title: Ath root nuclei processed 2h post cut after 2h on TSA with multiome ATAC

city: Gif-sur-Yvette

first: Bruno

last: Guillotin

address: Bâtiment 630, Avenue des Sciences

institute: Institute of Plant Sciences of Paris-Saclay - IPS2

description:
Library name: Cut_2h_TSA_multiome_ATAC
10x Genomics

library_source: genomic single cell

data_processing:
Raw base calls were demultiplexed using Illumina's bcl2fastq.
Alignment, barcode and UMI quantification were performed with Chromium 10x Cell Ranger software package. Samples were normalized, and cell clusters determined using Seurat.
Differential gene expression analyses between cell clusters was perfomed using the SCT algorithm from Seurat.
Assembly: Arabidopsis_thaliana.TAIR10.38
Supplementary files format and content: dgMatrix table with raw counts for every cell  (column) and gene (rows). Seurat Object of Arabidopsis single cell or nuclei

organism: Arabidopsis thaliana

source_name: Whole root

growth_protocol: Arabidopsis seeds were imbibed for 48h at 4°C before being surface sterilized and placed on a nylon mesh (110um) and agar plates-1/2 × Murashige and Skoog salts (Sigma M5524), 0.5% sucrose, 0.8% Agar (Sigma A1296). Plant were transferred vertically in growth chambers set to 23°C and a 16 h light/8 h dark cycle (400 μmol m−2 s−1). Root tips were collected 7 days after transfer, cut with a feather scalpel at 100um from the tip and directly transferred to either the protoplast solution at room temperature

extract_protocol:
Root tip were incubated in a enzymatic solution to digest cell walls and produce protoplasts and used as input for the 10x Chromium Single Cell 3' kit
Libraries were prepared using Chromium Single Cell 3' Reagent Kit V2 and V3 protocol and the multiome kit from 10xgenomics

treatment_protocol: For chemical treatment seeds are grown on nylon mesh and transfer to MS plates with the chemicals x h before processing

value: Whole root

value: all

tag: ecotype

value: Root cut 2h TSA


title: ChIP3, dcr1Δ, H3, heat-treatment 5min, rep1

status: Public on Feb 25 2026

type: SRA

city: Bunkyo, Tokyo

first: Soichi

last: Inagaki

department: Department of Biological Sciences

country: Japan

institute: Graduate School of Science, The University of Tokyo

library_source: genomic

data_processing:
ChIP-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created using deeptools software.
RNA-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using STAR aligner with -- outFilterType, BySJout; -- alignSJoverhangMin, 8; -- alignSJDBoverhangMin, 1; -- quantMode GeneCounts parameters. When we analyzed the expression of DNA sequence inculding repeat regions such as heterochromatin genes, we calculated the readcounts from bedgraph file, which was produced using the coverage function of BEDTools ver 2.17.0. Those readcount files were named as “mRNA_XXX_for_HGs.txt".
PRO-seq reads were mapped on S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created from bedgraph files using bedGraphToBigWig program.
Assembly: ASM294v2
Supplementary files format and content: bigwig file for ChIP-seq and PRO-seq
Supplementary files format and content: tab-delimited text file for RNA-seq

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: S.pombe cells

growth_protocol: Cells were grown in YES medium until mid-log phase at 30 ºC.

extract_protocol:
Total RNA for mRNA-seq was extracted by the hot-phenol method, as previously described (Iyer,V. and Struhl,K. 1996). Cell permeabilization and extraction of biotinylated RNA for PRO-seq was performed as previously described (Mahat et al., 2016). Chromatin for ChIP-seq, extracted from cell lysate of 1% formaldehyde fixed-cells, was sonicated using a Picoruptor (Diagenode).
ChIP-seq libraries were constructed using the ThruPLEX DNA-seq Kit (Clontech). mRNA-seq libraries were constructed using the KAPA mRNA HyperPrep Kit (Kapa Biosystems). cDNA libraries for PRO-seq were converted from the RNA, to which 3' and 5' adaptors were ligated, by revearse transcription.

treatment_protocol: The non-treated samples (0 min) were harvested immediately, and the heet-treated samples were moved from a 30 ºC water bath to 37.5 ºC and incuvated during the designated term (2.5, 5 and 25 min) with shaking.

tag: cell type

value: S.pombe cells

tag: genotype

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ dcr1{delta}::KanMX6

tag: treatment

value: 5 min atter heat-treatment


title: ChIP3, ago1Δ, H3K9me2, heat-treatment 5min, rep2

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ ago1{delta}::HphMX6


title: liver, sham HFD, 4

city: Mineola

first: Louis

last: Ragolia

state: New York

address: 101 Mineola Blvd, Suite 4-004

department: Foundations of Medicine

country: USA

institute: NYU Grossman Long Island School of Medicine

description:
Library name: Sample14
Sample name in raw counts sHFD4

library_source: transcriptomic

data_processing:
Raw sequencing reads were processed using Trimmomatic v0.36 with default parameters to remove adapters, poly-N regions, and low-quality reads. Quality of trimmed reads was assessed using FastQC. Cleaned reads were aligned to the Mus musculus reference genome (mm10) using HISAT2 v2.1.0 with default settings. Gene-level counts were generated using FeatureCounts v1.5.0-p3 from the Subread package.
Assembly: mm10
Supplementary files format and content: csv file contains raw count data for each sample

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA extraction was performed using Trizol reagent (Ambion, Life Technologies, Carlsbad, CA), followed by purification and concentration using RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany; #74204). RNA purity was assessed by 260/280 and 260/230 ratios and samples were sent for sequencing.
mRNA was enriched from total RNA using poly-T oligo-attached magnetic beads, then fragmented using divalent cations at elevated temperature. First-strand cDNA synthesis was performed using random hexamer primers and reverse transcriptase, followed by second-strand synthesis using DNA Polymerase I and RNase H with dUTP incorporation to maintain strand specificity. After end repair, A-tailing, and adapter ligation, cDNA fragments were size-selected and amplified. Library quality and concentration were assessed using an Agilent Bioanalyzer, Qubit Fluorometer, and qPCR.

tag: tissue

value: liver


title: Ath root nuclei processed 2h post cut after 2h on TSA with multiome RNA

department: Biology

country: France

description:
Library name: Cut_2h_TSA_multiome_RNA
10x Genomics

library_source: transcriptomic single cell

molecule: polyA RNA

tag: batch


title: H-2D 1

city: Changsha

first: Chaoyong

last: He

address: Tianma road

country: China

institute: Hunan university

description:
Library name: Sample 5
High 1

data_processing:
Reads mapping and gene expression quantification: cDNA library samples were sequenced as described above. After removing the reads with adapters, any reads containing ‘n’ (> 10%) and low-quality reads (sQ ≤ 5), the remaining clean reads were checked by FastQC (v.0.11.5). Clean reads were aligned to the Rattus norvegicus Rnor 6.0.98 using STAR (v.2.5.3a) and the raw counts matrix were obtained by featureCounts. The expression level of genes was calculated using CPM (count per millon) as a metric, and filtered using the sum of relative abundance to eliminate the effects of sequencing depths.
PCA analysis, DEG obtain and clustering: Normalized gene expression values used to calculate the correlation coefficient among biological replicates for PCA and hierarchical clustering. The PCA was calculated with the prcomp function in R with default settings. Hierarchical clustering was performed using the pheatmap package with default settings using Pearson’s correlation. The DEGs in pairwise comparisons were identified by the R package edgeR, which performs data normalization using the trimmed mean of M-values (TMM) method. Genes with at least a two-fold change in expression and P value < 0.05 were considered to be expressed differentially. A k-means approach was used (R package pheatmap) to cluster all the DEGs identified through pairwise comparisons.
Assembly: rn6
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

organism: Rattus norvegicus

source_name: brain tissue from SD rats at 1 day

growth_protocol: NSCs were isolated from cerebral cortices of 1–day-old neonatal Sprague-Dawley rats.

extract_protocol:
NSCs were expanded as neutrospheres at 37°C, 5% CO2 for 3-4 days in proliferation culture medium, which contained DMEM/F12 supplemented with 1% glutamine (Gibco), 1% sodium pyruvate (Gibco), 1% NEAA (Gibco), 2% B27 (Gibco), 0.02 ng/mL EGF, 0.02 ng/mL bFGF, 1.83 ng/mL heparin and 1% streptomycin penicillin (Gibco). The proliferation medium was replaced every 2 days. Thereafter, the NSCs neutrospheres were gathered through centrifugation (300×g, 5min), and digested with 0.25% trypsin-EDTA (Gibco) at 37℃ for 18 min. After terminating digestion mixture using 10% FBS, the cells were collected by countrification and filtered through 70 μm and 40 μm mech of cell strainer successively to obtain the NSCs of single-cell suspension. 0.2% (W/V) of Col solution mixed with equal volume of NSCs single-cell suspension to obtain final 0.75, 1.5, 3 million/mL of cell packing density system.
RNA-seq library preparation. Total RNA was isolated from each sample using the RNAmini kit (Qiagen, Germany). RNA quality was examined by gel electrophoresis and with Qubit (Thermo, Waltham, MA, USA). Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), through reverse transcription using S1000TM Touch Thermal Cycler (Bio Rad) at 53°C (45 min) - 85°C (5 min) - 4°C cycle. The generated cDNA was amplified, and quality estimated using Agilent 4200 (performed by CapitalBio Technology, Beijing). The sequences of libraries were finally obtained using the Illumina Novaseq6000 sequencer with pair-end 150 bp (PE150).

treatment_protocol: tissue pieces of dissociation, the mixed cortical cells were first passed through a 100 μm mesh of nylon cell strainer, then plated into tissue culture flasks.

value: brain tissue

value: Neural Stem Cells

value: wild type

value: High crowding


title: ChIP3, dcr1Δ, H3, heat-treatment 5min, rep2


title: ChIP3, ago1Δ, H3K9me2, heat-treatment 0min, rep2

value: 0 min (non treated)


title: liver, sham HFD, 3

description:
Library name: Sample13
Sample name in raw counts sHFD3


title: ChIP3, ago1Δ, H3K9me2, heat-treatment 5min, rep1


title: Cortical neurons derived from 2L20 iPSCs with heterozygous CHMP2B G26403C mutation, biological replicate 3

city: Worcester

first: Evan

middle: Phillip

last: Hass

state: MA

address: 264 Plantation Street, LRB 560D

department: MCCB

institute: UMass Chan Medical School

description: Library name: Subject1_CHMP2B_het_mut_rep3

data_processing:
Adpater sequences were removed from reads using trimmomatic with the following parameters: ILLUMINACLIP:NexteraPE-PE.fa:2:25:7:1:true TRAILING:3 SLIDINGWINDOW:4:10 TRAILING:3 MINLEN:10
Trimmed reads were aligned to hg38 using bowtie2 using -N 1 -X 1000.
PCR duplicate reads were removed using Picard SortSam followed by MarkDuplicates with REMOVE_DUPLICATES=TRUE.
Samtools was used to remove reads with a MAPQ score less than 10, mitochondrial reads were removed using the grep command, and fragments longer than 100 bp in length were removed using awk.
The HOMER suite was used to make tag directories and bedGraph files, which were in turn converted to bigWig files using bedGraphToBigWig.
Assembly: hg38
Supplementary files format and content: All processed data files are in bigWig format and show ATAC-seq coverage.

organism: Homo sapiens

growth_protocol: iPSCs were cultured on Matrigel-coated wells (Corning, 354230) and passaged using Accutase (EMD Millipore, SCR005) at approximately 60% confluency. The following day, the culture medium was replaced with neuroepithelial progenitor (NEP) medium, and differentiation was induced through sequential stages, including NEP induction, neural progenitor expansion, and neuronal maturation. Differentiated neurons were plated on chambered coverslips (ibidi, 80826 or 80426) pre-coated with poly-L-lysine (0.1 mg/mL, overnight at 37 °C) and laminin (10 µg/mL, for at least 2 h at 37 °C), on poly-D-lysine/laminin-coated glass coverslips (Corning, 354087), or on Matrigel-coated plates, and maintained for 1–3 months before use.

extract_protocol:
ATAC-seq DNA was isolated as described previously (Grandi et al. 2022, Nature Protocols) with the following modifications. 1x105 cells were used to generate each library. Tagmentase (Diagenode) and home-made 2x TD Buffer (20 mM Tris-HCl pH 7.5, 10 mM MgCl2, 20% dimethylformamide) were used in place of the previously described TDE1 enzyme and 2x TD Buffer from Illumina. After tagmentation, DNA was isolated using the Qiagen MinElute PCR Purification Kit.
Libraries were generated from isolated DNA essentially as described previously (Grandi et al. 2022, Nature Protocols). Libraries were amplified with 10 cycles of PCR, and fragments between 150 and 500 bp were gel purified using the Qiagen Gel Extraction Kit.

tag: cell line

value: iPSC-derived cortical neurons

value: CHMP2B G26403C heterozygous


title: Ath root nuclei processed 2h post cut after 2h on DMSO with multiome RNA

description:
Library name: Cut_2h_DMSO_multiome_RNA
10x Genomics

value: Root cut 2h DMSO


title: ChIP3, dcr1Δ, H3, heat-treatment 0min, rep2


title: liver, sham HFD, 2

description:
Library name: Sample12
Sample name in raw counts sHFD2


title: Ath root nuclei processed 0h post cut after 2h on TSA with multiome ATAC

description:
Library name: Cut_0h_TSA_multiome_ATAC
10x Genomics

value: Root cut 0h TSA


title: Ath root nuclei processed 2h post cut after 2h on DMSO with multiome ATAC

description:
Library name: Cut_2h_DMSO_multiome_ATAC
10x Genomics

value: Whole root


title: liver, sham HFD, 1

description:
Library name: Sample11
Sample name in raw counts sHFD1


title: Cortical neurons derived from 2L20 iPSCs with heterozygous CHMP2B G26403C mutation, biological replicate 2

description: Library name: Subject1_CHMP2B_het_mut_rep2


title: Cortical neurons derived from 2L20 iPSCs with heterozygous CHMP2B G26403C mutation, biological replicate 1

description: Library name: Subject1_CHMP2B_het_mut_rep1


title: liver, RYGB chow, 5

description:
Library name: Sample10
Sample name in raw counts rChow5


title: Ath root nuclei processed 0h post cut after 2h on TSA with multiome RNA

description:
Library name: Cut_0h_TSA_multiome_RNA
10x Genomics

value: all


title: Ath root nuclei processed 0h post cut after 2h on DMSO with multiome ATAC

description:
Library name: Cut_0h_DMSO_multiome_ATAC
10x Genomics

value: Root cut 0h DMSO


title: ChIP3, ago1Δ, H3, heat-treatment 5min, rep2

value: S.pombe cells


title: ChIP3, ago1Δ, H3, heat-treatment 0min, rep2


title: ChIP3, ago1Δ, H3, heat-treatment 5min, rep1


title: Cortical neurons derived from 2L20 iPSCs, biological replicate 3

description: Library name: Subject1_CHMP2B_WT_rep3

value: CHMP2B wild type


title: liver, RYGB chow, 4

description:
Library name: Sample9
Sample name in raw counts rChow4


title: Cortical neurons derived from 2L20 iPSCs, biological replicate 2

description: Library name: Subject1_CHMP2B_WT_rep2


title: liver, RYGB chow, 3

description:
Library name: Sample8
Sample name in raw counts rChow3


title: Cortical neurons derived from 2L20 iPSCs, biological replicate 1

description: Library name: Subject1_CHMP2B_WT_rep1


title: Ath root protoplast processed 14h post cut on curcumin

description:
Library name: Cut_14h_Curcumin
10x Genomics

value: Root cut 14h Curcumine


title: ChIP3, ago1Δ, H3, heat-treatment 0min, rep1

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ ago1{delta}::HphMX6


title: Nasal cells 4

city: Seoul

first: Gyeongyeob

last: Kim

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Otorhinolaryngology

country: South Korea

institute: Yonsei University College of Medicine

description:
Library name: NB244_GT
gDNA data for genotyping

data_processing:
The sequencing data were demultiplexed using the mkfastq function (Cell Ranger, 10X Genomics, v7.1.0) to generate fastq files.
Assembly: GRCH38
Supplementary files format and content: 10x Genomics output files: filtered_feature_bc_matrix.h5

source_name: Nasal brushing

extract_protocol:
To collect nasal brushing(NB) samples, flocked swabs (Pap brush; SGS, Daejeon, Korea) were inserted into the nasal cavity of the donors and rotated 10–20 times. The swabs were then placed in tubes containing Dulbecco's Modified Eagle's Medium/F-12 (1:1) (1X) media (Gibco, Grand Island, NY, USA). The tubes were vigorously vortexed to dislodge the cells and pelleted via centrifugation. Nasal tissue (NT) was mechanically dissociated, and single-cell suspensions were prepared using a Tumor Dissociation Kit (Miltenyi Biotec, Auburn, CA, USA) in combination with a gentleMACS dissociator (Miltenyi Biotec) and 70-µm cell strainers (SPL Life Sciences, Gyeonggido, Korea).
The scRNA-seq libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3` v3.1 chemistry. Libraries were constructed and sequenced at a depth of approximately 20,000 reads per cell using the NovaSeq X Plus platform (Illumina, San Diego, CA, USA).

value: Nasal brushing

value: Nasal cell


title: Ath root nuclei processed 0h post cut after 2h on DMSO with multiome RNA

description:
Library name: Cut_0h_DMSO_multiome_RNA
10x Genomics


title: liver, RYGB chow, 1

description:
Library name: Sample6
Sample name in raw counts rChow1

value: liver


title: Ath root protoplast processed 14h post cut on roscovitine

description:
Library name: Cut_14h_Roscovitine
10x Genomics

value: Root cut 14h Roscovitinee


title: Cortical neurons derived from BIONi010-C iPSCs, biological replicate 1

description: Library name: Subject2_CHMP2B_WT_rep1


title: Nasal cells 3

description:
Library name: N362_GT
gDNA data for genotyping

source_name: Nasal tissue

value: Nasal tissue


title: ChIP3, swi6Δ, H3K9me2, heat-treatment 0min, rep2

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ swi6{delta}::KanMX6

value: 0 min (non treated)


title: liver, sham chow, 5

description:
Library name: Sample5
Sample name in raw counts sChow5


title: Nasal cells 2

description:
Library name: N359_GT
gDNA data for genotyping


title: Ath root protoplast processed 14h post cut on TSA

description:
Library name: Cut_14h_TSA
10x Genomics

value: Root cut 14h TSA


title: liver, RYGB chow, 2

description:
Library name: Sample7
Sample name in raw counts rChow2


title: ChIP3, swi6Δ, H3K9me2, heat-treatment 5min, rep2

value: 5 min atter heat-treatment


title: ChIP3, swi6Δ, H3K9me2, heat-treatment 5min, rep1


title: liver, sham chow, 4

description:
Library name: Sample4
Sample name in raw counts sChow4


title: ChIP3, swi6Δ, H3K9me2, heat-treatment 0min, rep1


title: Ath root protoplast processed 14h post cut on DMSO

description:
Library name: Cut_14h_DMSO
10x Genomics

value: Root cut 14h DMSO


title: liver, sham chow, 3

description:
Library name: Sample3
Sample name in raw counts sChow3


title: liver, sham chow, 2

description:
Library name: Sample2
Sample name in raw counts sChow2


title: Ath uncut root protoplast on 14h on roscovitine

description:
Library name: Uncut_Roscovitine
10x Genomics

value: Whole root

value: Root uncut Roscovitinee treatment 14h


title: ChIP3, swi6Δ, H3, heat-treatment 0min, rep2


title: Ath uncut root protoplast on 14h on curcumin

description:
Library name: Uncut_Curcumin
10x Genomics

value: all

value: Root uncut Curcumine treatment 14h


title: Nasal cells, nasal tissue + nasal brushing

description:
Library name: GEM_2
10x Genomics

source_name: Nasal tissue + brushing

value: Nasal tissue + brushing


title: liver, sham chow, 1

description:
Library name: Sample1
Sample name in raw counts sChow1


title: Nasal cells, nasal tissue

description:
Library name: GEM_1
10x Genomics


title: ChIP3, swi6Δ, H3, heat-treatment 5min, rep2

value: S.pombe cells


title: Nasal cells 1

description:
Library name: N333_GT
gDNA data for genotyping


title: liver, sham HFD, 5

description:
Library name: Sample15
Sample name in raw counts sHFD5


title: Sample8_aav ntn1

city: Shanghai

first: Jiahui

last: Zhao

address: Dongan road 130

institute: Fudan university

description:
Library name: Sample16
Colume name in raw_counts_All_Samples.txt:Ntn1-4

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim_galore
Trimmed sequence reads were mapped to mm10 using Hisat2
Read count extraction were performed using featureConts
Read count normalization and differential expression analysis were performed using DESeq2
Assembly: mm10
Supplementary files format and content: raw counts for each Sample

source_name: Liver

growth_protocol: Mice were housed in pathogen-free facilities under 12-h light-dark cycles with free access to food and water.

extract_protocol:
Total RNA was extracted from using Trizol. 200ng of total RNA was used for the construction of  sequencing libraries.
RNA libraries for RNA-seg were prepared using VAHTS® Universal V8 RNA-seg Library Prep Kit for Illumina

treatment_protocol: Ntn1fl/fl & Ntn1fl/flLrat-Cre mice or aav vec & aav Ntn1 mice are fed with Gan Diet for 5 months to induce MASH.

value: Liver

value: aav ntn1

value: Gan diet feeding for 5 months


title: Ath uncut root protoplast on 14h on DMSO

description:
Library name: Uncut_DMSO
10x Genomics

value: Root uncut no treatment


title: L4_IR+

city: Nanchang

first: Yi

last: Sang

state: Jiangxi

address: No.128,Xiangshan North Road

institute: Nanchang University

description: Library name: Sample 4

data_processing:
The sequencing data was processed and filterd with cutadapt(v1.18) leaving only the sgRNA sequence for further analysis
The sgRNA reads were mapped to the PTM sgRNA library with Bowtie2 (v2.3.5)
The count of each mapped reads was calculated by Model-bassed Analysis of PTM CRISPR/Cas9 Knockout algorithm
Assembly: Pooled PTM sgRNA library
Supplementary files format and content: tab-delimited text files include normalized read counts for each Sample
Library strategy: CRISPR Screen

source_name: lung cancer

extract_protocol:
The genomic DNA was extracted by Tissue DNA Kit(Omega, cat: D3396-01)
Libraries were prepared according to Illumina's instructions

value: lung cancer

value: irradiated at 9 Gy


title: Ath uncut root protoplast on 14h on TSA

description:
Library name: Uncut_TSA
10x Genomics

value: Root uncut TSA treatment 14h


title: Sample7_aav ntn1

description:
Library name: Sample15
Colume name in raw_counts_All_Samples.txt:Ntn1-3


title: Nasal cells, nasal brushing

description:
Library name: GEM_3
10x Genomics

value: Nasal brushing

value: Nasal cell


title: ChIP3, chp1Δ, H3K9me2, heat-treatment 5min, rep2

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ chp1{delta}::KanMX6

value: 5 min atter heat-treatment


title: Sample6_aav ntn1

description:
Library name: Sample14
Colume name in raw_counts_All_Samples.txt:Ntn1-2


title: Ath root protoplast processed 36h post cut

description:
Library name: Cut_36h
10x Genomics

value: Whole root

value: Root cut 36h


title: Ath uncut root protoplast processed on the same day as Cut_36h

description:
Library name: Uncut_36h
10x Genomics

value: all


title: L1_IR+

description: Library name: Sample 2


title: L4_IR-

description: Library name: Sample 3

value: nonirradiated


title: ChIP3, chp1Δ, H3K9me2, heat-treatment 0min, rep2

value: 0 min (non treated)


title: Ath root protoplast processed 24h post cut

description:
Library name: Cut_24h
10x Genomics

value: Root cut 24h


title: L1_IR-

description: Library name: Sample 1


title: ChIP3, chp1Δ, H3K9me2, heat-treatment 5min, rep1

value: S.pombe cells


title: Tubuloids normal 4

city: Bunkyo

first: Yuki

last: Nakao

state: Tokyo

address: Yushima 1-5-45

institute: Institute of Science Tokyo

description: Library name: Tb0mcm_4

data_processing:
Raw reads were trimmed and filtered using fastp (v0.22.0) with the options: -q 20 -u 30 -n 10 -l 30 -w 8. Quality control was performed before and after trimming using FastQC (v0.12.1), and consolidated quality reports were generated using MultiQC (v1.28).
Transcript-level quantification was performed using Salmon (v1.10.3). The transcriptome index was built using GENCODE Human Release 45 (GRCh38), with the files gencode.v45.transcripts.fa and gencode.v45.annotation.gtf downloaded in April 2025 from https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_45/.
Assembly: GENCODE Human Release 45 (GRCh38)
Supplementary files format and content: Tab-dilineated text file includes raw counts.

source_name: kidney

growth_protocol: The hRPTECs were seeded onto ultralow attachment plates at a density of 5.0 × 105 cells/well using Advanced RPMI 1640 medium (ThermoFisher Scientific) supplemented with 5% FBS. After a 2–3-day incubation period, Matrigel (Corning, NY, USA) was added to stimulate tubuloid formation. The following day, the culture medium was changed to Advanced RPMI 1640 medium with 5% FBS, EGF, FGF2, and HGF (tubuloids media). The media was changed three times a week to maintain optimal cell growth conditions.

extract_protocol:
Total RNA was extracted by initially homogenizing tubuloids in Sepasol-RNA I Super G (Nacalai Tesque, Japan), followed by purification using the Direct-zol RNA Miniprep Plus Kit (Zymo Research, R2070) according to the manufacturer’s protocol.Given the limited amount of RNA, quality control was conducted using an Agilent TapeStation. Samples with DV500 values greater than 75% were confirmed by Relixa Inc.
RNA-seq library preparation and sequencing were also outsourced to Relexa Inc. The library was prepared using the SMART-Seq mRNA HT LP (Takara Bio) kit. The sequencing was performed on an Illumina NovaSeq X Plus system, generating 2 × 150 bp paired-end reads (PE150), with approximately 6 giga bases of data and 40 million reads (20 million read pairs) per sample.

treatment_protocol: Following a 14-day culture period, the matured tubuloids were exposed to 0.1% DMSO for 48 hours in three consecutive cycles, after which they were collected

value: kidney

value: primary RPTECs

value: Vehicle(DMSO)for 6days


title: Sample4_aav vec

description:
Library name: Sample12
Colume name in raw_counts_All_Samples.txt:Vec4

value: Liver

value: aav vec

value: Gan diet feeding for 5 months


title: Ath uncut root protoplast processed on the same day as Cut_24h

description:
Library name: Uncut_24h
10x Genomics

value: Root uncut no treatment


title: ChIP3, chp1Δ, H3K9me2, heat-treatment 0min, rep1


title: Ath root protoplast processed 14h post cut

description:
Library name: Cut_14h
10x Genomics

value: Root cut 14h


title: Tubuloids normal 2

description: Library name: Tb0mcm_2


title: Sample3_aav vec

description:
Library name: Sample11
Colume name in raw_counts_All_Samples.txt:Vec3


title: Tubuloids normal 3

description: Library name: Tb0mcm_3


title: ChIP3, chp1Δ, H3, heat-treatment 5min, rep2

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ chp1{delta}::KanMX6


title: Sample5_aav ntn1

description:
Library name: Sample13
Colume name in raw_counts_All_Samples.txt:Ntn1-1

value: aav ntn1


title: Sample2_aav vec

description:
Library name: Sample10
Colume name in raw_counts_All_Samples.txt:Vec2


title: ChIP3, chp1Δ, H3, heat-treatment 0min, rep2


title: Ath root protoplast processed 9h post cut

description:
Library name: Cut_9h
10x Genomics

value: Whole root

value: Root cut 9h


title: Tubuloids normal 1

description: Library name: Tb0mcm_1


title: Sample1_aav vec

description:
Library name: Sample9
Colume name in raw_counts_All_Samples.txt:Vec1


title: Ath uncut root protoplast processed on the same day as Cut_9h and 14h

description:
Library name: Uncut_9_14h
10x Genomics

value: all


title: ChIP3, chp1Δ, H3, heat-treatment 5min, rep1

value: 5 min atter heat-treatment


title: Sample8_Ntn1flflLrat-Cre

description:
Library name: Sample8
Colume name in raw_counts_All_Samples.txt:Ntn1-4


title: Ath root protoplast processed 4h post cut

description:
Library name: Cut_4h
10x Genomics

value: Root cut 4h


title: RNA-POL-II-WT_input_1

city: Bethesda

first: Caroline

last: Esnault

state: md

address: 9000 Rockville Pike,

institute: NICHD NIH

data_processing:
Raw sequence reads were processed through lcdb-wf v1.6rc (https://github.com/lcdb/lcdb-wf). Briefly, raw sequence reads were trimmed with cutadapt v3.4 to remove adapters and do quality trimming with parameters “-u 3 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 20 –minimum-length=25” for paired-end reads or “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -q 20 – minimum-length=25” for single read. fastqc v0.11.9 with default parameters and multiqc v1.10.1 were used to estimate the sequencing library quality. The presence of common sequencing contaminants was evaluated with fastq_screen v0.14.0 with parameters “–subset 100000 –aligner bowtie2.” Trimmed reads were mapped to the human reference genome Gencode v19 GRCh37.p13) using bowtie2 v2.4.2 with parameter “--no-unal”, followed by samtools v1.12 functions view with parameter “-Sb” and function sort to sort the BAM files. Multimapping reads were filtered using samtools view with parameter “-b -q 20”. PCR duplicates were removed with picard v2.25.2 MarkDuplicates with parameters “REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT”. Bigwig files were generated with deeptools v3.5.1 bamCoverage with “--binSize 1 --minMappingQuality 20 --ignoreDuplicates --normalizeUsing CPM --extendReads 300” to visualize the signal in genome browsers. Significant ChIPseq signal peaks were computed with MACS2 v2.2.7.1 callpeak with parameters “-f BAMPE -B” or “-f BAM -B” for paired-end or single read respectively.
Assembly: hg19
Supplementary files format and content: bigwig files contain the mapped reads distribution. Technical replicates were concatenated.
Supplementary files format and content: narrowPeak files are the results of MACS2 peak calling on the IP / input.

source_name: Human cell line (HEK293T)

growth_protocol: HEK293T cells were propagated in Dulbecco’s modified Eagle’s media supplemented to contain fetal bovine serum (10%) and penicillin-streptomycin (1%; 100 U/ml) (DMEM). Cells were grown at 37 °C in humified tissue culture cell incubators.

extract_protocol:
Antibodies for ChIPSeq: FLAG (Sigma; Cat# F1804), RNA Pol II (8WG16 BioLegend; Cat# 664912), H3K4me3 (C42D8 Rabbit mAb #9751 cell signaling), H3K36me3 (Invitrogen; MA5-24687), and MLL1 (Rabbit anti-MLL1 antibody Bethyl; Cat#A300-374A).
ChIP-Seq libraries were constructed from 40 ng of ChIP DNA using Ovation Ultralow System V2 1-96 (Tecan) with 15 cycles of PCR amplification. The final libraries were twice purified using Ampure XP PCR Purification Beads (Agencourt). The pooled libraries were sequenced on a NovaSeq 6000 (Illumina) using version 1.5 chemistry to achieve approximately 80 million 151-base read pairs. The data was processed using RTA version 3.4.4.

treatment_protocol: HEK293T cells were modified with CRIPSR to prevent expression of both the p52 and p75 isoforms of LEDGF. Cas9 with two sgRNAs targeting exon 2 of PSIP1 generated a clone with one allele encoding a frameshift after amino acid 30 adding seven additional amino acids and a second allele with a stop codon at amino acid 24. RNA-seq data from this LEDGF KO cell line revealed nonsense mediated decay allowed only trace levels of expression at any position in the PSIP1 gene. A clone of HEK293T with homozygous alleles of PSIP1 encoding C-terminal 3XFLAG tags were produced with CRISPR and a donor sequence carrying only a silent mutation that removed the PAM sequence.  We expressed N-terminal tagged LEDGF from Sleeping Beauty vectors introduced into the HEK293T cells with the LEDGF KO. A Sleeping Beauty vector, a gift from Todd McFarlan, containing 5’ and 3’ terminal inverted repeats, puro and a PGK promoter to express coding sequence with an N-terminal 3XFLAG tag. At 5’ NcoI and 3’ NheI sites we introduced synthesized coding sequences for wild type LEDGF, LEDGF lacking amino acids 1-93 (deletes PWWP) and LEDGF-1-325 (deletes IBD). We co-transfected these vectors with pCMV-SB100X that expresses the Sleeping Beauty transposase that stably integrated the LEDGF sequences.

value: Human cell line (HEK293T)

value: LEDGF-WT

tag: chip antibody

value: input

tag: experiment run_number

tag: fraction


title: Sample7_Ntn1flflLrat-Cre

description:
Library name: Sample7
Colume name in raw_counts_All_Samples.txt:Ntn1-3


title: Ath uncut root protoplast processed on the same day as Cut_4h

description:
Library name: Uncut_4h
10x Genomics


title: RNA-POL-II-WT_IP_2

value: RNA-POL-II

value: IP


title: ChIP3, WT, H3K9me3, heat-treatment 5min, rep2

value: S.pombe cells

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+


title: RNA-POL-II-WT_IP_1


title: ChIP3, chp1Δ, H3, heat-treatment 0min, rep1

value: 0 min (non treated)


title: Sample6_Ntn1flflLrat-Cre

description:
Library name: Sample6
Colume name in raw_counts_All_Samples.txt:Ntn1-2

value: Liver

value: Gan diet feeding for 5 months


title: ChIP3, WT, H3K9me3, heat-treatment 2.5min, rep2

value: 2.5 min atter heat-treatment


title: ChIP3, WT, H3K9me3, heat-treatment 0min, rep2


title: Sample5_Ntn1flflLrat-Cre

description:
Library name: Sample5
Colume name in raw_counts_All_Samples.txt:Ntn1-1


title: ChIP3, ago1Δ, H3K9me2, heat-treatment 0min, rep1

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ ago1{delta}::HphMX6


title: ChIP3, swi6Δ, H3, heat-treatment 0min, rep1

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+ swi6{delta}::KanMX6


title: RNA-POL-II-LEDGF-KO_input_1

value: LEDGF-KO


title: Sample4_Ntn1flfl

description:
Library name: Sample4
Colume name in raw_counts_All_Samples.txt:Vec4


title: ChIP3, WT, H3K9me3, heat-treatment 5min, rep1


title: Sample3_Ntn1flfl

description:
Library name: Sample3
Colume name in raw_counts_All_Samples.txt:Vec3


title: RNA-POL-II-LEDGF-KO_IP_1


title: ChIP3, WT, H3K9me3, heat-treatment 0min, rep1


title: RNA-POL-II-LEDGF-KO_IP_2


title: ChIP3, swi6Δ, H3, heat-treatment 5min, rep1


title: MLL1-WT_input_1


title: Sample2_Ntn1flfl

description:
Library name: Sample2
Colume name in raw_counts_All_Samples.txt:Vec2


title: Control Offspring Mouse Testes 3

type: RNA

city: hefei

first: Hua-Long

last: Zhu

address: No. 81, Meishan Road, Hefei City

department: department of toxicology

institute: anhui medical university

description:
C43.txt
Biological replicate 3 of 3. Control offspring mice and their mothers were not treated during pregnancy.

hyb_protocol: Cy3 and Cy5 labeled cRNAs were combined together and hybridized to ArraystarMouse mRNA&IncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65'c for 17hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

source_name: Control Offspring Mouse Testes

label_protocol: The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar RNA Labeling protocol

growth_protocol: Pregnant mice were given RO water or high-dose cadmium (150 mg/L) from the eighth day of gestation until delivery, and the offspring male mice were euthanized until 70 days after birth, and the offspring testicles were obtainedand.

extract_protocol: Total RNAs were immunoprecipitated with anti-N6-methyadenosine(m6Aantibody. The immunoprecipitated lp fraction contained enriched m6Amethylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs.

treatment_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: strain

value: ICR

tag: gender

value: male

tag: age

value: day 70

value: Mouse Testes


title: Sample1_Ntn1flfl

description:
Library name: Sample1
Colume name in raw_counts_All_Samples.txt:Vec1


title: Control Offspring Mouse Testes 2

description:
C19.txt
Biological replicate 2 of 3. Control offspring mice and their mothers were not treated during pregnancy.


title: liver, RYGB HFD, 3

description:
Library name: Sample18
Sample name in raw counts rHFD3

value: liver


title: High Dose Cadmium exposure Offspring Mouse Testes 2

description:
Hcd37.txt
Biological replicate 2 of 3.  The offspring of the high cadmium group were not treated and their mothers were exposed to cadmium during pregnancy.


title: MLL1-WT_IP_3

value: Human cell line (HEK293T)

value: LEDGF-WT


title: Control Offspring Mouse Testes 1

description:
C14.txt
Biological replicate 1 of 3. Control offspring mice and their mothers were not treated during pregnancy.


title: ChIP3, WT, H3K9me1, heat-treatment 5min, rep2

value: 5 min atter heat-treatment


title: ChIP3, WT, H3K9me1, heat-treatment 2.5min, rep2

value: S.pombe cells


title: MLL1-LEDGF-KO_input_1

value: input


title: High Dose Cadmium exposure Offspring Mouse Testes 3, IP

description:
Hcd42.txt
Biological replicate 3 of 3.  The offspring of the high cadmium group were not treated and their mothers were exposed to cadmium during pregnancy.


title: MLL1-WT_IP_1

value: IP


title: High Dose Cadmium exposure Offspring Mouse Testes 3


title: CDK20.D cell line, replicate 2

city: Madrid

first: Cristian

last: Suarez Cabrera

state: Madrid

address: Av. Complutense 40

country: Spain

institute: CIEMAT

description: Library name: CK20DR2

data_processing:
Adapter trimming and quality filtering of the FASTQ files were performed with Trimmomatic. The quality of the reads was evaluated with FastQC. Alignment to the GRCm38 mouse reference genome (mm10) was performed with STAR aligner.
Quantification at the gene level was performed with featureCounts.
Counts were normalized using DESeq2’s median-of-ratios method.
Assembly: GRCm38 mouse reference genome (mm10)
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample (Genes are annotated using Ensembl Gene IDs)

growth_protocol: For the establishment of primary cell cultures, tumor specimens obtained from the different GEMMs were washed and minced into small pieces. Tumor dissociation was carried out by enzymatic digestion with 200 µg/mL of collagenase P, 800 µg/mL dispase II, and 100 µg/mL DNase I at 37°C, mixing samples every 20 minutes until the sample was disaggregated. Disaggregated tissue was filtered through a 40 µm strainer and centrifuged at 16 g for 7 minutes. Cells were cultured with DMEM GlutaMAX  with 10% FBS and 1% antibiotic-antimycotic at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted from cells using the RNeasy Mini kit (Qiagen) following the manufacturer’s instructions.
RNA sequencing analysis was performed using total RNA extracted from mouse BC cell lines, processed into biological duplicates. Stranded mRNA libraries were prepared with the TruSeq Stranded mRNA kit (Illumina), following the manufacturer's protocols. Pairwise sequencing (2 × 150 bp) was performed on a NovaSeq 6000 platform (Illumina) at the Centro Nacional de Análisis Genómico (CNAG, Barcelona, Spain), obtaining more than 60 million reads per sample.

value: Bladder cancer cell

tag: mouse strain_of_origin

value: QKO

tag: targeted cell_(adenovirus)

value: Suprabasal cells (Ad5-Krt20-Cre)


title: K5.6 cell line, replicate 1

description: Library name: K56R1

value: Basal cells (Ad5-Krt5-Cre)


title: CDK20.D cell line, replicate 1

description: Library name: CK20DR1


title: ChIP3, WT, H3K9me1, heat-treatment 0min, rep2

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

value: 0 min (non treated)


title: K5.6 cell line, replicate 2

description: Library name: K56R2


title: ChIP3, WT, H3K9me1, heat-treatment 2.5min, rep1

value: 2.5 min atter heat-treatment


title: ChIP3, WT, H3K9me3, heat-treatment 2.5min, rep1


title: MLL1-WT_IP_2


title: CK5.A cell line, replicate 2

description: Library name: CK5AR2


title: MLL1-LEDGF-KO_IP_2

value: LEDGF-KO


title: CK5.A cell line, replicate 1

description: Library name: CK5AR1


title: High Dose Cadmium exposure Offspring Mouse Testes 1

description:
Hcd14.txt
Biological replicate 1 of 3.  The offspring of the high cadmium group were not treated and their mothers were exposed to cadmium during pregnancy.

value: ICR

value: male

value: day 70


title: High Dose Cadmium exposure Offspring Mouse Testes 2, IP

value: Mouse Testes


title: Control Offspring Mouse Testes 3, IP


title: ChIP3, WT, H3K9me1, heat-treatment 5min, rep1


title: ChIP3, WT, H3, heat-treatment 5min, rep2


title: 3K20 cell line, replicate 2

description: Library name: 3K20R2

value: DKO


title: Control Offspring Mouse Testes 1, IP


title: ChIP3, WT, H3K9me1, heat-treatment 0min, rep1


title: LEDGF-3XFLAG-MLL1-WT_input_1

value: Human cell line (HEK293T)


title: ChIP3, WT, H3, heat-treatment 2.5min, rep2

value: S.pombe cells


title: MLL1-LEDGF-KO_IP_1


title: High Dose Cadmium exposure Offspring Mouse Testes 1, IP


title: HCT116 cells, 18hrs, Pore-C rep1 and rep2

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

country: Germany

institute: Max-Planck-Institut für molekulare Genetik

description: Library name: HCT116_18hrs_Pore-C_rep1_rep2

data_processing:
The raw pod5 reads were basecalled and demultiplexed using Dorado basecaller v0.5.3 with a model dna_r10.4.1_e8.2_400bps_sup@v4.2.0. Sequencing reads were aligned to the hg38 human genome using the published pipeline from HiPore-C (Zhong et al, 2023) with default parameters.
Assembly: hg38
Supplementary files format and content: hic

extract_protocol:
Protocol was adapted from the published method (Xiao et al. 2022) with additional RNA digestion using 10U of RNase A/T1 Mix (ThermoScientific, cat. no. EN0551) at 37°C for 20min before Pronase decrosslinking. After decrosslinking the DNA was extracted by Phenol/Chloroform extraction and ethanol precipitation as described before. 4.5x106 endogenous Halo-SON SRRM2-SNAP-FKBP HCT116 cells were incubated with 1µM HaloPROTAC3 (MedChemExpress, cat #HY-111997) and 1µM dTAG13 (Tocris, cat. no 6605) for 0 hours (untreated) 6 hours, 12 hours or 18 hours as well as DMSO for 18 hours. After the incubation the cells were fixed with 4mL 1% formaldehyde (final) in PBS (Pierce™ 16% Formaldehyde (w/v), Methanol-free, cat. no. 28908) for 10 min at room temperature and blocked with 125mM Glycine. Pellet of the fixed cells was frozen at -80°C for at least 1 hour. Nuclei were then isolated at 4°C for 30 min with Cytoplasm lysis buffer (10mM Tris-HCl, 10mM NaCl, 0.2% Igepal, 1x cOmplete protease inhibitors (MERCK, cat. no. COEDTAF-RO)). Cells were then permeabilized with 0.5% SDS at 62°C, which was subsequently inactivated 2% Triton-X-100 (37°C, 15min). DNA was then fragmented in-situ using 100U of NlaIII (NEB, cat. no. R0125S) in 1x CutSmart buffer (NEB, cat. no. B6004S) at 37°C for 16 hours. Next, The restriction enzyme was heat inactivated at 62°C for 20 min and restriction fragments ligated for 4 hours in 16°C followed by 1 hour in 25°C using 4000U of T4 ligase (NEB, cat. no.µg M0202L) in 1x T4 ligase buffer (NEB, cat. no. B0202S) with 1.25% Triton-X-100 and 10µg of BSA. The sample was decrosslinked for 16 hours at 63°C by addition of SDS to 0.5% and proteinase K to 1mg/mL (Invitrogen, cat. no. 25530-049). DNA was then extracted using phenol:chloroform: isoamyl alcohol (25:24:1). RNA in purified sample was digested with 10U of RNase A/T1 Mix (ThermoScientific, cat. no. EN0551) at 37°C for 20min followed by inactivation and second round of decrosslinking for 40min at 37°C with 2mg/mL pronase in 1x pronase buffer (5mM Tris, 10mM EDTA, 0.5% SDS).
ONT native barcoding library preparation according to ONT protocol SQK-NBD114.24

value: SON-HaloTag SRRM2-dTAG


title: HCT116 cells, 18hrs, Pore-C rep2

description: Library name: HCT116_18hrs_Pore-C_rep2


title: 3K20 cell line, replicate 1

description: Library name: 3K20R1


title: 4K5 cell line, replicate 2

description: Library name: 4K5R2


title: HCT116 cells, 0hrs, Pore-C rep2

description: Library name: HCT116_0hrs_Pore-C_rep2

value: control


title: ChIP3, WT, H3, heat-treatment 2.5min, rep1


title: LEDGF-3XFLAG-MLL1-WT_IP_1

value: IP


title: LEDGF-3XFLAG-MLL1-WT_IP_3


title: ChIP3, WT, H3, heat-treatment 0min, rep2


title: LEDGF-3XFLAG-MLL1-WT_IP_2


title: HCT116 cells, 0hrs, Pore-C rep1 and rep2

description: Library name: HCT116_0hrs_Pore-C_rep1_rep2


title: 4K5 cell line, replicate 1

description: Library name: 4K5R1

value: Bladder cancer cell


title: NIH3T3, Mic-628, rep4

city: Kanazawa

first: Hajime

last: Tei

state: Ishikawa

address: Kakuma-cho

department: Science and Technology

institute: Kanazawa University

description: Library name: Blaplus4

data_processing:
Illumina bcl2fastq was used for conversion into Fastq files.
Trimmotatic (version 0.39) was used to remove adaptor sequences (Bolger et al. 2014). Sequence reads were mapped to mouse genome GRCm39/mm39 with STAR (2.7.10a) (Dobin et al. 2013). To obtain reliable alignments, the reads with mapping quality less than 10 were removed by SAM tools  (1.7) (Li et al. 2009).
The bigWig files were normalized to display uniquely mapped reads per 10 million uniquely mapped reads with duplicates. There are separate bigWig files for + and - genomic strands.
The University of California, Santa Cruz (UCSC) known canonical gene set (78,298) were used for annotation, and the reads mapped to the exons were quantified using analyzeRNA.pl script in the Homer software with an option of –rpkm or -noadj for FPKM or raw read counts, respectively
Raw reads and Fragments Per Kilobase per Million mapped reads (FPKM) were calculated using HOMER (v4.11) (Heinz et al. 2010)
Assembly: GRCm39/mm39
Supplementary files format and content: bigWig and tab-delimited text files include raw read counts and FPKM values for each Sample.

growth_protocol: Mouse NIH3T3 cells were cultured in Dulbecco’s minimum essential medium (DMEM) (Nissui Co.) with 10% fetal bovine serum (FBS) (Biowest) at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted with Trizol reagent (Thermo Fisher Scientific).
RNA sequencing libraries were constructed using a TruSeq Stranded mRNA Library Preparation kit (Illumina Inc.) and sequenced on the NovaSeq 6000 System (Illumina, Inc.) with 101-bp paired-end reads in Macrogen Japan Corp.

treatment_protocol: NIH3T3 cells were treated with Mic-628 or vehicle for 1 day.

value: fibroblast

value: WT


title: ChIP3, WT, H3, heat-treatment 5min, rep1

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

value: 5 min atter heat-treatment


title: HCT116 cells, 18hrs, Pore-C

description:
instrument model: PromethION P2
R10.4.1 flow-cell

data_processing:
The raw pod5 reads were basecalled and demultiplexed using Dorado basecaller v0.5.3 with a model dna_r10.4.1_e8.2_400bps_sup@v4.2.0. Resulting bamfiles were converted to fastq format using GATK SamToFastq (Picard).
QC file generated with bwa mem mapped reads using the multiqc as part of pairtools
Assembly: hg38
Supplementary files format and content: HTML report generated with multiqc via pairtools

extract_protocol:
Protocol was adapted from the published method (Xiao et al. 2022) with additional RNA digestion using 10U of RNase A/T1 Mix (ThermoScientific, cat. no. EN0551) at 37°C for 20min before Pronase decrosslinking. After decrosslinking the DNA was extracted by Phenol/Chloroform extraction and ethanol precipitation as described before. 4.5x106 endogenous Halo-SON SRRM2-SNAP-FKBP HCT116 cells were incubated with 1µM HaloPROTAC3 (MedChemExpress, cat #HY-111997) and 1µM dTAG13 (Tocris, cat. no 6605) for 0 hours (untreated) 6 hours, 12 hours or 18 hours as well as DMSO for 18 hours. After the incubation the cells were fixed with 4mL 1% formaldehyde (final) in PBS (Pierce™ 16% Formaldehyde (w/v), Methanol-free, cat. no. 28908) for 10 min at room temperature and blocked with 125mM Glycine. Pellet of the fixed cells was frozen at -80°C for at least 1 hour. Nuclei were then isolated at 4°C for 30 min with Cytoplasm lysis buffer (10mM Tris-HCl, 10mM NaCl, 0.2% Igepal, 1x cOmplete protease inhibitors (MERCK, cat. no. COEDTAF-RO)). Cells were then permeabilized with 0.5% SDS at 62°C, which was subsequently inactivated 2% Triton-X-100 (37°C, 15min). DNA was then fragmented in-situ using 100U of NlaIII (NEB, cat. no. R0125S) in 1x CutSmart buffer (NEB, cat. no. B6004S) at 37°C for 16 hours. Next, The restriction enzyme was heat  inactivated at 62°C for 20 min and restriction fragments ligated for 4 hours in 16°C followed by 1 hour in 25°C using 4000U of T4 ligase (NEB, cat. no.µg M0202L) in 1x T4 ligase buffer (NEB, cat. no. B0202S) with 1.25% Triton-X-100 and 10µg of BSA. The sample was decrosslinked for 16 hours at 63°C by addition of SDS to 0.5% and proteinase K to 1mg/mL (Invitrogen, cat. no. 25530-049). DNA was then extracted using phenol:chloroform: isoamyl alcohol (25:24:1). RNA in purified sample was digested with 10U of RNase A/T1 Mix (ThermoScientific, cat. no. EN0551) at 37°C for 20min  followed by inactivation and second round of decrosslinking  for 40min at 37°C with 2mg/mL pronase in 1x pronase buffer (5mM Tris, 10mM EDTA, 0.5% SDS).
ONT native barcoding library preparation according to ONT protocol SQK-NBD114.24


title: LEDGF-3XFLAG-MLL1-KO_input_1

value: input


title: HCT116 cells, 12hrs, Pore-C


title: PRO1, WT, heat-treatment 5min, rep2

library_source: other

data_processing:
library strategy: PRO-seq
ChIP-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created using deeptools software.
RNA-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using STAR aligner with -- outFilterType, BySJout; -- alignSJoverhangMin, 8; -- alignSJDBoverhangMin, 1; -- quantMode GeneCounts parameters. When we analyzed the expression of DNA sequence inculding repeat regions such as heterochromatin genes, we calculated the readcounts from bedgraph file, which was produced using the coverage function of BEDTools ver 2.17.0. Those readcount files were named as “mRNA_XXX_for_HGs.txt".
PRO-seq reads were mapped on S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created from bedgraph files using bedGraphToBigWig program.
Assembly: ASM294v2
Supplementary files format and content: bigwig file for ChIP-seq and PRO-seq
Supplementary files format and content: tab-delimited text file for RNA-seq

molecule: other


title: NIH3T3, Mic-628, rep3

description: Library name: Blaplus3


title: ChIP3, WT, H3, heat-treatment 0min, rep1

value: 0 min (non treated)


title: LEDGF-3XFLAG-MLL1-KO_IP_3


title: HCT116 cells, 6hrs, Pore-C


title: NIH3T3, Mic-628, rep2

description: Library name: Blaplus2


title: PRO1, WT, heat-treatment 0min, rep2


title: NIH3T3, vehicle, rep4

description: Library name: Control4

value: Vehicle


title: NIH3T3, Mic-628, rep1

description: Library name: Blaplus1


title: TP1_2_3

data_processing:
The sequencing data was filtered with SOAPnuke(v1.5.6) by removing reads with adapter, low-quality base and unknown base.
The clean reads were mapped to the reference genome using HISAT2 (v2.1.0)
Ericscript(v0.5.5) and rMATS(V3.2.5) were used to detect fusion gene and differential splicing genes, respectively.
Bowtie2(2.3.4.3) was applied to align the clean reads to the gene set built by BGI(Beijing Genomic Institute in ShenZhen), the expression level of gene was calculated by RSEM(v1.3.1).
Assembly: Alignment was to the transcriptome (GCF_000001405.39_GRCh38.p13)
Supplementary files format and content: tab-delimited text files include read counts for each Sample ...

source_name: lung cancer cell lines

extract_protocol:
RNA was harvested using Trizol reagent. A certain amount of RNA samples for the construction of sequencing libraries.
Libraries were prepared according to DNBSEQ' instructions

treatment_protocol: we treated lung cancer cells with equivalent volume of DMSO or TP1 for 48 hours

value: lung cancer cell lines


title: HCT116 cells, 0hrs, Pore-C


title: Cortical neurons derived from BIONi010-C iPSCs, biological replicate 2

description: Library name: Subject2_CHMP2B_WT_rep2

value: iPSC-derived cortical neurons

value: CHMP2B wild type


title: NIH3T3, vehicle, rep3

description: Library name: Control3


title: TP1_2_2


title: LEDGF-3XFLAG-MLL1-KO_IP_1


title: LEDGF-3XFLAG-MLL1-KO_IP_2


title: PRO1, WT, heat-treatment 5min, rep1


title: PRO1, WT, heat-treatment 2.5min, rep2

value: 2.5 min atter heat-treatment


title: PRO1, WT, heat-treatment 2.5min, rep1


title: 3XFLAG-LEDGF-WTrun9_IP_3

value: Human cell line (HEK293T)

value: LEDGF-WT


title: 3XFLAG-LEDGF-WTrun9_input_1


title: NIH3T3, vehicle, rep1

description: Library name: Control1


title: PRO1, WT, heat-treatment 0min, rep1

value: S.pombe cells


title: 3XFLAG-LEDGF-WTrun9_IP_2


title: RNA2, WT, heat-treatment 5min, rep3


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with HFD, replicate5

city: Hangzhou

first: Xuejing

last: Shao

address: 866, Yuhangtang Road

department: Zhejiang University

institute: College of Pharmaceutical Sciences

description: Library name: SAMPLE 20

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GRCm38/GRCh38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCm38/GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: colon

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Paired-end libraries were synthesized by using the TruSeq® RNA sample preparation kit (Illumina, USA) following TruSeq® RNA sample preparation guide.

treatment_protocol: For colonic tissue, Male C57BL/6 mice at 8 weeks old were administrated with 1.5% DSS diluted in drinking water for 7 days following 7 days of untreated drinking water.  This treatment cycle was repeated three times and followed by 7 days of 1.5% DSS solution. The entire experimental period is 50 days in total. Meanwhile, mice were randomly subjected to 4 groups fed with different diets: 7.5% PAD (7.5% PAD contains 7.5% (w/w) palmitic acid with 26.6% Kcal fat), 15% PAD (15% PAD contains 15% (w/w) palmitic acid with 45% Kcal fat), HFD (HFD contains 19.5% (w/w) lard with 45% Kcal fat) and ND as control (Normal diet contains 12.5 % Kcal fat supplemented with soybean oil). For HCT116 xenografts, Female nude mice at 4-5 weeks old were supplied with ND or 7.5% PAD for two weeks in advance (and supplied throughout the whole experimental period). Then 1×106 HCT116 cells were injected subcutaneously into these nude mice. The HCT116 xenografts were harvested after 15 days.

value: colon

value: mice exposed to DSS-induced colitis fed with HFD


title: DMSO_2_3

value: DMSO


title: 3XFLAG-LEDGF-WTrun9_IP_1

value: IP


title: TP1_2_1


title: 3XFLAG-LEDGF-1-325_input_1


title: DMSO_2_2


title: RNA2, WT, heat-treatment 2.5min, rep3

data_processing:
ChIP-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created using deeptools software.
RNA-seq reads were trimmed using Trimmomatic ver 0.33 with SE, CROP:50, ILLUMINACLIP:TruSeq3-SE.fa:2:10:10, SLIDINGWINDOW:5:20, MINLEN:30 parameters. Trimmed reads were mapped on the S.pombe ASM294v2 genome using STAR aligner with -- outFilterType, BySJout; -- alignSJoverhangMin, 8; -- alignSJDBoverhangMin, 1; -- quantMode GeneCounts parameters. When we analyzed the expression of DNA sequence inculding repeat regions such as heterochromatin genes, we calculated the readcounts from bedgraph file, which was produced using the coverage function of BEDTools ver 2.17.0. Those readcount files were named as “mRNA_XXX_for_HGs.txt".
PRO-seq reads were mapped on S.pombe ASM294v2 genome using Bowtie ver 0.12.9. The read count for each transcription unit was calculated using the coverage function of BEDTools ver 2.17.0. The bigwig files were created from bedgraph files using bedGraphToBigWig program.
Assembly: ASM294v2
Supplementary files format and content: bigwig file for ChIP-seq and PRO-seq
Supplementary files format and content: tab-delimited text file for RNA-seq


title: NIH3T3, vehicle, rep2

description: Library name: Control2

value: fibroblast

value: WT


title: RNA2, WT, heat-treatment 0min, rep3

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+


title: 3XFLAG-LEDGF-1-325_IP_3


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with HFD, replicate4

description: Library name: SAMPLE 19


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with HFD, replicate3

description: Library name: SAMPLE 18


title: 3XFLAG-LEDGF-1-325_IP_2


title: RNA2, WT, heat-treatment 5min, rep2

value: 5 min atter heat-treatment


title: 3XFLAG-LEDGF-1-325_IP_1


title: TP1_1_2


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with HFD, replicate1

description: Library name: SAMPLE 16


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with HFD, replicate2

description: Library name: SAMPLE 17


title: RNA2, WT, heat-treatment 2.5min, rep2


title: LEDGF-3XFLAG_input_1

value: input


title: TP1_1_1


title: DMSO_2_1


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with 15% PAD, replicate5

description: Library name: SAMPLE 15

value: mice exposed to DSS-induced colitis fed with 15%PAD


title: RNA2, WT, heat-treatment 5min, rep1


title: DrogADcdxB::Pxyl-cdxB-flag rep 2

city: Norwich

first: Tung

last: Le

address: Colney Lane

department: Molecular Microbiology

country: United Kingdom

institute: John Innes Centre

description: Library name: TLE18

data_processing:
All data processing was done in the Galaxy platform.
Sequencing reads were checked for quality using FastQC.
Reads were then mapped to the NA1000 reference genome using Hisat2
The sequencing coverage for each nucleotide position was determined using bedtools genome-cov.
Peaks were called using MACS2 callpeak (comparing test sample to negative control) with a significance cut off q value of <0.01
Assembly: Caulobacter crescentus NA1000 reference genome (NC_011916.1)
Supplementary files format and content: MACS2 callpeak data in .txt format

organism: Caulobacter vibrioides

source_name: bacterial cell

growth_protocol: Caulobacter crescentus cells were grown for 20h at 30 C, then back-diluted to an OD600 of 0.1 and grown for a further 20h to stationary phase.

extract_protocol:
Cells were sonicated in lysis buffer and pellted. Supernatant was incubated with anti-FLAG antibody beads at 4 C overnight. DNA was then isolated from the beads.
Libraries were prepared for Illumina sequencing using the NEXT Ultra II library preparation kit (NEB) according to the manufacturer's protocol

treatment_protocol: Cells were fixed with a final concentration of 1% formaldehyde then quenched with 250 mM glycine.

value: bacterial cell


title: DMSO_1_2

value: lung cancer cell lines


title: RNA2, WT, heat-treatment 2.5min, rep1

extract_protocol:
Total RNA for mRNA-seq was extracted by the hot-phenol method, as previously described (Iyer,V. and Struhl,K. 1996). Cell permeabilization and extraction of biotinylated RNA for PRO-seq was performed as previously described (Mahat et al., 2016). Chromatin for ChIP-seq, extracted from cell lysate of 1% formaldehyde fixed-cells, was sonicated using a Picoruptor (Diagenode).
ChIP-seq libraries were constructed using the ThruPLEX DNA-seq Kit (Clontech). mRNA-seq libraries were constructed using the KAPA mRNA HyperPrep Kit (Kapa Biosystems). cDNA libraries for PRO-seq were converted from the RNA, to which 3' and 5' adaptors were ligated, by revearse transcription.


title: DMSO_1_3


title: TP1_1_3


title: DMSO_1_1


title: LEDGF-3XFLAG_IP_1


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with 15% PAD, replicate4

description: Library name: SAMPLE 14


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with 15% PAD, replicate3

description: Library name: SAMPLE 13


title: RNA2, WT, heat-treatment 0min, rep1

value: 0 min (non treated)


title: Mouse_aorta_sections

city: Stanford

first: Thomas

last: Quertermous

state: CA

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

hyb_protocol: A total of 5000 genes (5k mouse panel) were included in the analysis. Gene panel probe hybridization occurred overnight for 18 hours at 50C. Slides were washed the next day to remove unbound probes. Ligase was added to circularize the paired ends of bound probes (2 hours at 37C) followed by enzymatic rolling circle amplification (2 hours at 30C). Slides were washed in TE buffer before background fluorescence was chemically quenched.

scan_protocol: Imaging processing, decoding quality score generation and DAPI-based cell segmentation was automatically performed by the Xenium Analyzer system.

data_processing: R using Seurat V5.0.1 and associated packages

label: Xenium probe set

source_name: Aorta

label_protocol: Xenium probe set

growth_protocol: C57BL/6 mice were treated with tamoxifen at 7 weeks of age and started on high fat diet. This diet was continued for 16 weeks prior to capture

extract_protocol: tissue preparation protocol: Tissue sections were cut at a thickness of 10uM and placed onto a Xenium slide followed by fixation and permeabilization

value: Aorta

tag: tissue preservation method

value: Fresh Frozen

value: ApoE-/-, Rosa26-Tdt+/+


title: RNA2, WT, heat-treatment 0min, rep2

value: S.pombe cells


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with 15% PAD, replicate2

description: Library name: SAMPLE 12

value: colon


title: ChIP2, WT, H3K9me2, heat-treatment 5min, rep2


title: DrogADcdxB::Pxyl-cdxB-flag rep 1

description: Library name: TLE17


title: DrogADcdxB::Pxyl-cdxB negative control rep 1

description: Library name: TLE15


title: JE2_3

city: Guelph

first: Georgina

last: Cox

state: Ontario

address: Summerlee Science Complex

department: Molecular and Cellular biology

country: Canada

institute: University of Guelph

description: Library name: Sample 7

data_processing:
usegalaxy.org  (version 24.2.rc1)
Quality control of raw reads, demultiplexing and adapter trimming were completed in advance by the SeqCenter.
Reads were aligned to the USA300 reference genome (GenBank: CP000255.1) using HISAT2 (Galaxy Version 2.2.1+galaxy1).
The number of reads mapped to the annotated genome (GCA_000013465, GFF3, EnsemblBacteria) were counted using featureCounts (Galaxy Version 2.0.8+galaxy0).
Analysis of differentially expressed genes was performed using the DESeq2 package (Galaxy Version 2.11.40.8+galaxy0)
Assembly: USA300_FPR3757
Supplementary files format and content: Text file containg raw counts for each sample

organism: Staphylococcus aureus

growth_protocol: JE2 cells were grown in tryptic soy broth to an OD600nm of 0.6

extract_protocol:
RNA was harvested using the RNeasy Mini Kit (Qiagen)
Library preparation was conducted at the SeqCenter

treatment_protocol: Cells were treated with 10 µM geranylgeranoic acid

value: Wildtype JE2


title: JE2_4

description: Library name: Sample 8


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with 7.5% PAD, replicate5

description: Library name: SAMPLE 10

value: mice exposed to DSS-induced colitis fed with 7.5%PAD


title: ChIP2, WT, H3K9me2, heat-treatment 0min, rep2

city: Bunkyo, Tokyo

first: Soichi

last: Inagaki

institute: Graduate School of Science, The University of Tokyo


title: DrogADcdxB::Pxyl-cdxB negative control rep 2

description: Library name: TLE16


title: JE2_2

description: Library name: Sample 6


title: DcdxB::Pxyl-cdxB-flag rep 1

description: Library name: TLE13


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with 7.5% PAD, replicate3

description: Library name: SAMPLE 8


title: JE2_1

description: Library name: Sample 5


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with 7.5% PAD, replicate4

description: Library name: SAMPLE 9


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with 15% PAD, replicate1

description: Library name: SAMPLE 11


title: ChIP2, WT, H3K9me2, heat-treatment 2.5min, rep1

value: 2.5 min atter heat-treatment


title: GGA_4

description: Library name: Sample 4

value: GGA


title: DcdxB::Pxyl-cdxB negative control rep 1

description: Library name: TLE11


title: ChIP2, WT, H3K9me2, heat-treatment 5min, rep1


title: DcdxB::Pxyl-cdxB negative control rep 2

description: Library name: TLE12


title: ChIP2, WT, H3K9me2, heat-treatment 2.5min, rep2


title: DcdxB::Pxyl-cdxB-flag rep 2

description: Library name: TLE14


title: SAM, 26DAS, ATAC-seq, Rep2

city: Shenzhen

first: liang

last: dong

address: No. 66, Gongchang Road, Guangming District, Shenzhen

institute: Sun Yat-Sen University

description: Library name: AT26DAS rep2

data_processing:
For bulk RNA-seq, raw sequencing data quality was assessed using Trimmomatic (v.0.33) with parameters “LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:20”. Clean reads underwent alignment to the B73 AGPv4 reference genome via HISAT2 under default settings. Uniquely mapped reads were extracted using SAMtools (v.1.9)  with filtering criteria “rmdup and mapq > 10”. For tsCUT&Tag and ATAC-seq, raw sequencing data quality control was performed using Trimmomatic with parameters “LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:20”. Clean tsCUT&Tag and ATAC-seq reads were mapped to the maize genome (B73 AGPv4) via bowtie2. Post-alignment processing involved removing PCR duplicates and low-quality reads (mapping quality < 10) using samtools. For bulk RNA-seq, clean UMI data were aligned to the maize genome using STAR mapping with customized parameters to derive UMI counts per sample. All scRNA-seq preprocessing was executed in Seurat (v.4.3.0). Cellular metrics including detected total genes (nFeature_RNA), molecules (nCount_RNA), and mitochondrial/chloroplast genome mapping percentages (percent.mt/percent.pt) were quantified per sample. Quality control applied sequential filters: cells retaining 1,800-10,000 expressed genes and 2,800-50,000 UMIs; genes detected in at least 3 cells; exclusion of cells with percent. mt or percent.pt ≥ 10%; and doublet removal via DoubletFinder (v.2.0.3).
Assembly: B73 RefGen_v4
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample
Supplementary files format and content: matrix files

organism: Zea mays

source_name: 26DAS SAM

extract_protocol:
For bulk RNA-seq, SAM samples at 14, 16, 18, 22, 26, and 28 DAS were flash-frozen with liquid nitrogen immediately after collection. Total RNA was extracted using the Direct-zol RNA Microprep Kit (Zymo Research). For ATAC-seq, approximately 25 freshly dissected SAMs were digested in 15 μl protoplast lysis buffer at the bottom of 1.5 ml tube for 2 h at room temperature in the dark with gentle shaking. For scRNA-seq, approximately ~300 SAMs with two youngest leaf primordia were dissected and enzymatically digested in 50 μl protoplast lysis buffer at the bottom of 2 ml tube for 2 h at room temperature in the dark with gentle shaking to release protoplasts. After digestion, the reaction was stopped by dilution using 1.5 ml protoplast washing buffer (lysis buffer without enzyme) and filtered through 30-μm strainers to remove debris and large aggregates. The filtrate was then centrifuged at 300 g for 3 min at room temperature to collect protoplasts. Pellets were gently resuspended and washed twice with protoplast washing buffer under the same centrifugation conditions. After washing, a final filtration step was performed to remove cell aggregates and obtained a suspension of single, dissociated cells. Cell concentration and viability were assessed by fluorescein diacetate (FDA) staining using a hemocytometer. Only samples with ≥ 75% viable cells were used.
For bulk RNA-seq, sequencing libraries were constructed with the MGIEasy RNA Library Prep Kit according to the manufacturer’s instructions. Nuclei were released by adding 1 ml release buffer (1 × PBS, 1 × protease inhibitor, 0.3% Triton X-100) and gentle pipetting. For ATAC-seq, nuclei were then collected by centrifugation and resuspended in 20 μl 1 × TTBL buffer (Vazyme, TD501). Nuclei integrity and concentration were assessed by DAPI staining. Approximately 5,000 nuclei were subjected to Tn5 transposition (Vazyme, TD501) in the presence of 0.3% Triton X-100 at 37 °C for 30 min. Transposed DNA was immediately purified using Qiagen MinElute kits and amplified for 10-13 PCR cycles according to the manufacturer’s instructions (VAHTS, TD501). Amplified DNA was size-selected using KAPA DNA Clean Beads (150-650 bp) to generate the final library, which was sequenced on an Illumina HiSeq X Ten platform (paired-end, 2 × 150 bp). For  tsCUT&Tag, full-length coding sequences of ZmMADS69 and ZmRap2.7 were cloned into the PM999-GFP vector, and plasmids were purified to transfection grade. Protoplasts were prepared from etiolated B73 seedlings grown in the dark and transfected with the GFP-tagged constructs using PEG-mediated transformation. After overnight incubation, protoplasts were processed using the Hyperactive In-Situ ChIP Library Prep Kit (Vazyme, Nanjing, China) according to the manufacturer’s instructions. Chromatin was immunoprecipitated with anti-GFP antibody (1:100 dilution), and tagmented DNA fragments were PCR-amplified and size-selected to generate sequencing libraries. Libraries were subjected to paired-end sequencing (2 × 150 bp) on an Illumina NovaSeq 6000 platform. For scRNA-seq, approximately 15,000 protoplasts were loaded into the BD Rhapsody™ Single-Cell Capture system (BD Biosciences) for scRNA-seq library construction according to the manufacturer’s protocol. Libraries were sequenced on an Illumina NovaSeq 6000 platform with paired-end 150 bp reads.

value: 26DAS SAM


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with 7.5% PAD, replicate1

description: Library name: SAMPLE 6

value: WT


title: SAM, 26DAS, ATAC-seq, Rep1

description: Library name: AT26DAS rep1


title: ChIP2, WT, H3, heat-treatment 5min, rep2

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

value: 5 min atter heat-treatment


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with ND, replicate5

description: Library name: SAMPLE 5

value: mice exposed to DSS-induced colitis fed with ND


title: GGA_3

description: Library name: Sample 3


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with 7.5% PAD, replicate2

description: Library name: SAMPLE 7


title: ChIP2, WT, H3, heat-treatment 2.5min, rep2


title: ChIP2, WT, H3K9me2, heat-treatment 0min, rep1


title: SAM, 22DAS, ATAC-seq, Rep2

description: Library name: AT22DAS rep2

source_name: 22DAS SAM

value: 22DAS SAM


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with ND, replicate4

description: Library name: SAMPLE 4


title: ChIP2, WT, H3, heat-treatment 0min, rep2

source_name: S.pombe cells


title: GGA_1

description: Library name: Sample 1


title: SAM, 22DAS, ATAC-seq, Rep1

description: Library name: AT22DAS rep1


title: SON_KD_rep3

description: Library name: SON_KD_rep3

data_processing:
Base calling, demultiplexing and FASTQ conversion
Read alignment to the human genome (GRCh38 assembly) using STAR 2.7.9a
Read alignments (.bam files) converted to bigWigs using bamCoverage 3.5.1
Assembly: hg38
Supplementary files format and content: RPKM normalized RNA-seq coverage in bigWig format

organism: Gallus gallus

extract_protocol:
Total RNA was extracted from cells with Quick-RNA MicroPrep kit (Zymo) after fractionation. Polyadenylated RNA was then isolated using Dynabeads™ mRNA Purification Kit. Purification was done twice to increase purity.
Strand-specific libraries were generated using KAPA Stranded RNA-seq Library Preparation Kit (Roche)

value: SON siRNA pool


title: GGA_2

description: Library name: Sample 2


title: SON_KD_rep1

description: Library name: SON_KD_rep1


title: colonic tissue derived from DSS-treated  C57BL/6 mice fed with ND, replicate3

description: Library name: SAMPLE 3


title: ChIP2, WT, H3, heat-treatment 5min, rep1


title: ChIP2, WT, H3, heat-treatment 0min, rep1

value: 0 min (non treated)


title: ChIP2, WT, H3, heat-treatment 2.5min, rep1


title: colonic tissue derived from DSS-treated C57BL/6 mice fed with ND, replicate2

description: Library name: SAMPLE 2


title: 3#DZCiCreb5-L, Dox+

city: Boston

first: Andrew

middle: Bruce

last: Lassar

address: 240 Longwood Ave.

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description: Library name: TRA00238152

data_processing:
For RNA-Seq analysis, all samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/). Raw RNA-Seq reads were assessed with FastQC 0.11.3 followed by MultiQC 1.2 aggregation to determine sequence quality, per-base sequence quality, per-read GC content (~50), and per base N content.
Read pairs were aligned to the bovine genome (ARS-UCD1.2/bosTau9) using STAR 2.5.2b and quality of alignments was assessed by checking for evenness of coverage, rRNA content, genomic context of alignments, complexity and other metrics with the use of Qualimap.
Expression quantification was performed with Salmon to identify transcript-level abundance estimates and then collapsed down to the gene-level using the R Bioconductor package tximport.
Principal components analysis (PCA) and hierarchical clustering methods validated clustering of samples by group. Differential expression was performed at the gene level using the R Bioconductor package DESeq2.  Counts were normalized using the median of ratios method and differentially expressed genes were identified using the Wald test, followed by Benjamini-Hochberg multiple testing correction (FDR) set at < 0.05.
Assembly: ARS-UCD1.2/bosTau9
Supplementary files format and content: tsv of nominal and adjusted p values, log2foldchange and other DESeq2 output for each gene
Supplementary files format and content: csv of normalized gene counts for each sample

organism: Bos taurus

source_name: Articular cartilage

growth_protocol: After three days of culture, RNA was harvested from lentivirus infected deep zone articular chondrocytes from three independently collected bovine knees using Trizol reagent.

extract_protocol:
RNA was extracted using Trizol agents (Life Technologies).
mRNA was purified and used to prepare the libraries using the KAPA mRNA HyperPrep Kits (Roche) following the manufacturer’s instructions.

treatment_protocol: Newly isolated bovine deep zone articular chondrocytes were cultured for at least 2-3 days before infection. Ultracentifuge-concentrated doxycycline-inducible bovine CREB5 lentivirus was added into DMEM/F12 medium (with 10% FBS) containing 7.5 μg/ml DEAE-Dextran (to increase infection efficiency).  24 hours after infection, medium was replaced with new DMEM/F12 medium (with 10% FBS) containing 500 μg/ml G418 (for 11 days) for selection. After G418 selection, infected bovine deep zone articular chondrocytes were re-plated onto low attachment tissue culture plates (Corning #3471 or #3473) in DMEM/F12 medium (with 10% FBS) in the presence of TGFb2 (20 ng/ml), TGFa (100 ng/ml) and doxycycline (1 µg/ml), without G418 (3#DZCiCreb5-L, Dox+).

value: Articular cartilage

value: Chondrocytes

value: TGFb2 (20 ng/ml), TGFa (100 ng/ml)

tag: doxycycline treatment

value: Dox+


title: SON_KD_rep2

description: Library name: SON_KD_rep2


title: NOD.B10 cLN Replicate 2

city: Buffalo

first: Jill

last: Kramer

state: NY

address: 3435 Main St

institute: SUNY at Buffalo

description: Library name: Sample4_cLN_B_NOD

data_processing:
Alignment was performed usiing HiSat2 v2.1.0
Sam files converted to sorted bam files using Samtools v1.3
Reads were counted using subread v1.6.5
Assembly: mm10
Supplementary files format and content: tab-delimited featureCount text files for each bulk RNA-seq sample

source_name: ervical lymph nodes

extract_protocol:
cLN were removed sorted purified directly into RNA storage buffer and RNA was harvested using Qiagen RNAeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ervical lymph nodes

value: cervical lymph node B-cells


title: control_rep3

description: Library name: control_rep3

value: control


title: NOD.B10 cLN Replicate 1

description: Library name: Sample3_cLN_B_NOD


title: SAM, 14DAS, ATAC-seq, Rep1

description: Library name: AT14DAS rep1

source_name: 14DAS SAM

value: 14DAS SAM


title: RNA1, WT, heat-treatment 25min, rep3

value: S.pombe cells

value: 25 min atter heat-treatment


title: SAM, 14DAS, ATAC-seq, Rep2

description: Library name: AT14DAS rep2


title: control_rep2

description: Library name: control_rep2


title: 2#DZCiCreb5-L, Dox+

description: Library name: TRA00238150


title: Control BL/10 cLN Replicate  2

description: Library name: Sample2_cLN_B_BL10


title: control_rep1

description: Library name: control_rep1


title: Control BL/10 cLN Replicate 1

description: Library name: Sample1_cLN_B_BL10


title: RNA1, WT, heat-treatment 0min, rep3


title: G4_1.0

description: Library name: WT4+GGA_1.0

data_processing:
usegalaxy.org  (version 25.1.rc1)
Quality control of raw reads, demultiplexing and adapter trimming were completed in advance by the AAC.
Reads were aligned to the USA300 reference genome (GenBank: CP000255.1) using HISAT2 (Galaxy Version 2.2.1+galaxy1).
The number of reads mapped to the annotated genome (GCA_000013465, GFF3, EnsemblBacteria) were counted using featureCounts (Galaxy Version 2.0.8+galaxy0).
Analysis of differentially expressed genes was performed using the DESeq2 package (Galaxy Version 2.11.40.8+galaxy0)
Assembly: USA300_FPR3757
Supplementary files format and content: Text file containg raw counts for each sample

growth_protocol: JE2 and JE2-saeS::Tn cells were grown in tryptic soy broth to an OD600nm of 0.3, 0.6 and 1.0

extract_protocol:
RNA was harvested using PuroSPIN Total RNA Purification Kit (Luna Nanotech).
Library preparation was conducted at the Advanced Analysis Centre (AAC) at the University of Guelph, Ontario, Canada

treatment_protocol: Cells were treated with or without 10 µM geranylgeranoic acid

value: Wildtype JE2

value: GGA


title: 1#DZCiCreb5-L, Dox+

description: Library name: TRA00238148


title: RNA1, WT, heat-treatment 5min, rep3

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

value: 5 min atter heat-treatment


title: G3_1.0

description: Library name: WT3+GGA_1.0


title: colonic tissue derived from DSS-treated C57BL/6 mice fed with ND, replicate1

description: Library name: SAMPLE 1

value: colon

value: WT

value: mice exposed to DSS-induced colitis fed with ND


title: RNA1, WT, heat-treatment 25min, rep2


title: RNA1, WT, heat-treatment 5min, rep2


title: 2#DZCiCreb5-L, Dox-

description: Library name: TRA00238144

value: Articular cartilage

value: Dox-


title: G2_1.0

description: Library name: WT2+GGA_1.0


title: B16-F10, Melanoma, B16-VC

city: Beijing

first: yanyan

last: zhu

state: Beijing

address: 10 Xitoutiao, Youanmen Wai, Fengtai District

institute: Chinese Institutes for Medical Research, Beijing

description:
Library name: Sample2
10X Genomics

data_processing:
Raw sequencing data were processed using the 10X Genomics single-cell platform. Reads were aligned to the mouse reference transcriptome mm10-2020-A
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Tumor tissues were dissected from the B16F10 mouse models. Tumors were collected 14 days post injections (n=3 for each group). Tissues were digested with agitation with 2mg/ml collagenase D and 30μg/ml DNase I for 45 minutes at 37°C. Single-cell suspensions containing tumor cells were passed through 70 μm filters and stained with LIVE/DEAD Aqua (Invitrogen; Cat #L34957) for viability, as well as APC anti-mouse CD45 (Clone 30F11; BioLegend; Cat #103112).
Viable CD45+ single cells were sorted using BD FACSAriaTM III flow cytometer. Then, the cells were sent to the 10X Genomics company for library construction and sequencing.

value: Melanoma


title: 3#DZCiCreb5-L, Dox-

description: Library name: TRA00238146

value: Chondrocytes

value: TGFb2 (20 ng/ml), TGFa (100 ng/ml)


title: B16-F10, Melanoma, B16-D

description:
Library name: Sample1
10X Genomics

value: DGAT1-knockout (KO)


title: 1#DZCiCreb5-L, Dox-

description: Library name: TRA00238142


title: G1_1.0

description: Library name: WT1+GGA_1.0


title: ZmRap2.7, tsCUT&Tag, Rep2

description: Library name: ZmRap2.7 rep2

data_processing:
For bulk RNA-seq, raw sequencing data quality was assessed using Trimmomatic (v.0.33) with parameters “LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:20”. Clean reads underwent alignment to the B73 AGPv4 reference genome via HISAT2 under default settings. Uniquely mapped reads were extracted using SAMtools (v.1.9)  with filtering criteria “rmdup and mapq > 10”. For tsCUT&Tag and ATAC-seq, raw sequencing data quality control was performed using Trimmomatic with parameters “LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:20”. Clean tsCUT&Tag and ATAC-seq reads were mapped to the maize genome (B73 AGPv4) via bowtie2. Post-alignment processing involved removing PCR duplicates and low-quality reads (mapping quality < 10) using samtools. For bulk RNA-seq, clean UMI data were aligned to the maize genome using STAR mapping with customized parameters to derive UMI counts per sample. All scRNA-seq preprocessing was executed in Seurat (v.4.3.0). Cellular metrics including detected total genes (nFeature_RNA), molecules (nCount_RNA), and mitochondrial/chloroplast genome mapping percentages (percent.mt/percent.pt) were quantified per sample. Quality control applied sequential filters: cells retaining 1,800-10,000 expressed genes and 2,800-50,000 UMIs; genes detected in at least 3 cells; exclusion of cells with percent. mt or percent.pt ≥ 10%; and doublet removal via DoubletFinder (v.2.0.3).
Assembly: B73 RefGen_v4
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample
Supplementary files format and content: matrix files
Library strategy: CUT&Tag

source_name: Leaf protoplasts

value: Leaf protoplasts


title: Citeseq, HTO, CD45+ lung cells, tube 4

city: Basel

first: Carolyn

last: King

address: Hebelstrasse 28

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description:
Library name: CD45-4_HTO
conditions and mice hashtagged, see hashtags.tsv

data_processing:
Sequencing reads were mapped to the mouse transcriptome (mm39) using STARsolo for both gene expression and antibody-bound hashtag oligos using cell barcode whitelist from cellranger-7.0.0.
Analysis steps were performed using Bioconductor packages: SingleCellExperiment, scater, scran, scuttle, SingleR. Demultiplexing hashtag oligos and doublet detection were done using DropletUtils. Cells were further filtered for library size, library complexity and mitochondrial content using adaptive thresholding provided by the R package scuttle's perCellQCFilters function with default arguments. Normalization was performed using the R package scran’s deconvolution method.
Assembly: mm39
Supplementary files format and content: tsv: UMI count matrix, cell and gene metadata, hashtag oligo metadata
Library strategy: CITE-seq

molecule: protein

source_name: lung

extract_protocol:
Lungs were digested with Liberase TL (33.3 μg/ml) and Dnase I (58 μg/ml), shaken at 37C for 30 minutes, mashed through 70 um filters, treated with ACK lysis buffer, washed and resuspended in antibody mix, washed again and resuspended, and sorted.
Library preparation was performed according to manufacturer's instructions using 10x Genomics kit version

treatment_protocol: Tamoxifen was administered days 20-24 post influxenza infection, harvest at day 35

value: lung

value: mixed (HIF KO and HIF Control)


title: RNA1, WT, heat-treatment 25min, rep1

value: S.pombe cells

value: 25 min atter heat-treatment


title: RNA1, WT, heat-treatment 0min, rep2

value: 0 min (non treated)


title: WT-4_1.0

description: Library name: WT4_1.0

value: Wildtype JE2


title: ZmRap2.7, tsCUT&Tag, Rep1

description: Library name: ZmRap2.7 rep1


title: RNA1, WT, heat-treatment 5min, rep1

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

value: 5 min atter heat-treatment


title: Citeseq, HTO, CD45+ lung cells, tube 3

description:
Library name: CD45-3_HTO
conditions and mice hashtagged, see hashtags.tsv


title: Citeseq, HTO, CD45+ lung cells, tube 2

description:
Library name: CD45-2_HTO
conditions and mice hashtagged, see hashtags.tsv


title: WT-3_1.0

description: Library name: WT3_1.0


title: Citeseq, HTO, CD45+ lung cells, tube 1

description:
Library name: CD45-1_HTO
conditions and mice hashtagged, see hashtags.tsv


title: WT-1_1.0

description: Library name: WT1_1.0


title: ZmMADS69, tsCUT&Tag, Rep2

description: Library name: ZmMADS69 rep2


title: RNA1, WT, heat-treatment 0min, rep1


title: Citeseq, scRNA-seq, CD45+ lung cells, tube 4

description:
Library name: CD45-4_GEX
conditions and mice hashtagged, see hashtags.tsv


title: WT-2_1.0

description: Library name: WT2_1.0


title: ChIP1, WT, H3K9me2, heat-treatment 25min, rep2


title: INPUT, tsCUT&Tag

description: Library name: INPUT


title: ZmMADS69, tsCUT&Tag, Rep1

description: Library name: ZmMADS69 rep1


title: sae4_1.0

description: Library name: 1.0_saeS_4

value: JE2- saeS transposon


title: Shoot, 26DAS, scRNA-seq

description: Library name: sc26DAS

source_name: 26DAS Shoot

value: 26DAS Shoot


title: ChIP1, WT, H3K9me2, heat-treatment 0min, rep2


title: sae3_1.0

description: Library name: 1.0_saeS_3


title: ChIP1, WT, H3K9me2, heat-treatment 5min, rep2


title: Citeseq, scRNA-seq, CD45+ lung cells, tube 2

description:
Library name: CD45-2_GEX
conditions and mice hashtagged, see hashtags.tsv


title: Citeseq, scRNA-seq, CD45+ lung cells, tube 3

description:
Library name: CD45-3_GEX
conditions and mice hashtagged, see hashtags.tsv


title: ChIP1, WT, H3K9me2, heat-treatment 25min, rep1


title: sae2_1.0

description: Library name: 1.0_saeS_2


title: Control Offspring Mouse Testes 2, IP

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

extract_protocol: Total RNAs were immunoprecipitated with anti-N6-methyadenosine(m6Aantibody. The immunoprecipitated lp fraction contained enriched m6Amethylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs.

value: ICR

value: male

value: day 70

value: Mouse Testes


title: 42C_5

city: Callahagn

first: benjamin

last: Robinson

state: NSW

address: University Drive

department: School of Biomedical Science and Pharmacy

country: Australia

institute: University of Newcastle

description: Library name: Sample 10

data_processing:
FASTQ data generated by Illumina DRAGEN BCL Convert 07.021.609.3.9.3 pipeline
Adapters and poor quality bases/reads were trimmed with trim_galore (cutadapt)
Trimmed sequecne reads were mapped to GRCm38
Performed TEtranscripts to generate gene and TE counts
Assembly: mm10
Supplementary files format and content: Merged tab deliminated text file contains raw TE and gene counts

source_name: Round Spermatids

extract_protocol:
RNA was extracted using Rneasy Mini plus kit (Qiagen).
Ribo-zero stranded protocol performed by Australian Genome Research Facility (AGRF)

treatment_protocol: Mice were aneanesthetised with (5% isoflurane 2L/min) then placed on a floating block with a hole cut allowing the testis to be in contact with a thermally controlled water bath. Anestesia was maintained via nose cone (1.5-2% isoflurane 2L/min). Water temperature was maintaiend at 42°C or 33°C for 30 minutes. Mice were allowed to recover from anestesia then immediatley sacrificed and round spermatids isolated.

value: Round Spermatids

value: 42°C 30 minutes


title: Citeseq, scRNA-seq, CD45+ lung cells, tube 1

description:
Library name: CD45-1_GEX
conditions and mice hashtagged, see hashtags.tsv


title: Shoot, 14DAS, scRNA-seq

description: Library name: sc14DAS

source_name: 14DAS Shoot

value: 14DAS Shoot


title: sae1_1.0

description: Library name: 1.0_saeS_1


title: Scar, PR1-Y1, scRNAseq

city: Birmingham

first: Yung-Yi

last: Chen

address: Vincent Drive

institute: University of birmingham

description:
Library name: PR1Y1
10x Genomics

data_processing:
Cellranger v7.0.0 used to generate count matricies and aggregate samples.
Assembly: hg38
Supplementary files format and content: Barcode (.tsv), matrix (.mtx) and feature (.tsv) files

source_name: skin

extract_protocol:
Skin biopsy samples (n=16) were thawed and washed with Dulbecco's Phosphate-Buffered Saline (DPBS) supplemented with 5% foetal calf serum (FCS) once before incubating with 1mg/ml collagenase P (Sigma Aldrich, UK) and 100mg/ml DNase I (Sigma Aldrich, UK) for 3.5 hours at 37°C in a humidified CO2 incubator. Cell suspensions were filtered through a 70mm cell strainer. Dissociated cells were then labelled with live and dead dye before live cell sorting using a BD LSR FORTESSAÔ X-20 Cell Analyzer (BD Biosciences, USA). Single cells were captured and barcoded using 10x Chromium platform and the sequencing libraries were prepared following manufacturer’s instructions using dual index Chromium Next GEM G Single Cell 3’ kit v3.1 (10xGemonics, California, USA)
Single cells were captured and barcoded using 10x Chromium platform and the sequencing libraries were prepared following manufacturer’s instructions using dual index Chromium Next GEM G Single Cell 3’ kit v3.1 (10xGemonics, California, USA). Libraries were quantified using an Agilent Bioanalyzer High Sensitivity DNA chip and pooled together to get similar numbers of reads from each single cell before sequencing. Overall, approximately 50,000 cells per sample were used for construction libraries and sequenced using Novogene single cell RNA sequencing services.

value: skin

value: All primary isolated skin cells

value: total RNA

value: Y1 end point


title: Shoot, 22DAS, scRNA-seq

description: Library name: sc22DAS

source_name: 22DAS Shoot

value: 22DAS Shoot


title: ChIP1, WT, H3K9me2, heat-treatment 5min, rep1

value: S.pombe cells


title: Scar, PR1-M6, scRNAseq

description:
Library name: PR1M6
10x Genomics

value: 6 Month post treatment


title: Scar, PR1-W3, scRNAseq

description:
Library name: PR1W3
10x Genomics

value: 3 Weeks post treatment


title: 1.0_JE2_3

description: Library name: 1.0_JE2_3

value: Wildtype JE2


title: 42C_3

description: Library name: Sample 8


title: 1.0_JE2_4

description: Library name: 1.0_JE2_4


title: ChIP1, WT, H3K9me2, heat-treatment 0min, rep1

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

value: 0 min (non treated)


title: MLL1-LEDGF-KO_IP_3

city: Bethesda

first: Caroline

last: Esnault

institute: NICHD NIH

data_processing:
Raw sequence reads were processed through lcdb-wf v1.6rc (https://github.com/lcdb/lcdb-wf). Briefly, raw sequence reads were trimmed with cutadapt v3.4 to remove adapters and do quality trimming with parameters “-u 3 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -q 20 –minimum-length=25” for paired-end reads or “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -q 20 – minimum-length=25” for single read. fastqc v0.11.9 with default parameters and multiqc v1.10.1 were used to estimate the sequencing library quality. The presence of common sequencing contaminants was evaluated with fastq_screen v0.14.0 with parameters “–subset 100000 –aligner bowtie2.” Trimmed reads were mapped to the human reference genome Gencode v19 GRCh37.p13) using bowtie2 v2.4.2 with parameter “--no-unal”, followed by samtools v1.12 functions view with parameter “-Sb” and function sort to sort the BAM files. Multimapping reads were filtered using samtools view with parameter “-b -q 20”. PCR duplicates were removed with picard v2.25.2 MarkDuplicates with parameters “REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT”. Bigwig files were generated with deeptools v3.5.1 bamCoverage with “--binSize 1 --minMappingQuality 20 --ignoreDuplicates --normalizeUsing CPM --extendReads 300” to visualize the signal in genome browsers. Significant ChIPseq signal peaks were computed with MACS2 v2.2.7.1 callpeak with parameters “-f BAMPE -B” or “-f BAM -B” for paired-end or single read respectively.
Assembly: hg19
Supplementary files format and content: bigwig files contain the mapped reads distribution. Technical replicates were concatenated.
Supplementary files format and content: narrowPeak files are the results of MACS2 peak calling on the IP / input.

source_name: Human cell line (HEK293T)

extract_protocol:
Antibodies for ChIPSeq: FLAG (Sigma; Cat# F1804), RNA Pol II (8WG16 BioLegend; Cat# 664912), H3K4me3 (C42D8 Rabbit mAb #9751 cell signaling), H3K36me3 (Invitrogen; MA5-24687), and MLL1 (Rabbit anti-MLL1 antibody Bethyl; Cat#A300-374A).
ChIP-Seq libraries were constructed from 40 ng of ChIP DNA using Ovation Ultralow System V2 1-96 (Tecan) with 15 cycles of PCR amplification. The final libraries were twice purified using Ampure XP PCR Purification Beads (Agencourt). The pooled libraries were sequenced on a NovaSeq 6000 (Illumina) using version 1.5 chemistry to achieve approximately 80 million 151-base read pairs. The data was processed using RTA version 3.4.4.

value: Human cell line (HEK293T)

value: LEDGF-KO

value: IP


title: 42C_1

description: Library name: Sample 6

value: Round Spermatids


title: 1.0_JE2_2

description: Library name: 1.0_JE2_2


title: ChIP1, WT, H3K4me3, heat-treatment 25min, rep2

value: 25 min atter heat-treatment


title: ChIP1, WT, H3K4me3, heat-treatment 5min, rep2

value: 5 min atter heat-treatment


title: sae4_0.6

description: Library name: 0.6_saeS_4

value: JE2- saeS transposon


title: ChIP1, WT, H3K4me3, heat-treatment 0min, rep2


title: Scar, PR1-D0, scRNAseq

description:
Library name: PR1D0
10x Genomics

value: skin

value: All primary isolated skin cells

value: Baseline- before treatment


title: 42C_2

description: Library name: Sample 7

value: 42°C 30 minutes


title: ChIP1, WT, H3K4me3, heat-treatment 5min, rep1

value: S.pombe cells


title: ChIP1, WT, H3K4me3, heat-treatment 25min, rep1


title: 33C_5

description: Library name: Sample 5

value: 33°C 30 minutes


title: sae3_0.6

description: Library name: 0.6_saeS_3


title: 42C_4

description: Library name: Sample 9


title: Scar, GR1-Y1, scRNAseq

description:
Library name: GR1Y1
10x Genomics

value: total RNA

value: Y1 end point


title: 33C_4

description: Library name: Sample 4


title: Scar, GR1-M6, scRNAseq

description:
Library name: GR1M6
10x Genomics

value: 6 Month post treatment


title: ChIP1, WT, H3K4me3, heat-treatment 0min, rep1

value: h+ ade6-DN/N leu1-32 ura4-DS/E imr1L::ura4+ otr1R::ade6+

value: 0 min (non treated)


title: 33C_3

description: Library name: Sample 3


title: sae2_0.6

description: Library name: 0.6_saeS_2


title: 1.0_JE2_1

description: Library name: 1.0_JE2_1

value: Wildtype JE2


title: Scar, GR1-D0, scRNAseq

description:
Library name: GR1D0
10x Genomics


title: ChIP1, WT, H3K4me2, heat-treatment 25min, rep2


title: sae1_0.6

description: Library name: 0.6_saeS_1


title: 33C_2

description: Library name: Sample 2


title: Scar, GR1-W3, scRNAseq

description:
Library name: GR1W3
10x Genomics

value: 3 Weeks post treatment