title: BHdeltarnc_MinusN_rep2

city: Bremen

first: Shanmugam

last: Solaiyappan Mani

address: Leobner strasse

department: Department of Microbe-Plant Interactions

institute: University of Bremen

description:
BHΔrnc (RNase III Knockout mutant of strain BH72)
rRNA eliminated total RNA

data_processing:
The Illumina sequencing reads were trimmed using the fastp tool based on the adapter sequence (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) and read quality. Reads with at least one “N” base or more than 10 bases with Phred score less than 10 were removed.From the 5’ and 3’ end of the reads, bases up to a 3 nucleotide window that had a mean quality score less than 10 were also dropped.
Processed reads were aligned to the genome sequence of Azoarcus olearius strain BH72 using the READemption tool with its default parameters. Only reads that mapped uniquely were considered for quantification.
Raw coverage values for the annotated CDSs, tRNAs and predicted ncRNAs were rounded and used for differential expression analysis using DEseq2 tool. The results were optimized for an FDR cutoff value of 0.05 by independent filtering of genes based on mean normalized counts.
Genes with Padj < 0.05 and Fold-change > 1.8 were considered to be differentially regulated
Assembly: AM406670.1 Azoarcus olearius BH72, complete genome
Supplementary files format and content: Matrix table in xlsx with raw gene counts for every CDS , tRNA and ncRNA from every sample

organism: Azoarcus olearius

source_name: BH{delta}rnc (RNase III Knockout mutant of strain BH72)

growth_protocol: Azoarcus olearius strain BHΔrnc was grown in minimal SM medium ([Reinhold B, Hurek T, Fendrik I (1985) Strain-specific chemotaxis of Azospirillum spp. J Bacteriol 162: 190–195.]) microaerobically (0.3% O2) in a bioreactor (Minifors, infors HT) at 37 °C with constant stirring at 600 rpm. The medium was either supplemented with 10 mM ammonium chloride (ammonium-based growth) or not (N2-fixing).

extract_protocol:
30 mL of harvested culture was frozen in liquid N2. RNA was extracted from the frozen cells using Hot phenol method. Genomic DNA was eliminatedby using RNeasy Plus Mini Kit (Qiagen, Catalog no. 74134). Ribosomal RNA was depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina, Catalog no. MRZB12424).
The samples were fragmented by 4 pulses of ultrasound, 30 s each, at 4 °C. To aid in directional sequencing, 3’ Illumina TruSeq sequencing adapter, with barcodes, was ligated to the 3’ end of the fragmented RNA molecules. First-strand cDNA was synthesized using M-MLV reverse transcriptase and a primer binding to the adapter sequence. Synthesized cDNA was purified, and to its 3’ end the 5’ Illumina TruSeq sequencing adapter, also containing barcodes, was ligated. The cDNA was amplified through 13 cycles of PCR, using a high fidelity DNA polymerase, to obtain about 10-20 ng/µl of DNA. Amplified cDNA was purified using AgencourtAMPure XP kit (Beckman Coulter Genomics). The six samples were pooled in approximately equimolar amounts and size-fractionated using a preparative agarose gel to obtain the size range between 200 and 400 bp. The sample pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length.

treatment_protocol: Three replicates supplemented with 10 mM ammonium chloride (ammonium-based growth), two replicates without ammonium chloride (N2-fixing).

value: Without ammonium chloride

value: RNase III Knockout mutant


title: NFkB_act_input_A549_rep2

status: Public on Jun 30 2026

type: SRA

city: Vienna

first: Tomas

last: Pachano

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description:
Library name: Sample 16
164bp

library_source: genomic

data_processing:
Adapters were trimmed using trim galore
Trimmed reads were aligned with Bowtie2 to a custom dictionary indexes of BCs, where each BC is associated to its assigned ORF
The resulting BAM file was used to construct a raw count matrix for each BC
The resulting BC count matrix was used as an input to MAGeCK tool (https://doi.org/10.1186/s13059-014-0554-4) to identify ORFs that are enriched in each screen.
Assembly: custom Dictionary of BC-eORFs
Supplementary files format and content: tab-delimited text file includes raw counts for each BC id. Each BC id contains a number and the id of its associated ORF (e.g. BC23_1893 correspond to the BC 23 of ORF 1893, and the ORF id can be associated to a specific ORF through table S1).

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: A549 cells were cultured at 37ºC in DMEM (In-house) supplemented with 10% heat inactivated FBS (Gibco, S0615), L-glutamine (Gibco, 25030081) and penicillin-streptomycin (Gibco, 15140122) and passaged every 3 days. U937 cells were cultured at 37ºC in RPMI (Gibco, 11875093) supplemented with 10% FBS (Gibco, S0615) and passaged every 3 days.

extract_protocol:
Genomic DNA (gDNA) was isolated by lysing cell pellets overnight at 55°C in a buffer containing 10 mM Tris-HCl (pH 8.0), 5 mM EDTA, 100 mM NaCl, 1% SDS, and 0.5 mg/ml proteinase K. The lysate was then treated with RNase A (Qiagen) for 2 hours at 37°C. Subsequently, gDNA was purified through two sequential extractions with phenol:chloroform:isoamyl alcohol followed by a final extraction with chloroform:isoamyl alcohol. For barcode (BC) recovery, the entire gDNA yield from sorted/selected samples and 40 µg of gDNA from input samples were used as templates.
To generate NGS libraries,  40 individual PCR reactions were performed for each gDNA sample. The PCR adds Illumina adaptors and indexes for each sample. Following amplification, all PCR reactions for a given sample were pooled. The pooled amplicons were concentrated and purified using the Monarch PCR & DNA Cleanup Kit (NEB), using six columns for each input sample and one column for each sorted/selected sample. The final purified barcode amplicons were gel-extracted and submitted for next-generation sequencing.

treatment_protocol: For each biological replicate, cells were transduced at a multiplicity of infection (MOI) below 0.2 to ensure single-copy integration while maintaining a library representation of at least 10,000-fold. Twenty-four hours post-transduction, cells were selected with 1 µg/ml puromycin, after which eORF expression was induced with 1 µg/ml doxycycline for 24 hours. For the reporter-based screens, procedures were as follows: for the NF-κB activation screen, a baseline sample of 15 million cells was collected as the "input" control before the remaining cells were sorted for the GFP-positive population (top 5%) using a BD FACSAria III sorter. For the inhibition screens, cells were first treated with either 20 ng/mL TNFα (NF-κB inhibition) or 2.5 µM Nutlin (p53 inhibition) for 16 hours. After this treatment, the 15 million cell "input" sample was collected, and the remaining cells were sorted to isolate the GFP-low or mCherry-low populations (bottom 5%), respectively, using a BD FACSAria III sorter. For the apoptosis inhibition screen, transduced A549-Eco cells were split post-induction into two conditions: a control group maintained in doxycycline and a treatment group cultured with both doxycycline and etoposide (0.1 uM). These populations were maintained for 10 days, splitting them at a 1:4 ratio upon reaching confluency. At the conclusion of each screen, genomic DNA was isolated from all collected cell populations (input, sorted, or treated) for subsequent barcode analysis (see below). All screens were performed in two independent biological replicates.

tag: cell line

tag: treatment

value: input


title: BHdeltarnc_MinusN_rep1

country: Germany

library_source: transcriptomic

molecule: total RNA

tag: strain

value: BH{delta}rnc (RNase III Knockout mutant of strain BH72)

tag: genotype


title: BHdeltarnc_plusN_rep3

value: With 10 mM ammonium chloride


title: BU-LF-41

city: Jacksonville

last: Zhao

state: FL

address: 4500 San Pablo Rd S

department: Neuroscience

country: USA

institute: Mayo Clinic

description: Library name: BU-LF-41

data_processing:
RNA sequencing reads were processed through the Mayo Clinic RNA sequencing analytic pipeline, MAPRSeq Version 3.1.3. Briefly, reads were aligned to the mouse reference genome mm10 using STAR version 2.6.1c. Quality control (QC) was performed using RSeQC version 2.6.4. Gene counts were generated using featureCounts version 1.5.1. Genes were filtered out from further analyses if there were not at least four samples with 10 counts of the gene.
Conditional quantile normalization (CQN) was performed on the raw gene counts to correct for gene length differences, GC bias, and global technical variations and to obtain similar quantile-by-quantile distributions of gene expression levels across samples.
Based on the bimodal distribution of the CQN-normalized and log2-transformed reads per kilobase per million (RPKM) gene expression values, genes with log2 RPKM ≥ 2 in all samples were considered expressed. Using this selection threshold, 18,592 genes were included in the downstream analysis.
Assembly: mm10
Supplementary files format and content: .tsv of raw gene counts

organism: Mus musculus

source_name: Cortical RNA

extract_protocol:
Total RNA was extracted from the cortex using Trizol reagent and cleaned using RNeasy spin columns with DNase treatment to remove contaminating genomic DNA.
RNA libraries were prepared from 200 ng of total RNA using the TruSeq Stranded RNA Sample Prep Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions, employing poly-A mRNA enrichment using oligo-dT magnetic beads. The final adaptor-modified cDNA fragments were enriched by 15 cycles of PCR using Illumina TruSeq PCR primers. The concentration and size distribution of the completed libraries were determined using an Agilent Tape Station, (Agilent, Santa Clara, CA) and Qubit fluorometer (Invitrogen, Carlsbad, CA).
Libraries from all samples were sequenced on Illumina’s NovaSeq 6000 at 50 million fragment reads/sample following Illumina’s standard protocol on two S2 flow cells. S2 flow cells were sequenced at 101 x 2 paired end reads using a NovaSeq S2 sequencing kit, NovaSeq Control Software v1.7.0 and base-calling was analyzed using Illumina’s RTA version 3.4.4.

treatment_protocol: For each APOE genotype group, 12-month-old mice were assigned to one of two feeding regimens for 32 weeks: AL feeding with a normal diet or 30% CR with a normal diet. CR feeding was provided daily during a fixed time slot (3–4 pm).

tag: tissue

value: Cortical RNA

value: AL

tag: Sex

value: Female


title: NFkB_act_input_A549_rep1

description:
Library name: Sample 15
164bp


title: BU-LF-40

description: Library name: BU-LF-40

value: male


title: BHdeltarnc_plusN_rep2


title: BHdeltarnc_plusN_rep1


title: BU-LF-38

description: Library name: BU-LF-38

value: CR


title: normal skin5, Sup

type: RNA

city: Changsha

first: Wei

last: Liu

state: Hunan

address: 139 Renmin central road,Furong district

department: Otolaryngology

country: China

institute: the second xiangya hospital of central south university

description:
S5 Sup
Biological replicate 5 of 5 S.
lncRNA/mRNA SUP (m6A unmodified RNA).

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human epitranscriptomic Arrays (8x60K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing:
Data was extracted using Agilent Feature Extraction software. A series of data processing including quantile normalization were performed using the R software package.
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and/or Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.

source_name: normal skin

label_protocol: Total RNAs were immunoprecipitated with anti-N6-methyladenosine (m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs. IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit (Arraystar, Inc.)

growth_protocol: Middle ear cholesteatoma and normal skin.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Tissues from middle ear cholesteatoma surgery and promptly frozen in liquid nitrogen.

value: normal skin

tag: gender

value: female

tag: age


title: BU-LF-35

description: Library name: BU-LF-35


title: normal skin3, IP

description:
S3 IP
Biological replicate 3 of 5 S.
lncRNA/mRNA IP (m6A modified RNA).


title: normal skin3, Sup

description:
S3 Sup
Biological replicate 3 of 5 S.
lncRNA/mRNA SUP (m6A unmodified RNA).


title: normal skin2, Sup

description:
S2 Sup
Biological replicate 2 of 5 S.
lncRNA/mRNA SUP (m6A unmodified RNA).


title: p53_2_input_A549_rep1

description:
Library name: Sample 11
164bp


title: BU-LF-34

description: Library name: BU-LF-34


title: normal skin2, IP

description:
S2 IP
Biological replicate 2 of 5 S.
lncRNA/mRNA IP (m6A modified RNA).


title: Tcell-3

city: kisarazu

first: Keiko

last: Nakano

state: chiba

address: kazusa-kamatari 2-6-7

country: Japan

institute: Kazusa DNA Research institute

description:
Library name: Tcell-3
Column name in CPM_count1.tsv: Tcell-3

data_processing:
For 3' mRNA sequencing (QuantSeq), single-end reads (101 bp) were processed using fastp (version 0.23.4) to remove adapter sequences and poly(A) tails.
Clean reads were aligned using STAR (version 2.7.10a) to the following reference genomes: - Mus musculus: GRCm39 (mm39; GCA_000001635.9) - Homo sapiens: GRCh38 (hg38; GCA_000001405.15)
Gene-level read counts were generated using Subread featureCounts (version 2.0.6) at the meta-feature (exon) level using Ensembl annotations: - Mus musculus: Ensembl release 113 (Mus_musculus.GRCm39.113.gtf) - Homo sapiens: Ensembl release 115 (Homo_sapiens.GRCh38.115.gtf)
Counting was performed with strand-specific settings (forward), assigning reads to gene_id.
CPM values were calculated for each sample using a scaling factor (1,000,000 divided by the total assigned reads).
Assembly: Mus musculus: GRCm39 (Ensembl release 113 / GCA_000001635.9) Homo sapiens: GRCh38 (Ensembl release 115 / GCA_000001405.15)
Supplementary files format and content: Excel files include CPM values for each Sample

source_name: T cell

extract_protocol:
See method in article
Quant-Seq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)

tag: cell type

value: T cell

value: WT


title: normal skin1, IP

description:
S1 IP
Biological replicate 1 of 5 S.
lncRNA/mRNA IP (m6A modified RNA).


title: p53_2_screen_A549_rep1

description:
Library name: Sample 9
164bp

value: screen


title: htz-1(bon101), young adult, rep 3

city: Bonn

first: Daniele

last: Bano

state: NRW

address: Venusberg Campus 1/99

institute: DZNE, German Center for Neurodegenerative Diseases

description: Library name: Sample3

data_processing:
RNA sequencing was performed using 75 bp paired-end reads (PE75) on a NovaSeq X Plus (Illumina) with a 10B flow cell. Total RNA was extracted using the miRNeasy Micro Kit and quality-controlled for concentration and size distribution on a TapeStation 4200 system using RNA ScreenTape.
Libraries were prepared following the bulk SMART-Seq2 protocol from 200 pg input RNA and assessed using D1000 ScreenTape on the TapeStation 4200. Sequencing reads were pseudo-aligned to the C. elegans reference genome (Ensembl release 109) using Kallisto (v0.48).
Assembly: WBcel235
Supplementary files format and content: csv file includes normalized counts for each sample.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Nematode animals were cultured on OP50-1 E. coli at 20 ℃.

extract_protocol:
Young adult worms were collected and dissolved in 1ml Trizol (Invitrogen). Total RNA was extracted using miRNeasy Micro Kit (Qiagen).
Libraries were prepared using SMART-Seq2 protocol (Picelli et al., 2014).

value: whole animal

tag: batch


title: BU-LF-58

description: Library name: BU-LF-58


title: normal skin1, Sup

description:
S1 Sup
Biological replicate 1 of 5 S.
lncRNA/mRNA SUP (m6A unmodified RNA).


title: BU-LF-26

description: Library name: BU-LF-26


title: middle ear cholesteatoma5, Sup

description:
C5 Sup
Biological replicate 5 of 5 C.
lncRNA/mRNA SUP (m6A unmodified RNA).

source_name: middle ear cholesteatoma

value: middle ear cholesteatoma


title: BU-LF-51

description: Library name: BU-LF-51


title: htz-1(bon101), young adult, rep 1

description: Library name: Sample1


title: middle ear cholesteatoma5, IP

description:
C5 IP
Biological replicate 5 of 5 C.
lncRNA/mRNA IP (m6A modified RNA).


title: ATAC_4_KO1_Treg_melanoma_RbpdeltaFoxp3a

city: Heraklion

first: Matthieu

middle: David

last: Lavigne

address: Nikolaou Plastira 100

country: Greece

institute: IMBB-FORTH

description:
Library name: ATAC_4_KO1
KO1.bam
Rbpj_ATACseq_counts_table.csv

data_processing:
For full-length mRNA-seq, Raw sequence data were quality-controlled using FastQC version 0.12.0 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Adapter sequences and poor-quality bases were removed with Cutadapt version 1.1656. Paired-end reads were aligned to the mouse genome GRCm38 using Rsubread version 2.12.3. Alignments were performed using default parameters. Reads associated with annotated genes were counted using the Rsubread function ‘featureCount’. Differentially expressed genes were identified using an FDR cut-off below 0.05 after normalization in EdgeR version 3.40.2 (PMID: 19910308)
Quant-seq: The quality of the FASTQ files was assessed with the FastQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads were aligned to the mouse (mm10) genome  with the Hisat2 aligner (hisat2 -p32 -x $REFERENCE_GENOME -q fastq/$FILE_ID.fastq -S $FILE_ID.sam --score-min L,0,-0.5 -k 2). Htseq-counts was utilized to summarize reads at the gene level (htseq-count -f bam -s yes-igene_idbam/$FILE_ID.bamdata/refs/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf>$COUNTS_DIR/NGS$FILE_ID). Differential expression analysis (DEA) was conducted by running EdgeR via SARTools 1.5.0. For each comparison, DEGs were defined by applying the following thresholds adj. p-value <0.05, which was considered statistically significant.
Read quality was assessed using FastQC version 0.12.0 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Adapters and poor-quality bases were trimmed using fastp version 0.23.4 (PMID: 30423086). Samples were aligned to the mouse reference genome GRCm38 using default parameters in Rsubread version 2.12.3 (PMID: 30783653).  Mitochondrial reads were removed using SAMtools version 1.18. PCR duplicates were removed using the ‘MarkDuplicates’ function in Picard Tools version 17.0.13 (Java) (http://broadinstitute.github.io/picard/). Open chromatin was detected using MACS2 version 2.2.9.1 with an FDR < 0.05. The number of reads in each peak was determined using featureCounts embedded in Rsubread version 2.12.3. Differentially accessible peaks were identified using an FDR cut-off below 0.05 after normalization in DESeq2 version 1.38.3 (PMID: 25516281). Peaks were annotated using the ‘annotatePeak’ function using ChIPseeker version 1.34.1.  The bamCoverage function from deepTools version 3.5.6 was used to generate coverage track (BigWig) files. Trackplot version 1.6.0 was utilized to create IGV-style track plots (also known as locus plots) from BigWig files. Pheatmap version 1.0.12 was used to generate the heatmap of differentially accessible regions (DARs).
Assembly: mm10
Supplementary files format and content: Quant-seq: raw_counts_table_LTvT_quant-seq.txt, This matrix includes  counts of reads in ESMUSG Ensemble genes id  for 3 biological replicates (sample LT1,LT2,LT3 - TDLN_Treg cells_Foxp3EGFP mice; sample T1, T2, T345 - tumor_Treg cells_Foxp3EGFP mice)
Supplementary files format and content: ATAC-seq count matrix (Rbpj_ATACseq_counts_table.csv: This matrix excludes blacklisted regions, mitochondrial reads, and peaks detected in only one sample  (WT1, WT2, WT3:  biological Replicates of Tregs from Foxp3YFPcre;   KO1, KO2, KO3: biological Replicates of Tregs from Foxp3YFPcre RbpjΔFoxp3)
Supplementary files format and content: full length mRNA-seq raw count data (Rbpj_RNAseq_countdata.csv): Row names correspond to gene IDs, and column names represent the samples: (WT1, WT2, WT3:  biological Replicates of Tregs from Foxp3YFPcre;   KO2 KO3, KO4: biological Replicates of Tregs from Foxp3YFPcre RbpjΔFoxp3)

source_name: tumor melamoma

growth_protocol: murine B16.F10 melanoma, were cultured at 37°C under 5% CO2 in complete medium [RPMI-1640 medium (GlutaMAXTM, Gibco, #61870) supplemented with 10% foetal bovine serum (FBS, Gibco, #10270), 0.1% β-mercaptoethanol (Gibco, #31350) and 1% of a mix of Penicillin/Streptomycin (P/S, Gibco, #15140)]. B16.F10 melanoma and MB49 urothelial cancer cells were split at 90%–100% confluence.

extract_protocol:
For Full length strand-specific mRNA-seq, Treg cells (CD45+CD4+ Foxp3YFP+) were FACS-sorted from melanoma tumors of Foxp3YFPcre or RbpjΔFoxp3and RNA was extracted using the ArcturusTM PicoPure TM RNA isolation kit (Thermo Fisher, #12204-01) according to the manufacturer’s protocol. For Quant-seq (T1-345, LT1-3), total RNA was extracted from FACS-sorted Tregs cells derived TDLNs or tumors of Foxp3EGFP melanoma-bearing mice, using NucleoSpin RNA XS (Macherey-Nagel; cat. #740955.50) as per the manufacturer’s protocol. The quantity and quality of RNA samples were analyzed using Agilent RNA 6000 Nano kit with the bioanalyzer from Agilent.
For Full length strand-specific mRNA-seq, RNA-seq libraries were prepared using NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module according to manufacturer’s instructions and starting with three replicates per group and 50-120 ng of pure total RNA extracted from 18-28.000 sorted cells. Libraries were prepared using sample specific combinations of i5 and i7 indexed adapters, amplified for 16-18 cycles according to qPCR estimates and were size selected for sizes around 400 bp. Paired-end reads (2*111) were sequenced on an Illumina NextSeq 2000 at Genecore EMBL, DE. For Quant-seq (T1-345, LT1-3,) RNA samples with RNA integrity number (RIN)>7 were used for library construction using the 3′ mRNA-Seq Library Prep Kit FWD for Illumina (QuantSeq-LEXOGEN) as per the manufacturer’s instructions. Amplification was controlled for obtaining optimal unbiased libraries across samples by assessing the number of cycles (ranging from 19-20 cycles) required by qPCR. DNA High Sensitivity Kit for bioanalyzer was used to assess the quantity and quality of libraries, according to the manufacturer’s instructions (Agilent). Libraries were multiplexed and sequenced on an Illumina Nextseq 500 at the genomics facility of IMBB FORTH, GR. according to the manufacturer’s instructions.
The ATAC-seq protocol was performed as previously described57,58. In brief, 2-5 x 104 Treg cells were FACS-sorted (CD45+CD4+Foxp3YFP+) from melanoma tumors of Foxp3YFPcre or RbpjΔFoxp3, washed with ice-cold PBS and resuspended in lysis buffer [0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin in Resuspension Buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2)]. Cell nuclei were washed (0.1% Tween-20 in Resuspension Buffer) and the transposition reaction was performed by using Tn5 Transposase in tagmentation buffer (Illumina Tagment DNA enzyme and Buffer, #20034210), 10%Tween-20, 1%Digitonin and incubating for 30min at 37oC. DNA was purified with the the MinElute Cleanup Kit (Qiagen, #28204) and amplified using the NEBNext High-Fidelity PCR Master Mix (New England BioLabs) and Nextera PCR primers with sample specific combinations of i5 and i7 indexes. Library were size selected for sizes between 200 and 500 bp using AMPure XP beads (Beckman Coulter). Paired-end reads (2*111) were sequenced on an Illumina NextSeq 2000 at Genecore EMBL, Heidelberg.

treatment_protocol: melanoma tumors growth in Foxp3YFPcre, RbpjΔFoxp3 and  Foxp3EGFP mice was monitored after implanting subcutaneously on the back 3 x 10^5 B16.F10 melanoma cells in each tested mouse.

value: tumor melamoma

value: Treg

value: subcutaneous implantation 3 x 10^5 B16.F10 melanoma cells


title: BU-LF-25

description: Library name: BU-LF-25


title: NFkB_screen_A549_rep2

description:
Library name: Sample 8
164bp


title: NFkB_screen_A549_rep1

description:
Library name: Sample 7
164bp


title: middle ear cholesteatoma4, Sup

description:
C4 Sup
Biological replicate 4 of 5 C.
lncRNA/mRNA SUP (m6A unmodified RNA).


title: ATAC_1_WT1_Treg_melanoma_Foxp3YFPcre

description:
Library name: ATAC_1_WT1
WT1.bam
Rbpj_ATACseq_counts_table.csv


title: middle ear cholesteatoma4, IP

description:
C4 IP
Biological replicate 4 of 5 C.
lncRNA/mRNA IP (m6A modified RNA).


title: BU-LF-22

description: Library name: BU-LF-22


title: middle ear cholesteatoma3, Sup

description:
C3 Sup
Biological replicate 3 of 5 C.
lncRNA/mRNA SUP (m6A unmodified RNA).


title: NFkB_input_A549_rep2

description:
Library name: Sample 6
164bp

value: input


title: BU-LF-42

description: Library name: BU-LF-42


title: NFkB_act_screen_A549_rep2

description:
Library name: Sample 14
164bp


title: BU-LF-19

description: Library name: BU-LF-19


title: middle ear cholesteatoma3, IP

description:
C3 IP
Biological replicate 3 of 5 C.
lncRNA/mRNA IP (m6A modified RNA).


title: NFkB_input_A549_rep1

description:
Library name: Sample 5
164bp


title: middle ear cholesteatoma2, Sup

description:
C2 Sup
Biological replicate 2 of 5 C.
lncRNA/mRNA SUP (m6A unmodified RNA).


title: BU-LF-18

description: Library name: BU-LF-18


title: middle ear cholesteatoma2, IP

description:
C2 IP
Biological replicate 2 of 5 C.
lncRNA/mRNA IP (m6A modified RNA).


title: RA -FLS siFUNDC1 6

city: Guangzhou

first: Yaxiong

last: FANG

address: No.1 Du Xue Rd, Nansha District

institute: HKUSTGZ

description:
Library name: Sample 12
12_siFUNDC1

data_processing:
Sequencing was performed on an AVITI instrument (Element Biosciences, San Diego, CA, USA) using a paired-end (PE150) strategy, which provides 150 base pair reads from each end of the RNA fragments.
Assembly: hg19
Supplementary files format and content: csv files include TPM values for each sample

source_name: synovial tissues

extract_protocol:
Total RNA was extracted from the samples using TRIzol reagent (Takara, 9108, Japan) according to the manufacturer's instructions.
RNA-seq libraries were prepared using the Watchmaker Genomics protocols. Specifically, the 7K0077-096 Polaris Depletion Kit  was employed for rRNA depletion, followed by library preparation using the 7K0078-096 Watchmaker RNA Library Prep Kit. The libraries were generated according to the manufacturer's guidelines, ensuring the incorporation of unique adapter sequences for multiplexing.

value: synovial tissues

value: fibroblast-like synoviocytes

value: FUNDC1 knockdown


title: Setaria italica leaf H3K27ac CUT&Tag GCSY_K27_R1

city: Xi'an

first: Huiying

last: Shang

address: Cuihua Road No. 17

institute: Xi'an Botanical Garden

description:
Library name: SITALICA_leaf_H3K27ac_GCSY_K27_R1
H3K27ac CUT&Tag source sample used to build the S. italica regulatory atlas. Source sample id GCSY_K27_R1. Plant material: Xiaomi early-maturing foxtail millet mutant, provided by the Minor Grain Molecular Breeding Team Germplasm Resource Bank, Shanxi Agricultural University. Growth conditions: 14 h light at 28 C and 10 h dark at 22 C, 50% humidity.

data_processing:
Raw paired-end reads were quality controlled and aligned to the corresponding reference genome using Bowtie 2 compatible workflows.
Duplicate reads were evaluated using Picard MarkDuplicates outputs where available, and deduplicated alignments were used for downstream summaries.
Normalized signal tracks were generated in bigWig format for H3K27ac signal visualization.
Sample-level H3K27ac peaks were called and exported as broadPeak files. S. italica source peak sets were merged to generate a nonredundant consensus H3K27ac atlas.
The S. viridis CUT&Tag dataset was processed as a single validation sample and used only for representative locus-level support.
Assembly: Setaria italica v1.0, Setaria viridis v4.0 GCA_005286985.2
Supplementary files format and content: bigWig files contain normalized H3K27ac signal tracks for each CUT&Tag library.
Supplementary files format and content: broadPeak files contain sample-level H3K27ac peak calls, and the BED file contains the merged S. italica consensus H3K27ac peak atlas.
Library strategy: CUT&Tag

organism: Setaria italica

source_name: leaf

growth_protocol: Plants were grown under standard conditions for the source experiment. Heading-stage stem, leaf, and panicle tissues were used where tissue information was available.

extract_protocol:
Nuclei or chromatin-associated material was prepared for CUT&Tag profiling of H3K27ac. Antibody details must be confirmed before final submission, including vendor, catalog number, and lot number.
CUT&Tag libraries were prepared for H3K27ac profiling and sequenced as paired-end genomic DNA libraries. Sequencing platform and instrument model must be confirmed before final submission.

treatment_protocol: No experimental treatment was applied. Samples represent tissue-specific H3K27ac CUT&Tag profiling and one S. viridis validation library.

value: leaf

value: Xiaomi early-maturing mutant

tag: antibody

value: H3K27ac antibody, Active Motif, catalog 39685, mouse polyclonal; lot not available


title: BU-LF-17

description: Library name: BU-LF-17

value: Cortical RNA

value: AL

value: Female


title: BU-LF-36

description: Library name: BU-LF-36

value: CR

value: male


title: middle ear cholesteatoma1, Sup

description:
C1 Sup
Biological replicate 1 of 5 C.
lncRNA/mRNA SUP (m6A unmodified RNA).


title: Setaria italica stem H3K27ac CUT&Tag GCSJ_K27_R1

description:
Library name: SITALICA_stem_H3K27ac_GCSJ_K27_R1
H3K27ac CUT&Tag source sample used to build the S. italica regulatory atlas. Source sample id GCSJ_K27_R1. Plant material: Xiaomi early-maturing foxtail millet mutant, provided by the Minor Grain Molecular Breeding Team Germplasm Resource Bank, Shanxi Agricultural University. Growth conditions: 14 h light at 28 C and 10 h dark at 22 C, 50% humidity.

source_name: stem

value: stem


title: RA -FLS siFUNDC1 5

description:
Library name: Sample 11
11_siFUNDC1


title: middle ear cholesteatoma1, IP

description:
C1 IP
Biological replicate 1 of 5 C.
lncRNA/mRNA IP (m6A modified RNA).

value: middle ear cholesteatoma


title: normal skin4, Sup

description:
S4 Sup
Biological replicate 4 of 5 S.
lncRNA/mRNA SUP (m6A unmodified RNA).

value: normal skin

value: female


title: normal skin5, IP

description:
S5 IP
Biological replicate 5 of 5 S.
lncRNA/mRNA IP (m6A modified RNA).


title: NFkB_act_screen_A549_rep1

description:
Library name: Sample 13
164bp

value: screen


title: p53_2_input_A549_rep2

description:
Library name: Sample 12
164bp

value: input


title: Setaria italica panicle H3K27ac CUT&Tag GCSS_K27_R1

description:
Library name: SITALICA_panicle_H3K27ac_GCSS_K27_R1
H3K27ac CUT&Tag source sample used to build the S. italica regulatory atlas. Source sample id GCSS_K27_R1. Plant material: Xiaomi early-maturing foxtail millet mutant, provided by the Minor Grain Molecular Breeding Team Germplasm Resource Bank, Shanxi Agricultural University. Growth conditions: 14 h light at 28 C and 10 h dark at 22 C, 50% humidity.

source_name: panicle

value: panicle


title: BU-LF-14

description: Library name: BU-LF-14


title: Setaria italica leaf H3K27ac CUT&Tag G_BJ_Y_K27_r1

description:
Library name: SITALICA_leaf_H3K27ac_G_BJ_Y_K27_r1
H3K27ac CUT&Tag source sample used to build the S. italica regulatory atlas. Source sample id G_BJ_Y_K27_r1. Plant material: Xiaomi early-maturing foxtail millet mutant, provided by the Minor Grain Molecular Breeding Team Germplasm Resource Bank, Shanxi Agricultural University. Growth conditions: 14 h light at 28 C and 10 h dark at 22 C, 50% humidity.


title: normal skin4, IP

description:
S4 IP
Biological replicate 4 of 5 S.
lncRNA/mRNA IP (m6A modified RNA).


title: BU-LF-10

description: Library name: BU-LF-10


title: Stage 28 gonad, female, rep2

city: Dos Hermanas

first: Iván

last: Barberá Aura

address: Avenida Rectora Rosario Valpuesta 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo (CABD)

description:
Library name: female_28_rep2
10x genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, alignment to genome and transcriptome, gene counting and aggregation was performed using the Cell Ranger software (v7.0.2)
Assembly: UM_NZW_1.0 (GCA_009806435.2)
Supplementary files format and content: Barcode, feature tsv files and matrix files from filtered CellRanger output.

organism: Oryctolagus cuniculus

source_name: Embryonic gonad

growth_protocol: Pregnant New Zealand White rabbits at the stages 13-21 dpc were obtained from Charles River (France branch). For 24 and 28 dpc, fetal ovaries were obtained from New Zealand rabbits bred at the SAJ rabbit facility (Jouy-en-Josas, France).

extract_protocol:
Pregnant New Zealand White rabbits at the stages 13-21 dpc were obtained from Charles River (France branch). Dissected gonads were dissociated into single-cells by incubating them with 0.05% Trypsin-EDTA (Gibco cat#25300-054) in addition to 1/10 portion of 5% BSA (Sigma-Aldrich cat#A7030-50G) /DPBS for 7-10 minutes at 37ºC. Dissociation was facilitated by pipetting gently every 2-3 minutes. Residual connective tissue, which appeared as whitish clumps at the end of the dissociation process, was discarded. Trypsin activity was halted by adding 2 portions of 5% BSA/DPBS. Cell suspension was passed through a 40 µm FlowMi cell strainer (Fisher Scientific cat#15342931) to remove cell clumps and debris. Filtrated cells were collected by centrifugation at 250-300g for 5 minutes at 4°C. The cell pellet was resuspended in DPBS for counting and viability check using 50% v/v trypan blue staining (Sigma Aldrich cat#T8154-20ML) under a light microscope. Only samples with ≥ 80% were used for downstream single-cell library preparation. Finally cells were fixed with 98% methanol added drop by drop and stored in -80°C freezer. For ovaries collected at 24 and 28 dpc, gonads were obtained from New Zealand rabbits bred at the SAJ rabbit facility (Jouy-en-Josas, France). The two gonads from the same fetus were pooled per stage in 500 µl of Trypsin-EDTA 0.05% at 37°C for 30 min. Dissociation was facilitated by gently pipetting every 5 minutes. Tryspin activity was stopped by adding SVF for a final 2% concentration. The cell suspension was passed through a 70 µm filter, then a 40 µm FlowMi Cell Strainer (Sigma-Aldrich cat #BAH136800040) to remove cell clumps and debris. The filtrated cells were collected by centrifugation at 300g for 10 minutes. The cell pellet was resuspended in 500 µL (24 dpc) or 1 mL (28 dpc) of DMEM/F12-SVF 2%. To determine whether the obtained cells were suitable for downstream analysis (cell viability > 80%), cell viability was evaluated using trypan blue staining with a haemocytometer r (TC20, Bio-Rad cat#1450102). The cell concentration was then adjusted to around 1000 cells/μl before loading onto the single-cell chip.
For the data from gonads at the stages 13-21 dpc, fixed cells were equilibrated to 4ºC on ice for at least 5 minutes. Subsequently, the cells were pelleted at 1,000g for 5 minutes at 4℃. The cells were rehydrated and gently washed with rehydration buffer (0.04% BSA, 1mM DTT (Life Technologies cat#707265ML), 0.4U/µl RNaseIn (Life Technologies cat#AM2682), 0.2U/µl SuperaseIn (Life Technologies cat#AM2696), in DPBS), using wide-bore tips (Corning Axygen Cat#T- 205-WB-C-R-S). Cell number and quality after rehydration were assessed using 50% v/v trypan blue staining. Cell suspensions were adjusted to a final concentration of 700-1,200 cells/µl. Single-cell libraries were generated using the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics), according to manufacturer’s instructions, targeting 10,000 cells per reaction. Two libraries were prepared for each developmental stage and sex, except for female gonads at stage 15, for which only one library was prepared. Libraries were sequenced to a minimum depth of 200 million reads per library using the paired-end sequencing format: Read 1, 28 cycles; I7 index, 10 cycles; I5 index, 10 cycles; Read 2, 90 cycles.  For the data from ovaries at 24 and 28 dpc, Gel-Bead in Emulsions (GEMs) were generated using a Chromium 10X Single Cell System (10X Genomics) and cDNA libraries were prepared using the Chromium Next GEM Single Cell 5' Reagent v2 (10X Genomics). Two libraries were prepared for each developmental stage. The I2BC High-throughput Sequencing Platform (https://www.i2bc.paris-saclay.fr/sequencing/ng-sequencing/; Université Paris-Saclay, Gif-sur-Yvette, France) provided the facilities and expertise for library preparation and sequencing (Paired-end 28-64 bp, Illumina NextSeq500).

value: Embryonic gonad

value: WT

value: Stage 28


title: RA -FLS siFUNDC1 3

description:
Library name: Sample 9
9_siFUNDC1

value: synovial tissues

value: fibroblast-like synoviocytes

value: FUNDC1 knockdown


title: Setaria italica stem H3K27ac CUT&Tag G_BJ_J_K27_r1

description:
Library name: SITALICA_stem_H3K27ac_G_BJ_J_K27_r1
H3K27ac CUT&Tag source sample used to build the S. italica regulatory atlas. Source sample id G_BJ_J_K27_r1. Plant material: Xiaomi early-maturing foxtail millet mutant, provided by the Minor Grain Molecular Breeding Team Germplasm Resource Bank, Shanxi Agricultural University. Growth conditions: 14 h light at 28 C and 10 h dark at 22 C, 50% humidity.

value: Xiaomi early-maturing mutant

value: H3K27ac antibody, Active Motif, catalog 39685, mouse polyclonal; lot not available


title: Setaria italica leaf H3K27ac CUT&Tag gcsyk27r1

description:
Library name: SITALICA_leaf_H3K27ac_gcsyk27r1
H3K27ac CUT&Tag source sample used to build the S. italica regulatory atlas. Source sample id gcsyk27r1. Plant material: Xiaomi early-maturing foxtail millet mutant, provided by the Minor Grain Molecular Breeding Team Germplasm Resource Bank, Shanxi Agricultural University. Growth conditions: 14 h light at 28 C and 10 h dark at 22 C, 50% humidity.

value: leaf


title: BU-LF-7

description: Library name: BU-LF-7

value: Cortical RNA

value: AL

value: Female


title: Stage 28 gonad, female, rep1

description:
Library name: female_28_rep1
10x genomics


title: RA -FLS siFUNDC1 2

description:
Library name: Sample 8
8_siFUNDC1


title: Stage 24 gonad, female, rep2

description:
Library name: female_24_rep2
10x genomics

value: Stage 24


title: RA -FLS siFUNDC1 1

description:
Library name: Sample 7
7_siFUNDC1


title: BU-LF-4

description: Library name: BU-LF-4

value: CR

value: male


title: Setaria italica panicle H3K27ac CUT&Tag gcssk27r1

description:
Library name: SITALICA_panicle_H3K27ac_gcssk27r1
H3K27ac CUT&Tag source sample used to build the S. italica regulatory atlas. Source sample id gcssk27r1. Plant material: Xiaomi early-maturing foxtail millet mutant, provided by the Minor Grain Molecular Breeding Team Germplasm Resource Bank, Shanxi Agricultural University. Growth conditions: 14 h light at 28 C and 10 h dark at 22 C, 50% humidity.


title: Setaria italica leaf H3K27ac CUT&Tag CGYK27R1

description:
Library name: SITALICA_leaf_H3K27ac_CGYK27R1
H3K27ac CUT&Tag source sample used to build the S. italica regulatory atlas. Source sample id CGYK27R1. Plant material: Xiaomi early-maturing foxtail millet mutant, provided by the Minor Grain Molecular Breeding Team Germplasm Resource Bank, Shanxi Agricultural University. Growth conditions: 14 h light at 28 C and 10 h dark at 22 C, 50% humidity.


title: Stage 24 gonad, female, rep1

description:
Library name: female_24_rep1
10x genomics

value: female


title: SENP7 siRNA (Replicate 3)

city: hannover

first: arnab

last: nayak

address: carl-neuberg-str 1

institute: MHH

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version v2.20.0.422 (Illumina).
Raw data processing was conducted by use of nfcore/rnaseq (v 1.4.2). The pipeline uses Nextflow ( v20.01.0) workflow tool and includes read trimming (Trim Galore! v0.6.4), alignment (STAR v2.6.1d), and counting (featureCounts  v1.6.4).
Normalization and differential expression analysis was performed on the internal Galaxy (version 20.05) instance of the RCU Genomics, Hannover Medical School, Germany with DESeq2 (Galaxy Tool Version 2.11.40.6) with default settings except for “Output normalized counts table”, which was set to “Yes” and all additional filters were disabled (“Turn off outliers replacement”, “Turn off outliers filtering”, and “Turn off independent filtering” set “Yes”).
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text files include normalized espression values as a matrix table for all samples (DESeq2 output)

source_name: mouse C2C12 myotubes

growth_protocol: DMEM+2% horse serum with antibiotics (1X penicillin streptomycin)

extract_protocol:
Total RNA extraction by using kit from Roche
Library generation, quality control, and quantification:   500ng of total RNA per sample were utilized as input for mRNA enrichment procedure with ‘NEBNext® Poly(A) mRNA Magnetic Isolation Module’ (E7490L; New England Biolabs) followed by stranded cDNA library generation using ‘NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina’ (E7760L; New England Biolabs). All steps were performed as recommended in user manualE7760 (Version 1.0_02-2017; NEB) except that all reactions were downscaled to 2/3 of initial volumes.   cDNA libraries were barcoded by dual indexing approach, using ‘NEBNext Multiplex Oligos for Illumina – 96 Unique Dual Index Primer Pairs’ (6440S; New England Biolabs). All generated cDNA libraries were amplified with 7 cycles of final pcr.   One additional purification step was introduced at the end of the standard procedure, using 1.2x ‘Agencourt® AMPure® XP Beads’ (#A63881; Beckman Coulter, Inc.). Fragment length distribution of individual libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific).     Library denaturation and Sequencing run:   Equal molar amounts of individually barcoded libraries were pooled for a common sequencing run in which each analyzed library constituted 16.7% of overall flowcell / run capacity. The library pool was denatured with NaOH and was finally diluted to 1.8pM according to the Denature and Dilute Libraries Guide (Document # 15048776 v02; Illumina). 1.3ml of the denatured pool was loaded on an Illumina NextSeq 550 sequencer using a Mid Output Flowcell (130M cluster) for 2x75bp paired-end reads (20024904; Illumina). Sequencing was performed with the following settings: Sequence reads 1 and 2 with 76 bases each; Index reads 1 with 8 bases each; no index reads 2.

treatment_protocol: 100 pmol siRNA treatment for three days

tag: replicate

value: Replicate 3

value: SENP7 siRNA


title: BU-LF-3

description: Library name: BU-LF-3


title: RA-FLS siNC 6

description:
Library name: Sample 6
6_siNC

value: WT

value: siNC


title: RA-FLS siNC 5

description:
Library name: Sample 5
5_siNC

value: synovial tissues


title: BU-LF-6

description: Library name: BU-LF-6


title: neurons,cK2c,week18,male,rep3 (9407_H3K4me3)

city: Philadelphia

first: Matthew

last: Edwards

state: PA

address: 450 Clinical Research Building

department: Genetics

institute: University of Pennsylvania School of Medicine

description: Library name: 9407_H3K4me3

data_processing:
CUT&Tag profiles for all four histone marks were trimmed using Cutadapt and aligned to the mm10 using bowtie2.  Reads were then centered and extended to represent the full DNA fragment, and were normalized using base-pair normalization with the Deeptools BamCoverage function.
Assembly: mm10
Supplementary files format and content: Bigwig tracks of histone modifications after BPM normalization
Library strategy: CUT&Tag

source_name: Cortex

extract_protocol:
Cut&Tag was used to profile H3K4me3, H3K4me2, H3K4me1 and H3K27ac in eighteen-week-old cortical neurons. The CUT&Tag-direct V.3 protocol31,32 were performed with minor modifications. For each sample, 50,000 GFP⁺/NeuN⁺ excitatory neuron nuclei were bound to Concanavalin-A beads (3.5 µL bead slurry per reaction) and incubated with primary antibodies (1:50 dilution) overnight at 4°C: H3K4me1 (EpiCypher #13-0057), H3K4me2 (EpiCypher #13-0027), H3K4me3 (Active Motif #39159), or H3K27ac (Active Motif #39133). After washing, bead-bound nuclei were incubated with guinea pig anti-rabbit secondary antibody for 30 min at room temperature. Protein A–Tn5 transposome (pAG-Tn5; EpiCypher #15-1117) was added (2.5 µL per reaction) and incubated for 1 hr at room temperature, followed by tagmentation at 37°C for 1 hour.Tagmented chromatin was released by incubation with 0.1% SDS at 58°C for 1 hr and neutralized with 0.67% Triton-X100.
Libraries were amplified using NEBNext High-Fidelity 2× PCR Master Mix (non-hot-start) (NEBNext #M0541L) with unique dual indexes (Buenrostro-style i7/i5 indexing) for 11–12 cycles depending on mark abundance. PCR products were cleaned with 1.3× SPRI bead purification, eluted in 13.2 µL, and assessed by Qubit and Bioanalyzer.

value: Cortex

value: In vivo

value: Excitatory neurons

value: conditional kmt2c knockout


title: GL2 (control) siRNA (replicate 3)


title: p53_2_screen_A549_rep2

description:
Library name: Sample 10
164bp

value: screen


title: neurons,cK2c,week18,male,rep3 (9407_H3K4me2)

description: Library name: 9407_H3K4me2


title: Setd2-ISC-KO

city: Shanghai

first: Yue

last: Xu

address: 上海市徐汇区华山路

institute: 上海交通大学

description: Library name: Sample4

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

source_name: intestine

extract_protocol:
The ATAC experiments were performed as described (Buenrostro et al., 2013).
Cells were  vehicle treated and then collected and treated with transposase Tn5 (Nextera DNA Library Preparation Kit, Illumina). DNA was purified using MinElute PCR Purification Kit (Qiagen). All samples were then amplified by PCR using NEBNextHigh-Fidelity 2× PCR Master Mix (New Englands Labs) with primers containing a barcode to generate libraries. DNA was again purified using AMPure Beads.DNA libraries for ATAC-seq were prepared using NextEra Library Prep Kit following manufacturer's protocols.

value: intestine

value: Intestinal stem cell


title: RA-FLS siNC 4

description:
Library name: Sample 4
4_siNC

value: fibroblast-like synoviocytes


title: SENP7 siRNA (Replicate 2)

value: Replicate 2


title: Setd2-ISC-WT

description: Library name: Sample3


title: BU-LF-31

description: Library name: BU-LF-31

value: Cortical RNA

value: CR

value: Female


title: RA -FLS siFUNDC1 4

description:
Library name: Sample 10
10_siFUNDC1

value: FUNDC1 knockdown


title: RA-FLS siNC 3

description:
Library name: Sample 3
3_siNC


title: GL2 (control) siRNA(replicate 2)


title: Nsd2-ISC-KO

description: Library name: Sample2


title: neurons,cK2c,week18,male,rep3 (9407_H3K4me1)

description: Library name: 9407_H3K4me1


title: Nsd2-ISC-WT

description: Library name: Sample1


title: RA-FLS siNC 1

description:
Library name: Sample 1
1_siNC


title: GL2 (control) siRNA (Replicate 1)

value: Replicate 1


title: Setd2-ISC-KO

description: Library name: Sample3


title: neurons,cK2c,week18,male,rep2 (497_H3K4me3)

description: Library name: 497_H3K4me3


title: neurons,cK2c,week18,male,rep2 (497_H3K4me2)

description: Library name: 497_H3K4me2


title: Rat gut spatial transcriptomics high fat diet tirzepatide

city: Saskatoon

first: Changting

last: Xiao

state: SK

address: 107 Wiggins Rd

country: Canada

institute: University of Saskatchewan

description:
Library name: HFD_TZP
10x Genomics Visium spatial transcriptomics of rat intestinal tissue from chow diet control treated with PBS (library Li52152-A-C5)

data_processing:
Raw sequencing reads were processed with SpaceRanger to generate spatial gene expression matrices. Downstream analyses were performed in Seurat v5, including quality control, SCTransform normalization, integration, PCA, UMAP, differential expression analysis using the Wilcoxon rank-sum test, and Gene Ontology enrichment analysis using clusterProfiler.
Assembly: Rattus norvegicus reference genome used by SpaceRanger; exact assembly version not provided in the manuscript.
Supplementary files format and content: Processed data files include filtered_feature_bc_matrix.h5 files containing spatial gene-by-barcode count matrices and tissue_positions.csv files containing spot coordinate information for each Visium library.
Library strategy: Spatial Transcriptomics

organism: Rattus norvegicus

source_name: gut

extract_protocol:
Male Sprague-Dawley rats were fed chow diet or high-fat diet, treated with PBS or tirzepatide, and jejunal tissue was collected at the end of the experiment. Jejunal tissue sections (10 µm) were prepared for spatial transcriptomics analysis.
Jejunal tissue sections (10 µm) were processed using the 10x Genomics Visium V1 platform according to the manufacturer's protocol to generate spatially barcoded cDNA libraries.

value: gut

value: intestinal tissue (Visium spatial transcriptomics capture spots)

value: High fat diet + tirzepatide


title: neurons,cK2c,week18,male,rep2 (497_H3K4me1)

description: Library name: 497_H3K4me1

value: Cortex


title: apoptosis_screen_A549_rep1

description:
Library name: Sample 3
164bp


title: ISC-WT

description: Library name: Sample1


title: neurons,cK2c,week18,male,rep2 (497_H3K27ac)

description: Library name: 497_H3K27ac

value: In vivo


title: apoptosis_input_A549_rep2

description:
Library name: Sample 2
164bp

value: input


title: Rat gut spatial transcriptomics CD tirzepatide

description:
Library name: CD_TZP
10x Genomics Visium spatial transcriptomics of rat intestinal tissue from chow diet control treated with PBS (library Li52152-A-C5)

value: Chow diet + tirzepatide


title: neurons,cK2c,week18,male,rep1 (174_H3K4me3)

description: Library name: 174_H3K4me3

value: Excitatory neurons

value: conditional kmt2c knockout


title: apoptosis_input_A549_rep1

description:
Library name: Sample 1
164bp


title: Setd2-ISC-KO-H3K27me3

description: Library name: Sample12-SETD2-KO-H3K27me3

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

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

value: intestine

value: Intestinal stem cell


title: Rat gut spatial transcriptomics high fat diet PBS

description:
Library name: HFD_PBS
10x Genomics Visium spatial transcriptomics of rat intestinal tissue from chow diet control treated with PBS (library Li52152-A-C5)

value: High fat diet + PBS


title: Rat gut spatial transcriptomics CD PBS

description:
Library name: CD_PBS
10x Genomics Visium spatial transcriptomics of rat intestinal tissue from chow diet control treated with PBS (library Li52152-A-C5)

value: Chow diet + PBS


title: Setd2-ISC-KO-H3K4me3

description: Library name: Sample11-SETD2-KO-H3K4me3


title: neurons,cK2c,week18,male,rep1 (174_H3K4me2)

description: Library name: 174_H3K4me2


title: Sojd_CHR_H3K4me3_Passage38

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description:
Library name: Sojd_CHR_H3K4me3_Passage38
cut_and_tag_later_timepoints_H3K4me3_peaks.tsv.gz

data_processing:
Quality control, trimming and mapping of the FASTQ files was performed using the cutandrun pipeline (version 3.2.1), distributed by nf-core [doi: 10.5281/zenodo.2634132]. The pipeline was configured so that each constituent component was under version control and executed within a Singularity container [https://sylabs.io].  The following command was used to execute the pipeline:  nextflow run nf-core/cutandrun -r 3.2.1 --input samplesheet.csv --genome homo_sapiens.GRCh38.release_102 -config config.config --blacklist ENCFF356LFX.txt --normalisation_mode CPM --use_control false --skip_heatmaps --outdir results -bg  These parameters generally adhered to the defaults set by the nf-core cutandrun pipeline.  Reads were mapped to the human reference genome (GRCh38 / release 102), but reads mapping to regions blacklisted by the ENCODE project [https://www.encodeproject.org/files/ENCFF356LFX/] were removed. The pipeline was also passed a sample list detailing the forward and reverse FASTQ file pairings, along with the sample identities, antibodies used, and how technical and biological replicates should be grouped together. The pipeline used the software SEACR (version 1.3)102 to identify peaks i.e genomic regions with a localised high abundance of mapped reads. SEACR was run using the default settings for the cutandrun pipeline, but no IgG control was provided.
Consensus peaks were identified separately for the H3K4me3 and the H3K27me3 antibodies. Peaks present in at least 2 of any of the biological replicates were considered as “consensus peaks” and retained.  Since the start and end positions of peaks rarely match to the exact base position between samples, overlapping peak regions from different biological replicates were merged together.
The number of reads mapping to each peak was quantitated using the genome browser and analysis software SeqMonk (version 1.48.1) [https://www.bioinformatics.babraham.ac.uk/projects/seqmonk]. To achieve this, the aligned reads BAM files generated by the nf-core cutandrun pipeline were imported into SeqMonk, along with a text-format list detailing peak genomic locations. By using the “Feature Probe Generator” and “Read Count Quantitation” SeqMonk functions, an “Annotated Probe Report” was created listing the raw read counts for each peak. A separate file was also created using this method, but instead it reported the log2-transformed normalised data (counts per million reads) for each peak.
FASTQ files could not be submitted for male HipSci cell lines owing to donor confidentiality regarding chromosome Y sequence information. Instead, BAM files generated by the nf-core atacseq pipeline (described previously) were submitted.  The BAM files were filtered by using samtools v1.21  to   contain only reads mapping to autosomes and chromosome X.
Assembly: GRCh38
Supplementary files format and content: The processed data files list the coordinates of the peak regions and the associated log2-transformed read count (per million reads) mapping to each peak, as quantitated by the genome browser and analysis software SeqMonk.
Library strategy: CUT&Tag

growth_protocol: All cell lines were cultured under atmospheric oxygen, 5% CO2 and at 37 degrees C in Essential 8 (E8) medium (Thermo Fisher A1517001) on TC-treated 6 well plates (Corning 3506) coated with rh-VTN (Thermo Fisher A14700) at 10 mcg/well in PBS without calcium or magnesium. For CHR lines culture plates were coated with rhL521 (Gibco A29249) at 5mcg per well of a 6 well plate in DPBS with calcium and magnesium (Gibco 14040133) and cells were cultured in Stemflex (ThermoFisher, A3349401) supplemented with 3mcM IWP2 (Cayman Chemicals 13951).

extract_protocol:
CUT&Tag was carried out using EpiCypher CUTANA™ CUT&Tag Protocol v 1.7. 120,000 cells per CUT&Tag experiment were harvested for nuclei extraction. The cell suspension was centrifuged for 3 minutes at 300 RCF at RT. The cell pellet was resuspended in 100 µl/sample of cold nuclei extraction buffer (20 mM HEPES–KOH, pH 7.9, 10 mM KCl, 0.1% Triton X-100, 20% Glycerol, 0.5 mM Spermidine (Sigma-Aldrich, 05292), 1x Roche cOmpleteTM, Mini, EDTA-free Protease Inhibitor) and incubated on ice for 10 minutes, followed by centrifugation for 3 minutes at 600 RCF and 4°C. The nuclei pellet was resuspended in nuclei extraction buffer to achieve a final concentration of 1.2 million nuclei/ml and frozen at -80°C until library preparation. Upon thawing of the nuclei suspension, 100µl of the suspension (120,000 nuclei) was aliquoted to be used per CUT&Tag reaction.
Concavalin A (ConA) beads (EpiCypher, 21-1401) were transferred to a 1.5ml Eppendorf tube on a magnetic stand and washed twice with cold bead activation buffer (20 mM HEPES pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). Beads and buffer were added at 11µl and 100µl per sample, respectively, and after washing, the beads were resuspended in a final volume of 11μl of buffer per sample. 10µl of ConA bead slurry was aliquoted into each sample tube of an 8-strip tube containing 100µl nuclei per tube for batch processing. The ConA bead and nuclei mixture was vortexed gently to mix and incubated at RT for 10 minutes. The tubes were placed on a magnetic stand and the supernatant removed. Each nuclei sample was resuspended in 50µl of cold Antibody150 buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin (Sigma-Aldrich, D141-100MG), 2mM EDTA) containing primary antibody (anti-H3K27me3 (Active Motif; 39157; dilution 1:50), anti-H3K4me3 (Active Motif; 39160; dilution 1:50), anti-IgG negative control antibody (EpiCypher; 13-0042; dilution 1:50). Samples were then gently mixed and incubated overnight at 4°C on an orbital shaker. The next day, the tubes were placed on a magnet and the supernatant discarded. Each sample was resuspended in 50µl Digitonin150 buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin) containing 0.5μg of secondary antibody (anti-rabbit Epicypher; 13-0047) for 1 hr at RT on a nutator. After the incubation, the samples were placed on a magnet and washed twice with Digitonin150 buffer. The samples were then resuspended in 50µl Digitonin300 buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin), and 1.25μl of CUTANA pAG-TN5 (EpiCypher, 15-1017) was added. Samples were then gently mixed and incubated for 1hr at RT on a nutator. After the incubation, the samples were placed on a magnet and washed twice with Digitonin300 buffer (20mM HEPES, pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1x Roche cOmpleteTM, Mini, EDTA-free Protease Inhibitor, 0.01% digitonin). The samples were then resuspended in 50 µl of Tagmentation buffer (Digitonin 300 Buffer, 10 mM MgCl2) and incubated for 1hr at 37°C in a thermocycler. Then the sample tubes were placed on a magnet and the supernatant discarded, the samples were then resuspended in 50µl TAPS buffer (10 mM TAPS, pH 8.5, 0.2 mM EDTA). The tubes were returned to the magnet and the supernatant removed, followed by addition of 5µl SDS release buffer (0.5M HEPES-NaOH pH 8.5, 10% SDS). The reaction mixture was vortexed on maximum speed for 10s and briefly centrifuged. The samples were then incubated on the thermocycler for 1hr at 58℃. The SDS was neutralised by the addition of 15µl SDS quench buffer (0.67% Triton-X 100), vortexed at maximum speed for 10s, and centrifuged briefly. The libraries were amplified using KAPA HiFi HotStart ReadyMix (Roche Diagnostics Ltd, KK2602). 25ul KAPA HiFi HotStart ReadyMix per CUT&Tag reaction (mastermix only) was incubated at 95℃ for 3 min and cooled to 22℃ in a thermocycler. 1μl of each of barcoded i5 and i7 primers (5μM stock) and 25µl of the previously heated mastermix was added to the DNA. PCR was conducted using the following programme: extension step at 72°C for 5 min, denaturation at 98°C for 45 s, 13-15 cycles (denaturation at 98°C for 10s and short extension at 60°C for 10s), and final extension at 72°C for 1 min. Amplified libraries were cleaned twice using 1X volume of AMPure XP Beads (Beckman Coulter; A63881) and resuspended in 15μl of 0.1X TE buffer. Size distribution and yield quantification of the CUT&Tag libraries were tested using an Agilent 2100 Bioanalyzer high sensitivity DNA chip (Agilent 5067–4626). Libraries were then multiplexed and sequenced (paired-end 150 bp) on a NovaSeq X Plus Series PE150 (Illumina) to a depth of a minimum 10 million reads per replicate.

treatment_protocol: no treatment

value: human pluripotent stem cells


title: LPA4-KO, SNI, rep4

city: izunokuni mifuku

first: takahisa

last: shimoda

state: Shizuoka

institute: Asahi Kasei Pharma

description: Library name: sample16

data_processing:
Sequencing was conducted on the Illumina NovaSeq platform in paired-end mode (150 bp × 2) (performed by Takara Bio, Shiga, Japan).
Raw sequencing reads were subjected to quality control using fastp (v0.22.0).
High-quality reads were aligned to the rat reference genome (mRatBN7.2) using STAR aligner (v2.7.9a).
Gene-level counts and transcripts per million (TPM) were calculated using RSEM (v1.3.1).
Assembly: mRatBN7.2
Supplementary files format and content: CSV (Comma-Separated Values) file includes raw counts for each sample

molecule: polyA RNA

source_name: spinal dorsal horn

extract_protocol:
Total RNA was purified using the Monarch Total RNA Miniprep Kit (Catalog # NEB #T2110, New England Biolabs, Ipswich, MA, USA) .
Total RNA was processed for sequencing using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA, USA).

value: spinal dorsal horn


title: neurons,cK2c,week18,male,rep1 (174_H3K4me1)

description: Library name: 174_H3K4me1


title: Setd2-ISC-KO-H3K4me1

description: Library name: Sample10-SETD2-KO-H3K4me1


title: Sojd_CHR_H3K27me3_Passage_38

description:
Library name: Sojd_CHR_H3K27me3_Passage_38
cut_and_tag_later_timepoints_H3K27me3_peaks.tsv.gz


title: Setd2-ISC-KO-H3K27ac

description: Library name: Sample9-SETD2-KO-H3K27ac


title: neurons,cK2c,week18,male,rep1 (174_H3K27ac)

description: Library name: 174_H3K27ac


title: Sojd_CHR_H3K4me3_Passage_37

description:
Library name: Sojd_CHR_H3K4me3_Passage_37
cut_and_tag_later_timepoints_H3K4me3_peaks.tsv.gz


title: neurons,WT,week18,male,rep3 (9771_H3K4me3)

description: Library name: 9771_H3K4me3

value: wild-type


title: Sojd_CHR_H3K27me3_Passage_37

description:
Library name: Sojd_CHR_H3K27me3_Passage_37
cut_and_tag_later_timepoints_H3K27me3_peaks.tsv.gz


title: Nsd2-ISC-KO-H3K4me3

description: Library name: Sample7-NSD2-KO-H3K4me3


title: Sojd3_CHR_Passage38

description:
Library name: Sojd3_CHR_Passage38
p37_p38_salmon.merged.gene_tpm.tsv.gz

data_processing:
Quality control, trimming and mapping of the FASTQ files was performed using the rnaseq pipeline (version 3.12.0), distributed by nf-core [doi: https://zenodo.org/records/7998767]. The pipeline was configured so that each constituent component was under version control and executed within a Singularity container [https://sylabs.io]. The following command was used to execute the pipeline:  nextflow run nf-core/rnaseq -r 3.12.0 --input samplesheet.csv --genome homo_sapiens.GRCh38.release_102 -config config.txt --extra_trimgalore_args '--nextseq 20' --outdir results --deseq2_vst -bg  These parameters generally adhere to the defaults set by the nf-core rnaseq pipeline. That pipeline release used STAR (version 2.7.9a) as the aligner, mapping reads to the human reference genome (GRCh38 / release 102). The specified read trimming parameter (--nextseq 20) were sequencing platform-specific, to account for the Illumina colour chemistry in which high quality calls for guanine nucleotides may actually reflect no signal on a flow cell. The pipeline was also passed a sample list detailing the forward and reverse FASTQ file pairings, along with the sample identities and how any technical and biological replicates should be grouped together. The nf-core rnaseq pipeline produces quantitated expression values for every gene for each sample, reporting raw counts and TPM values. These expression matrices were used in subsequent analyses.
FASTQ files could not be submitted for male HipSci cell lines owing to donor confidentiality regarding chromosome Y sequence information. Instead, BAM files generated by the nf-core atacseq pipeline (described previously) were submitted.  The BAM files were filtered by using samtools v1.21  to   contain only reads mapping to autosomes and chromosome X.
Assembly: GRCh38
Supplementary files format and content: The processed data files list the TPM expression values for each gene, segmented by biological replicate.  These data were produced by the nf-core rnaseq pipeline.

extract_protocol:
700,000 hiPSCs or hESCs were used for RNA extraction for each biological replicate. Cells were washed once with 1ml Dulbecco's Phosphate Buffered Saline (DPBS) and harvested using 500µl Accutase (StemCell Technologies, 07922) for 3 minutes at 37°C. Dissociated cells were then collected with 5ml of corresponding hPSC medium and centrifuged for 3 min at 400 RCF at RT. Supernatant was aspirated and the cells were resuspended in 1ml cold DPBS. RNA extraction from hiPSCs/hESCs was conducted using the Monarch Total RNA Miniprep Kit (NEB T2010S) according to the manufacturer’s protocol, with DNase I treatment used to enzymatically remove residual gDNA. RNA concentration was quantified using Nanodrop and the RNA Integrity Number (RIN) was assessed using the Agilent RNA 6000 Pico Kit (Agilent, 5067-1513) on Agilent 2100 Bioanalyzer (Agilent). A RIN value of >7 was deemed to be of good quality and used for downstream RNA-seq library processing. The isolated RNA was frozen and stored at -80°C until RNA-seq library preparation.
RNA-seq library preparation was performed on the isolated RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module, which isolated mRNA from total RNA (100ng input) by poly(A)-enrichment. RNA-seq libraries were subsequently prepared from the isolated mRNA using the NEBNext Ultra II Directional RNA Library Prep Kit from Illumina, the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L), and the NEBNext Multiplex Oligos from Illumina (Index Primers Set 1, 2, 3 and 4, NEB, E7335S, E7500S, E7710S, E7730S), following the manufacturer’s protocols. The final sequencing-ready libraries were amplified using the protocol’s PCR programme with 12 cycles. Size distribution and yield quantification of the RNA-seq libraries were assessed using an Agilent 2100 Bioanalyzer high sensitivity DNA chip (Agilent 5067–4626).


title: Nsd2-ISC-KO-H3K4me1

description: Library name: Sample6-NSD2-KO-H3K4me1


title: Nsd2-ISC-KO-H3K27me3

description: Library name: Sample8-NSD2-KO-H3K27me3


title: neurons,WT,week18,male,rep3 (9771_H3K4me1)

description: Library name: 9771_H3K4me1


title: Sojd3_CHR_Passage37

description:
Library name: Sojd3_CHR_Passage37
p37_p38_salmon.merged.gene_tpm.tsv.gz


title: Nsd2-ISC-KO-H3K27ac

description: Library name: Sample5-NSD2-KO-H3K27ac


title: neurons,WT,week18,male,rep3 (9771_H3K27ac)

description: Library name: 9771_H3K27ac


title: Nsd2-ISC-WT-H3K27me3

description: Library name: Sample4-WT-H3K27me3


title: Fiaj1_organoids_Day20

description:
Library name: Fiaj1_organoids_Day20
day20_salmon.merged.gene_tpm.tsv.gz


title: Nsd2-ISC-WT-H3K4me3

description: Library name: Sample3-WT-H3K4me3


title: neurons,WT,week18,male,rep2 (9768_H3K4me2)

description: Library name: 9768_H3K4me2


title: Feec2_organoids_Day20

description:
Library name: Feec2_organoids_Day20
day20_salmon.merged.gene_tpm.tsv.gz


title: Nsd2-ISC-WT-H3K4me1

description: Library name: Sample2-WT-H3K4me1


title: neurons,WT,week18,male,rep2 (9768_H3K4me1)

description: Library name: 9768_H3K4me1


title: WT, SNI, rep3

description: Library name: sample7


title: Nsd2-ISC-WT-H3K27ac

description: Library name: Sample1-WT-H3K27ac


title: neurons,WT,week18,male,rep2 (9768_H3K27ac)

description: Library name: 9768_H3K27ac


title: Sojd3_organoids_Day20

description:
Library name: Sojd3_organoids_Day20
day20_salmon.merged.gene_tpm.tsv.gz


title: WT, SNI, rep2

description: Library name: sample6


title: neurons,cK2c,week18,male,rep3 (9407_H3K27ac)

description: Library name: 9407_H3K27ac


title: RA-FLS siNC 2

description:
Library name: Sample 2
2_siNC

value: synovial tissues

value: fibroblast-like synoviocytes

value: WT

value: siNC


title: SENP7 siRNA (Replicate 1)

value: Replicate 1

value: SENP7 siRNA


title: apoptosis_screen_A549_rep2

description:
Library name: Sample 4
164bp

data_processing:
Adapters were trimmed using trim galore
Trimmed reads were aligned with Bowtie2 to a custom dictionary indexes of BCs, where each BC is associated to its assigned ORF
The resulting BAM file was used to construct a raw count matrix for each BC
The resulting BC count matrix was used as an input to MAGeCK tool (https://doi.org/10.1186/s13059-014-0554-4) to identify ORFs that are enriched in each screen.
Assembly: custom Dictionary of BC-eORFs
Supplementary files format and content: tab-delimited text file includes raw counts for each BC id. Each BC id contains a number and the id of its associated ORF (e.g. BC23_1893 correspond to the BC 23 of ORF 1893, and the ORF id can be associated to a specific ORF through table S1).

extract_protocol:
Genomic DNA (gDNA) was isolated by lysing cell pellets overnight at 55°C in a buffer containing 10 mM Tris-HCl (pH 8.0), 5 mM EDTA, 100 mM NaCl, 1% SDS, and 0.5 mg/ml proteinase K. The lysate was then treated with RNase A (Qiagen) for 2 hours at 37°C. Subsequently, gDNA was purified through two sequential extractions with phenol:chloroform:isoamyl alcohol followed by a final extraction with chloroform:isoamyl alcohol. For barcode (BC) recovery, the entire gDNA yield from sorted/selected samples and 40 µg of gDNA from input samples were used as templates.
To generate NGS libraries,  40 individual PCR reactions were performed for each gDNA sample. The PCR adds Illumina adaptors and indexes for each sample. Following amplification, all PCR reactions for a given sample were pooled. The pooled amplicons were concentrated and purified using the Monarch PCR & DNA Cleanup Kit (NEB), using six columns for each input sample and one column for each sorted/selected sample. The final purified barcode amplicons were gel-extracted and submitted for next-generation sequencing.

value: screen


title: mSIorg_84h

city: Basel

first: Prisca

last: Liberali

address: Klingelbergstrasse 48

department: D-BSSE

country: Switzerland

institute: ETHZ

description: Library name: mSIorg_84h

library_source: genomic single cell

data_processing:
Demultiplexing was performed using bcl2fastq version 2.20.0.422. All analyses, unless stated otherwise, were performed within R (version 4.2.0) and Bioconductor (version 3.15), using SeuratObject version 4.1.0, Seurat version 4.1.1, and Signac version 1.7.0.
Fragment files with aligned read coordinates were generated for each sample (one file per each of the timepoints: 24h, 36h, 48h, 60h, 72h, 84h), using CellRanger ATAC (version 1.2.0) with the “count” subtool and reference “refdata-cellranger-atac-mm10-1.2.0”. For initial quantification, genomic features were obtained by combining promoters (transcription start sites (TSS) expanded to 1000 base pairs centered on the TSS) and enhancer from the cellranger annotation. All overlapping regions were collapsed, and any region overlapping a cellranger annotated blacklist region was removed. Alignments in these regions were then quantified with Signac::FeatureMatrix() from the fragment files.
Cells with fewer than 300 detected features were excluded, and features detected in fewer than 10 cells were removed, yielding 83,493 cells across 302,405 features. Quality control metrics were calculated using TSSenrichment() and NucleosomeSignal(). Cells with TSS enrichment ≤ 2, nucleosomal signal ≥ 5, ≤ 2,500 fragments, or ≤ 25% fragments in promoters (calculated using FRiP()) were excluded, resulting in 68,905 cells. Normalization was performed with RunTFIDF() (method = 1, scale.factor = 10,000), and variable features were selected using FindTopFeatures() (min.cutoff = "q50"), yielding 151,214 features. Dimensionality reduction was performed using RunSVD() (n = 50). The first component of the resulting Latent Semantic Index (LSI) was excluded from all subsequent analysis as it showed high correlation with sequencing depth (as shown by DepthCor()). Using the remaining LSI components as input, a total of 38 clusters were identified using FindNeighbors() and FindClusters() (resolution = 3).
Gene coordinates were extracted from the reference (genes gtf file in refdata-cellranger-atac-mm10-1.2.0) including type = “gene” and gene_type = “protein_coding”. Only standard chromosomes were retained, using GenomeInfoDb::keepStandardChromosomes(), with pruning.mode = “coarse”. Predicted gene expression was quantified with GeneActitity(), with extend.upstream = 2000, extend.downstream = 0, biotypes = NULL (as only protein coding genes were already pre-selected), and max.width = 5e+05. The RNA count matrix was normalized with NormalizeData(), normalize.method = “LogNormalize” and scale.factor = median(seurat$nCount_RNA)[2]  (the median total predicted RNA count per cell). Coarse-grain cell type annotation was performed by assigning the 38 clusters to cell types based on predicted RNA expression of known markers of intestinal lineages averaged over cells in each cluster (see Fig. S3D). We removed 1,929 cells (2 of the 38 clusters) showing high expression of stress markers (including Hsp90aa1, and Hsp90b1). Peaks were identified for each of these preliminary cell types with Signac::CallPeaks() using MACS2 (version 2.1.3.3) (15), with effective.genome.size = 1.87e9, extsize = 200, and shift = -100, and merged across clusters, yielding 252,049 peaks. A second fragment quantification was then performed using Signac::FeatureMatrix(), replacing the initial generic promoter/enhancer features by the sample specific peaks identified in our data.
Assembly: GRCm38/mm10
Supplementary files format and content: barcodes.tsv.gz: gzipped, tab-separated text file with column annotation of the (sparse) alignment count table (peaks versus cells). The columns correspond to cell_id (cell identifier), timepoint (24h, 36h, 48h, 60h, 72h or 84h), cell_type (annotated celltype label), UMAP1 (first coordinate for UMAP embedding), UMAP2 (second coordinate for UMAP embedding)
Supplementary files format and content: features.tsv.gz: gzipped, tab-separated text file with row annotation of the (sparse) alignment count table (peaks versus cells). The single column corresponds to the peak identifiers in the format chromosome-start-end
Supplementary files format and content: matrix.mtx.gz: gzipped, tab-separated text file with the number of ATAC fragments per peak (row) and cell (column), as a sparse matrix in MatrixMarket format.

source_name: mouse small intestinal organoids

growth_protocol: Organoids were kept in IntestiCult Organoid Growth Medium (STEMCELL Technologies) with 100 μg/ml Penicillin-Streptomycin for amplification and maintenance. For the first 24h, we used ENR (advanced DMEM/F-12 with 15mM HEPES (STEM CELL Technologies) supplemented with 100 μg/ml Penicillin and Streptomycin, 1×Glutamax (Thermo Fisher Scientific), 1×B27 (Thermo Fisher Scientific), 1xN2 (Thermo Fisher Scientific), 1mM N-acetylcysteine (Sigma), 500ng/ml R-Spondin (kind gift from Novartis), 100 ng/ml Noggin (PeproTech) and 100 ng/ml murine EGF (R&D Systems)) with 20% Wnt3a-conditioned medium (Wnt3a-CM), 10 μM Y-27632 (ROCK inhibitor, STEMCELL Technologies) and 3 µM of CHIR99021 (GSK3B inhibitor, STEMCELL Technologies). From 24h to 72h we supplemented ENR with 20% Wnt3a-CM and 10 μM Y-27632 (ROCK inhibitor, STEMCELL Technologies). From day 72h to 84h, only ENR was added to the cells. Wnt3a-CM was produced in-house by Wnt3a L-cells (kind gift from Novartis).

extract_protocol:
The sorted and cryopreserved cells from each organoid time point were thawed in a 37°C water bath and washed three times with 0.8% BSA-PBS. After the third wash, cells were transferred into BSA-coated 0.2 mL PCR tubes. Nuclei were then isolated using a low-input nuclei isolation protocol (Demonstrated protocol CG000169 • Rev D, 10x Genomics), with an 8-minute lysis time. Propidium iodide was used to identify the nuclei, and counting was performed using the MoxiGo II counter (Orflo Technologies). Nuclei were loaded to achieve a target recovery of 10,000 nuclei; if recovery was insufficient, all available nuclei were loaded instead.
scATAC-seq libraries were generated using the Chromium Single Cell ATAC Library & Gel Bead Kit (PN-1000110) following the user guide (CG000168 • Rev A, 10x Genomics). Libraries were sequenced on the Illumina NovaSeq platform.

value: mouse small intestinal organoids

value: intestinal epithelial cells

value: wildtype


title: neurons,WT,week18,male,rep1 (9278_H3K4me3)

description: Library name: 9278_H3K4me3

value: Cortex

value: In vivo

value: Excitatory neurons


title: HUES8_organoids_Day20

description:
Library name: HUES8_organoids_Day20
day20_salmon.merged.gene_tpm.tsv.gz


title: Nsd2-ISC-KO

description: Library name: Sample2

value: intestine

value: Intestinal stem cell


title: WT, SNI, rep1

description: Library name: sample5

value: spinal dorsal horn


title: mSIorg_72h

description: Library name: mSIorg_72h


title: neurons,WT,week18,male,rep1 (9278_H3K4me2)

description: Library name: 9278_H3K4me2

value: wild-type


title: neurons,WT,week18,male,rep1 (9278_H3K4me1)

description: Library name: 9278_H3K4me1


title: mSIorg_60h

description: Library name: mSIorg_60h


title: H9_organoids_Day20

description:
Library name: H9_organoids_Day20
day20_salmon.merged.gene_tpm.tsv.gz

value: human pluripotent stem cells


title: WT, sham, rep3

description: Library name: sample3


title: mSIorg_48h

description: Library name: mSIorg_48h


title: H1_organoids_Day20

description:
Library name: H1_organoids_Day20
day20_salmon.merged.gene_tpm.tsv.gz


title: neurons,WT,week18,male,rep1 (9278_H3K27ac)

description: Library name: 9278_H3K27ac


title: LPA4-KO, SNI, rep1

description: Library name: sample13


title: WT, sham, rep2

description: Library name: sample2


title: 11_20_18_TWM1_C_TACCTT_R1

city: Brookings

first: Anne

last: Fennell

state: SD

address: Raven Precision Ag Building Box 2100A

department: Agronomy, Horticulture & Plant Science

institute: South Dakota State University

description:
Library name: 12685_5751_144681_HW3JMBGXJ_NSF023_H02_11_20_18_TWM1_C_TACCTT_R1
Total RNA single illumina

data_processing:
1. Quality Control of Raw Reads- Raw RNA-seq reads were assessed for quality using FastQC, and summary reports across all samples were generated using MultiQC.
2. Adapter Trimming and Filtering- Adapter sequences and low-quality bases were removed using Trimmomatic. Since the data consisted of single-end reads, the TruSeq2 single-end adapter file was used during trimming.
3. Reference Genome Preparation- The Vitis vinifera 12Xv2 reference genome assembly and V2.20 GFF3 annotation file were downloaded and prepared for downstream analysis.
4. Genome Index Generation - Genome indices were generated using STAR to facilitate efficient alignment of RNA-seq reads.
5. Read Alignment - Trimmed reads were aligned to the Vitis vinifera reference genome using STAR, producing BAM alignment files for each sample.
Assembly: 6. Gene Expression Quantification- Gene-level read counts were generated using featureCounts  with the V2.20 GFF3 annotation file, retaining gene IDs for downstream expression analysis.
Supplementary files format and content: The processed data file consists of a tab-delimited text matrix file generated by featureCounts. The matrix contains raw, un-normalized digital gene-level counts, where rows correspond to specific unique Gene IDs derived from the Vitis vinifera 12Xv2 (V2.20 GFF3) reference annotation, and columns represent the individual biological samples (replicates) mapped using single-end RNA-seq reads. No normalized values (such as FPKM or TPM) are included in this specific file.

organism: Vitis hybrid cultivar

source_name: Bud

growth_protocol: Standard commercial vineyard management, Tuckers Walk, Garretson SD.

extract_protocol:
Total RNA was extracted from grapevine bud tissue using a modified CTAB protocol or standard commercial RNA isolation kit optimized for woody plant tissues. RNA quality and quantity were assessed using an Agilent Bioanalyzer or NanoDrop spectrophotometer to ensure high-quality material prior to library preparation.
Sequencing libraries were constructed using the Illumina TruSeq RNA Library Prep Kit following the manufacturer's standard protocols. Poly-A selected mRNA was fragmented, converted to cDNA, ligated with TruSeq adapters, and PCR amplified to generate single-end sequencing libraries.

treatment_protocol: Controled chilling (4ºC) in dark.  Field natural chilling temperatures.

value: Bud

value: Controlled Chilling

value: total RNA

value: single


title: LPA4-KO, WT, rep4

description: Library name: sample12


title: 3_4_19_TWM1_F_CCTAAG_R1

description:
Library name: 12685_5751_144678_HW3JMBGXJ_NSF023_E02_3_4_19_TWM1_F_CCTAAG_R1
Total RNA single illumina

value: Field Chilling


title: Macrophage treated with 100ng/ml lipopolysaccharide (LPS)-1

city: Saint Louis

first: Gabriel

last: Mbalaviele

state: Missouri

address: 425 S. Euclid Ave., Steven & Susan Lipstein BJCIH, Floor: 11, Room 11203

institute: WashU School of Medicine

description: Library name: MA_LPS_1

data_processing:
Clustering of the index-coded samples was performed on a cBot Cluster Generation System using the PE Cluster Kit cBot-HS (Illumina), according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform, and paired-end reads were generated
Raw FASTQ reads were processed with fastp to remove adapters, poly-N sequences, and low-quality reads. Clean paired-end reads were aligned to the reference genome (downloaded from NCBI/UCSC/Ensembl) using STAR.
FeatureCounts was used to quantify gene-level expression, and RPKM values were calculated.
Differential expression analysis (three biological replicates per group) was performed using DESeq2, with p-values adjusted by the Benjamini-Hochberg method. Genes with adjusted p < 0.05 were considered differentially expressed.
Assembly: mm10
Supplementary files format and content: tab delimited text file containing fpkm for all samples

source_name: Bone marrow derived macrophages

growth_protocol: The femurs and tibiae were harvested from WT mice and used to expand BMDMs in vitro. Bone marrow cells were flushed from the bones as previously described by Wang et al., 2024. Cells were cultured in 10 cm Petri dishes in the presence of CMG (a source of macrophage colony-stimulating factor, M-CSF) for 4–5 days. Expanded BMDMs were trypsinized and seeded into appropriate well plates at a density of 3 × 10⁴ cells per well in 24-well plates and 0.4 × 10⁶ cells per well in 6-well plates. OC differentiation was induced by the addition of receptor activator of nuclear factor kappa-B ligand (RANKL, 50–100 ng/mL) for 5–6 days.

extract_protocol:
RNA was isolated using the PureLink RNA Mini Kit, and on-column DNase I treatment (Ambion) was performed to eliminate any DNA contamination. RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
One microgram (1 μg) of RNA per sample was used as input material for RNA library preparation. Sequencing libraries were generated using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA), following the manufacturer’s instructions. Library quality was assessed using the Agilent Bioanalyzer 2100 system.

treatment_protocol: BMDMs were cultured for 5–6 days in 2% CMG, with or without RANKL, to induce mature osteoclasts. On day 5, both cell types were treated with or without LPS (100 ng/mL) for 3 hours.

value: D5, no RANKL, LPS treated

value: Bone marrow derived macrophages

value: WT


title: neurons,cK2c,week18,female,rep3 (9776_H3K4me3)

description: Library name: 9776_H3K4me3

value: conditional kmt2c knockout


title: mSIorg_36h

description: Library name: mSIorg_36h

value: mouse small intestinal organoids

value: intestinal epithelial cells

value: wildtype


title: Deyz2_organoids_Day20

description:
Library name: Deyz2_organoids_Day20
day20_salmon.merged.gene_tpm.tsv.gz


title: WT, sham, rep1

description: Library name: sample1


title: LPA4-KO, WT, rep3

description: Library name: sample11


title: mSIorg_24h

description: Library name: mSIorg_24h


title: Kolf2_organoids_Day20

description:
Library name: Kolf2_organoids_Day20
day20_salmon.merged.gene_tpm.tsv.gz


title: Foxa1_ChIP_rep2

description: Library name: Foxa1_ChIP_rep2

data_processing:
Illumina RTA 3.4.4 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. All analyses, unless stated otherwise, were performed within R (version 4.3.2) and Bioconductor (version 3.18) (14). ChIP-seq read pairs were aligned to the GRCm38/mm10 mouse genome assembly using the qAlign function from the QuasR package (Gaidatzis et al., Bioinformatics 2015) with default parameters.
BigWig files with alignment fragment coverage along the genome were generated from the bam files using bedtools version 2.30, by first extracting a bed file with fragment coordinates (bedtools bamtobed), calculating genome coverage in a bedGraph file (bedtools genomecov) and then converting it to BigWig format using bedGraphToBigWig from KentTools version 442.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig files with alignment fragment coverage along the genome

growth_protocol: Organoids were generated from isolated crypts of mice, as previously described (Sato et al.,Nature 2009). Maintenance of organoid cultures was performed in ENR medium (advanced DMEM/F-12 with 15mM HEPES (STEM CELL Technologies) supplemented with 100 μg/ml Penicillin and Streptomycin, 1×Glutamax (Thermo Fisher Scientific), 1×B27 (Thermo Fisher Scientific), 1xN2 (Thermo Fisher Scientific), 1mM N-acetylcysteine (Sigma), 500ng/ml R-Spondin (kind gift from Novartis), 100 ng/ml Noggin (PeproTech) and 100 ng/ml murine EGF (R&D Systems)).

extract_protocol:
A total of 10⁷ cells were crosslinked for 8 minutes at room temperature in 10 mL PBS supplemented with 1% formaldehyde (Sigma, F8775). The reaction was quenched by adding glycine to a final concentration of 0.125 mM. Cells were pelleted by centrifugation at 500 × g for 3 minutes at 4°C, washed once with PBS, pelleted again, flash-frozen in liquid nitrogen, and stored until further processing.
30µL of a 1:1 mixture of Protein A/G Dynabeads (Invitrogen, 10002D and 10004D) was pre-coupled with 3 µL of FOXA1 antibody (ab170933) for 1 hour at room temperature, followed by three washes with 1× ChIP buffer and stored on ice until use. The cells were lysed in 10 mL of buffer A (50 mM HEPES pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) on ice for 10 minutes. After centrifugation, the pellet was resuspended in 5 mL of buffer B (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl) and incubated on ice for 5 minutes. Nuclei were pelleted by centrifugation at 500 × g for 3 minutes at 4°C, resuspended in 150 µL of buffer C (50 mM Tris pH 8.0, 5 mM EDTA, 1% SDS, 100 mM NaCl), and incubated on ice for 10 minutes. TE buffer (1.3 mL) was then added, and chromatin was sheared in 15 mL tubes using a Bioruptor Pico device for two sessions of 10 cycles (30 seconds ON / 30 seconds OFF). After shearing, 160 µL of 10× ChIP buffer (0.1% SDS, 10% Triton X-100, 12 mM EDTA, 167 mM Tris-HCl pH 8.0, 1.67 M NaCl) was added. The chromatin was transferred to fresh tubes and centrifuged at 13,000 × g for 10 minutes at 4°C. Per sample, 30 µL of 1:1 pre-coupled beads were added to the chromatin, and the mixture was incubated with rotation for 4 hours at 4°C. The ChIP samples were washed four times with LSB (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate), twice with HSB (same as LSB but with 500 mM NaCl), twice with LiSB (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate), and once with TE+ buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 50 mM NaCl). During the final wash, beads were transferred to fresh tubes, and the wash buffer was completely removed. DNA was eluted twice from the beads using 75 µL of elution buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 150 mM NaCl, 1% SDS) by incubation at 65˚C with shaking. The eluates were pooled, and 2 µL of RNase A (20 µg/µL) was added, followed by incubation for 1 hour at 37°C. Input samples were adjusted to a total volume of 150 µL with elution buffer and processed in the same manner as ChIP samples. Proteinase K (2 µL, 20 mg/mL) was added, and samples were incubated for 2 hours at 55°C and then for 6 hours at 65°C. Afterward, 9 µL of 5 M NaCl, 30 µL of AMPure XP beads, and 190 µL of isopropanol were added. Samples were vigorously mixed, incubated at room temperature for 10 minutes, and the beads were collected on a magnetic rack. The beads were washed twice with 80% ethanol, and DNA was eluted in 30 µL of 10 mM Tris-HCl pH 8.0 for 5 minutes at 37°C. For library preparation, 25 µL of ChIP DNA or 50 ng of input DNA was used with the NEBNext Ultra II Library Prep Kit for Illumina (NEB), following the manufacturer’s protocol but with reactions scaled down to half-volume. Libraries were sequenced on the NovaSeq 6000 platform (Illumina) with paired-end reads (2x 56 bp).

value: Lgr5::DTR-EGFP (Genentech, de Sauvage laboratory)

tag: chip antibody

value: FOXA1 antibody ab170933


title: LPA4-KO, WT, rep1

description: Library name: sample9

value: spinal dorsal horn


title: Kolf2_untreated_Rep2

description:
Library name: Kolf2_untreated_Rep2
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: Micro-C of synTAD cell line, replicate 2

first: James

middle: Martin

last: Jusuf

state: MA

address: Building 56 Room 787B, 32 Vassar Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

description:
Library name: synTAD_G2_rep2
Cell line containing 3xCTCF sites forming synthetic loop (synTAD) on chr2 and flanking synBsr1 and Anchor3 arrays for fluorescent labeling

data_processing:
Base calls for NovaSeq output were obtained using bcl2fastq (v2.20.0.422).
Paired-end reads were aligned to the mm39 reference genome or modified versions of mm39 using bwa-mem2 (v2.2.1). The modified genomes contained the synthetic DNA sequences inserted at the anchors of the Fbn2, Npr3, or synTAD loops.
Aligned paired-end reads were then parsed with pairtools (v1.0.3) parse with --add-columns mapq --walks-policy all --min-mapq 30.
When aligning to the modified genomes only, a custom pipeline was implemented to recover multiply mapping reads in the synthetic regions by randomly assigining them to unique positions.
Parsed reads were filtered for PCR duplicates and unmapped/mutiply mapping reads with pairtools dedup with --max-mismatch 1.
For all samples, trans reads were downsampled in order to ensure that trans reads constituted a fixed 5% of total reads.
These filtered reads were subsequently converted to .cool format with cooler (v.0.9.3) cload pairs and subsequently to .mcool format with cooler zoomify with --balance --balance-args '--ignore-dist 20000'
Assembly: mm39
Supplementary files format and content: mcool files contain all valid Micro-C pairs stored in HDF5 format with multiple resolutions
Supplementary files format and content: mESC_merged_54B_mm39.mcool contains all valid Micro-C pairs of untreated mESC cells from this study, Hansen et al. 2019, Hsieh et al. 2020, Hsieh et al. 2022, Narducci & Hansen 2025, and Paldi et al. 2026.

growth_protocol: Fbn2, Fbn2_lowCTCF, and synTAD cell line: Cells were cultured on plates pre-coated with 0.1% gelatin solution (Sigma-Aldrich, G1890) in KnockOut Dulbecco's Modified Eagle Medium (Thermo Fisher, 10829018) supplemented with 15% fetal bovine serum (HyClone, SH30396.03),  2 mM GlutaMAX (Thermo Fisher, 35050061), 1% MEM Non-Essential Amino Acid Solution (Thermo Fisher, 11140050), 0.1 mM 2-mercaptoethanol (Sigma-Aldrich, M3148), 1000 U/mL leukemia inhibitory factor (home-made [Hansen et al 2017]), 10 μM MEK inhibitor (Tocris, PD0325901), 3 μM GSK3 inhibitor (Sigma-Aldrich, SML1046), and 100 μg/ml Penicillin-Streptomycin (Thermo Fisher, 15140122) in 5% CO2 at 37 °C. In addition, synTAD cells were grown with GSK-3484862 (TargetMol, cat. no. T11469) at a 2 µM concentration at all times. Npr3 cell line: Cells were cultured on plates pre-coated with 0.1% gelatin solution (Sigma-Aldrich, G2500) in Glasgow Minimum Essential Medium (Sigma-Aldrich, G5154) supplemented with 15% fetal calf serum (Eurobio Abcys), 1% L-Glutamine (Thermo Fisher, 25030024), 1% Sodium Pyruvate MEM (Thermo Fisher, 11360039), 1% MEM Non-Essential Amino Acids (Thermo Fisher, 11140035), 0.1 mM 2-mercaptoethanol (Thermo Fisher, 31350010), 20 U/mL leukemia inhibitory factor (Miltenyi Biotec, premium grade), 1 µM MEK inhibitor (Axon, 1408), and 3 µM GSK3 inhibitor (Axon, 1386) in 8% CO2 at 37 °C.

extract_protocol:
Cells were fixed with 3 mM DSG for 35 minutes, followed by an additional 10 minutes with 1% formaldehyde. Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and chromatin crosslinks were reversed. DNA was purified by the DNA Clean and Concentrator kit (Zymo), and size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments.
Size selected DNA fragments bound to streptavidin coated beads were used to prepare Micro-C libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with 7 PCR cycles on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled in a 1:1 ratio. Following qPCR quantification, the library pool was submitted for sequencing.

treatment_protocol: Micro-C was performed on cells in untreated condition.

value: Embryonic stem cells


title: neurons,cK2c,week18,female,rep3 (9776_H3K27ac)

description: Library name: 9776_H3K27ac

value: Cortex

value: In vivo

value: Excitatory neurons


title: Kolf2_untreated_Rep1

description:
Library name: Kolf2_untreated_Rep1
cell_lines_salmon.merged.gene_tpm.tsv.gz

value: human pluripotent stem cells


title: Foxa1_Input_rep4

description: Library name: Foxa1_Input_rep4


title: Micro-C of Npr3 cell line, replicate 4

description:
Library name: Npr3_rep4
Cell line containing 3xCTCF sites forming synthetic Npr3 loop on chr15 and flanking TetO and LacO arrays for fluorescent labeling


title: neurons,cK2c,week18,female,rep2 (501_H3K4me3)

description: Library name: 501_H3K4me3


title: neurons,cK2c,week18,female,rep3 (9776_H3K4me1)

description: Library name: 9776_H3K4me1


title: Fiaj1_untreated_Rep2

description:
Library name: Fiaj1_untreated_Rep2
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: Micro-C of Npr3 cell line, replicate 3

description:
Library name: Npr3_rep3
Cell line containing 3xCTCF sites forming synthetic Npr3 loop on chr15 and flanking TetO and LacO arrays for fluorescent labeling


title: WT, SNI, rep4

description: Library name: sample8


title: Foxa1_Input_rep3

description: Library name: Foxa1_Input_rep3


title: Burb1_organoids_Day20

description:
Library name: Burb1_organoids_Day20
day20_salmon.merged.gene_tpm.tsv.gz


title: Fiaj1_untreated_Rep1

description:
Library name: Fiaj1_untreated_Rep1
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: neurons,cK2c,week18,female,rep2 (501_H3K4me2)

description: Library name: 501_H3K4me2


title: Micro-C of Fbn2 cell line, replicate 4

description:
Library name: Fbn2_rep4
Cell line containing TetO and Anchor3 arrays for fluorescent labeling of the Fbn2 loop on chr18


title: neurons,cK2c,week18,female,rep2 (501_H3K4me1)

description: Library name: 501_H3K4me1


title: Foxa1_Input_rep2

description: Library name: Foxa1_Input_rep2


title: Fiaj1_CHR_Rep2

description:
Library name: Fiaj1_CHR_Rep2
cell_lines_salmon.merged.gene_tpm.tsv.gz


title: Micro-C of Fbn2 cell line, replicate 3

description:
Library name: Fbn2_rep3
Cell line containing TetO and Anchor3 arrays for fluorescent labeling of the Fbn2 loop on chr18