title: scWAT, HY, CE3

data_processing:
FastQC was used to check the quality of sequencing reads from fast files.
Fastp was used to filter out low-quality reads and adapters from fastq files of RNA-seq reads.
RNA-seq reads were aligned to the mouse mm10 genome by using STAR2.
FPKM tables of RNA-seq were calculated by using Stringtie with the GENOCODE comprehensive gene annotation set M25 release.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include reads per genes values for each sample.

source_name: scWAT

extract_protocol:
Total RNA was extracted using ISOGEN (Nippongene) following manufacturer's protocol.
Libraries were prepared by TruSeq sample purification kit (Illumina) following manufacturer's protocol.

value: scWAT

value: Jmjd1a HY/HY

value: Cold exposed (CE)


title: 18-3_unstimulated_1

status: Public on Mar 12 2024

type: SRA

city: Neuherberg

first: Sebastian

last: Schmidt

address: Ingolstädter Landstraße 1

department: Institute of Developmental Genetics

country: Germany

institute: Helmholtz Zentrum München

description:
18-3; unstimulated; replicate 1
countmatrix.txt
22L001578

library_source: transcriptomic

data_processing:
RNA-seq data were analyzed using a local Galaxy v 22.05 instance.
The quality of sequencing reads stored in FASTQ files was assessed using FastQC v0.72.
Paired-end reads were trimmed, and short reads (<20 bp) were removed using Trimmomatic v0.38.1.
RNA STAR Aligner v2.7.8a was used to align sequence reads to the human reference genome GRCh38.
Alignment summary statistics were reported using samtools idxstats v2.0.3.
Alignment quality was further assessed using RSeQC v1.1 and its provided annotation BED files for the human reference genome GRCh38.
The number of reads mapped to each gene was extracted from the STAR aligner BAM output file using featureCounts v1.6.4 and gene annotations (release 32) were obtained from GENCODE.
Gene counts were converted to a matrix using Count matrix v0.0.3.
Output results from FastQC, Trimmomatic, STAR aligner, samtools idxstats, featureCounts, and RSeQC were aggregated using MultiQC v1.9
Assembly: GRCh38
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Neuronal precursor cells (NPCs) were cultivated at 37°C, 5% CO2, 21%O2 on Geltrex-coated plates (Thermo Fisher Scientific, A1413302) in maintenance medium (50% DMEM/F12-GlutaMAX (Life Technologies, 31331093), 50% Neurobasal (Life Technologies, 21103049) supplemented with 1% B27 minus vitamin A (Life Technologies, 12587010), 0.5% N2 (Life Technologies, 17502048), 10 µM SB431542 (Miltenyi Biotec, 130-106-275), 1 µM dorsomorphin (Tocris Bioscience, 3093/10), 4.44 nM FGF-8b (Miltenyi Biotec, 130-095-741), 150 µM ascorbic acid 2-phosphate (Sigma, A8960-5G), and 0.02% beta-mercaptoethanol (Life Technologies, 31350010)).

extract_protocol:
RNA was isolated using the RNeasy Plus Mini Kit (Qiagen, 74134) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA kit (Illumina) following manufacturar's protocols.

treatment_protocol: NPCs were stimulated for 48h with 3 µM CHIR99021 (Tocris Bioscience, 4423/10).

tag: cell line

tag: cell type

value: neuronal precursor cells

tag: genotype

value: WT

tag: treatment

value: unstimulated


title: scWAT, HY, CE2

city: Tokyo

first: Juro

last: Sakai

address: 4-6-1, Komaba, Meguro-ku

department: Division of Metabolic Medicine

country: Japan

institute: Research Center for Advanced Science and Technology, The University of Tokyo

molecule: total RNA

organism: Mus musculus

tag: tissue


title: K562 cells, SF3B1 wild type, 4 days, replicate 1 [RNAPIINTDChIPseq_K562_WT_Replicate1]

city: NEW HAVEN

first: MANOJ

last: PILLAI

state: CT

address: 300 GEORGE STREET #786

country: USA

institute: YALE UNIVERSITY

library_source: genomic

data_processing:
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 using Bowtie2 aligners
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bases toward the interior of the sequenced fragment and were normalized to total reads aligned (RPKM) and Drosophila reads. Bam files were then reformatted in the bigWig file format.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: K562 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Formaldehyde was directly added to the media to a final concentration of 1% and 1 million cells were incubated for 15 min. Glycine was added to quench the reaction for 5 min. Cells were spun down and pellet was washed twice with PBS .  The cell pellet was lysed on ice in cell lysis buffer, pelleted and resuspended in MNase digestion buffer containing MNase, followed by nuclear lysis in nuclear lysis buffer. Sonication was performed with a sonic Dismembranator.5-10 μg of chromatin was used for each IP. ChIP spike in normalization for the RNAPII ChIP assays was performed using Drosophila-specific chromatin and Drosophila-specific histone variant (H2Av) antibody. 50 ng of Drosophila S2 sheared crosslinked-chromatin was added to 10 μg of chromatin as spike-in control. RNAPII NTD antibody was mixed with diluted chromatin and subjected to IP performed on a rotating wheel at 4°C overnight. Pierce Protein A/G Magnetic beads were added to the chromatin-antibody mixture and 4°C rotation continued for 3 more hours. Beads were washed with wash buffers. Immuno-bound chromatin was eluted at 55°C for 1 hour with elution buffer and de-crosslinked overnight at 65°C. DNA was extracted with phenol:chloroform:isoamyl alcohol and precipitated for 60 min at −20°C with sodium acetate and ethanol. Pellet was washed with 70% ethanol and resuspended in TE buffer. DNA quality and size distribution were checked on Fragment Analyzer.
10 ng of DNA was used for library preparation according to NEBNext® Ultra II DNA Library Prep Kit. Purity and size distribution of the libraries were estimated using Fragment Analyzer.

treatment_protocol: Modified allele expression induced with doxycycline (1ug/ml) and maintained for 4 days

value: Immortalized epithelial cells


title: ATAC_WT_DM_Rep2

city: Beijing

first: Yuting

last: Liu

state: Beijing

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Science

country: China

institute: Peking University

data_processing:
Fastq files were aligned to the reference genome using bowtie262 with the setting of ‘-very-sensitive’. Duplicate reads were removed using PicardTools. Only uniquely mapped reads (MAPQ>30) were kept for the following processing. RPM-normalized coverage tracks were calculated by deepTools. Peaks were called using MACS2 with the settings ‘macs2 callpeak -q 0.01 –nomodel –extsize 147’.
Assembly: mm9
Supplementary files format and content: xlsx file includes FPKM values for each sample
Supplementary files format and content: txt file include positionS of identified narrow peakS by MACS2

source_name: skeletal muscle

extract_protocol:
Cells were lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630)
A Nextera DNA Library Preparation kit (Illumina) was used to perform the transposition according to the manufacturer’s manual.

value: skeletal muscle

value: myocyte

value: wild type

value: myogenic differentiation for 24 h


title: ATAC_WT_DM_Rep1


title: 15-1_unstimulated_3

description:
15-1; unstimulated; replicate 3
countmatrix.txt
22L001577


title: scWAT, HY, CE1


title: K562 cells, SF3B1 K700E, 4 days, replicate 2, Input [CDK9ChIPseq_K562_SF3B1K700E_Input_Replicate2]

description: CDK9ChIPseq_K562_SF3B1K700E_IP_Input_Replicate2.bw

data_processing:
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 using Bowtie2 aligners
The respective IP and Input BAM files were compared to each other while being simultaneously normalized for sequencing depth (using RPKM), and reformatting to the bigWig file format using deepTools BamCompare program.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Formaldehyde was directly added to the media to a final concentration of 1% and 10 million cells were incubated for 15 min. Glycine was added to quench the reaction for 5 min. Cells were spun down and pellet was washed twice with PBS .  The cell pellet was lysed on ice in cell lysis buffer, pelleted and resuspended in MNase digestion buffer containing MNase, followed by nuclear lysis in nuclear lysis buffer. Sonication was performed with a sonic Dismembranator.100 μg of chromatin was used for each IP. CDK9 antibody was mixed with diluted chromatin and subjected to IP performed on a rotating wheel at 4°C overnight. Pierce Protein A/G Magnetic beads were added to the chromatin-antibody mixture and 4°C rotation continued for 3 more hours. Beads were washed with wash buffers. Immuno-bound chromatin was eluted at 55°C for 1 hour with elution buffer and de-crosslinked overnight at 65°C. DNA was extracted with phenol:chloroform:isoamyl alcohol and precipitated for 60 min at −20°C with sodium acetate and ethanol. Pellet was washed with 70% ethanol and resuspended in TE buffer. DNA quality and size distribution were checked on Fragment Analyzer.
10 ng of DNA was used for library preparation according to NEBNext® Ultra II DNA Library Prep Kit. Purity and size distribution of the libraries were estimated using Fragment Analyzer.


title: ATAC_WT_GM_Rep3

value: myoblast


title: scWAT, WT, CE3

value: Jmjd1a +/+


title: 15-1_unstimulated_2

description:
15-1; unstimulated; replicate 2
countmatrix.txt
22L001576


title: ATAC_MKO_GM_Rep2

value: MyoD knocout


title: K562 cells, SF3B1 K700E, 4 days, replicate 1, Input [CDK9ChIPseq_K562_SF3B1K700E_Input_Replicate1]

description: CDK9ChIPseq_K562_SF3B1K700E_IP_Input_Replicate1.bw


title: 15-1_unstimulated_1

description:
15-1; unstimulated; replicate 1
countmatrix.txt
22L001575


title: scWAT, WT, CE1


title: ATAC_WT_GM_Rep2


title: 4-5_unstimulated_3

description:
4-5; unstimulated; replicate 3
countmatrix.txt
22L001571


title: K562 cells, SF3B1 wild type, 4 days, replicate 2, Input [CDK9ChIPseq_K562_WT_Input_Replicate2]

description: CDK9ChIPseq_K562_WT_IP_Input_Replicate2.bw


title: ATAC_WT_GM_Rep1


title: K562 cells, SF3B1 wild type, 4 days, replicate 1, Input [CDK9ChIPseq_K562_WT_Input_Replicate1]

description: CDK9ChIPseq_K562_WT_IP_Input_Replicate1.bw


title: scWAT, WT, CE2


title: scWAT, HY, TN3

value: Thermoneutral (TN)


title: scWAT, HY, TN2


title: K562 cells, SF3B1 K700E, 4 days, replicate 2, IP [CDK9ChIPseq_K562_SF3B1K700E_IP_Replicate2]


title: RNA_siCTCF_Rep2

data_processing:
Fastq files were aligned to the reference genomeusing STAR with default settings. The UCSC database was used for gene annotation. The numbers of reads mapped to genes were counted by the summarizeOverlap function of the GenomicAlignments package. FPKM-normalized counts were calculated using the CQN package.
Assembly: mm9
Supplementary files format and content: xlsx file includes FPKM values for each sample
Supplementary files format and content: txt file include positionS of identified narrow peakS by MACS2

source_name: muscle

extract_protocol:
total RNA was extracted using TRIZOL (Ambion)
RNA-seq libraries were constructed using a NEBNext UltraTM RNA Library Prep kit for Illumina  following the manufacturer’s recommendations.

value: muscle

value: CTCF knockdown


title: 4-5_unstimulated_2

description:
4-5; unstimulated; replicate 2
countmatrix.txt
22L001570


title: RNA_siCTCF_Rep3


title: 4-4_unstimulated_3

description:
4-4; unstimulated; replicate 3
countmatrix.txt
22L001568


title: RNA_siCTCF_Rep1


title: 4-5_unstimulated_1

description:
4-5; unstimulated; replicate 1
countmatrix.txt
22L001569


title: 4-4_unstimulated_2

description:
4-4; unstimulated; replicate 2
countmatrix.txt
22L001567


title: K562 cells, SF3B1 wild type, 4 days, replicate 2, IP [CDK9ChIPseq_K562_WT_IP_Replicate2]


title: scWAT, WT, TN3

value: scWAT


title: RNA_ctrl_Rep3


title: CD34 cells, SF3B1-mutant MDS, replicate 6, ATAC-seq

data_processing:
Sequence reads were trimmed for adaptors with Cutadaptv4.1
Trimmed sequence reads were mapped to hg38 (for human samples) and mus musculus (for murine samples) using Bowtie2 aligner
To create promoter nucleosome occupancy plots, the locations of the mapped ATAC-seq reads were extended to 150 bp to represent sequenced fragments, and the resulting Bam files were used in the NucleoATAC page to generate output files in the bigWig file format. For ATAC peak analysis in K562 cell data, Epic2 package was used to call differentially enriched domains in WT and SF3B1K700E, using default parameters. Differentially ATAC-seq peaks were determined as those with a |log2 fold change(L2FC)| > 0.58 and adjusted p value < 0.05, calculated with DESeq2.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: K562 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. For the healthy volunteer and MDS patient samples, CD34 cells were isolated using FACS analysis. For the murine samples, cKit+Sca1+Lin- cells were isolated from bone marrow aspirates using FACS analysis

extract_protocol:
50,000 K562 cells or 5000 CD34+/murine HSC cells (flow sorted) were harvested, washed, and resuspended in PBS. Washed cells were resuspended in ATAC-seq resuspension buffer and  centrifuged at 500g for 5 min in a 4 °C. Cell pellets were then resuspended in 50 μl of ATAC resuspension buffer. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of RSB containing 0.1% Tween-20 (without NP-40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500g at 4 °C. Supernatant was carefully removed and nuclei were resuspended in transposition mix containing transposase enzyme by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 rpm.
DNA quality and size distribution were checked on Fragment Analyzer. 10 ng of DNA was used for library preparation according to NEBNext® Ultra II DNA Library Prep Kit

treatment_protocol: Modified allele expression induced with doxycycline (1ug/ml) and maintained for 4 days (in 562 cells). For the murine model, SF3B1 mutant (and WT counterparts) were treated with tamoxifen daily x 5 days at 5 weeks of age. Mice were euthanized at end of week 8 and bone marrow was harvested to isolate the HSC progenitors.

value: Hematopoietic progenitor cells

value: SF3B1 K700E


title: scWAT, HY, TN1

value: Jmjd1a HY/HY


title: RNA_ctrl_Rep2


title: scWAT, WT, TN2


title: 4-3_unstimulated_3

description:
4-3; unstimulated; replicate 3
countmatrix.txt
22L001565

value: neuronal precursor cells

value: WT


title: scWAT, WT, TN1


title: 4-4_unstimulated_1

description:
4-4; unstimulated; replicate 1
countmatrix.txt
22L001566

value: unstimulated


title: RNA_ctrl_Rep1


title: CD34 cells, SF3B1-mutant MDS, replicate 5, ATAC-seq


title: cKIT+Sca1+Lin- cells, Murine Sf3b1 K700E, replicate 2, ATAC-seq

source_name: cKIT+Sca1+Lin- cells

value: cKIT+Sca1+Lin- cells

value: Sf3b1 K700E


title: 4-3_unstimulated_1

description:
4-3; unstimulated; replicate 1
countmatrix.txt
22L001563


title: CD34 cells, SF3B1-mutant MDS, replicate 4, ATAC-seq


title: cKIT+Sca1+Lin- cells, Murine Sf3b1 K700E, replicate 1, ATAC-seq


title: 4-3_unstimulated_2

description:
4-3; unstimulated; replicate 2
countmatrix.txt
22L001564


title: Esophagus,GEJ and Stomach, from E15, E19, Pup and Adult, CMO

city: Würzburg

first: Cindrilla

last: Chumduri

address: Am Hubland

department: Chair of Microbiology, Biozentrum

institute: University of Wuerzburg

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing data were processed using Cell Ranger software (v.6.1.1, 10X Genomics).
Processing of raw sequencing reads, demultiplexing, read mapping and UMI counting were done using the standard ‘cellranger multi’ pipeline with default parameters
Assembly: mm10-2020-A
Supplementary files format and content: Supplementary_files_format_and_content: 1) Cell-level data: matrix.mtx.gz, barcodes.tsv.gz and features.tsv.gz  2) csv format: Metadata (sample ID, cluster, time point, CMO tag etc) for each cell contained in the UMI count matrix.  3) csv format: Demultiplexed sample-cell barcode assignment indicating the sample membership for each cell barcode with experimental time point information 4) csv format: Information regarding CMO and Feature Barcode and their corresponding experimental condition, sequence etc. 5) csv format: Reference file mapping information of CMO tags and their respective experimental/sample ID

source_name: Esophagus,GEJ and Stomach

extract_protocol:
Following gut extraction from prenatal (E15, E19) and postnatal (Pup, Adult) mice, the esophagus, gastroesophageal junction, and stomach were cut out. Tissue samples were washed in sterile PBS (Gibco, 14190-094) and minced with scissors. Minced tissue was processed separately by incubating in 0.5 mg ml−1 collagenase II (Calbiochem, 234155) in a shaker (45 min, 37 °C). Tissue and dissociated cells were pelleted (7 min, 1,000g, 4 °C), and the supernatant was discarded. The pellet was resuspended in  0.04% BSA-PBS solution and passed through a 40 µm cell strainer (BD Falcon, 352340).
Cells from biological replicates were pooled and multiplexed based on the tissue region of origin and time point and library preparation for tissue were performed using 10x Genomics  3' CellPlex Kit and Single-Cell 3′ v3.1 RNA-seq kits according to manufacturer's protocol.

value: Epithelia, Stroma, Immune

value: Esophagus,GEJ and Stomach

tag: strain

value: wild type

tag: age

value: E15, E19, Pup (day-2) and Adult (8-week old)


title: K562 cells, SF3B1 K700E, 4 days, replicate 1, IP [CDK9ChIPseq_K562_SF3B1K700E_IP_Replicate1]

value: Immortalized epithelial cells


title: Esophagus,GEJ and Stomach, from E15, E19, Pup and Adult, GEX

description: 10x Genomics


title: CD34 cells, SF3B1-mutant MDS, replicate 3, ATAC-seq


title: 25-19_unstimulated_3

description:
25-19; unstimulated; replicate 3
countmatrix.txt
22L001550

value: EN1 ko


title: cKIT+Sca1+Lin- cells, Murine Sf3b1 WT, replicate 1, ATAC-seq

value: Sf3b1 WT


title: CD34 cells, SF3B1-mutant MDS, replicate 2, ATAC-seq


title: ATAC-seq: MutuIII Replicate 2

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Quality control of raw sequencing reads was performed using the DNA Accessibility Pipeline v2.2.0 from the ENCODE Project.
ATAC-seq reads were aligned to the human genome (hg19) using Bowtie2 .
Aligned reads were then sorted using samtools (v.1.8) and duplicate reads were removed using Picard (v. 1.89)
Peaks were called using the default parameters of MACS2 (q < 0.01).
Irreproducibility Discovery Rate (IDR) optimal peaks, generated from the ENCODE pipeline, were obtained for each cell type and used for downstream analyses.
Assembly: hg19
Supplementary files format and content: Peaks called by MACS2 in narrowPeak format. Peaks are filtered based on q-value and contain only those with a q-value < 0.01
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing BPM --binSize 10

source_name: MutuIII

growth_protocol: The AG876, Jiyoye, GM12878, and MutuIII cell lines were grown in RPMI medium supplemented with 2 mM L-glutamine, 10% FBS, 1X antibiotic-antimycotic , and 0.2% Normocin at 200,000 – 500,000 viable cells/mL. Cells were incubated in flasks at 37C with 5% carbon dioxide in an upright position with vented.

extract_protocol:
Transposase Tn5 with sequencing adapter sequences was used to cut the accessible DNA as detailed in Buenrostro et al. 2015
The resulting accessible DNA sequences were isolated, and libraries were prepared from 50,000 cells from each cell line using the OMNI ATAC protocol as detailed in Corces et al 2017

value: MutuIII

tag: virus type

tag: virus strain

value: Mutu


title: 25-19_unstimulated_1

description:
25-19; unstimulated; replicate 1
countmatrix.txt
22L001548


title: K562 cells, SF3B1 wild type, 4 days, replicate 1, IP [CDK9ChIPseq_K562_WT_IP_Replicate1]


title: CD34 cells, SF3B1-mutant MDS, replicate 1, ATAC-seq

value: Hematopoietic progenitor cells


title: D9 CARD9 WT replicate 1, scRNAseq

city: Cambridge

first: Ramnik

last: Xavier

state: MA

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

description:
10x Genomics
D9_WT_INF_1201

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were conducted using Cell Ranger software v6.0.0
Assembly: mm10
Supplementary files format and content: Processed Seurat object containing count matrices for all samples and cell metadata, both provided in RDS format.  These can be read into R with the readRDS() command.

source_name: skin

extract_protocol:
Skin was harvested with sterile tools, cut into small pieces with scissors and incubated for 1.5h in digestion solution containing Liberase (Roche #385040) and DNAse I (Roche #10104159001) at 370C with agitation. After the digestion, samples were placed on ice and the reaction was stopped using stop buffer containing 5% FBS and 1mM EDTA. Cells were centrifuged  5min 1500 rpm at 40C and washed 1x with PBS. Cells were passed through a 100uM cell strainer and counted.
Single cell suspensions were processed using the Chromium Single Cell 3’ Gene Expression kit (v3.1, 10x Genomics) per manufacturer’s instructions. Libraries were sequenced on the Illumina NovaSeq SP per manufacturer’s instructions.

value: Immune stromal epithelial

value: skin

value: Trichophyton rubrum

tag: timepoint

value: D9 post-infection


title: 5-12_unstimulated_3

description:
5-12; unstimulated; replicate 3
countmatrix.txt
22L001547

value: neuronal precursor cells

value: unstimulated


title: 5-12_unstimulated_2

description:
5-12; unstimulated; replicate 2
countmatrix.txt
22L001546


title: liver, Sham, input

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
reads were quality checked with fastqc and preprocessed in order to remove adapters with trimmomatic (v0.39)
reads were aligned to the mm10 reference genome with the BWA aligner (bwa mem) and reads annotated as PCR duplicates with picard or mapping to the mitochondrial genome were excluded
ChIP-seq peaks were called with HOMER using the input as control sample and with the preset for brod histone peaks for H3K27ac
bigwig coverage files were generated using python deeptools (with options --effectiveGenomeSize 2654621783 --normalizeUsing CPM)
Assembly: mm39
Supplementary files format and content: bed
Supplementary files format and content: bigwig

source_name: liver

extract_protocol:
ChIP was performed on 200-400 mg of snapfrozen liver tissue. First, DynabeadsTM protein G (Thermo Fisher Scientific) were washed three times with BSA/PBS and coupled to a primary antibody against H3K27ac or H3K4me3 overnight at 4°C. Afterwards, the beads with coupled antibody were washed with BSA/PBS twice. Livers were homogenized and fixed in Farnham Lysis buffer with 1% formaldehyde, supplemented with protease inhibitor cocktail (Roche), for 10 min at RT. the material was sonicated (Bioruptor, Diagenode) at 4°C for 40 cycles (30s ON, 30s OFF) with high settings to yield 200-800 bp DNA fragments. Cell debris was removed by centrifugation at full speed for 20-30 min at 4°C. Sonication efficiency was checked (after reverse crosslinking with proteinase K for 1h at 65°C and DNA purification) on a 1.5% agarose gel. For immunoprecipitation (IP), antibody-coupled magnetic beads were added to the sonicated samples and incubated overnight at 4°C . The day after, bead-antibody-DNA complexes were washed 5 times with LiCl wash buffer (100 mM Tris-HCl; pH 7.5, 500 mM LiCl, 1% IGEPAL, 1% sodium deoxycholate) at 4°C and 2 times with TE buffer (10 mM Tris-HCl; pH 7.5, 0.1 mM EDTA) at 4°C. Chromatin was eluted by incubating the IP samples with elution buffer (1% SDS, 0.1M NaHCO3) 1h at 65°C. Samples  were incubated with proteinase K for 4h at 65°C for reverse crosslinking and DNA was purified in 50 µL elution buffer according to the manufacturer’s protocol by using the Monarch PCR&DNA Cleanup kit (Biolabs).
15 ng of purified chromatin was used to generate a ChIP-Seq library according to the manufacturer’s protocol using NEBNext Ultra II DNA Library Prep kit (E7645L, NEB)

treatment_protocol: mice were subjected to SHAM or CLP surgery and livers are isolated 8h after the procedure and snap frozen in liquid nitrogen

value: liver

tag: antibody

value: none; input

value: WT

value: CLP


title: CD34 cells, healthy volunteer, replicate 3, ATAC-seq

value: SF3B1 WT


title: 5-12_unstimulated_1

description:
5-12; unstimulated; replicate 1
countmatrix.txt
22L001545


title: D9 CARD9 R101C replicate 3, scRNAseq

description:
10x Genomics
D9_HOMO_INF_1220

value: CARD9 R101C


title: liver, CLP, input

value: Sham


title: D9 CARD9 R101C replicate 2, scRNAseq

description:
10x Genomics
D9_HOMO_INF_1219


title: liver, H3K4me3, Sham rep4


title: K562 cells, SF3B1K700E, 4 days, replicate 2, ATAC-seq

value: Immortalized epithelial cells

value: SF3B1 K700E


title: D9 CARD9 R101C replicate 1, scRNAseq

description:
10x Genomics
D9_HOMO_INF_1206


title: CD34 cells, healthy volunteer, replicate 2, ATAC-seq


title: 5-6_unstimulated_3

description:
5-6; unstimulated; replicate 3
countmatrix.txt
22L001544

value: EN1 ko


title: 25-19_unstimulated_2

description:
25-19; unstimulated; replicate 2
countmatrix.txt
22L001549


title: CD34 cells, healthy volunteer, replicate 1, ATAC-seq

value: Hematopoietic progenitor cells


title: D2 CARD9 WT replicate 3, scRNAseq

description:
10x Genomics
D2_WT_INF_1242

value: Immune stromal epithelial

value: D2 post-infection


title: K562 cells, SF3B1K700E, 4 days, replicate 1, ATAC-seq


title: liver, H3K4me3, Sham rep2


title: D9 CARD9 WT replicate 3, scRNAseq

description:
10x Genomics
D9_WT_INF_1204

value: skin

value: Trichophyton rubrum


title: liver, H3K4me3, Sham rep3


title: D2 CARD9 WT replicate 2, scRNAseq

description:
10x Genomics
D2_WT_INF_1238


title: K562 cells, SF3B1 wild type, 4 days, replicate 2, ATAC-seq


title: 5-6_unstimulated_2

description:
5-6; unstimulated; replicate 2
countmatrix.txt
22L001543

value: neuronal precursor cells


title: liver, H3K4me3, Sham rep1


title: ATAC-seq: MutuIII Replicate 1

value: MutuIII

value: Mutu


title: D2 CARD9 WT replicate 1, scRNAseq

description:
10x Genomics
D2_WT_INF_1230


title: D9 CARD9 WT replicate 2, scRNAseq

description:
10x Genomics
D9_WT_INF_1202

value: D9 post-infection


title: liver, H3K27ac, Sham rep4

value: liver

value: WT


title: HeLa S3, shSETD3, RNase, rep2

city: Wuhan

first: Shuang

last: Wang

address: Hubei province

institute: Wuhan University

description: NS-seq

data_processing:
Sequencing adapters were trimmed by fastp (v0.23.2)
The clean reads were mapped to human genome (GRCh38) using bowtie2 (v2.3.5.1)
Peaks were called by Macs2 (v2.1.1)
Assembly: GRCh38
Supplementary files format and content: narrowPeak
Library strategy: NS-seq

source_name: Human cervical carcinoma

growth_protocol: Human cervical carcinoma cell (HeLa S3) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were lysed with DNAzol (Invitrogen, 10503027) at room temperature for 5 min. Genomic DNA was purified according to the manufactory’s instructions. DNA was denatured by boiling 10 min at 100 °C and then loaded onto 13 mL neutral 5%-30% sucrose gradients prepared in TEN500 (10mM Tris, pH7.9, 2mM EDTA, 500mM NaCl) in ultraclear tubes. The mixture was centrifuged in SW40 rotor at 25,000 rpm for 20 h. An 1 mL-fraction was withdrawn from the top of the gradients. DNA fragments ranging from 0.5-2.5 kb were collected and purified.
the VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (ND607, Vazyme)

value: Human cervical carcinoma

value: HeLa S3

value: Human cervical carcinoma cell


title: 5-6_unstimulated_1

description:
5-6; unstimulated; replicate 1
countmatrix.txt
22L001542

value: unstimulated


title: D2 CARD9 R101C replicate 3, scRNAseq

description:
10x Genomics
D2_HOMO_INF_1231

value: CARD9 R101C


title: HeLa S3, shSETD3, RNase, rep1

description: NS-seq


title: D2 CARD9 R101C replicate 2, scRNAseq

description:
10x Genomics
D2_HOMO_INF_1228


title: liver, H3K27ac, Sham rep3

value: Sham


title: HeLa S3, shSETD3, NS, rep2

description:
NS-seq
sh-rep2_peaks.narrowPeak


title: liver, H3K27ac, Sham rep2


title: L1_DP_AID_Auxin_biol_rep1

city: Paris

first: Germano

last: Cecere

address: Institut Pasteur, 28 Rue Du Docteur Roux, Batiment Monod, 4eme Etage

department: Development and stem cell biology

country: France

institute: Institut Pasteur

description: RNA-seq from hatched L1 larvae

data_processing:
For all of the library, normalized bigwig files were generated from the mapping results using millions of non-structural mappers as a normalization factor. This normalized coverage information was computed for 10 bp bins using the bedtoolsand bedopsv.2.4.26 packages.
Assembly: ce11 C. elegans Sequencing Consortium WBcel235
Supplementary files format and content: normalized big wig files will be provided for each libraries

organism: Caenorhabditis elegans

source_name: Hatched L1 larvae

growth_protocol: Strains were maintained at 20°C, using standard methods (Brenner, 1974). Bristol N2 was the wild-type strain used.

extract_protocol:
To obtain synchronized non-starved L1, we used the NemaSync C. elegans synchronizer model 5000. L1 larvae were frozen in dry ice with TRIzol Reagent (Invitrogen), and after six repetitions of freeze and thaw, RNA was extracted using the Direct-zol RNA Microprep kit (ZymoResearch, R2062). The small RNA fragments (17 to 200 nucleotides) were separated from the large RNAs (>200 nucleotides) using the Quick-RNA MicroPrep kit (ZymoResearch, R1051). The large RNA was DNAse treated using the reagent provided along with the Quick-RNA Microprep kit. Using these size separation kits, we were able to sequence both the small RNA and the mRNA coming from the same samples. An Agilent 2200 TapeStation System was used to evaluate the RIN indexes of the large RNAs (>200 nucleotides), and only samples with RNA integrity number RIN  > 8 were used for RNA-seq. For 2-cell embryo RNA extraction, precisely staged 2-cell embryos were obtained by alkaline hypochlorite treatment of synchronized gravid adult hermaphrodites, and fifty 2-cell embryos were collected using a mouth pipet. Embryos were lysed for 10min at 65˚C and 1min at 85˚C in a lysis solution containing Tris pH8 5mM final, EDTA 0.25mM final, Triton 100X 0.5%, Tween 20 0.5%, Proteinase K 0.5% and Water. The lysates were subjected to RNA purification using the Quick-RNA MicroPrep kit (ZymoResearch, R1051), and small RNAs (RNA fraction from 17 to 200 nucleotides) and mRNAs (RNA fraction >200 nucleotides) were collected separately. The RNA fraction > 200 nucleotides were used for preparing RNA-seq libraries.
DNase-treated total RNA with RIN > 8 was used to prepare strand-specific RNA libraries. Ribosomal and mitochondrial rRNAs were depleted using a custom RNAse-H-based method to degrade rRNAs using complementary oligos as described in42.Strand-specific RNA libraries were prepared using at least 100 ng of rRNA-depleted RNAs using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S). RNA libraries were analysed on Agilent 2200 TapeStation System using high sensitivity D1000 screentapes and quantified using the Qubit Fluorometer High Sensitivity dsDNA assay kit (Thermo Fisher Scientific, Q32851). Multiplexed libraries were sequenced on a NextSeq 2000 Illumina platform.

treatment_protocol: To induce the degradation of DROSHA and PASHA in C. elegans intestine, we used the AID degron system. Mothers were treated with Auxin at L3 stages and embryos or hatched L1 were collected for the RNA-seq experiment. 250 mM auxin stock solution was prepared in ethanol and stored at 4 °C. Auxin plates or ethanol plates were prepared by the addition of auxin or only ethanol to NGM plates (final concentration: 500 µM auxin, 0.2% ethanol for auxin plates and 0.2% ethanol for ethanol plates). Plates were seeded with OP50 Escherichia coli.

value: Hatched L1 larvae

value: MHE229 (Drosha Pasha intestinal degron)

value: drsh-1(luc82[myc::AID::3XFLAG::4xGGSG::drsh-1::4xGGSG::3xFLAG::AID::myc])pash-1(luc71[pash-1::2xGGSG::3xFLAG::AID::myc]) I; reSi12 [ges-1p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II:0.77)

value: Auxin


title: D2 CARD9 R101C replicate 1, scRNAseq

description:
10x Genomics
D2_HOMO_INF_1221

value: Immune stromal epithelial

value: skin

value: Trichophyton rubrum

value: D2 post-infection


title: HeLa S3, shSETD3, NS, rep1

description:
NS-seq
sh-rep1_peaks.narrowPeak


title: L1_DP_AID_EtOH_biol_rep2

description: RNA-seq from hatched L1 larvae

value: EtOH


title: liver, H3K27ac, Sham rep1

value: liver


title: Stomach epithelial organoid

institute: Julius-Maximilians-Universität Würzburg

description:
Single cells
Bar11

data_processing:
Sequencing data were processed using Cell Ranger software (v3.1.0, 10X Genomics).
Raw sequencing data were converted to FASTQs with the command “cellranger mkfastq” and default parameters.
Read mapping to mouse genome, UMI counting and generating the count matrix were performed with the command “cellranger count” and default parameters.
MultiSeq barcode libraries were processed with the R package deMULTIplex (v1.0.2) to determine the sample origin of each cell barcode.
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: Supplementary_files_format_and_content: 1) Cell-level data: matrix.mtx, barcodes.tsv and features.tsv  2) csv format: MULTI-seq barcode UMI count matrix: Cell-by-barcode matrix of MULTI-seq barcode counts for each cell that was used for sample demultiplexing. 3) csv format: Demultiplexed sample-cell barcode assignment indicating the sample membership for each cell barcode (post-filter, "negative" and "multiplet" cell barcodes excluded) 4) xlsx format: Information regarding MULTI-Seq sample barcodes and their corrsponding experimental condition, sequence etc.

source_name: Stomach Organoids

growth_protocol: Mouse epithelial stem cells derived from esophagus and stomach tissues were grown into 3D organoids using a unique cocktail of growth factors using the protocol described in the accompanying manuscript (Materials and Methods).

extract_protocol:
Esophageal and stomach organoids were harvested with ice-cold PBS, pelleted by centrifugation (5 Min, 300g, 4˚C), and Matrigel was removed. The process was repeated twice to remove Matrigel completely. Organoids were then incubated with warm TrypLE in a shaker (15 min, 37˚C, 180 rpm). Organoids were sheared using a 1 mL pipette by pipetting up and down 20 times. Dissociated cells were passed through a 40 µm cells strainer to obtain suspension of single cells, and the cells were washed with 0.1% BSA in 1XPBS.   Following the preparation of single-cell suspension, multiplexing of samples was performed according to the MULTI-seq protocol (McGinnis CS et al., Nat Methods. 2019). The barcoded samples were pooled together equally, and cell numbers were adjusted to 1000 cells/µl. A 10x Genomics Chromium™ Controller was used for partitioning single cells into nanoliter-scale Gel Bead-In-EMulsions (GEMs) and Single Cell 3′ v3.1 RNA-seq kit for reverse transcription, cDNA amplification and library construction (10xGenomics). The detailed protocol was provided by 10xGenomics.
Chromium Next GEM Single Cell 3’ v3.1 (10X Genomics)

treatment_protocol: Esophagus and stomach 3D organoids using a unique cocktail of growth factors were harvested for single cells isolation.

value: Untreated

value: Stomach epithelial organoid


title: K562 cells, SF3B1 wild type, 4 days, replicate 1, ATAC-seq

value: Immortalized epithelial cells

value: SF3B1 WT


title: HeLa S3, shSETD3, input,rep2

description: NS-seq

value: Human cervical carcinoma

value: HeLa S3

value: Human cervical carcinoma cell


title: L1_DP_AID_EtOH_biol_rep1

description: RNA-seq from hatched L1 larvae

value: Hatched L1 larvae


title: Esophageal epithelial oragnoid

description:
Single cells
Bar8

source_name: Esophageal Organoids

value: Esophageal epithelial oragnoid


title: 2C_EMB_DP_AID_Auxin_biol_rep2

description: RNA-seq from 2-cell embryos

source_name: embryo

value: embryo

value: MHE229 (Drosha Pasha intestinal degron)

value: 2-cell embryos

value: drsh-1(luc82[myc::AID::3XFLAG::4xGGSG::drsh-1::4xGGSG::3xFLAG::AID::myc])pash-1(luc71[pash-1::2xGGSG::3xFLAG::AID::myc]) I; reSi12 [ges-1p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II:0.77)


title: liver, H3K4me3, CLP rep4

value: WT

value: CLP


title: 2C_EMB_DP_AID_Auxin_biol_rep1

description: RNA-seq from 2-cell embryos

value: Auxin


title: liver, H3K4me3, CLP rep3

value: liver


title: HeLa S3, shSETD3, input,rep1

description: NS-seq


title: ileal crypt cells, CPT4

city: Shanghai

first: Min

last: Huang

address: 555, Zuchongzhi Road

institute: Shanghai Institute of Materia Medica

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38.p6 whole genome using bowtie2 v2.4.1
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: ileal crypt cells

extract_protocol:
mice ileum was dissected, flushed, opened and incubated in cold PBS containing 20 mM EDTA for 90 min followed by shaking. Incubation (30 min for each time) and shaking were repeated for two more times, and the supernatant was filtered through a 70-μm strainer and centrifuged at 350 g, 4℃ for 5 min to collect crypts. Isolated crypts were then incubated in 0.05% trypsin at 37℃ for 10 min to obtain single cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with CPT-11 (20 mg/kg) for 7 days.

value: ileal crypt cells


title: HeLa S3, shvec, RNase, rep2

description: NS-seq

value: shvec


title: L1_DP_AID_Auxin_biol_rep2

description: RNA-seq from hatched L1 larvae


title: liver, H3K4me3, CLP rep2


title: ileal crypt cells, CPT3


title: HeLa S3, shvec, RNase, rep1

description: NS-seq


title: ileal crypt cells, CPT2


title: liver, H3K4me3, CLP rep1


title: HeLa S3, shvec, NS, rep2

description:
NS-seq
vec-rep2_peaks.narrowPeak


title: 2C_EMB_DP_AID_EtOH_biol_rep2

description: RNA-seq from 2-cell embryos

value: EtOH


title: 2C_EMB_DP_AID_EtOH_biol_rep1

description: RNA-seq from 2-cell embryos


title: liver, H3K27ac, CLP rep4


title: ileal crypt cells, CPT1


title: HeLa S3, shvec, NS, rep1

description:
NS-seq
vec-rep1_peaks.narrowPeak


title: liver, H3K27ac, CLP rep3


title: HeLa S3, shvec ,input, rep2

description: NS-seq


title: DP_AID_Auxin_50mM_biol_rep2

data_processing:
For all of the library, normalized bigwig files were generated from the mapping results using millions of non-structural mappers as a normalization factor. This normalized coverage information was computed for 10 bp bins using the bedtoolsand bedopsv.2.4.26 packages. For the 2-cell embryo small RNA sequencing, counts were normalized in each sample using spike-ins counts (scaling factor per sample = 10^3 x total_nb_spikes_counted / total_nb_reads_aligned) in a dataset. Scaling factors were then generally "minimized" : all scaling factors of the dataset were divided by the smallest scaling factor in the dataset).
Assembly: ce11 C. elegans Sequencing Consortium WBcel235
Supplementary files format and content: normalized big wig files will be provided for each libraries

source_name: small RNAs from 2-cell embryos

extract_protocol:
Synchronous populations of worms were grown at 20°C on NGM plates seeded with OP50 E. coli concentrated food at a density of maximum 40,000 animals per 15 cm Petri dish and harvested at Young Adult stage at 48 hours post hatching. The harvested animals were washed three times with M9 buffer and 40 µl of worm pellet was frozen in dry ice with TRI Reagent (MRC, Inc.). After five repetitions of freeze and thaw, total RNA was isolated according to the TRI Reagent protocol. For the 2-cell embryo RNA extraction, precisely staged 2-cell embryos were obtained by alkaline hypochlorite treatment of synchronized gravid adult hermaphrodites, and fifty 2-cell embryos were collected using a mouth pipet. Embryos were lysed for 10min at 65˚C and 1min at 85˚C in a lysis solution containing Tris pH8 5mM final, EDTA 0.25mM final, Triton 100X 0.5%, Tween 20 0.5%, Proteinase K 0.5% and Water. The lysates were subjected to RNA purification using the Quick-RNA MicroPrep kit (ZymoResearch, R1051), and small RNAs (RNA fraction from 17 to 200 nucleotides) and mRNAs (RNA fraction >200 nucleotides) were collected separately. A small RNA spike-in was added before embryo lysis.
The small RNA library preparation was performed essentially as described previously by Barucci et al., 2020.

treatment_protocol: In all experiments using AID strains, 250 mM auxin stock solution was prepared in ethanol and stored at 4 °C. Auxin plates or ethanol plates were prepared by the addition of auxin or only ethanol to NGM plates (final concentration: 500 µM auxin, 0.2% ethanol for auxin plates and 0.2% ethanol for ethanol plates). Plates were seeded with OP50 Escherichia coli. Synchronized worms were placed on auxin or ethanol plates from L3 stage. To collect embryos from day 3 adult AID strains the auxin treatment was initiated at day 1 of adulthood. For experiments using the AID2 system, 10mM stock solution of 5-Ph-IAA was prepared in ethanol and stored at -20 ˚C for not more than a month. 5-Ph-IAA plates were prepared at a final concentration of 1µM. For osmotic stress treatment, synchronized populations of L1 larvae, obtained by hypochlorite treatment of gravid adults, were grown on NGM plates for 48 hours. After 48 hours, worms were washed from the NGM plates and divided on two NGM plates seeded with OP-50 E. coli and containing 50mM NaCl (control treatment) or 300mM NaCl (mild osmotic stress). After 24 hours of exposure, adults were collected and washed from the plates. Adults were pelleted by sedimentation rather than centrifugation to avoid collecting laid eggs derived from not fully exposed worms. Eggs from adults were collected by hypochlorite treatment and 2-cell stage embryos were manually picked for small RNA sequencing.

value: mothers exposed to 50mM NaCl and Auxin


title: ileal crypt cells, CON4

value: vehicle


title: DP_AID_Auxin_50mM_biol_rep3


title: liver, H3K27ac, CLP rep2


title: liver, H3K27ac, CLP rep1


title: DP_AID_Auxin_300mM_biol_rep3

value: mothers exposed to 300mM NaCl and Auxin


title: DP_AID_Auxin_50mM_biol_rep1


title: HeLa S3, shvec, input, rep1

description: NS-seq

value: Human cervical carcinoma

value: HeLa S3

value: Human cervical carcinoma cell


title: Vehicle-treated_L003

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

data_processing:
The standard 10x Genomics protocol (CellRanger V6.0172) was used to generate gene-cell expression matrices. Preliminary QC including correcting for batch effects on the FASTQ files was performed (CellRanger) before aggregating the libraries. Seurat (V3.1, R package) was used for normalization, to merge replicates and determine filter criteria according to the median number of genes and mitochondrial gene percent via QC plots. The integrative analysis workflow from Seurat was implemented to compare the vehicle- and FAKi-treated samples. Bootstrapping (jackstraw and elbow heuristics) were used to identify/validate significant principal components from sequenced cells as input UMAPs. Graph-based clustering (Seurat) was used for cluster generation, and cell types were annotated based on canonical marker genes, and unbiased cell type annotation using relevant references. Differentially expressed genes were identified across the clusters, and false discovery rate correction was done using Benjamini-Hochberg correction. Functional enrichment was done using clusterProfiler resources from MSigDB. Psedutime analysis was performed using Slingshot, and differentially expressed genes along the trajectory were identified using Monocle2, and visualized as heatmaps ordered based on the pseudotime.
Assembly: mm10
Supplementary files format and content: scRNAcounts and metadata files

source_name: isolated islets

extract_protocol:
Single cells were stained using trypan blue for visualization, counting and viability assessment using the Countess II Automated Cell Counter and diluted as needed to a final concentration of 700-1200 cells/ml in 1x PBS + 0.04% BSA.
Single cells were stained using trypan blue for visualization, counting and viability assessment using the Countess II Automated Cell Counter and diluted as needed to a final concentration of 700-1200 cells/ml in 1x PBS + 0.04% BSA.  A minimum of two reproducible counts with SD <25% were required before droplet preparation. Cell viability was 75-76%. A total of 8832 for the vehicle- and 8437 cells for the FAKi-treated samples were used for sequencing. Cells were processed with Chromium Next Gem single Cell 3’ GEM Library and Gel Bead Kit v 3.1 (10X Genomics) according to manufacturer instructions. Briefly, cells diluted in master mix containing reverse transcription reagents and primer and were transferred to the ChromiumChip with gel beads and partitioning oil for preparation of nanoliter-scale Gel Bead-In-Emulsions (GEMs). Reverse transcription produced cDNA with a cellular 10X barcode and UMI, and was recovered with Dynabeads MyOne SILANE magnetic beads.  Subsequently the cDNA underwent 12 cycles of amplification before clean-up using SPRIselect Reagent (Beckman).  Total cDNA yield was calculated following quality assessment (High Sensitivity D5000 ScreenTape, Agilent) and fluorometric quantitation (Qubit, ThermoFisher).
Libraries were constructed by enzymatic fragmentation, end repair and A-tailing according to the manufacturer’s instructions.  A double sided SPRIselect Reagent (Beckman) clean up prepared samples for adapter ligation and another round of magnetic bead clean-up before sample indexing PCR for 12 cycles. A further double sided size selection produced libraries of approximately 400bp, which were quantified for paired end sequencing (26bp x 98bp).

value: isolated islets

value: Vehicle-treated


title: ileal crypt cells, CON3


title: OE-ALKBH5-2

city: Shenyang

first: Lingyue

last: Gao

address: Wenhua Road

institute: Shenyang Pharmaceutical University

data_processing:
Paired-end reads were harvested from sequencer, and were quality controlled by Q30.
Sequence reads were trimmed for 3’ adaptor/low-quality reads using  cutadapt software (v1.9.3)
The  high quality reads were aligned to the reference genome (HG19) with hisat2 software (v2.0.4).
HTSeq software (v0.9.1) was used to get the raw count as the expression profiling
The edgeR (v3.16.5) was used to perform normalization and differential expressed mRNAs were identified by p-value and Fold change.
Assembly: HG19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes normalized values for each Sample

source_name: NSCLC

extract_protocol:
Total RNA of lung cancer cells were harvested using Trizol reagent. The rRNAs was removed from total RNA with GenSeq® rRNA Removal Kit (GenSeq, Inc.).
RNA libraries for RNA-seq were prepared using GenSeq® Low Input RNA Library Prep Kit following manufacturer’s protocol

tag: group

value: NSCLC


title: ileal crypt cells, CON2


title: DP_AID_EtOH_50mM_biol_rep3

value: embryo

value: MHE229 (Drosha Pasha intestinal degron)

value: 2-cell embryos

value: drsh-1(luc82[myc::AID::3XFLAG::4xGGSG::drsh-1::4xGGSG::3xFLAG::AID::myc])pash-1(luc71[pash-1::2xGGSG::3xFLAG::AID::myc]) I; reSi12 [ges-1p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II:0.77)

value: mothers exposed to 50mM NaCl and EtOH


title: OE-ALKBH5-3


title: Vehicle-treated_L002


title: ileal crypt cells, CON1

value: ileal crypt cells


title: DP_AID_Auxin_300mM_biol_rep1


title: Vehicle-treated_L001


title: DP_AID_Auxin_300mM_biol_rep2


title: OE-ALKBH5-1


title: GCs_week2, scRNAseq

city: Hong Kong

first: Tongzhou

last: Liang

state: Hong Kong

address: 30 Ngan Ching Street

department: Department of Orthopaedics and Traumatology

institute: The Chinese University of Hong Kong

description: 10x genomics

data_processing:
The raw gene expression matrix generated from each sample were aggregated using CellRanger(v5.0.1) provided on the 10x genomics website. Downstream analysis was done using the R package Seurat (v 3.2.0). Quality control was applied to cells based on number of detected genes and proportion of mitochondrial reads per cell. Specifically, cells with less than 200 detected genes or cells with >90% of the proportion of the maximum genes were filtered out.  For the mitochondrial metric, sorted the cells in descending order of mitochondrial read ratio, and filtered out the top 15% of cells. Potential doublets were identified and removed by DoubletDetection. Cell cycle analysis was performed by using CellCycleScoring function in Seurat program. The gene expression dataset was normalized, subsequent principal component (n=15) analysis was conducted using only the 2000 highly variable genes in the dataset.
U-MAP was then used for two-dimensional visualization of the resulting clusters. For each cluster, the marker genes were identified using the FindAllMarkers function as implemented in the Seurat package (logfc. threshold >0.25, minPct >0.1 and Padj≤0.05). Then, clusters were remarked to a known cell type by SCSA method. Differently expressed gene across different samples were identified using the FindMarkers function in Seurat with parameters ‘logfc. threshold >0.25, minPct>0.1 and Padj≤0.05’.
Assembly: mm10
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Trabecular bone tissue

extract_protocol:
The callus and trabecular digested subjected to enzyme digestion to produce single-cell suspension.  To isolate trabecular bone and callus cells, marrow plugs were flushed. The remaining bone fragments were crushed and digested following the same methods as the marrow plugs. The digestion buffer contained Collagenase II, Dispase II and DNase I. The bone fractions were pooled and filtered through 70 μm cell strainers, washed twice with ice-cold staining buffer and centrifugation at 600 × g for 5 min.
Single-cell RNA-seq libraries were prepared using the Kit v2 from 10x Genomics, following the manufacturer’s instructions.The cellular or nuclei suspension is stained with 0.4% trypan blue to assess cell viability under microscopic observation. Cells with greater than 80% viability are qualified for library construction process. Prepared single-cell suspension is then partitioned into GEMs (Gel Beads in Emulsions) in the automated Chromium Controller, and then mRNAs are reverse transcribed into cDNAs. The reaction system is configured for breaking GEMs. After reacting at the suitable temperature for a fixed period of time, the products are purified.The reaction system is configured for PCR. After reacting at the suitable temperature for a fixed period of time, the products are purified. The reaction system is configured. A certain amount of cDNA amplified products is taken. After reacting at the suitable temperature for a fixed period of time, the cDNAs are subjected to fragmentation, end repair and addition of “A” base at the 3'-end of each strand. Finally, the products are purified. The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, the cDNAs are subjected to adaptor ligation. Finally, the products are purified.

treatment_protocol: Glucocorticoid-induced bone loss model: 20-week-old C57BL/6J male mice were used. All the mice were anesthetized, and prednisolone slow-release pellets (or placebo control) were applied by subcutaneous implantation (6.25 mg/kg/d). The sample were collected at week 2. Glucocorticoid-induced bone loss model: 20-week-old C57BL/6J male mice were used. All the mice were anesthetized, and prednisolone slow-release pellets (or placebo control) were applied by subcutaneous implantation (6.25 mg/kg/d). The sample were collected at week 2.

value: Trabecular bone tissue

value: GCs


title: GCs_fracture, scRNAseq

description: 10x genomics

source_name: Fracture callus tissue

value: Fracture callus tissue


title: DP_AID_EtOH_50mM_biol_rep1


title: Ctrl_fracture, scRNAseq

description: 10x genomics

value: Ctrl


title: OE-CON1

value: Control


title: Faki-treated_L003

value: Faki-treated


title: HSM2_T6_R2

city: Melbourne

first: Akriti

last: Varshney

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

data_processing:
Processing is automated using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools), and proceeds as follows:
Reads are stripped of trailing poly(A) sequence.
Reads are aligned using STAR aligner (v2.6.0A https://github.com/alexdobin/star). Multi-mapping reads are assigned to one location at random.
Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.
Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 2000 bases down-strand of a gene are counted towards that gene. Total reads per gene and reads with a poly(A) tail per gene are tabulated.
Genome_build: Homo sapiens ensembl version 93
Supplementary_files_format_and_content: genewise-count.csv contains counts of reads aligning to each gene and peakwise-count.csv contains counts of reads aligning to each peaks called by the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools).

source_name: primary human skeletal muscle cells

growth_protocol: Primary human skeletal muscle cells were cultivated in Hams F-10 with 20% Fetal Bovine Serum and basic Fibroblast Growth Factor (bFGF) at 37˚C until 80% confluent.

extract_protocol:
Total RNA was harvested in Trizol and stored at -80˚C until Quant-seq analysis.
The Library was made using Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit FWD according to the manufacturer's instructions, which was then sequenced on Illumina HiSeq 3000.
Sequencing was by the MHTP Medical Genomics Facility and applied Illumina directional RNA-seq on the Illumina Hiseq3000 using 150bp forward read. Libraries were purifified using AMPureXp beads and QC’d by Qubit, Bioanalyzer and qPCR. Mean size 343bp; 7.8nM.
[Cluster Generation]  c-bot clustering using 200pM of library pool. Illumina Protocol 15006165 v02 Jan 2016
[Sequencing Chemistry]  PE sequencing using Illumina HiSeq 3000. Illumina Protocol 15066493 Rev A, February 2015

treatment_protocol: Cells were differentiatiated in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 2% horse serum. Samples were collected 1, 3, 5 and 7 days post treatment.

value: 7 days with horse serum


title: Faki-treated_L002


title: HSM2_T6_R1


title: Ctrl_week2, scRNAseq

description: 10x genomics


title: OE-CON2


title: OE-CON3


title: Faki-treated_L001


title: HSM2_T5_R2

value: 5 days with horse serum


title: Human parathyroid adenoma cells; sample Y11

city: New Haven

first: Diane

middle: S

last: Krause

address: 10 Amistad St.

department: Laboratory Medicine

institute: Yale University

description: 10x Genomics Next GEM Single Cell 3' V3.1

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mmul_10 with transcriptome annotation v10.104; GRch38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Dissociate human paratyhroid

extract_protocol:
Freshly collected parathroid adenomas from human subjects were obtained with signed informed consent in compliace with the Declaration of Helsinki. Human tissue was dissociated with a gentleMACS on setting "mouse spleen program 1". The digestate was then passed through a 100 µm cell strainer, rinsed with 4 mL ice cold RBC lysis buffer (155mM NH4Cl, 10 mM KHCO3, 0.1 mM EDTA or BD Pharm Lyse solution from Becton Dickinson #555899), and pelleted by centrifugation at 200 x g for 3 minutes. Supernatant was discarded and cells were resuspended again in 5 mL RBC lysis buffer, pelleted, then resuspended in sterile PBS. Cells were counted, pelleted again, then resuspended at a concentration of 1E6 cells/mL in sterile PBS containing 0.1% BSA in preparation for downstream processing. Primate tise
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, parathyroids were dissociated with Collagenase B and agitation, then resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Parathyroid adenoma cells

value: Dissociated human parathyroid

tag: cell abundance

value: primarily oxyphil cells by analysis of H&E stained slide from same tissue


title: DP_AID_EtOH_300mM_biol_rep2

value: embryo

value: mothers exposed to 300mM NaCl and EtOH


title: DP_AID_EtOH_50mM_biol_rep2

value: MHE229 (Drosha Pasha intestinal degron)

value: 2-cell embryos


title: Faki-treated_L004

value: isolated islets


title: DP_AID_EtOH_300mM_biol_rep1

value: drsh-1(luc82[myc::AID::3XFLAG::4xGGSG::drsh-1::4xGGSG::3xFLAG::AID::myc])pash-1(luc71[pash-1::2xGGSG::3xFLAG::AID::myc]) I; reSi12 [ges-1p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II:0.77)


title: WT_N2_50mM_biol_rep2

value: Wild-type embryos from mother exposed to 50mM NaCl

value: mothers exposed to 50mM NaCl


title: Human parathyroid adenoma cells; sample Y7

value: primarily chief cells by analysis of H&E stained slide from same tissue


title: Human parathyroid adenoma cells; sample Y9


title: Sham_Saline_S20

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

data_processing:
RNASeq reads were aligned to the mouse genome (Mm10 genome assembly) using Partek Flow (Star 2.3.7), with an alignment rate of 98%. Genes and transcripts were annotated with Genocode 25 and the number of reads within exons on average 84%.
Assembly: Mm10
Supplementary files format and content: tab-delimited text file of gene counts for each sample

source_name: Left Ventricle

extract_protocol:
RNA was extracted from hearts using TRIzol (ThermoFisher)/chloroform method
mRNA libraries were prepared using NEBNext Ultra II

value: Left Ventricle

tag: Sex

value: male

value: Sham Saline


title: Sham_Saline_S19


title: WT_N2_50mM_biol_rep1


title: HSM2_T4_R2

value: 3 days with horse serum


title: NCH53: PA-IVS iPSC-CMs

city: Memphis

first: Zhaohui

last: Xu

state: TN

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequences were removed, then mapped to GRCh38 whole genome using hisat2
Gene counts were calculated using featureCounts with provided GTF file (GENCODE)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene count values for each Sample

source_name: iPSC-CMs

extract_protocol:
iPSC-CMs derived from PA-IVS-1v patients and healthy controls were lysed by the TRIzol Reagent (Zymo Research) and total RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research)
RNA libraries were prepared using standard in-house library prep protocols (Novogene)

tag: disease state

value: iPSC-CMs

value: differentiation for 13 days


title: TAC_29P_S18

value: TAC 29P


title: DP_AID_EtOH_300mM_biol_rep3


title: HSM2_T4_R1


title: WT_N2_300mM_biol_rep2

value: Wild-type embryos from mother exposed to 300mM NaCl

value: mothers exposed to 300mM NaCl


title: Human parathyroid adenoma cells; sample Y13

value: Parathyroid adenoma cells

value: Dissociated human parathyroid

value: primarily oxyphil cells by analysis of H&E stained slide from same tissue


title: NCH52: PA-IVS iPSC-CMs


title: HSM2_T3_R2

value: 1 day with horse serum


title: WT_N2_300mM_biol_rep1

value: embryo

value: 2-cell embryos


title: NCH51: PA-IVS iPSC-CMs


title: Sham_29P_S15

value: Sham 29P


title: NCH33: Control iPSC-CMs

value: healthy control


title: HSM2_T5_R1

value: 5 days with horse serum


title: Sham_29P_S14

value: Left Ventricle

value: male


title: HSM2_T3_R1


title: WT_N2_Day3_biol_rep2

value: Wild-type embryos from day 3 mothers


title: WT_N2_Day3_biol_rep3


title: Sham_Saline_S13

value: Sham Saline


title: NCH31: Control iPSC-CMs

value: iPSC-CMs

value: differentiation for 13 days


title: WT_N2_Day3_biol_rep1


title: TAC_Saline_S12

value: TAC Saline


title: HSM2_T2_R1

value: no treatment


title: WT_N2_Day2_biol_rep3

value: Wild-type embryos from day 2 mothers


title: HSM2_T1_R2


title: NCH32: Control iPSC-CMs


title: TAC_29P_S11

value: TAC 29P


title: H9 crowded rep 2

city: Pohang-si

first: Seungbok

last: Yang

address: 47, Jigok-ro

country: South Korea

institute: POSTECH

description: Crowded DEG.csv

data_processing:
The libraries were quantified using KAPA Library Quantificatoin kits for Illumina Sequecing platforms and qualified using the TapeStation D1000 ScreenTape.
The raw reads from the Illumina NovaSeq were trimmed using TRIMMOMATIC to remove adapter and low quality sequence, than aligned to the Homo sapiens (GRCh37) using HISAT v2.1.0.
Transcript assembly of known transcripts was processed by StringTie v2.1.3b
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts and normalized data for each Sample.

source_name: human embryonic cells

growth_protocol: H9 cells were routinely passaged every 3-4 days onto culture plate coated with Matrigel with stem cell media mTeSR1 or TeSR-E8.

extract_protocol:
total RNAs were extracted using Trizol reagent. TruSeq Stranded mRNA LT Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic stem cell

value: H9 (WiCell WA09)

value: crowded


title: HSM2_T1_R1


title: H9 crowded rep 1

description: Crowded DEG.csv


title: TAC_29P_S9


title: TAC_Saline_S16


title: HSM1_T6_R2

value: 7 days with horse serum


title: WT_N2_Day2_biol_rep2

value: embryo

value: 2-cell embryos


title: WT_N2_Day2_biol_rep1


title: H9 small rep 2

description: Crowded DEG.csv

value: small


title: TAC_29P_S8

value: Left Ventricle


title: HSM1_T6_R1


title: HSM2_T2_R2


title: H9 small rep 1

description: Crowded DEG.csv


title: WT_N2_Day1_biol_rep3

value: Wild-type embryos from day 1 mothers


title: HSM1_T5_R2

value: 5 days with horse serum


title: HSM1_T5_R1


title: WT_N2_Day1_biol_rep2


title: Sham_Saline_S6

value: male

value: Sham Saline


title: Vehicle-treated_L004

value: isolated islets

value: Vehicle-treated


title: WT_N2_Day1_biol_rep1


title: H9 ETV4 KD rep 2

description: ETV4 KD DEG.csv

value: ETV4 KD


title: Sham_Saline_S5


title: HSM1_T4_R2

value: 3 days with horse serum


title: H9 Ctrl rep 2

description: ETV4 KD DEG.csv

value: Ctrl


title: H9 ETV4 KD rep 1

description: ETV4 KD DEG.csv

value: embryonic stem cell


title: HSM1_T4_R1


title: TAC_Saline_S2

value: TAC Saline


title: DP_AID_Auxin_biol_rep2

value: MHE229 (Drosha Pasha intestinal degron)

value: drsh-1(luc82[myc::AID::3XFLAG::4xGGSG::drsh-1::4xGGSG::3xFLAG::AID::myc])pash-1(luc71[pash-1::2xGGSG::3xFLAG::AID::myc]) I; reSi12 [ges-1p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II:0.77)

value: Auxin


title: TAC_29P_S3

value: TAC 29P


title: TAC_29P_S1


title: H9 Ctrl rep 1

description: ETV4 KD DEG.csv

value: H9 (WiCell WA09)


title: HSM1_T3_R2

value: 1 day with horse serum


title: DP_AID_EtOH_biol_rep3

value: embryo

value: 2-cell embryos

value: EtOH


title: HSM1_T2_R2

value: no treatment


title: DP_AID_EtOH_biol_rep2


title: colo205 cells,SB204741_3

city: Buk-gu, Gwangju

first: Suhyeon

last: Park

state: Gwangju

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호

institute: GIST

data_processing:
kallisto  2023 Pachter Lab
pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
Pseudoalignment of reads were mapped to human GRCh38 cDNA as a reference
the expected counts were used
Assembly: h38
Supplementary files format and content: tab-delimited txt file includes expected counts for each sample

source_name: human colon

growth_protocol: The Colo 205 cells were cultured in RPMI 1640 with 10% FBS and 100μg ml-1 P/S in a humidified atmosphere of 5% CO2 at 37℃.

extract_protocol:
The total RNA was isolated by TRIzol (Thermo, 15596018). From 1 ug input of total RNA, sequencing libraries were generated.
the Illumina Stranded mRNA prep was used according to the manufacturer’s protocol.

treatment_protocol: Colo 205 was treated with 500nM SB204741 for 3 days.

value: human colon

value: Human Caucasian colon adenocarcinoma

value: WT


title: HSM1_T2_R1


title: colo205 cells,SB204741_2

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호


title: DP_AID_EtOH_biol_rep1


title: Sham_29P_S4

value: Left Ventricle

value: male

value: Sham 29P


title: colo205 cells,SB204741_1

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호


title: HSM1_T1_R2


title: rme2_AID2_5PhIAA_biol_rep3

value: MHE235 (rme-2 degron)

value: wrdSi51 [mex-5p::TIR1F79G::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II:0.77) ; rme-2(gcp080[rme-2::AID::2XHA]) IV


title: colo205 cells,control3

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호


title: DP_AID_Auxin_biol_rep3

value: MHE229 (Drosha Pasha intestinal degron)

value: drsh-1(luc82[myc::AID::3XFLAG::4xGGSG::drsh-1::4xGGSG::3xFLAG::AID::myc])pash-1(luc71[pash-1::2xGGSG::3xFLAG::AID::myc]) I; reSi12 [ges-1p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II:0.77)


title: DP_AID_Auxin_biol_rep1

value: Auxin


title: rme2_AID2_5PhIAA_biol_rep2


title: HSM1_T3_R1


title: colo205 cells,control2

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호


title: rme2_AID2_5PhIAA_biol_rep1


title: slgols2-2

first: Huidong

last: Zhang

address: No.120 Dongling Road, Shenhe District, Shenyang, Liaoning Province, P.R.C.

institute: Shenyang Agricultural University

data_processing:
Fastp (0.22.0) software was used to filter the raw data to get high quality sequence for further analysis.
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
The difference expression of genes was analyzed by DESeq (v1.38.3) with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05.
Assembly: Reference genome Solanum lycopersicum SL3.0 was downloaded from tomato genome website (https://solgenomics.net/).
Supplementary files format and content: The tab-delimited text file includes the fpkm values for each sample.

organism: Solanum lycopersicum

source_name: pericarp

growth_protocol: All plants were grown in the greenhouse under 16 h light (25 °C) and 8 h dark (18 °C).

extract_protocol:
For RNA-Seq analysis, tomato pericarps of WT and slgols2 mutations were harvested at 30 DPA. Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies).
RNA library was prepared for sequencing using Illumina protocols.

value: pericarp

value: slgols2 knock-out

tag: cultivar

value: Ailsa Craig

tag: developmental stage

value: 30 DPA


title: rme2_AID2_NGM_biol_rep3

value: embryo

tag: cell line

value: 2-cell embryos


title: slgols2-3


title: slgols2-1


title: GSC387, KD, CBP ChIP

city: CLEVELAND

first: Haidong

state: OH

address: 9500 EUCLID AVE RK-15

department: Cancer Biology

institute: Cleveland Clinic Foundation

data_processing:
Raw fastq files were trimmed using Trim Galore and aligned to the GRCh38 human genome using Bowtie2 with the default parameters.
Samtools was used to sort the BAM file. Sambamba was used to filter out duplicated reads and bedtools was used to filter out blacklisted regions.
BAMs files were used to call peaks with MASC2 with the narrow peak mode.
Bigwig files were generated using the Deeptools bamCoverage for visualization. Deeptools was used to generate heat maps and profile plots. Signal tracks were visualized using Integrative Genomics Viewer web app.
Assembly: GRCh38
Supplementary files format and content: BW (BigWig) files

growth_protocol: GSC line 387 was maintained in Neurobasal-A medium with B27 supplement, 20 ng/ml EGF and 20 ng/ml FGF, 1 mM L-Glutamine, 100 units/mL penicillin, and 100 μg/mL streptomycin) at 37 °C with 5% CO2.

extract_protocol:
Cells were crosslinked and sonicated. HIF1A or CBP antibodies were used for ChIP.
Purified DNAs were used to prepare sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: Cells were treated with 1ug/ml doxyxycline and incubated in 1% O2 for 24 hours.

tag: cell type

value: glioma stem cell


title: WT-3

tag: genotype

value: wild type


title: HSM1_T1_R1

tag: treatment

value: no treatment


title: GSC387, KD, HIF1a ChIP


title: GSC387, KD, input for CBP ChIP


title: GSC387, KD, input for HIF1a ChIP


title: rme2_AID2_NGM_biol_rep1

tag: tissue


title: WT-1


title: colo205 cells,control1

address: 광주광역시 북구 첨단과기로 123 다산빌딩 403호

value: human colon

value: Human Caucasian colon adenocarcinoma

value: WT


title: unsorted_OP50_biol_rep2

source_name: unsorted fraction

value: whole worm

value: wrdSi51 [mex-5p::TIR1::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II:0.77) ; rme-2(gcp072[rme-2::AID::2xHA])IV line 3; vit-2(crg9070[vit-2::gfp]) X


title: unsorted_OP50_biol_rep3


title: WT-2


title: GSC387, control, CBP ChIP


title: unsorted_OP50_biol_rep1


title: M. mulatta parathyroid gland cells; animal 4

organism: Macaca mulatta

source_name: Dissociated primate parathyroid

value: Parathyroid cells

value: Dissociated primate parathyroid

value: 23 years


title: rme2_AID2_NGM_biol_rep2

value: MHE235 (rme-2 degron)

value: wrdSi51 [mex-5p::TIR1F79G::F2A::mTagBFP2::AID*::NLS::tbb-2 3'UTR] (II:0.77) ; rme-2(gcp080[rme-2::AID::2XHA]) IV


title: M. mulatta parathyroid gland cells; animal 3

value: 22 years


title: GSC387, control, HIF1a ChIP


title: GSC387, control, input for HIF1a ChIP


title: GFP_sorted_OP50_biol_rep3

source_name: yolk sorted fraction


title: GSC387, control, input for CBP ChIP


title: M. mulatta parathyroid gland cells; animal 2


title: GFP_sorted_OP50_biol_rep1


title: BMDM WT 6.0h R2

status: Public on Mar 11 2024

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

data_processing:
Demultiplexed and trimmed reads where mapped to the NCBI37/mm9 genome using Hisat2.
After alignment samples were processed into BAM files using Samtools.
Raw reads were extracted using SeqMonk. Normalized read counts (RPKMs) were generated by normalizing for sequencing depth (per million reads) and gene length (kilobases).
Assembly: mm9
Supplementary files format and content: tab-deliminated text file included RPKM values for each sample.

molecule: nuclear RNA

source_name: BMDM

growth_protocol: Bone marrow was extracted from hip, femur, tibia, and fibula of wild type or cRel-/- mice. Cells were differentiated for 6-days in cell culture using 8% CMG.

extract_protocol:
Cellular fractionation was used to isolate nuclei and extract chromatin. Once chromatin was isolated, it was resuspended in Trizol. ~100ng of chromatin-assosiated RNA was used for library construciton.
RNA-seq libraries were constructed using the Illumina Stranded Tru-Seq Kit adapted from the manufacturers instructions.

value: BMDM

value: Wild type

value: 6.0h Lipid A


title: GFP_sorted_OP50_biol_rep2


title: M. mulatta parathyroid gland cells; animal 1

value: 24 years


title: BMDM WT 1.0h R2

value: 1.0h Lipid A


title: BMDM cRel-/- 0.5h R2

value: cRel-/-

value: 0.5h Lipid A


title: BMDM WT 2.0h R2

value: 2.0h Lipid A


title: BMDM cRel-/- 1.0h R2


title: BMDM cRel-/- 0.0h R2

value: Unstimulated


title: BMDM WT 0.5h R2


title: BMDM WT 0.0h R2


title: BMDM cRel-/- 2.0h R1


title: BMDM cRel-/- 1.0h R1


title: Normal 5

type: genomic

city: Kolkata

first: Susanta

last: Roychoudhury

state: West Bengal

address: Mahatma Gandhi Road, Thakurpukur

country: India

institute: Saroj Gupta Cancer Centre & Research Institute

description: SAMPLE 15

hyb_protocol: The bisulfite converted DNA extracts were hybridized to Infinium EPIC BeadChips using standard Illumina Protocol

scan_protocol: Arrays were imaged using iScan System using standard recommended Illumina scanner setting

data_processing: GenomeStudio v2011.1 (Methylation Module 1.9.0) was used to transform the data. No normalisation was performed.

label: biotin

source_name: Patient

label_protocol: 500ng of DNA are used for bisulfite conversion using the Zymo Research EZ-96 DNA Methylation Kit and labelling was done by standard Illumina Protocol using biotin

growth_protocol: Primary uterine cervical lesions and normal ectocervix were collected from the hospital section of Chittaranjan National Cancer Institute, Kolkata, India after appropriate approval of the Institutional Ethical Committee and written informed consent from respective patients were taken.

extract_protocol: Genomic DNA from cryosections (5µm) of microdissected tumor tissue specimen and ectocervix were isolated by standard phenol/chloroform method.

tag: gender

value: Female

value: HPV negative normal cervical epithelium


title: BMDM cRel-/- 6.0h R1


title: Normal 4

description: SAMPLE 14


title: BMDM cRel-/- 0.0h R1


title: BMDM WT 1.0h R1


title: BMDM WT 0.0h R1


title: NSLA_72

city: daejeon

first: Seung-Jin

address: gwahakro

institute: KRIBB

description: SWAN normalization

hyb_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
CpG methylation values were calculated as average-values using Minfi (v3.11), with the following equation: average = M/(M + U + 100), where M and U are the methylated and unmethylated signal intensities, respectively. Measurements with a p-value <0.05 were considered significant above the background. Additionally, redundant probes, including multi-hit probes and SNPs, which could affect the analysis results, were filtered using the ChAMP package filter function.
processed data value definition: SWAN normalization

label: Cy5 and Cy3

source_name: Lung

label_protocol: Standard Illumina Protocol

extract_protocol: not provided

tag: Stage

tag: age

value: FEMALE

tag: disease

value: Never-smoker lung adenocarcinoma


title: BMDM WT 0.5h R1


title: BMDM cRel-/- 0.5h R1


title: BMDM WT 6.0h R1


title: Primary Tumor 8

description: SAMPLE 8

value: hrHPV positive cervical squamous cell carcinoma stage III/IV


title: Normal 1

description: SAMPLE 11


title: BMDM cRel-/- 2.0h R2


title: NSLA_696

description: SWAN normalization

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting


title: Primary Tumor 4

description: SAMPLE 4

value: hrHPV positive cervical squamous cell carcinoma stage I/II


title: BMDM WT 2.0h R1


title: NSLA_677

description: SWAN normalization


title: BMDM cRel-/- 6.0h R2


title: Primary Tumor 10

description: SAMPLE 10


title: NSLA_698

description: SWAN normalization


title: NSLA_675

description: SWAN normalization


title: NSLA_666

description: SWAN normalization


title: NSLA_693

description: SWAN normalization


title: NSLA_699

description: SWAN normalization


title: NSLA_674

description: SWAN normalization


title: NSLA_689

description: SWAN normalization


title: NSLA_66

description: SWAN normalization


title: Normal 2

description: SAMPLE 12


title: Primary Tumor 6

description: SAMPLE 6


title: NSLA_682

description: SWAN normalization


title: Primary Tumor 3

description: SAMPLE 3


title: NSLA_649

description: SWAN normalization


title: NSLA_679

description: SWAN normalization


title: NSLA_680

description: SWAN normalization


title: NSLA_663

description: SWAN normalization


title: NSLA_616

description: SWAN normalization


title: Primary Tumor 5

description: SAMPLE 5


title: NSLA_61

description: SWAN normalization


title: NSLA_667

description: SWAN normalization


title: NSLA_6

description: SWAN normalization


title: Normal 3

description: SAMPLE 13


title: NSLA_672

description: SWAN normalization


title: NSLA_665

description: SWAN normalization


title: Primary Tumor 9

description: SAMPLE 9


title: NSLA_598

description: SWAN normalization


title: Primary Tumor 2

description: SAMPLE 2


title: NSLA_587

description: SWAN normalization


title: NSLA_654

description: SWAN normalization


title: NSLA_581

description: SWAN normalization


title: Primary Tumor 1

description: SAMPLE 1


title: NSLA_657

description: SWAN normalization


title: NSLA_571

description: SWAN normalization


title: NSLA_631

description: SWAN normalization


title: NSLA_632

description: SWAN normalization


title: Primary Tumor 7

description: SAMPLE 7


title: NSLA_626

description: SWAN normalization


title: NSLA_611

description: SWAN normalization


title: NSLA_595

description: SWAN normalization


title: NSLA_540

description: SWAN normalization


title: NSLA_541

description: SWAN normalization


title: NSLA_589

description: SWAN normalization


title: NSLA_585

description: SWAN normalization


title: NSLA_608

description: SWAN normalization


title: NSLA_50

description: SWAN normalization


title: NSLA_563

description: SWAN normalization


title: NSLA_555

description: SWAN normalization


title: NSLA_56

description: SWAN normalization


title: NSLA_543

description: SWAN normalization


title: NSLA_542

description: SWAN normalization


title: NSLA_460

description: SWAN normalization


title: NSLA_469

description: SWAN normalization


title: NSLA_471

description: SWAN normalization


title: NSLA_459

description: SWAN normalization


title: NSLA_535

description: SWAN normalization


title: NSLA_519

description: SWAN normalization


title: NSLA_490

description: SWAN normalization


title: NSLA_407

description: SWAN normalization


title: NSLA_488

description: SWAN normalization


title: NSLA_483

description: SWAN normalization


title: NSLA_475

description: SWAN normalization


title: NSLA_479

description: SWAN normalization


title: NSLA_380

description: SWAN normalization


title: NSLA_464

description: SWAN normalization


title: NSLA_382

description: SWAN normalization


title: NSLA_429

description: SWAN normalization


title: NSLA_398

description: SWAN normalization


title: NSLA_362

description: SWAN normalization


title: NSLA_379

description: SWAN normalization


title: NSLA_377

description: SWAN normalization


title: NSLA_421

description: SWAN normalization


title: NSLA_356

description: SWAN normalization


title: NSLA_365

description: SWAN normalization


title: NSLA_350

description: SWAN normalization


title: NSLA_312

description: SWAN normalization


title: NSLA_311

description: SWAN normalization


title: NSLA_300

description: SWAN normalization


title: NSLA_310

description: SWAN normalization


title: NSLA_309

description: SWAN normalization


title: NSLA_426

description: SWAN normalization


title: NSLA_259

description: SWAN normalization


title: NSLA_271

description: SWAN normalization


title: NSLA_257

description: SWAN normalization


title: NSLA_251

description: SWAN normalization


title: NSLA_235

description: SWAN normalization


title: NSLA_216

description: SWAN normalization


title: NSLA_2_97

description: SWAN normalization

value: MALE


title: NSLA_345

description: SWAN normalization


title: NSLA_2_8

description: SWAN normalization


title: NSLA_653

description: SWAN normalization


title: NSLA_2_63

description: SWAN normalization


title: NSLA_20

description: SWAN normalization


title: NSLA_374

description: SWAN normalization


title: NSLA_2_55

description: SWAN normalization


title: NSLA_2_5

description: SWAN normalization


title: NSLA_2_41

description: SWAN normalization


title: NSLA_2_369

description: SWAN normalization


title: NSLA_2_363

description: SWAN normalization


title: NSLA_2_379

description: SWAN normalization


title: NSLA_291

description: SWAN normalization


title: NSLA_2_266

description: SWAN normalization


title: NSLA_2_275

description: SWAN normalization


title: NSLA_2_407

description: SWAN normalization


title: NSLA_2_28

description: SWAN normalization


title: NSLA_2_350

description: SWAN normalization


title: NSLA_2_265

description: SWAN normalization


title: NSLA_2_273

description: SWAN normalization


title: NSLA_2_263

description: SWAN normalization


title: NSLA_2_30

description: SWAN normalization


title: NSLA_2_411

description: SWAN normalization


title: NSLA_239

description: SWAN normalization


title: NSLA_2_252

description: SWAN normalization


title: NSLA_2_220

description: SWAN normalization


title: NSLA_2_184

description: SWAN normalization


title: NSLA_2_171

description: SWAN normalization


title: NSLA_2_121

description: SWAN normalization


title: NSLA_2_152

description: SWAN normalization


title: NSLA_2_136

description: SWAN normalization


title: NSLA_2_24

description: SWAN normalization


title: NSLA_2_118

description: SWAN normalization


title: NSLA_2_116

description: SWAN normalization


title: NSLA_14

description: SWAN normalization


title: NSLA_181

description: SWAN normalization


title: NSLA_198

description: SWAN normalization


title: NSLA_168

description: SWAN normalization


title: NSLA_179

description: SWAN normalization


title: NSLA_172

description: SWAN normalization


title: NSLA_138

description: SWAN normalization


title: NSLA_136

description: SWAN normalization


title: NSLA_1013

description: SWAN normalization


title: NSLA_1012

description: SWAN normalization


title: NSLA_1009

description: SWAN normalization


title: NSLA_1011

description: SWAN normalization


title: NSLA_101

description: SWAN normalization


title: NSLA_1008

description: SWAN normalization


title: NSLA_2_221

description: SWAN normalization


title: NSLA_1010

description: SWAN normalization


title: NSLA_1007

description: SWAN normalization


title: NSLA_1006

description: SWAN normalization


title: NSLA_2_19

description: SWAN normalization


title: NSLA_1005

description: SWAN normalization


title: NSLA_1004

description: SWAN normalization


title: NSLA_1001

description: SWAN normalization


title: NSLA_1003

description: SWAN normalization


title: NSLA_139

description: SWAN normalization


title: Primed-H9_RNAseq_rep1

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

data_processing:
The adapter sequences of RNA-seq data and low-quality reads with Phred score <5 were deleted with Cutadapt before further processing.
Clean reads of RNA-seq were mapped to hg38 using HISAT2(2.1.0)
Expression levels of all genes were count.txted and expression profile matrix was constructed with featureCounts (2.0.4)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with padj < 0.05 and fold change > 2 or < 1/2
Assembly: hg38
Supplementary files format and content: gene FPKM text file

growth_protocol: The naive hESCs (also named as prEpiSCs) were derived from the LTR7-GFP hESC_H9 cell line. The basal culture medium (500 ml) is prepared as follows, 240 ml DMEM/F12 (Thermo Fisher Scientific, catalog. no. 21331020), 240 ml Neurobasal medium (Thermo Fisher Scientific, catalog. no. 21103049), 2 mM L-glutamine (Thermo Fisher Scientific, catalog. no. 25030081), non-essential amino acids (Thermo Fisher Scientific, catalog. no. 11140050), 1% N2 supplement (Thermo Fisher Scientific, catalog. no. 17502048), 2% B27 supplement (Thermo Fisher Scientific, catalog. no. 12587010, minus vitamin A), 100 mg/ml Vitamin C (Sigma, catalog no. A4403), 50 ng/ml Bovine Albumin Fraction V (Thermo Scientific, cat. no. 15260-037), 20 ng/ml IL6 (PeproTech, catalog. no. AF-200-06), 20 ng/ml sIL-6R (PeproTech, catalog. no. 200-06R), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific, catalog. no. 21985023), Primocin (InvivoGen, catalog. no. ant-pm-2). The naive/prEpiSCs were cultured in the advanced GIX medium (basal culture medium plus chemical cocktail [0.2 μM Trametinib (GSK112022, Selleck S2673), 0.3 μM PD0325901, 2.0 μM XAV939, 0.5 μM Go6983]).IL6, IL-6R, Trametinib, PD0325901, XAV939, Go6983

extract_protocol:
the sample used to perform RNA-seq are prepared based on the commonly used method.
AS  for RNA-seq, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer (5x). First strand cDNA was synthesized using random hexamer primer and M-MLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected and cDNA adaptor ligated at 37 °C for 15 min followed by 5 min at 95 °C prior to PCR. PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index Primer. At last, PCR products were purified using AMPure XP system and library quality assessed on the Agilent Bioanalyzer 2100 system. Cluster of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform.

treatment_protocol: The medium was changed every other day. The dome-shaped colonies were dissociated with Accutase (Thermo Fisher Scientific, catalog. no. A1110501) into single cells, and then passaged onto new Matrigel- or feeder-coated plates every 3 - 4 days.

value: ESC

value: WT

value: Primed medium (E8)


title: Primed-H9_Cuttagseq_H3K27me3_rep2

data_processing:
Use FastQC v0.11.9 for quality control of raw sequencing readings.
Using TrimGalore v0.6.6 to remove raw readings from low-quality base and linker sequences
Clean reads of  were mapped to hg38 using Bowtie2(2.3.1) The options are: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
Use the sorting function of samtools v1.13 to sort aligned bam files based on chromosome coordinates
Use the genomecov function of bedtools v2.30 to summarize the sorted bam files into a bedgraph file (Quinlan et al., 2010).
Peak calling on all bedgraph files using SEACR v1.3 by selecting the top 1% of the call peak.
Assembly: hg38
Supplementary files format and content: cut&tag peak bigwig files

extract_protocol:
the sample used to perform RNA-seq, ATAC-seq, CUT&Tag-seq are prepared based on the commonly used method.
as for CUT&Tag, 20000~50000 cells per sample replicate were washed in Wash Buffer [1 mL 1 M HEPES pH 7.5 (Sigma–Aldrich, H3375), 1.5 mL 5 M NaCl (Sigma–Aldrich, S5886-1KG), 12.5 μL 2 M Spermidine (MCE, HY-B1776), Roche Complete Protease Inhibitor EDTA-Free tablet (Sigma–Aldrich, 4693132001), and bring the final volume to 50 mL with dH2O], then immobilized on 10 ul of Concanavalin A-coated beads (Bangs Laboratories, BP531). Cells were cleared on a magnetic rack, then permeabilized with cold Antibody buffer [20 mM HEPES pH 7.5, 150 mM NaCl, 2mM EDTA, 0.1% BSA, 0.5 mM Spermidine and 1× protease inhibitor cocktail containing 0.05% Digitonin (AbMole, M5020-100mg)] on ice. The cells were then incubated with anti-H3K9me3(Abcam, ab8898, 1:100 dilution), anti-H3K9ac (Abcam, ab32129, 1:100 dilution), anti-H3K27me3(Millipore, 07-449, 1:100 dilution), H3K27ac (Abcam, ab177178, 1:100 dilution), anti-CTCF (Millipore, ab128873,1:100 dilution) for 2h at RT on a shaker. The primary antibody was cleared on a magnetic rack. Goat anti-Rabbit IgG secondary antibody (Millipore, 07-449) was diluted 1:100 in Dig-wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine and 1× protease inhibitor cocktail containing 0.05% Digitonin) and incubated at RT for an hour. Cells were cleared on a magnetic rack and washed three times with 700ul of Dig-wash buffer. A 1:100 diluted of pA-Tn5 adapter complex combining adapter primers (Table S3) and pA-Tn5 according to the manufacturer’s instructions (Vazyme, S603-01) was prepared in Dig-300 Buffer [20 mM HEPES pH 7.5, 300 mM NaCl, 0.5 mM Spermidine and 1× protease inhibitor cocktail containing 0.05% Digitonin]. Cells were cleared on a magnetic rack and incubated by adding 100 ul of pA-Tn5 at RT for 1 h. Cells were washed with 700ul of Dig-300 buffer, resuspended in 300 ul of Tagmentation buffer [10 mM MgCl2 in Dig-300 Buffer], and incubated at 37 °C for 1 h. 10 ul of 0.5 M EDTA, 3 ul of 10% SDS, and 2.5 ul of 20 mg/mL Proteinase K was added to each reaction to stop the tagmentation at 37 °C overnight. DNA was purified using phenol/chloroform/isoamyl alcohol (PCI) extraction followed by chloroform extraction and precipitated with glycogen and ethanol. DNA was pelleted with a high-speed spin at 4 °C, washed, air dried for 5 min and resuspended in 25 ul of double-distilled water (ddH2O) containing 100ug/ml RNase. The DNA was then PCR amplified using TruePrep Index Kit V4 for Illumina (Vazyme, TD204), and cleaned up with VAHTS DNA Clean Beads (Vazyme, N411-01).


title: Primed-H9_Cuttagseq_H3K9me3_rep1


title: Primed-H9_RNAseq_rep2


title: Primed-H9_Cuttagseq_H3K9me3_rep2


title: Primed-H9_Cuttagseq_CTCF_rep1


title: Primed-H9_Cuttagseq_H3K9ac_rep2


title: Naive-H9_RNAseq_rep1

value: navie induced medium


title: NSLA_187

description: SWAN normalization


title: Primed-H9_Cuttagseq_H3K9ac_rep1


title: Naive-H9_Cuttagseq_H3K9me3_rep2


title: Primed-H9_Cuttagseq_H3K27me3_rep1


title: Naive-H9_Cuttagseq_CTCF_rep1


title: Primed-H9_Cuttagseq_H3K27ac_rep1


title: Primed-H9_Cuttagseq_H3K27ac_rep2


title: Naive-H9_Cuttagseq_H3K9me3_rep1


title: Naive-H9_Cuttagseq_H3K27ac_rep2


title: NSLA_1002

description: SWAN normalization


title: Naive-H9_RNAseq_rep2


title: Naive-H9_Cuttagseq_H3K27me3_rep2


title: Naive-H9_Cuttagseq_H3K27me3_rep1


title: Naive-H9_Cuttagseq_H3K27ac_rep1


title: Naive-H9_Cuttagseq_H3K9ac_rep2


title: ChIP_N2

city: Little Rock

first: Kimberly

middle: E

last: Stephens

state: AR

address: 4301 W. Markham St Slot 510

department: Neuroscience

institute: University of Arkansas for Medical Sciences

data_processing:
Casava v1.8.2 used for base calling
Reads trimmed for adapter sequence
reads mapped to rn6 genome using Bowtie2
Assembly: rn6
Supplementary files format and content: Align reads shifted 4 nucleotides upstream for 5' and 5 nucleotides downstream for 3' end; insertion sites identified by trimming to the 5'end. Insertion site extended in both directions by 75bp; Reads downsampled; peaks called by MACS2; limma used to count reads for CCI versus Naive.

organism: Rattus norvegicus

source_name: DRG

extract_protocol:
Dorsal root ganglion (L4-L6) harvested and homogenized
ATAC-seq with Illumina TDE1 enzyme after nuclei isolation

treatment_protocol: Chronic Constriction Injury and Naïve groups

value: naive

tag: strain

value: Sprague-Dawley


title: Primed-H9_ATACseq_rep1

data_processing:
ChiLin pipeline 2.0.0  (Qin et al., 2016) is used for QC and preprocess of the ATAC-seq.
We use Burrows-Wheeler Aligner (BWA)  as a read mapping tool, and Model-based Analysis of ChIP-Seq (MACS2)  as a peak caller, with a q-value (FDR) threshold of 0.01
Deeptools is used for the heatmap plots
Differential peaks between Naive and Primed were identified by DEseq2 with adjusted P ≤0.05, |log2fold change| ≥ 1.
Assembly: hg38
Supplementary files format and content: ATACseq peak bigwig files

extract_protocol:
the sample used to perform RNA-seq, ATAC-seq, CUT&Tag-seq are prepared based on the commonly used method.
AS for ATAC-seq, Cells were harvested and counted. Number of 500~1000 cells were used for ATAC-seq. The number of cells at this step is crucial, as the transposase-to-cell ratio determines the distribution of DNA fragments generated. Sample with 500~ 1000 cells was centrifuged for 5 min at 500 × g at 4 °C. Supernatant was removed and discarded. Cells were washed once with 50 μl of cold PBS buffer, centrifuged for 5 min at 500 × at 4 °C, and supernatant removed and discarded. The cell pellet in 50 μl of cold lysis buffer was resuspended by gently pipetting up and down and lysed for 10 min on ice, followed by centrifugation immediately for 10 min at 500 × g at 4 °C. The supernatant was discarded, and immediately continued to transposition reaction. Lysis buffer used was, 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40.For transposition reaction and purification, TruePrep® DNA Libraryaf Prep Kit V2 for Illumina (Vazyme, TD502, 5ng) for tagmentation was used. After tagmentation reaction, AMP XP beads for purifying was used. In preparation, AMPure XP beads were equilibrated at room temperature for 30 minutes and mixed well. 25 μl (0.6x) beads were pipetted into the 50 μl PCR product, gently pipetted and mixed, and incubated at room temperature for 5 min (to remove long fragments). The reaction tube was centrifuged briefly and placed on a magnetic stand. After clarification, the supernatant (75 μl) was transferred to a new tube (be careful to mark the tube cap and tube body), and the magnetic beads discarded. 60 μl (1.2x) beads were pipetted into the supernatant, mixed by pipetting, and incubated at room temperature for 5 min (magnetic beads can be added to the new EP tube during the first incubation). The reaction tube was centrifuged briefly and placed on a magnetic stand. After clarification, the supernatant was removed, the tube was kept on the magnetic stand.  200 μl of freshly prepared 80% ethanol was added to rinse the magnetic beads, incubated at room temperature for 30 s, and the supernatant carefully removed. The rinse was repeated three times. The tube was kept on the magnetic stand, the lid left open and dry (not too dry, no alcohol residue at the bottom of the tube). The tube was taken out of the magnetic stand, 25 μl of sterile ultrapure water added, the magnetic beads smashed from the wall, mixed well, and incubated at room temperature for 5 min. The reaction tube was dentrifuged briefly and placed on a magnetic stand. After clarification, 20 μl of supernatant was carefully transferred to a new tube and stored at −20°C.Library was constructed as follow. TruePrep TM Index V4 for Illumina (Vazyme TD204) was used to enrich DNA and PCR amplification. The PCR products were purified with VAHTS DNA Clean Beads (Vazyme N411). At last, DNA fragments of preferentially about 300 bp in length were selected, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA)


title: ChIP_CCI2

value: CCI


title: ATAC_N3


title: Naive-H9_Cuttagseq_CTCF_rep2


title: ATAC_CCI1


title: Naive-H9_ATACseq_rep2


title: Naive-H9_ATACseq_rep1