title: B0013T3 Visium

description:
B0013T3
Fresh frozen spatial transcriptomics sequencing


title: PANC1 CTR 3

status: Public on Jul 08 2025

type: RNA

city: Segrate

first: Marcella

last: Bonanomi

state: Milan

address: Via Fratelli Cervi 93

department: IBSBC

country: Italy

institute: CNR

description: Gene expression after 72 hours of multi-stage treatment

hyb_protocol: Labeled cRNA was hybridized to a SurePrint G3 Human Gene Expression v3 8x60K Microarray Gene Chip (Agilent Technologies) for 16h at 68°C

scan_protocol: Scanned using a SureScan Microarray Scanner (Agilent Technologies) using the Agilent G3_GX_1color default scan settings.

data_processing: Expression values were calculated by the software package Feature Extraction 12.2.0.7 (Agilent Technologies). Statistical analysis of the expression data was performed using the Gene Spring GX Software (Agilent Technologies).

molecule: total RNA

organism: Homo sapiens

source_name: whole cell homogenate

label_protocol: 100ng of total RNA were applied for Cy3-labelling reaction using the one-color Quick Amp Labeling protocol (Agilent Technologies).

growth_protocol: PANC-1 were grown in Roswell Park Memorial Institute (RPMI) 1640 supplemented with 10% FBS and 2 mM L-glutamine. All media were supplemented with 100 U/mL penicillin and 100 μg/mL streptomycin. Cells were grown at 37 °C in a 5% CO2 incubator.

extract_protocol: Total RNA for microarray analysis was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany), and its concentration, purity, and RNA integrity, measured as RNA integrity number (RIN), were assessed using a TapeStation 4150 (Agilent Technologies).

treatment_protocol: PANC-1 were plated in 6-well plates and treated with 0.6 uM erastin and 0.5 uM methothrexate for 72 h, then the medium was replaced with fresh medium without drugs for another 72 h. After that, the cells were placed in the presence or absence of the drugs for the next 72 hours and then harvested for analysis.

tag: cell line

tag: treated

value: no


title: ChIP_E13.5_M_H3K9me3_rep3

type: SRA

city: Beijing

first: Jiansen

last: Lu

address: No. 5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

country: China

institute: Peking University

library_source: genomic

data_processing:
For scATAC-seq, demultiplexed raw fastq files were trimmed by cutadapt (v3.3) to remove adapter sequences and short reads. ‘Clean reads’ were then mapped to mm10 using bowtie2 (v2.4.5) with parameters ‘--mm --no-unal --very-sensitive’, duplicated and low quality (MAPQ < 30) alignments were further removed with samtools (v1.11). Cell identifiers were attached to ‘CB’ tag of bam files manually, then fragment files of each cell were generated using sinto (v0.7.6) with default parameters. We followed the ArchR (v1.0.2) pipeline to perform downstream analysis of scATAC-seq data.
For ULI-NChIP-seq and low-input MNase-seq, raw data files were firstly trimmed by TrimGalore (v0.6.4) to remove sequencing adapters and low-quality reads. Bowtie2 were used to align reads to mm10 reference, duplicate alignments were identified and removed by ‘MarkDuplicates’ (v2.23.6) function of picard. Alignments with MAPQ < 30 were filtered. Aligned bam files were normalized to RPKM and converted to bigwig format for visualization by ‘bamCoverage’ function of deeptools (v3.4.3).
Assembly: mm10
Supplementary files format and content: .bed.gz: compressed bed files containing the scATAC-seq fragments for single cells
Supplementary files format and content: .bed.gz.tbi: index files related to compressed bed format fragment files
Supplementary files format and content: .bw: bigwig files containing RPKM normalized ChIP-seq signal

molecule: genomic DNA

organism: Mus musculus

source_name: gonad

extract_protocol:
Male mice homozygous for the Oct4-EGFP transgene in the C57BL/6J background were crossed with wild-type C57BL/6J females. When a copulatory plug was evident around noon, that time was counted as E0.5. Gonads were isolated from E13.5, E14.5, E15.5 and E16.5 embryos, female and male samples were collected separately.Gonads were treated with 0.25% trypsin-EDTA for 10 min at 37 °C, and then, trypsin was inactivated by addition of 15% fetal bovine serum (FBS)/DMEM. Cells were ﬁltered through 40 µ m cell strainers to obtain a single-cell suspension for FACS (FACSAria II SORP, BD Bioscience).
The sequence libraries were generated using the KAPA Hyper Prep Kit according to the manufacturer’s instructions.
scATAC-seq, ulltra-low-input native ChIP-seq (ULI-NChIP-seq) and low-input MNase-seq

tag: tissue

value: gonad

tag: cell type

value: somatic cell

tag: strain

tag: developmental stage

tag: Sex

value: male

tag: chip antibody


title: Neuron-WT, Rep3

city: Edinburgh

first: Graeme

last: Grimes

address: MRC Institute of Genetics & Molecular Medicine, Crewe Road,

country: United Kingdom

institute: University of Edinburgh

library_source: transcriptomic

data_processing:
The QuantSeq protocol generates one fragment per transcript, resulting in extremely accurate gene expression values, and the sequences obtained were close to the 3’ end of the transcripts. Library generation was initiated by oligo-dT priming (already containing Illumina- compatible linker sequences). After first strand synthesis the RNA was removed, and second strand synthesis initiated by random priming and a DNA polymerase. With the QuantSeq FWD kit the Read 1 linker sequence is contained in the second strand synthesis primer, so that NGS reads are generated towards the poly (A) tail and directly correspond to the mRNA sequence. Second strand synthesis was followed by a magnetic bead-based purification step before cDNA libraries were amplified for 18 cycles, introducing the sequences required for cluster generation and index sequences to allow multiplexing of sequencing libraries. After amplification, a final bead-purification removed any excess primers or adapter-dimers that may interfere with sequencing. Libraries were quantified by fluorometry using the Qubit dsDNA High Sensitivity assay and assessed for quality and fragment size using the Agilent Bioanalyser with the DNA High Sensitivity kit. Fragment size and quantity measurements were used to calculate molarity for each library pool. Single read (1x75bp) sequencing was performed on the NextSeq 550 platform (Illumina Inc, SY-415-1002) using the NextSeq 500/550 High-Output v2.5 kit (20024906). Libraries were combined in a single equimolar sample based on Qubit and Bioanalyser assay results, and run across a High Output v2.5 Flow Cell.
Reads alignment and differential data analyses were performed following pipeline integration onto the Bluebee genomics analysis platform (www.bluebee.com/quantseq).
Assembly: hg38
Supplementary files format and content: bam files aligned using the bluebee platform provided by Lexogen.
Supplementary files format and content: tab delimited text file with normalized counts generated from  Bluebee genomics analysis platform (www.bluebee.com/quantseq).

source_name: ATRX WT-clone3

growth_protocol: iPSCs were maintained on vitronectin (Stem Cell Technologies, 7180), with a complete media change every day in Essential 8 media (Life Technologies, A1517001); 0.5mM EDTA was used for passaging; Accutase (Stem cell Technologies 07920) and 10 μM Rho-associated kinase (ROCK) inhibitor (Sigma-Aldrich Y0503) were used for single-cell dissociation purposes. Neural progenitor cells (NPCs) were established following the STEMdiff Neural System based on STEMdiff SMADi Neural Induction kit (Stem cell Technologies, 08581). NPCs were used at passage 2, 3 or 5 to generate forebrain neurons following the instructions of STEMdiff Forebrain Neuron Differentiation Kit (Stem cell Technologies, 08600) and STEMdiff Forebrain Neuron Maturation Kit (Stem cell Technologies, 08605). Differentiating neurons were fed twice a week, and cultured for 3 to 4 weeks.

extract_protocol:
total RNA was extracted using RNeasy Micro Kit (Qiagen, 74004)
Individual libraries were generated from 100ng of each total RNA sample using the QuantSeq 3’mRNA-Seq Library Prep kit (FWD) protocol for Illumina (Lexogen Inc, #015), where enough material was available, 50ng was inputted otherwise.
QuantSeq 3’ mRNA-Seq

tag: time

value: 29 days of culture

value: forebrain neuron

tag: genotype

value: ATRX WT


title: B0013T1 Visium

city: Singapore

first: Pierce

middle: Kah Hoe

last: Chow

address: 11 Hospital Cres

country: Singapore

institute: National Cancer Center Singapore

description:
B0013T1
Fresh frozen spatial transcriptomics sequencing

data_processing:
Raw sequencing data were processed using 10x Genomics Space Ranger to generate processed files
Sequences were aligned to hg38 reference genome using Space Ranger with default setting and generated gene expression counts
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Liver

extract_protocol:
Fresh frozen tissues were OCT embedded and 10 microns frozen sections were cut using cryostat
Spatial transcriptome sequencing libraries were prepared with 10Xgenomics Visium Gene Expression Slides & Reagent kit according to manufacturer's protocol

value: Liver

value: Male

tag: tumour stage

value: TNM Stage IIIA


title: C004T1P Visium

description:
C004T1P
Fresh frozen spatial transcriptomics sequencing

value: Female

value: TNM Stage IB


title: HPAF CTR 2

growth_protocol: HPAF-2 were grown in Roswell Park Memorial Institute (RPMI) 1640 supplemented with 10% FBS and 2 mM L-glutamine. All media were supplemented with 100 U/mL penicillin and 100 μg/mL streptomycin. Cells were grown at 37 °C in a 5% CO2 incubator.

treatment_protocol: HPAF-2 were plated in 6-well plates and treated with 3 uM erastin and 15 uM alpelisib for 72 h, then the medium was replaced with fresh medium without drugs for another 72 h. After that, the cells were placed in the presence or absence of the drugs for the next 72 hours and then harvested for analysis.


title: HPAF CTR 1


title: Neuron-WT, Rep2

source_name: ATRX WT-clone2

value: 21 days of culture


title: A009T5 Visium

description:
A009T5
Fresh frozen spatial transcriptomics sequencing

value: TNM Stage II


title: ChIP_E13.5_M_H3K9me2_rep1


title: A009T4 Visium

description:
A009T4
Fresh frozen spatial transcriptomics sequencing


title: HPAF TREAT 8

value: yes


title: ChIP_E13.5_F_soma_H4ac_rep2

value: female


title: HPAF TREAT 7


title: Neuron-WT, Rep1

source_name: ATRX WT-clone1


title: ChIP_E13.5_F_soma_H4ac_rep1


title: HPAF TREAT 6


title: A009T3 Visium

description:
A009T3
Fresh frozen spatial transcriptomics sequencing


title: NPC-KI, Rep3

source_name: ATRX KI-clone3

value: passage number p2

value: neural progenitor cells

value: ATRX KI


title: HPAF TREAT 5


title: A009T2 Visium

description:
A009T2
Fresh frozen spatial transcriptomics sequencing


title: ChIP_E13.5_F_soma_H3K9me3_rep3

value: gonad

value: somatic cell


title: NPC-KI, Rep2

source_name: ATRX KI-clone2


title: NPC-KI, Rep1

source_name: ATRX KI-clone1

value: passage number p3


title: Neuron-WT, Rep4

value: 29 days of culture

value: forebrain neuron


title: A009T1 Visium

description:
A009T1
Fresh frozen spatial transcriptomics sequencing

value: Liver


title: B0013T2 Visium

description:
B0013T2
Fresh frozen spatial transcriptomics sequencing

value: Male


title: ChIP_E13.5_F_soma_H3K9me3_rep2


title: ChIP_E13.5_M_H3K9me2_rep2

value: male


title: HPAF CTR 4

value: no


title: ChIP_E13.5_F_soma_H3K9me3_rep1


title: A009N Visium

description:
A009N
Fresh frozen spatial transcriptomics sequencing

value: Female


title: NPC-WT, Rep3

value: ATRX WT


title: ChIP_E13.5_F_soma_H3K9me2_rep2


title: Rat skin: DHT+  FeCl₃

city: Los Angeles

first: Bo

last: Tao

state: CA

address: 675 Charles E Young Drive

department: Cardiology

country: USA

institute: University of California Los Angeles

description: Library name: WT_sc_DHT_FeCl3_1

library_source: other

data_processing:
Bulk RNA-seq data were processed using STAR (v2.7.10a) for alignment to the Rattus norvegicus reference genome (Rnor_6.0).  ScRNA-seq data were processed using Cell Ranger (v7.1.0) for demultiplexing and counting.
Gene counts were generated using featureCounts v2.0.3.
Assembly: Rattus norvegicus Rnor_6.0 (Ensembl release 107).
Supplementary files format and content: Bulk RNA-seq: Gene-level expression matrices in CSV format. Rows represent Ensembl gene IDs for Rattus norvegicus; columns represent individual samples. Values represent log2-transformed normalized expression from DESeq2 (using rlog transformation). File names: PBS_CPA_expression.csv, WT_SRG_expression.csv, main_groups_expression.csv, WT_SRG_expression.csv, LPS_DHT_LPS_expression.csv. ScRNA-seq:HDF5 (.h5) format expression matrix file. The file contains gene-by-cell expression count matrix for Rattus norvegicus skin tissue, generated using Cell Ranger (or Seurat/Scanpy). Rows are genes, columns are cell barcodes. Values are raw or normalized counts depending on processing step.

molecule: other

organism: Rattus norvegicus

source_name: WT rat,  DHT + FeCl₃, scRNA-seq

growth_protocol: Sprague-Dawley rats were housed in a temperature- and humidity-controlled facility with a 12 h light/dark cycle and ad libitum access to food and water.

extract_protocol:
For bulk RNA-seq: Total RNA was extracted from skin tissue using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. For scRNA-seq: Cell pellets were obtained from dissociated skin tissue using enzymatic digestion, followed by centrifugation. Cell pellets were directly used for RNA extraction or single-cell library preparation.
For bulk RNA-seq, RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB), following polyA enrichment or rRNA depletion. For scRNA-seq, chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) were used.

treatment_protocol: (1)Sprague-Dawley(SD) Rats were given vehicle (p.o.) + FeCl₃ (s.c.), DHT (p.o.) + FeCl₃ (s.c.), DHT (p.o.) + LPS (s.c.). (2) SD Rats and SRG rats were given DHT (p.o.) + FeCl₃ (s.c.). (3) SD Rats were given DHT (p.o.) + FeCl₃ (s.c.) with PBS/CPA/IgG/IL-17a treatments, as described in the Methods section.

value: skin

value: wiid type

tag: treatment

value: DHT (p.o.) + FeCl₃ (s.c.)


title: HPAF TREAT 3

value: yes


title: NPC-WT, Rep2

value: passage number p2

value: neural progenitor cells


title: PBMCs ADT

first: Shaun

last: Ngang

address: 14 Medical Drive, MD6 #14-01

department: iHealthtech

institute: National University of Singapore

description:
10X Genomics
Antibody derived oligotags (ADT): read1 contains cell barcode and UMI; read2 contains the ADT reads

data_processing:
The libraries for cDNA (large and small fraction), sample hashtag barcodes, and surface protein barcodes were indexed, pooled and sequenced in Illumina NextSeq platform. As the cDNA in scComplete-seq is expected to include many other species beyond conventional mRNA-sequencing, we generate a custom GTF file by merging the Ensembl Human Reference with external small non-coding RNA annotated in DASHR v2 and miRNA using MGCount  approach (Hita et al., 2022). We also append the putative eRNA annotations obtained from CAGE-seq in the custom GTF file. Standard pre-processing is employed for all single-cell RNA-seq dataset. Count data were retrieved for the following gene biotypes: protein coding, lncRNA, antisense, IG LV gene, IG V gene, IG V pseudogene, snRNA, IG D gene, IG J gene, IG J pseudogene, IG C gene, TR V pseudogene, TR D gene, TR J gene, TR J pseudogene, TR C gene, pre-miRNA, vault RNA, misc RNA, MT rRNA, MT tRNA, ribozyme, rRNA, sRNA, scaRNA, siRNA, piRNA, tRNA, miRNA, scRNA, snoRNA and eRNA. Raw cDNA FASTQ data were processed for cell barcodes calling and unique molecular identifier (UMI) counting of the cDNA library using STARSolo (v2.7.10b, Dobin et al, 2013: Kaminow et al., 2021) with modified parameters (--soloType CB_UMI_Simple --soloStrand Forward --outFilterMultimapNmax 50 --soloCBwhitelist celllranger3M-february-2018.txt --soloUMIlen 12 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --winAnchorMultimapNmax 100 --outFilterMatchNmin 15 --outFilterScoreMin 14 --outFilterMismatchNoverLmax 0.05 --seedMultimapNmax 100000 --seedSplitMin 9 --seedSearchStartLmax 25 --soloCellFilter EmptyDrops_CR --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIdedup 1MM_CR --soloFeatures Gene GeneFull SJ Velocyto --soloMultiMappers EM) and custom GTF. Cutadapt (v4.4., Martin, 2011) with following parameters -u 3 -m 16 -a AAAAAAAAAAAAAAA, and riboDetector (v0.2.7, Deng et al., 2022) with following parameters -l 147 -e rrna --chunk_size 256 were used to check the quality of reads, trimming, and removal of low-quality too short reads. The generated cell barcodes were used to find individual cell barcode-matched expression profiles of sample hashtags and surface proteins using CITE-seq-Count (v1.4.0) with a Hamming distance of 1 for both cell barcodes calling and UMI counting.
Assembly: GRCh38
Supplementary files format and content: STARSolo output format (GEXs): barcodes.tsv, features.tsv, matrix.mtx
Supplementary files format and content: Cite-Seq Count output format (HTOs): barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cite-Seq Count output format (ADTs): barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-Seq

molecule: protein

source_name: Peripheral Blood Mononuclear Cells

growth_protocol: Cell lines (K562, MCF7, HEK293T) were cultivated in Dulbecco’s Modified Eagle Medium with high glucose (#11965084, Life Technologies) supplemented with 10% fetal bovine serum Life Technologies, 1027016) and 1% Penicillin-Streptomycin (#15070063, Life Technologies) at 37 °C and 5% CO2. Adherent cell lines (MCF7 and HEK293T). PBMCs, ~10 million PBMCs were thawed at 37ºC immediately after removal from liquid nitrogen. Cells were rested at 37ºC for 2 hours in RPMI Complete Media (RPMI 1640 medium (Life Technologies, A1049101) with 10% fetal bovine serum (Life Technologies, 1027016 and 1% Penicillin-Streptomycin (Life Technologies, 15070063)) (5% CO2, 37 °C incubator).

extract_protocol:
Single cells of 3 cel lines and PBMCs were encapsulated in Gel-Bead-Emulsions (GEMs) using the 10X Controller with a Chromium Single Cell 3' GEM Library and Gel Bead Kit (Singleron, Singapore)
The cell lines after the aspiration of the supernatant, the cells were washed in washing buffer.  Phosphate buffered saline (PBS) with 0.02% FBS was used as the staining and washing buffer. K562, MCF7 and HEK293T cells were then blocked with Fc-blocking agent (BioLegend, 422301) at 4 °C for 30 min and labeled with sample identifier hashtags (0.5 µg each Ab-oligo per million cells, TotalSeq™-A0251/2/3 anti-human Hashtag 1/2/3). Cells were washed with wash buffer 3 times and pooled together (equal number of cells for each, loading 4,800 cells in total). PBMCs from different conditions were then blocked with Fc-blocking agent and labeled with sample identifier hashtags given above (0.5 µg each Ab-oligo per million cells) at 4 °C for 30 min. Cells were washed with wash buffer 2 times and pooled together (equal number of cells per condition, and loading 16,000 cells in total). An Ab-oligo cocktail (0.125 µg each Ab-oligo per million cells, TotalSeq™- A anti-human CD3, CD4, CD8, CD16, CD27, CD28, CD45, CD45RA, CD56, CD69, CD95, CD197) was prepared in 45 µl of staining buffer and 5 µl  of Fc-blocking reagents immediately before use. The pooled barcoded cell samples were stained with surface marker Ab-oligo cocktail at 4 °C for 40 min. Cells were washed with wash buffer 3 times and resuspended in PBS.

treatment_protocol: MCF7 and HEK293T cells were harvested with 1X TrypLE (Gibco, 12563011) treatment, pelleted at 350g for 3 minutes and the supernatant was aspirated.  PBMCs were seeded at ~2 million per well in 6 well plates in three conditions: 1) Unstimulated, 2) 2µl/mL PMA/Ionomycin (1X final dilution-eBioscience Cell Stimulation Cocktail 500X, 00-4970-93), and 3) 0.02 mg/mL LPS (4X final dilution-eBioscience Lipopolysaccharide Solution 500X, 00-4976-93) for 8 hours in RPMI Complete Media.

value: Peripheral Blood Mononuclear Cells

value: Human donor PBMCs

value: mixture of unstimulated, LPS and PMA/Ionomycin stimulated

tag: adt

value: TotalSeq-A0034 anti-human CD3, TotalSeq-A0045 anti-human CD4, TotalSeq-A0046 anti-human CD8,  TotalSeq-A0083 anti-human CD16,  TotalSeq-A0154 anti-human CD27,  TotalSeq-A0386 anti-human CD28,  TotalSeq-A0391 anti-human CD45,  TotalSeq-A0063 anti-human CD45RA,  TotalSeq-A0047 anti-human CD56, TotalSeq-A0146 anti-human CD69, TotalSeq-A0156 anti-human CD95(Fas), TotalSeq-A0148 anti-human CD197(CCR7)


title: HPAF TREAT 4


title: HPAF TREAT 1


title: NPC-WT, Rep1

value: passage number p5


title: PBMCs HTO

description:
10X Genomics
Hashtag derived oligotags (HTO): read1 contains cell barcode and UMI; read2 contains the HTO tag reads

tag: hto

value: (PBMCs run on separate day from Cell Lines) TotalSeq-A0251 anti-human Hashtag 1, TotalSeq-A0252 anti-human Hashtag 2, TotalSeq-A0253 anti-human Hashtag 3


title: HPAF TREAT 2


title: Rat skin: vehicle+ H₂O

description: Library name: WT_sc_H2O_1

source_name: WT rat, vehicle + H₂O, scRNA-seq

value: vehicle (p.o.) + FeCl₃ (s.c.)


title: ChIP_E13.5_F_soma_H3K4me3_rep2

value: gonad

value: somatic cell

value: female


title: PBMCs scComplete-seq GEX 0.6XSPRI

description:
10X Genomics
GEX (3'): read1 contains cell barcode and UMI; read2 contains the transcripts


title: MBT (mid-blastula embryos), derived from sperm_14day-post stripping, rep3

city: Vodnany

first: Yu

last: Cheng

state: South Bohemia

address: Zátiší 728/II

department: Faculty of Fisheries and Protection of Waters

country: Czech Republic

institute: University of South Bohemia in Ceske Budejovice

description: Library name: Sample 12

data_processing:
The clean data were obtained after filtering and then mapped to the reference genome (assembly accession: GCF_018340385.1) for bioinformatics analysis by BSMAP. Subsequently, the duplication reads were removed, and the mapping results were merged according to each library. The mapping rate and bisulfite conversion rate were calculated for each sample. The methylation level was calculated by dividing the number of reads covering each mC by the total number of reads covering that cytosine (Xiang et al., 2010), which was also equal to the mC/C ratio at each reference cytosine (Lister et al., 2009). Putative differentially methylated regions (DMRs) were identified by comparing the control and treated sample methylomes using windows that contained at least five CpG (CHG or CHH) sites with a two-fold change in the methylation level and a Fisher test P-value < 0.05. DMRs-related genes (DMGs) were annotated to pathways and processes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses.
Assembly: GCF_018340385.1
Supplementary files format and content: csv

organism: Cyprinus carpio

source_name: Embryos

extract_protocol:
Genomic DNA was extracted from 2 µL sperm samples obtained from three males using a DNA Mini Kit (Invitrogen, USA), or extracted from 50-60 mid-blastula embryos and 10-20 embryos at hatching using SDS-based methods; Total RNA was extracted from embryos using RNA isolation kits (Invitrogen, USA) in accordance with the instructions provided in the manual; Thirty embryos from each group were pooled and homogenized by a grinder with steel beads, containing 1X Cocktail, EDTA and SDS L3. The supernatant was extracted following centrifugation (25,000 g, 4°C for 15 min), and reduced with 10 mM DTT for 30 min at 37 oC. Samples were alkylated with iodoacetamide (55 mM final concentration) in the dark for 45 min. The treated samples were precipitated in cold acetone at a ratio of 1:5 for 2 h at -20 oC. After centrifugation at 25,000 g, the dry pellet was dissolved in 0.5 M triethylammoniumbicarbonate (TEAB) (Applied Biosystems). Bradford assay and SDS-PAGE were used for quality control of the protein extraction.
The construction of the library and bisulfite sequencing were conducted by BGI (Shenzhen, China). Briefly, DNA was fragmented by sonication using a Bioruptor (Diagenode, Belgium) to a mean size of c. 250 bp. This was followed by the blunt-ending, dA addition to the 3'-end, and finally, adaptor ligation, essentially according to the manufacturer’s instructions. Ligated DNA was subjected to bisulfite conversion using the EZ DNA Methylation-Gold kit (ZYMO). Following the administration of sodium bisulfite, unmethylated cytosine residues were converted to uracil, whereas 5-methylcytosine (5mC) remained unaffected. After the PCR amplification process, uracil residues were converted to thymine. Fragments of varying insert sizes were excised from a single lane of a 2% TAE agarose gel. The purification of the products was conducted using the QIAquick Gel Extraction Kit (Qiagen), while the amplification was achieved through PCR. Finally, sequencing was performed using the HighSeq4000 and 150-bp paired-end reads were generated.

value: Embryos


title: iPSC-KI, Rep3

value: passage number p40

value: induced pluripotent stem cells

value: ATRX KI


title: iPSC-KI, Rep2


title: ChIP_E13.5_F_soma_H3K4me3_rep1


title: MBT (mid-blastula embryos), derived from sperm_14day-post stripping, rep2

description: Library name: Sample 11


title: iPSC-KI, Rep1

value: passage number p39


title: MBT (mid-blastula embryos), derived from sperm_14day-post stripping, rep1

description: Library name: Sample 10


title: 3CellLines scComplete-seq GEX 0.6XSPRI

source_name: Breast (MCF7), lymphoblast (K562), human embryonic kidney (HEK293T)

value: Breast cancer (MCF7), chronic myelogenous  leukemia (K562), embryonic kindney (HEK293T)

value: untreated


title: MBT (mid-blastula embryos), derived from sperm_0day-post stripping, rep3

description: Library name: Sample 9


title: iPSC-WT, Rep3

value: passage number p38

value: ATRX WT


title: iPSC-WT, Rep2


title: ChIP_E13.5_F_soma_H3K4me1_rep1


title: 3CellLines scComplete-seq GEX 1XSPRI

value: Breast (MCF7), lymphoblast (K562), human embryonic kidney (HEK293T)


title: ChIP_E13.5_F_soma_H3K36me3_rep2


title: MBT (mid-blastula embryos), derived from sperm_0day-post stripping, rep2

description: Library name: Sample 8


title: ChIP_E13.5_F_soma_H3K36me3_rep1


title: iPSC-WT, Rep1


title: MBT (mid-blastula embryos), derived from sperm_0day-post stripping, rep1

description: Library name: Sample 7


title: 3CellLines scmRNA seq GEX 0.6XSPRI

molecule: polyA RNA


title: ChIP_E13.5_F_soma_H3K4me1_rep2


title: A375_A_BRAFi-MEKi_DOX_3

city: Philadelphia

first: Andrew

middle: E

last: Aplin

state: PA

address: 233 South 10th St.

institute: Thomas Jefferson University

description: A375TR-NR2F1 cells treated with BRAFi + MEKi + DOX

data_processing:
RNA sequencing fastq files were aligned to the GRCh38 reference genome using Star aligner and GENCODE (v35)
RSEM was used to quantify gene and transcript level expression
normalized counts data were calculated using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file of normalized counts

source_name: metastatic melanoma cells

growth_protocol: Melanoma cells, 1205Lu and WM793, were grown in Tu2% medium (MCDB153 80%, Leibovitz's L-15 20%, FBS 2%, Insulin (bovine) 5 5 ug/mL, CaCl2 1.68 mM). Melanoma cells, A375, were grown in DMEM implemented with 10%FBS and 1% P/S.

extract_protocol:
RNeasy Plant Mini Kit
TruSeq RNA Library Prep Kit v2

treatment_protocol: Melanoma cells were treated -/+ doxycycline (DOX, 100 ng/mL) for 24 hours. Then, cells were treated either with DMSO (1:1000) or BRAF inhibitor (PLX4720, 1uM) plus MEK inhibitor (PD0325901, 35nM), plus or minus doxycycline (DOX, 100 ng/mL) for 72 hours.

tag: cancer type

value: melanoma

value: BRAFi + MEKi + DOX


title: Replicate 2, Unsorted

city: Solna

first: Bernhard

last: Schmierer

state: (optional)

address: Biomedicum 9B, Solnavagen 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description:
Library name: Rep2_Unsorted
NextSeq 1000/2000 Control Software 1.4.1.39716/RTA 3.9.25) with a 53nt(Read1)-10nt(Index1)-6nt(Index2) setup using 'P2' flowcell

data_processing:
Readcounts were mapped to the library sequences using MAGeCK/0.5.9.4
Assembly: GRCh38
Supplementary files format and content: tab-delimited .txt file with mapped readcounts
Library strategy: CRISPR screen

source_name: Breast

growth_protocol: DMEM/10%FCS/100U/ml Pen/Strep

extract_protocol:
QIAamp DNA Blood Mini (Qiagen) according to manufacturer's instructions
PCR one amplicon with adaptor-containing primers

treatment_protocol: 48h with 5ng/ml TGF-beta1

value: Breast

value: CAGA-GFP

value: 5ng/ml TGFbeta


title: ChIP_E13.5_F_soma_H3K9me2_rep1

value: gonad

value: somatic cell


title: A375_A_BRAFi-MEKi_DOX_2


title: PBMCs scComplete-seq GEX 1XSPRI

value: Peripheral Blood Mononuclear Cells

value: Human donor PBMCs

value: mixture of unstimulated, LPS and PMA/Ionomycin stimulated


title: Replicate 2, Low CAGA-GFP expression

description:
Library name: Rep2_LowGFP
NextSeq 1000/2000 Control Software 1.4.1.39716/RTA 3.9.25) with a 53nt(Read1)-10nt(Index1)-6nt(Index2) setup using 'P2' flowcell


title: ChIP_E13.5_F_soma_H3K27ac_rep1

value: female


title: Sperm, 14day-post stripping, rep2

description: Library name: Sample 5

source_name: Sperm

value: Sperm


title: A375_A_BRAFi-MEKi_DOX_1


title: ChIP_E13.5_F_H4ac_rep2

value: fetal germ cell


title: 3CellLines HTO

value: Breast cancer (MCF7), chronic myelogenous  leukemia (K562), embryonic kindney (HEK293T)

value: untreated

value: TotalSeq-A0251 anti-human Hashtag 1, TotalSeq-A0252 anti-human Hashtag 2, TotalSeq-A0253 anti-human Hashtag 3


title: Sperm, 14day-post stripping, rep1

description: Library name: Sample 4


title: Replicate 2, Early time point

description:
Library name: Rep2_ETP
NextSeq 1000/2000 Control Software 1.4.1.39716/RTA 3.9.25) with a 53nt(Read1)-10nt(Index1)-6nt(Index2) setup using 'P2' flowcell

value: Untreated


title: Sperm, 0day-post stripping, rep3

description: Library name: Sample 3


title: Replicate 1, Unsorted

description:
Library name: Rep1_Unsorted
NextSeq 1000/2000 Control Software 1.4.1.39716/RTA 3.9.25) with a 53nt(Read1)-10nt(Index1)-6nt(Index2) setup using 'P2' flowcell


title: ChIP_E13.5_F_H4ac_rep1


title: A375_A_BRAFi-MEKi_NO_DOX_2

description: A375TR-NR2F1 cells treated with BRAFi + MEKi

value: melanoma

value: BRAFi + MEKi


title: Sperm, 0day-post stripping, rep2

description: Library name: Sample 2


title: ChIP_E13.5_F_H3K9me2_rep2


title: Sperm, 14day-post stripping, rep3

description: Library name: Sample 6


title: Sperm, 0day-post stripping, rep1

description: Library name: Sample 1


title: Replicate 1, High CAGA-GFP expression

description:
Library name: Rep1_HighGFP
NextSeq 1000/2000 Control Software 1.4.1.39716/RTA 3.9.25) with a 53nt(Read1)-10nt(Index1)-6nt(Index2) setup using 'P2' flowcell

value: Breast


title: MNase_E16.5_M_MNase_rep2

value: male


title: A375_A_Control_DOX_3

description: A375TR-NR2F1 cells treated with DMSO + DOX

value: DMSO + DOX


title: Replicate 1, Low CAGA-GFP expression

description:
Library name: Rep1_LowGFP
NextSeq 1000/2000 Control Software 1.4.1.39716/RTA 3.9.25) with a 53nt(Read1)-10nt(Index1)-6nt(Index2) setup using 'P2' flowcell

value: CAGA-GFP

value: 5ng/ml TGFbeta


title: Replicate 2, High CAGA-GFP expression

description:
Library name: Rep2_HighGFP
NextSeq 1000/2000 Control Software 1.4.1.39716/RTA 3.9.25) with a 53nt(Read1)-10nt(Index1)-6nt(Index2) setup using 'P2' flowcell


title: A375_A_Control_DOX_2


title: Replicate 1, Early time point

description:
Library name: Rep1_ETP
NextSeq 1000/2000 Control Software 1.4.1.39716/RTA 3.9.25) with a 53nt(Read1)-10nt(Index1)-6nt(Index2) setup using 'P2' flowcell


title: ChIP_E13.5_F_soma_H3K27ac_rep2

value: gonad

value: somatic cell


title: MNase_E16.5_M_MNase_rep1


title: A375_A_Control_DOX_1


title: yaa_hto

city: Cambridge

first: Nir

last: Hacohen

state: MA

address: 415 Main St

institute: Broad Institute of MIT and Harvard

description:
Library name: yaa_hto
10x Genomics

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: mm10_v1.2.0
Supplementary files format and content: H5 formattted tab separated values, genes x cells raw counts

source_name: kidney

extract_protocol:
Murine kidney dissociation and single cell suspension: Under terminal anesthesia, mice were perfused by gentle intracardiac injection of 10 ml prewarmed (37°C) PBS 1x and kidneys were harvested. To obtain single cell suspensions, kidneys were then incubated for 12 minutes in DMEM containing 1 mg/ml Collagenase D (Roche), 100U/ml DNAse I (Sigma), 0.25mg/ml Liberase (Invitrogen) at 37°C. Tissues were gently dissociated using a pipette and then passed through a 70 μm cell strainer (BD). This single cell suspension was finally enriched for myeloid cells or total CD45+ cells using Mouse anti-CD11b and anti-CD11c or anti-CD45 MicroBeads (Miltenyi) and LS magnetic Columns (Miltenyi) for flow cytometry or FACS sorting.
Up to 10,000 live cells were loaded into separate 10x channels for single cell RNAseq on the Chromium platform (10x Genomics). DNA amplification and library construction were carried out according to the manufacturer’s instructions.

value: kidney

value: myeloid

tag: library type

value: HTO


title: ChIP_E13.5_F_H3K36me3_rep2

source_name: gonad

value: fetal germ cell

value: female


title: ChIP_E13.5_F_H3K4me1_rep2


title: A375_A_BRAFi-MEKi_NO_DOX_3


title: yaa_rna

description:
Library name: yaa_rna
10x Genomics

library_source: transcriptomic single cell

value: mRNA


title: MNase_E16.5_F_MNase_rep2


title: MNase_E16.5_F_MNase_rep1


title: ChIP_E13.5_F_H3K9me3_rep3


title: A375_A_Control_NO_DOX_3

description: A375TR-NR2F1 cells treated with DMSO alone

value: DMSO alone


title: A375_A_BRAFi-MEKi_NO_DOX_1


title: MNase_E15.5_M_MNase_rep2


title: scATAC_E16_5_M_S4

library_source: genomic single cell


title: A375_A_Control_NO_DOX_2


title: A375_A_Control_NO_DOX_1


title: ChIP_E13.5_F_H3K9me2_rep1


title: nzbw_hto

description:
Library name: nzbw_hto
10x Genomics


title: MNase_E15.5_M_MNase_rep1


title: WM793_BRAFi-MEKi_DOX_3

description: WM793TR-NR2F1 cells treated with BRAFi + MEKi + DOX

value: BRAFi + MEKi + DOX


title: scATAC_E16_5_M_S2


title: Mouse mammary gland, KO group (combined three mice)

city: Lexington

first: Jinpeng

last: Liu

state: Kentucky

address: 800 Rose St

institute: Markey Cancer Center

description: Library name: 6Ho

data_processing:
scRNA-seq gene expression libraries were mapped to mm10 mouse reference (10X Genomics pre-built reference, mm10-2020-A) using Cell Ranger (v6.1, 10x Genomics).
Assembly: GRCm38
Supplementary files format and content: filtered_feature_bc_matrix.h5
Supplementary files format and content: barcode and feature matrix in h5 format

source_name: mammary gland

extract_protocol:
Mammary glands from both groups were dissected and mechanically dissociated. The finely minced tissue was transferred to a digestion mix consisting of DMEM/F12 (Gibco) + 10 mM HEPES (Gibco) + collagenase (Roche) + 200 U ml⁻¹ hyaluronidase (Sigma) + gentamicin (Gibco) for 3 hours at 37°C and vortexed every 30 minutes. After the lysis of red blood cells in NH4Cl, cells were briefly digested with warm 0.05% Trypsin-EDTA (Gibco), 5 mg ml−1 dispase (Sigma), and 1 mg ml−1 DNase (Sigma), and filtered through a cell strainer (BD Biosciences) to remove debris, yielding a single-cell preparation for sequencing. Propidium iodide (PI, Sigma) was used at a working concentration of 1 μg/ml, prepared by diluting the stock solution 1:1000 to detect dead cells. After sorting, cells were spun down and resuspended. Samples were manually counted using an improved Neubauer chamber, and the cell concentration was normalized. Equal numbers of cells per sample were processed for scRNA library preparation.
ScRNA-seq libraries for 5Ht and 6Ho mice were generated using the 10X Genomics Chromium platform.

value: mammary gland

value: K14-cre; P4HA1 fl/fl

value: P4HA1 KO


title: WM793_BRAFi-MEKi_DOX_2

value: melanoma


title: Mouse mammary gland, control group (combined three mice)

description: Library name: 5Ht

value: K14-cre; P4HA1 fl/+

value: Control


title: scATAC_E16_5_M5

value: male


title: MNase_E15.0_F_MNase_rep2

value: gonad


title: scATAC_E16_5_M_S1

value: somatic cell


title: scATAC_E16_5_M6


title: MNase_E14.5_M_MNase_rep1


title: MNase_E15.5_F_MNase_rep1


title: MNase_E15.0_F_MNase_rep1


title: WM793_BRAFi-MEKi_NO_DOX_1

description: WM793TR-NR2F1 cells treated with BRAFi + MEKi

value: BRAFi + MEKi


title: lv_2

city: Pamplona

first: Ana

last: Garcia Osta

state: Navarra

address: Juslarrocha 10, 3H

department: neuroscience

country: Spain

institute: Cima

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCm39 mouse assembly using STAR v2.7.0d with default parameters.
featureCounts v1.6.0 software and Gencode vM28 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Obtained gene counts were normalized using edgeR and voom function of limma.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: primary culture

extract_protocol:
Maxwell® RSC simplyRNA Tissue Kit (Promega)
TruSeq Stranded mRNA Kit (Illumina, San Diego, CA, USA)

value: primary culture

value: neurons

value: wild type

value: lentiviral particles expressing shRNA agains Pla2g4e


title: lv_1


title: scATAC_E16_5_M_S3


title: scATAC_E16_5_M3

value: fetal germ cell


title: scATAC_E16_5_M4


title: scATAC_E16_5_M_S5


title: C_3

value: lentiviral particles expressing shRNA control or scrambled


title: lv_3


title: WM793_BRAFi-MEKi_NO_DOX_2


title: MNase_E13.5_M_MNase_rep2


title: C_2


title: nzbw_rna

description:
Library name: nzbw_rna
10x Genomics

value: kidney

value: myeloid

value: mRNA


title: WM793_Control_DOX_3

description: WM793TR-NR2F1 cells treated with DMSO + DOX

value: DMSO + DOX


title: MNase_E13.5_M_MNase_rep1


title: WM793_BRAFi-MEKi_DOX_1

value: melanoma

value: BRAFi + MEKi + DOX


title: MNase_E14.5_F_MNase_rep1

value: female


title: WM793_Control_DOX_2


title: scATAC_E16_5_M2

value: male


title: WM793_BRAFi-MEKi_NO_DOX_3


title: scATAC_E16_5_M1

value: gonad


title: MNase_E13.5_F_MNase_rep2


title: WM793_Control_DOX_1


title: MNase_E13.5_F_MNase_rep1


title: ChIP_E16.5_M_H3K9me3_rep2


title: WT_3

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCm39 mouse assembly using STAR v2.7.9a with default parameters.
featureCounts v1.6.0 software and Gencode vM31 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Obtained gene counts were normalized using edgeR and voom function of limma.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: Prefrontal cortex

value: Prefrontal cortex


title: scATAC_E16_5_F_S7

value: somatic cell


title: WM793_Control_NO_DOX_2

description: WM793TR-NR2F1 cells treated with DMSO alone

value: DMSO alone


title: scATAC_E16_5_F_S6


title: WT_2


title: KO_2

value: Pla2g4e KO


title: KO_3


title: ChIP_E16.5_M_H3K4me3_rep1


title: ChIP_E16.5_M_H3K4me3_rep2


title: WM793_Control_NO_DOX_1


title: 1205LuTR_BRAFi-MEKi_DOX_3

description: 1205LuTR-NR2F1 cells treated with BRAFi + MEKi + DOX


title: WT_1

value: wild type


title: scATAC_E16_5_F_S2


title: scATAC_E16_5_F_S5


title: scATAC_E16_5_F_S3


title: C_1

value: primary culture

value: neurons


title: KO_1


title: 1205LuTR_BRAFi-MEKi_DOX_2


title: scATAC_E16_5_F_S4


title: 1205LuTR_BRAFi-MEKi_DOX_1


title: ChIP_E16.5_M_H3K4me1_rep2

value: fetal germ cell


title: scATAC_E16_5_F_S1


title: WM793_Control_NO_DOX_3


title: ChIP_E16.5_M_H3K4me1_rep1


title: 1205LuTR_BRAFi-MEKi_NO_DOX_3

description: 1205LuTR-NR2F1 cells treated with BRAFi + MEKi

value: BRAFi + MEKi


title: Ctrl 1st

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 20 -p 16 --no-discordant. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Pvalue <= 0.01 Qvalue <= 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: HeLa cell

growth_protocol: HeLa cells were cultured under standard conditions with Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion) and was further purified with two phenol-chloroform treatments.The purified RNA was then treated with RQ1 DNase (RNase free) (Promega, Madison, WI, USA) and its quality and quantity were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad, USA). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
For each sample, 10μg of the total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) before directional RNA-seq library preparation. The purified mRNAs were then iron fragmented at 95°C followed by end repair and 5' adaptor ligation. Then, reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified, amplified, and stored at -80°C until they were used for sequencing.  For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions. Illumina HiSeq 4000 was used to collect data from 150-bp pair-end sequencing (ABlife Inc., Wuhan, China).

treatment_protocol: Plasmids transfection of HeLa cells was performed using lipofectAMINE 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. Transfected cells were harvested after 48 h for q-PCR analysis.

value: HeLa cell

tag: genotype/variation

value: control plasmid


title: RBM4 2nd

tag: cell line

value: RBm4 overexpression


title: scATAC_E16_5_F7


title: Ctrl 2nd


title: 1205LuTR_BRAFi-MEKi_NO_DOX_2

value: melanoma


title: ChIP_E16.5_M_H3K36me3_rep1


title: ChIP_E16.5_M_H3K9me3_rep1


title: ChIP_E16.5_M_H3K36me3_rep2


title: RBM4 1st


title: 1205LuTR_BRAFi-MEKi_NO_DOX_1


title: scATAC_E16_5_F5


title: scATAC_E16_5_F6


title: ChIP_E16.5_M_H3K27ac_rep1


title: ChIP_E16.5_M_H3K27ac_rep2


title: 1205LuTR_Control_DOX_2

description: 1205LuTR-NR2F1 cells treated with DMSO + DOX

value: DMSO + DOX


title: scATAC_E16_5_F4

value: female


title: 235_3_S15 (LuCaP Series, Set 2)

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

institute: Fred Hutchinson Cancer Cancer

description: Library name: 235_3_S15

data_processing:
Reads were aligned to a concated human and mouse genome from human build hg38 and mouse build mm10 using bowtie2 v2.4.2 8. Reads aligning to mm10 were removed.
PCR duplicates were marked and removed using Picard MarkDuplicates v2.24.1 (https://broadinstitute.github.io/picard/).
Peaks were called using Genrich v0.6.1 in ATAC-Seq mode (https://github.com/jsh58/Genrich?tab=readme-ov-file#atacseq).
Called peaks had the ENCODE blacklisted regions removed.
Assembly: hg38
Supplementary files format and content: narrowPeak calls using Genrich

extract_protocol:
Nuclei isolation was performed using the OMNI-ATACseq protocol with tissue-specific modifications. Briefly, 200,000 cells were pelleted at 500 rcf for 5 minutes in a pre-chilled (4°C) fixed-angle centrifuge. Supernatant was carefully discarded in a 2-step method using a P1000 pipette followed by a P200 pipette. Pelleted cells were then resuspend-ed in 100 µL ice-cold lysis buffer comprising ATACseq resuspension buffer (A-RSB; 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2 in nuclease free H2O) supplemented with NP-40, tween-20 and digitonin at final concentrations of 0.1%, 0.1% and 0.01% respectively. After 3 minutes of lysis re-action on ice, 1ml of ice-cold wash buffer (A-RSB supplemented with tween-20; 0.1% final concen-tration) was added and the tubes inverted to mix. The nuclei were then pelleted by centrifugation, and suspension carefully discarded (as previously described). For transposition, nuclei were resus-pended in a 50 µL transposition mix (2x TD buffer, PBS, 0.01% digitonin, 0.1 % tween 20, nucle-ase-free H20 and TDE1Tn5 transposase enzyme). Transposition was performed at 37°C for 30 minutes in a thermomixer with shaking at 850 rpm. Transposed DNA was cleaned up using the MinElute® PCR purification kit.
Libraries were generated as previously described (2), double-sized selected using AMPure XP beads and eluted in EB buffer. For sequencing, 16 libraries were pooled together and sequenced pair-end in a NextSeq P3.

value: prostate tumor patient-derived xenograft


title: 235_2_S14 (LuCaP Series, Set 2)

description: Library name: 235_2_S14


title: scATAC_E16_5_F3

value: gonad


title: ChIP_E16.5_F_H3K9me3_rep2


title: ChIP_E16.5_F_H3K9me3_rep1


title: 1205LuTR_Control_NO_DOX_3

description: 1205LuTR-NR2F1 cells treated with DMSO alone


title: 1205LuTR_Control_DOX_1


title: 174_1_S12 (LuCaP Series, Set 2)

description: Library name: 174_1_S12


title: scATAC_E16_5_F1


title: ChIP_E16.5_F_H3K4me3_rep2


title: 1205LuTR_Control_NO_DOX_2


title: scATAC_E15_5_M_S5

value: male


title: ChIP_E16.5_F_H3K4me3_rep1


title: 136_1 (LuCaP Series, Set 2)

description: Library name: 136_1


title: 1205LuTR_Control_DOX_3


title: 246_2_S13 (LuCaP Series, Set 2)

description: Library name: 246_2_S13


title: CPA rat skin: DHT+  FeCl₃, replicate 5

description: Library name: CPA-5

source_name: CPA treated rat,  DHT + FeCl₃

value: skin

value: wiid type

value: CPA (i.p.) treated DHT (p.o.) + FeCl₃ (s.c.)


title: ChIP_E16.5_F_H3K4me1_rep2


title: scATAC_E15_5_M_S3

value: somatic cell


title: ChIP_E16.5_F_H3K4me1_rep1


title: CPA rat skin: DHT+  FeCl₃, replicate 4

description: Library name: CPA-4


title: s173_2_bulk

description: Library name: s173_2_bulk

source_name: prostate cancer patient-derived xenograft

extract_protocol:
Fragment of frozen tissues (PDX models) were cut and resuspended in 300 ul of cold 3-detergent-ATAC-Resuspension Buffer (RSB) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin. Tissues were dounced 10 times with a loose and a tight pestle each until complete homogenization. The homogenate was then transferred to a 1.5 ml pre-chilled microfuge tube and incubated on ice for 10 minutes to lyse. After lysis, 300 ul of ATAC-RSB containing 0.1% Tween-20 was added and the tubes were inverted to mix. Lysates were filtered through a 40 um cell strainer and nuclei were centrifuged for 10 minutes at 1500 RCF in a pre-chilled (4 ºC) fixed-angle centrifuge. Nuclei were resuspended with 300 ul of ATAC-RSB containing 0.1% Tween-20 and counted with a hemocytometer using Trypan blue stain.
Nuclei were resuspended in 50 µl of transposition mix (25 µl 2× TD buffer, 2.5 µl transposase [100 nM final], 16.5 µl PBS, 0.5 µl 1% Digitonin, 0.5 µl 10% Tween-20, 5 µl H₂O). Transposition reactions were incubated at 37 °C for 30 min on a thermomixer. Transposed DNA was purified using Qiagen columns.


title: 96

description: Library name: 96

value: prostate cancer patient-derived xenograft


title: ChIP_E16.5_F_H3K36me3_rep2


title: scATAC_E16_5_F2


title: CPA rat skin: DHT+  FeCl₃, replicate 3

description: Library name: CPA-3


title: 96_rep1

description: Library name: 96_rep1


title: 136_2 (LuCaP Series, Set 2)

description: Library name: 136_2


title: scATAC_E15_5_M_S2


title: scATAC_E15_5_M_S1


title: ChIP_E16.5_F_H3K36me3_rep1


title: 96CR_rep1

description: Library name: 96CR_rep1


title: CPA rat skin: DHT+  FeCl₃, replicate 2

description: Library name: CPA-2


title: CPA rat skin: DHT+  FeCl₃, replicate 1

description: Library name: CPA-1


title: scATAC_E15_5_M6


title: 93_rep2

description: Library name: 93_rep2


title: scATAC_E15_5_M5


title: ChIP_E16.5_F_H3K27ac_rep1


title: 1205LuTR_Control_NO_DOX_1

value: DMSO alone


title: scATAC_E15_5_M_S4


title: PBS rat skin: DHT+  FeCl₃, replicate 4

description: Library name: PBS-4

source_name: PBS treated rat,  DHT + FeCl₃

value: PBS (i.p.) treated DHT (p.o.) + FeCl₃ (s.c.)


title: ChIP_E15.5_M_H3K9me3_rep2

value: fetal germ cell


title: 93_2X

description: Library name: 93_2X


title: scATAC_E15_5_M3


title: ChIP_E15.5_M_H3K9me3_rep1


title: PBS rat skin: DHT+  FeCl₃, replicate 2

description: Library name: PBS-2


title: scATAC_E15_5_M4


title: PBS rat skin: DHT+  FeCl₃, replicate 3

description: Library name: PBS-3


title: ChIP_E15.5_M_H3K4me3_rep4


title: PBS rat skin: DHT+  FeCl₃, replicate 1

description: Library name: PBS-1


title: ChIP_E15.5_M_H3K4me3_rep3


title: 92_rep1

description: Library name: 92_rep1


title: RNA-seq in CD4+YFP+Foxp3+ Treg cells, Female heterozygous, Foxp1/p4 cDKO, repl3

city: Palo Alto

first: Jonathan

last: Maltzman

state: California

address: 3801 Miranda Ave

institute: Stanford University

description: Library name: Sample 12

data_processing:
RNA-seq were carried out on an Illumina HiSeq 2000 (Illumina), generating 100 base-pair single-end reads. Data were normalized to reads per million. Sequencing data were aligned and annotated to the mouse genome assembly MGSCv37/mm9 at Stanford Genomic Core. Differentially expressed genes were identified by Cuffdiff, then analyzed, and visualized in R.
Assembly: mm9
Supplementary files format and content: txt files include FPKM values for each Sample

source_name: Spleen

extract_protocol:
Naturally occurring FOXP3+ Treg cells (CD4+ CD25+ YFP+) were sorted from 2-month-old Control and cDKO spleens. RNA was isolated using RNeasy Plus Micro Kit (Qiagen) per manufacturer’s instruction.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB) according to the manufacturer’s protocol.

value: Spleen

value: Treg cells

value: Foxp3YFP-Cre/X Foxp1/p4fl/fl


title: scATAC_E15_5_M1


title: ChIP_E15.5_M_H3K4me3_rep2


title: ChIP_E16.5_F_H3K27ac_rep2


title: scATAC_E15_5_M2


title: 82CR_rep1

description: Library name: 82CR_rep1


title: 93_1X

description: Library name: 93_1X


title: RNA-seq in CD4+YFP+Foxp3+ Treg cells, Female heterozygous, Foxp1/p4 cDKO, repl2

description: Library name: Sample 11


title: 81

description: Library name: 81


title: scATAC_E15_5_F_S4


title: RNA-seq in CD4+YFP+Foxp3+ Treg cells, Female heterozygous, Foxp1/p4 cDKO, repl1

description: Library name: Sample 10


title: 81_rep1

description: Library name: 81_rep1


title: 93_rep1

description: Library name: 93_rep1


title: RNA-seq in CD4+YFP+Foxp3+ Treg cells, Female heterozygous, Ctrl, repl3

description: Library name: Sample 9

value: Foxp3YFP-Cre/X Foxp1/p4+/+


title: ChIP_E15.5_M_H3K4me1_rep2


title: ChIP_E15.5_M_H3K4me3_rep1


title: scATAC_E15_5_F_S5


title: 78

description: Library name: 78


title: scATAC_E15_5_F_S2


title: ChIP_E15.5_M_H3K4me1_rep1


title: RNA-seq in CD4+YFP+Foxp3+ Treg cells, Female heterozygous, Ctrl, repl1

description: Library name: Sample 7


title: RNA-seq in CD4+YFP+Foxp3+ Treg cells, Female heterozygous, Ctrl, repl2

description: Library name: Sample 8


title: 78_rep1

description: Library name: 78_rep1


title: scATAC_E15_5_F_S1


title: scATAC_E15_5_F6


title: ChIP_E15.5_M_H3K36me3_rep1


title: ChIP_E15.5_M_H3K27ac_rep2


title: scATAC_E15_5_F_S3


title: RNA-seq in CD4+Foxp3+ Treg cells, Male homozygous, Foxp1/p4 cDKO, repl3

description: Library name: Sample 6

value: Foxp3YFP-Cre/Y Foxp1/p4fl/fl


title: scATAC_E15_5_F5

value: female


title: RNA-seq in CD4+Foxp3+ Treg cells, Male homozygous, Foxp1/p4 cDKO, repl2

description: Library name: Sample 5


title: scATAC_E15_5_F4


title: 77

description: Library name: 77


title: ChIP_E15.5_F_H3K9me3_rep1


title: RNA-seq in CD4+Foxp3+ Treg cells, Male homozygous, Foxp1/p4 cDKO, repl1

description: Library name: Sample 4


title: ChIP_E15.5_M_H3K27ac_rep1


title: scATAC_E15_5_F3


title: ChIP_E15.5_F_H3K4me3_rep2


title: RNA-seq in CD4+Foxp3+ Treg cells, Male homozygous, Ctrl, repl3

description: Library name: Sample 3

value: Foxp3YFP-Cre/Y Foxp1/p4+/+


title: RNA-seq in CD4+Foxp3+ Treg cells, Male homozygous, Ctrl, repl2

description: Library name: Sample 2


title: scATAC_E15_5_F2

value: gonad


title: ChIP_E15.5_F_H3K4me3_rep1


title: 77CR_bulk_for_scATAC

description: Library name: 77CR_bulk_for_scATAC


title: 77_rep1

description: Library name: 77_rep1


title: ChIP_E15.5_F_H3K4me1_rep2


title: 78_rep2

description: Library name: 78_rep2


title: scATAC_E15_5_F1


title: 77CR_rep1

description: Library name: 77CR_rep1


title: RNA-seq in CD4+Foxp3+ Treg cells, Male homozygous, Ctrl, repl1

description: Library name: Sample 1


title: 73_rep1

description: Library name: 73_rep1


title: ChIP_E15.5_F_H3K4me1_rep1


title: scATAC_E14_5_M_S5

value: male


title: 77_rep2

description: Library name: 77_rep2


title: 73CR_rep1

description: Library name: 73CR_rep1


title: scATAC_E14_5_M_S4


title: ChIP_E14.5_F_H3K27ac_rep1


title: Human iPSC-derived, unconditioned, rep2

city: Seoul

first: Yongjin

last: Yoo

state: Seoul

address: 73, Goryeodae-ro, Seongbuk-gu

department: Department of Neuroscience

country: South Korea

institute: Korea University

description:
Library name: snRNAseq-wildtype
10x Genomics

data_processing:
The 10× Genomics Cell Ranger (v.6.1.2) analysis pipelines were used to align reads to the hg38 reference genome and count barcodes or unique molecular identifiers.
Assembly: Human hg38
Supplementary files format and content: Tab-separated values and matrix files

source_name: human Pluripotent Stem Cells (KOLF2.1J, WTC11, H1)

extract_protocol:
For single-cell sample collection, we followed the 10x Genomics cell preparation protocol (https://cdn.10xgenomics.com/image/upload/v1686678481/support-documents/CG00053_Handbook_CellPreparation_SingleCellProtocols_Rev_D.pdf). Briefly, we removed media from the samples, washed once with 1x PBS, and incubated with Accutase for 5 minutes at 37oC. The samples were checked at 2.5 minutes to ensure dissociation was proceeding as expected. 2mL of Triculture Media was gently added to the samples, which were transferred to a 15mL conical tube and spun down at 20g for 5 minutes at room temperature in a swinging bucket centrifuge. The supernatant was discarded and the pellet resuspended gently in 1x PBS before being strained through the MACS SmartStrainer (30µm), run through a tabletop cell sorter to confirm the absence of doublets and clumps, and adding the resulting cells to the 10x Single Cell workflow. For single-nuclear sample collection, we adapted the protocol described by 10x Genomics ://cdn.10xgenomics.com/image/upload/v1660261285/support-documents/CG000124_Demonstrated_Protocol_Nuclei_isolation_RevF.pdf]. Briefly, we prepared lysis buffer for single cell suspension (10mM Tris-HCL pH7.4, 10mM NaCl, 3mM MgCl2, and 0.025% NP-40). We prepared nuclei wash and resuspension buffer (1% BSA, 0.2U/μl RNase Inhibitor, in 1x PBS). To harvest nuclei, we removed culture media, washed once with 1x PBS, and added ice-cold lysis buffer (scaled up to accommodate larger cell quantities) and incubated the samples for 1 minute. Next, we collected the samples and added nuclei wash and resuspension buffer and mixed with gentle pipetting. The samples were spun down at 500g at 4oC and the supernatant was removed and discarded. Next, 1mL of ice-cold nuclei wash and resuspension buffer was added and mixed with gentle pipetting. The samples were spun down again at 500g and the supernatant was discarded. As a final step, the samples were resuspended in nuclei wash and resuspension buffer at a final concentration of 1,000 nuclei/μl (determined via manual counting with Trypan Blue staining) and used immediately in the 10x Genomics Single Cell Protocol.
Library construction was conducted using the Chromium Next GEM Single Cell 3ʹ Library Kit v.3.1 (10× Genomics, 1000128). All reaction and quality control steps were carried out according to the manufacturer’s protocol and with recommended reagents, consumables and instruments. We chose 11 PCR cycles for library generation. Quality control of cDNA and libraries was conducted using a bioanalyzer (Agilent) at the Stanford Protein and Nucleic Acid Facility.

value: KOLF2.1J (neuron), WTC11 (astrocytes), H1 (microglia)

value: human PSC-derived neuron, astrocytes and microglia

value: no

tag: batch


title: 70_rep1

description: Library name: 70_rep1

tag: tissue


title: Human iPSC-derived, unconditioned, rep1

description:
Library name: scRNAseq-wildtype
10x Genomics

value: human Pluripotent Stem Cells (KOLF2.1J, WTC11, H1)

tag: cell type


title: ChIP_E14.5_M_H3K9me3_rep2

tag: strain


title: scATAC_E14_5_M_S3

value: somatic cell

tag: developmental stage


title: scATAC_E14_5_M_S2

tag: Sex


title: 70CR_rep1

description: Library name: 70CR_rep1

value: prostate cancer patient-derived xenograft


title: scATAC_E14_5_M_S1


title: ChIP_E14.5_M_H3K4me3_rep3

tag: chip antibody


title: 58_rep1

description: Library name: 58_rep1


title: ChIP_E14.5_M_H3K4me3_rep2


title: 49_rep2

description: Library name: 49_rep2


title: hMP, donor2, CRISPRa, rep1, CRISPR guide capture

city: South San Francisco

first: Rebecca

middle: Yi-Shuan

last: Wang

address: 131 Oyster Point Blvd

institute: Alector Inc

description: Library name: D2-4a_CR

data_processing:
Cell Ranger 7.1.0 software (10x Genomics) was used for alignment of scRNA-seq reads to the transcriptome as well as the alignment of sgRNA reads to the library. The ‘cellranger count’ command with default parameters was used to map expression reads to the reference transcriptome (10x Genomics GRCh38 version 2020-A).
Assembly: 10x Genomics GRCh38 version 2020-A
Supplementary files format and content: rds files for procesed Seurat objects

source_name: blood

growth_protocol: Two donors of hMF were each transduced with adenovirus encoding either CRISPRi-IRES-GFP (Vector Biolabs, custom prep) or CRISPRa-IRES-GFP (Vector Biolabs, custom prep), and lentivirus encoding either the CRISPRi or CRISPRa sgRNA libraries, respectively. The cells were grown in macrophage media for 1 week then FACS sorted based on a live cell dye (Thermo Fisher, #C34858), RFP+ (indicating the presence of the guide casette), and GFP+ (marking dCas9 expression).

extract_protocol:
Sorted cells were resuspended in 1X PBS with 0.04% BSA.
A total of 20,000 cells per sample were loaded and library preparation was performed according to the manufacturer’s protocol (10x Genomics, CG000206 Rev D) using the 10x Genomics Chromium Single Cell 3’ Gene Expression v3.1 kit with Feature Barcode technology (10x Genomics PN-1000079), generating both gene expression and CRISPR guide capture libraries.

value: blood

value: primary, donor2

value: macrophage

tag: donor

value: CRISPRa


title: hMP, donor2, CRISPRa, rep3, CRISPR guide capture

description: Library name: D2-6a_CR


title: hMP, donor2, CRISPRi, rep3, CRISPR guide capture

description: Library name: D2-3i_CR

value: CRISPRi


title: scATAC_E14_5_M6

data_processing:
For scATAC-seq, demultiplexed raw fastq files were trimmed by cutadapt (v3.3) to remove adapter sequences and short reads. ‘Clean reads’ were then mapped to mm10 using bowtie2 (v2.4.5) with parameters ‘--mm --no-unal --very-sensitive’, duplicated and low quality (MAPQ < 30) alignments were further removed with samtools (v1.11). Cell identifiers were attached to ‘CB’ tag of bam files manually, then fragment files of each cell were generated using sinto (v0.7.6) with default parameters. We followed the ArchR (v1.0.2) pipeline to perform downstream analysis of scATAC-seq data.
For ULI-NChIP-seq and low-input MNase-seq, raw data files were firstly trimmed by TrimGalore (v0.6.4) to remove sequencing adapters and low-quality reads. Bowtie2 were used to align reads to mm10 reference, duplicate alignments were identified and removed by ‘MarkDuplicates’ (v2.23.6) function of picard. Alignments with MAPQ < 30 were filtered. Aligned bam files were normalized to RPKM and converted to bigwig format for visualization by ‘bamCoverage’ function of deeptools (v3.4.3).
Assembly: mm10
Supplementary files format and content: .bed.gz: compressed bed files containing the scATAC-seq fragments for single cells
Supplementary files format and content: .bed.gz.tbi: index files related to compressed bed format fragment files
Supplementary files format and content: .bw: bigwig files containing RPKM normalized ChIP-seq signal

extract_protocol:
Male mice homozygous for the Oct4-EGFP transgene in the C57BL/6J background were crossed with wild-type C57BL/6J females. When a copulatory plug was evident around noon, that time was counted as E0.5. Gonads were isolated from E13.5, E14.5, E15.5 and E16.5 embryos, female and male samples were collected separately.Gonads were treated with 0.25% trypsin-EDTA for 10 min at 37 °C, and then, trypsin was inactivated by addition of 15% fetal bovine serum (FBS)/DMEM. Cells were ﬁltered through 40 µ m cell strainers to obtain a single-cell suspension for FACS (FACSAria II SORP, BD Bioscience).
The sequence libraries were generated using the KAPA Hyper Prep Kit according to the manufacturer’s instructions.
scATAC-seq, ulltra-low-input native ChIP-seq (ULI-NChIP-seq) and low-input MNase-seq

value: fetal germ cell


title: 49_rep1

description: Library name: 49_rep1


title: hMP, donor2, CRISPRi, rep1, CRISPR guide capture

description: Library name: D2-1i_CR


title: hMP, donor2, CRISPRi, rep2, CRISPR guide capture

description: Library name: D2-2i_CR


title: ChIP_E14.5_M_H3K4me3_rep1


title: scATAC_E14_5_M4_M5


title: scATAC_E14_5_M3


title: ChIP_E14.5_M_H3K4me1_rep4


title: hMP, donor2, CRISPRa, rep2, CRISPR guide capture

description: Library name: D2-5a_CR


title: ChIP_E14.5_M_H3K4me1_rep3


title: 49_1X

description: Library name: 49_1X


title: ChIP_E14.5_M_H3K9me3_rep1


title: scATAC_E14_5_M2


title: scATAC_E14_5_M1


title: hMP, donor1, CRISPRa, rep4, CRISPR guide capture

description: Library name: D1-8a_CR

value: primary, donor1


title: hMP, donor1, CRISPRa, rep3, CRISPR guide capture

description: Library name: D1-7a_CR


title: ChIP_E14.5_M_H3K4me1_rep2


title: 49_2X

description: Library name: 49_2X


title: ChIP_E14.5_M_H3K4me1_rep1


title: hMP, donor1, CRISPRa, rep2, CRISPR guide capture

description: Library name: D1-6a_CR


title: 243_rep1

description: Library name: 243_rep1


title: 235.3_rep1

description: Library name: 235.3_rep1


title: ChIP_E14.5_M_H3K36me3_rep2


title: scATAC_E14_5_F_S5

value: female


title: scATAC_E14_5_F_S4


title: 235.3CR_rep1

description: Library name: 235.3CR_rep1


title: ChIP_E14.5_M_H3K36me3_rep1


title: scATAC_E14_5_F_S3


title: hMP, donor1, CRISPRi, rep4, CRISPR guide capture

description: Library name: D1-4i_CR


title: hMP, donor1, CRISPRi, rep3, CRISPR guide capture

description: Library name: D1-3i_CR


title: scATAC_E14_5_F_S2


title: 235.2_rep1

description: Library name: 235.2_rep1


title: scATAC_E14_5_F_S1


title: 35CR_rep1

description: Library name: 35CR_rep1


title: hMP, donor1, CRISPRa, rep1, CRISPR guide capture

description: Library name: D1-5a_CR


title: hMP, donor1, CRISPRi, rep2, CRISPR guide capture

description: Library name: D1-2i_CR


title: 23_1

description: Library name: 23_1


title: scATAC_E14_5_F8


title: ChIP_E14.5_F_H3K9me3_rep2


title: hMP, donor1, CRISPRi, rep1, CRISPR guide capture

description: Library name: D1-1i_CR


title: ChIP_E14.5_M_H3K27ac_rep1


title: ChIP_E14.5_M_H3K27ac_rep2


title: hMP, donor2, CRISPRa, rep2, gene expression

description: Library name: D2-5a_G


title: 35_rep1

description: Library name: 35_rep1


title: ChIP_E14.5_F_H3K9me3_rep1


title: 23.1_rep2

description: Library name: 23.1_rep2


title: scATAC_E14_5_F4


title: 208.2_rep1

description: Library name: 208.2_rep1


title: hMP, donor2, CRISPRa, rep3, gene expression

description: Library name: D2-6a_G


title: scATAC_E14_5_F7


title: 23.1_rep1

description: Library name: 23.1_rep1


title: scATAC_E14_5_F6


title: scATAC_E14_5_F5


title: hMP, donor2, CRISPRa, rep1, gene expression

description: Library name: D2-4a_G


title: ChIP_E14.5_F_H3K4me3_rep4


title: ChIP_E14.5_F_H3K4me3_rep1


title: 208.4_rep1

description: Library name: 208.4_rep1


title: hMP, donor2, CRISPRi, rep2, gene expression

description: Library name: D2-2i_G


title: ChIP_E14.5_F_H3K4me1_rep4


title: ChIP_E14.5_F_H3K4me3_rep3


title: hMP, donor2, CRISPRi, rep1, gene expression

description: Library name: D2-1i_G


title: ChIP_E14.5_F_H3K4me3_rep2


title: hMP, donor2, CRISPRi, rep3, gene expression

description: Library name: D2-3i_G


title: scATAC_E14_5_F1


title: scATAC_E14_5_F2


title: 189.3_rep1

description: Library name: 189.3_rep1


title: 189.4_rep1

description: Library name: 189.4_rep1


title: hMP, donor1, CRISPRa, rep4, gene expression

description: Library name: D1-8a_G


title: hMP, donor1, CRISPRa, rep2, gene expression

description: Library name: D1-6a_G


title: 176_rep1

description: Library name: 176_rep1


title: ChIP_E14.5_F_H3K4me1_rep2


title: 208.1_rep1

description: Library name: 208.1_rep1


title: 189.3CR_rep1

description: Library name: 189.3CR_rep1


title: hMP, donor1, CRISPRa, rep3, gene expression

description: Library name: D1-7a_G


title: scATAC_E13_5_M_S3


title: scATAC_E13_5_M_S1


title: 176CR_rep1

description: Library name: 176CR_rep1


title: ChIP_E14.5_F_H3K4me1_rep3


title: hMP, donor1, CRISPRa, rep1, gene expression

description: Library name: D1-5a_G


title: 173_1

description: Library name: 173_1


title: scATAC_E13_5_M_S2


title: ChIP_E14.5_F_H3K4me1_rep1


title: hMP, donor1, CRISPRi, rep4, gene expression

description: Library name: D1-4i_G


title: ChIP_E15.5_F_H3K36me3_rep1


title: 174.1_rep1

description: Library name: 174.1_rep1


title: 173_1_S6

description: Library name: 173_1_S6


title: scATAC_E14_5_F3


title: scATAC_E13_5_M5


title: scATAC_E13_5_M_S4


title: scATAC_E13_5_M6


title: ChIP_E15.5_F_H3K27ac_rep1


title: 173.1_rep3

description: Library name: 173.1_rep3


title: ChIP_E15.5_F_H3K27ac_rep2


title: hMP, donor1, CRISPRi, rep2, gene expression

description: Library name: D1-2i_G


title: ChIP_E15.5_F_H3K36me3_rep2


title: scATAC_E13_5_M4


title: hMP, donor1, CRISPRi, rep1, gene expression

description: Library name: D1-1i_G


title: 173.1_rep2

description: Library name: 173.1_rep2


title: scATAC_E13_5_M3


title: ChIP_E13.5_M_H3K9me3_rep1


title: NB4-RNAseq-FP54-rp3

city: Chicago

first: Chuan

last: He

state: IL

address: 929 E 57th St

department: Chemistry Department

institute: University of Chicago

description: Library name: NB4-RNAseq-6

data_processing:
For RNA-seq analysis, raw reads were trimmed by Cutadapt (version 4.8)to remove low-quality bases and adapters. Trimmed reads were subjected to Clumpify (BBMap package)to remove duplicates. The deduplicated reads were aligned to the human genome (hg38 from UCSC) using STAR (version 2.7.11b)  using default parameters. FeatureCounts software (version 2.0.3) was used to count reads mapped to protein-coding genes from hg38 Gencode V42, and differentially expressed gene analysis was conducted by DEseq2 software. Differentially expressed genes were identified with cutoff p < 0.01, |log2FC|≥0.5. For m6A-seq analysis, raw reads for both input and IP samples were trimmed by Cutadapt (version 4.8)  to remove low-quality bases and adapters. Trimmed reads were subjected to Clumpify (BBMap package) to remove duplicates. The deduplicated reads were aligned to the human genome (hg38 from UCSC) using STAR (version 2.7.11b)  using default parameters. Mapped reads were separated by strands with SAMtools (version 1.21) , using “samtools view -f 83 (and 163)” for forward strand and “samtools view -f 99 (and 147)” for reverse strand. m6A peaks on each strand were called using MACS2  with the parameter ‘--nomodel’ separately. Significant peaks with q < 0.01 identified by MACS2 were considered. Polysome-seq analysis: raw reads were trimmed by Cutadapt (version 4.8)  to remove low-quality bases and adapters. Trimmed reads were subjected to Clumpify (BBMap package) to remove duplicates. The deduplicated reads were aligned to the human genome (hg38 from UCSC) using STAR (version 2.7.11b)  using default parameters. FeatureCounts software (version 2.0.3)  was used to count reads mapped to protein-coding genes from hg38 Gencode V42. Translation efficiency (TE) was calculated as RPKM (from polysome-seq) divided by RPKM (from RNA-seq). Differentially translated genes were identified with cutoff p< 0.05, |log2(TE fold change)| ≥1.
Assembly: hg38
Supplementary files format and content: "MOLM13_DMSO_vs_FP54.DEresults.RNAseq.xlsx"  and "NB4_DMSO_vs_FP54.DEresults.RNAseq.xlsx" show the differentially expression levels of mRNA with and without FP54 treatment; "MOLM13-DMSO-FP54.m6A.FC.single_peak.xlsx" shows the differentially changed m6A levels of mRNA with and without FP54 treatment; "Polysome_seq_data_FP54_vs_DMSO.xlsx" shows the differentially translated genes with and without FP54 treatment.

growth_protocol: Cell were grown in RPMI-1640, with 10% FBS and 1% penicillin-streptomycin. Cells were maintained at 37°C with 5% CO2.

extract_protocol:
RNA was isolated using Trizol method and precipitated using ethanol.
RNAseq and m6A seq: NB4 or MOLM-13 cells were incubated with DMSO or FP-54 (2 μM) for 48 h at 37 °C and 5% CO2, cells were collected by centrifugation, washed with PBS, and suspended in TRIzol reagent (Invitrogen). Total RNAs were extracted following the manufacturer’s protocol through ethanol precipitation. mRNA enrichment: mRNA was purified with two rounds of polyA+ purification with Dynabeads mRNA DIRECT kit (Ambion) following the manufacturer’s protocol. RNA concentration was measured by NanoDrop 1000 (Thermo Fisher Scientific). 1 μg mRNA for each sample were fragmented and enriched by m6A antibody (Millipore). Fragmented mRNA (as “input”) and immunoprecipitated RNA (as “IP”) were subjected to RNA library construction following manufacturer’s instructions of SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara). polysome-seq: 20 million MOLM-13 cells were incubated with FP-54 (2 μM) for 48 h, Cycloheximide (CHX) was added to the media at 100 mg/ml and incubated at 37°C for 7 min. Cells were collected by centrifugation, washed with ice-cold PBS with CHX (100 mg/ml), the cell pellet was suspended in lysis buffer which was formulated as 20 mM HEPES, pH 7.6, 100 mM KCl, 5 mM MgCl2, 100 μg/ml CHX, 1% Triton-X-100, freshly add 1:100 protease inhibitor (Roche), 40 U/ml SUPERasin (Ambion). The lysate was loaded onto the sucrose gradient and centrifuged at 4°C at 28,000 rpm (Beckman, rotor SW28) for 3 h. The samples were then fractioned and the A260 absorbance of each fraction was analyzed. Total RNAs of polysome fractions were suspended in TRIzol LS (Invitrogen), and RNA were extracted by RNA Clean & Concentrator (Zymo), mRNAs were then purified with two rounds of polyA+ purification with Dynabeads mRNA DIRECT kit (Ambion), and the libraries were constructed using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara).

treatment_protocol: AML cells (MOLM13 and NB4) were treated with Mock (DMSO) or FP54 (2uM) for 48 h.

value: AML

tag: genotype

value: WT


title: 173.1_rep1

description: Library name: 173.1_rep1


title: scATAC_E13_5_M2

first: Jiansen

last: Lu

address: No. 5 Yiheyuan Road, Haidian District

institute: Peking University

value: gonad

value: male


title: ChIP_E13.5_M_H3K4me3_rep4


title: 170.2_rep1

description: Library name: 170.2_rep1


title: NB4-RNAseq-FP54-rp1

description: Library name: NB4-RNAseq-4


title: 170.1_rep1

description: Library name: 170.1_rep1


title: hMP, donor1, CRISPRi, rep3, gene expression

description: Library name: D1-3i_G


title: ChIP_E13.5_M_H3K4me3_rep3


title: NB4-RNAseq-DMSO-rp3

description: Library name: NB4-RNAseq-3

value: DMSO


title: ChIP_E13.5_M_H3K4me3_rep2


title: NB4-RNAseq-DMSO-rp2

description: Library name: NB4-RNAseq-2


title: scATAC_E13_5_F_S4


title: 167_rep1

description: Library name: 167_rep1


title: 167CR_rep1

description: Library name: 167CR_rep1


title: ChIP_E13.5_M_H3K9me3_rep2


title: ChIP_E13.5_M_H3K4me3_rep1


title: scATAC_E13_5_F_S3


title: ChIP_E13.5_M_H3K4me1_rep1


title: 147_rep1

description: Library name: 147_rep1


title: scATAC_E13_5_F_S2


title: ChIP_E13.5_M_H3K4me1_rep2


title: MOLM13-Polysome-seq-FP54-rp2

description: Library name: MOLM13-Polysome-seq-4

data_processing:
For RNA-seq analysis, raw reads were trimmed by Cutadapt (version 4.8)to remove low-quality bases and adapters. Trimmed reads were subjected to Clumpify (BBMap package)to remove duplicates. The deduplicated reads were aligned to the human genome (hg38 from UCSC) using STAR (version 2.7.11b)  using default parameters. FeatureCounts software (version 2.0.3) was used to count reads mapped to protein-coding genes from hg38 Gencode V42, and differentially expressed gene analysis was conducted by DEseq2 software. Differentially expressed genes were identified with cutoff p < 0.01, |log2FC|≥0.5. For m6A-seq analysis, raw reads for both input and IP samples were trimmed by Cutadapt (version 4.8)  to remove low-quality bases and adapters. Trimmed reads were subjected to Clumpify (BBMap package) to remove duplicates. The deduplicated reads were aligned to the human genome (hg38 from UCSC) using STAR (version 2.7.11b)  using default parameters. Mapped reads were separated by strands with SAMtools (version 1.21) , using “samtools view -f 83 (and 163)” for forward strand and “samtools view -f 99 (and 147)” for reverse strand. m6A peaks on each strand were called using MACS2  with the parameter ‘--nomodel’ separately. Significant peaks with q < 0.01 identified by MACS2 were considered. Polysome-seq analysis: raw reads were trimmed by Cutadapt (version 4.8)  to remove low-quality bases and adapters. Trimmed reads were subjected to Clumpify (BBMap package) to remove duplicates. The deduplicated reads were aligned to the human genome (hg38 from UCSC) using STAR (version 2.7.11b)  using default parameters. FeatureCounts software (version 2.0.3)  was used to count reads mapped to protein-coding genes from hg38 Gencode V42. Translation efficiency (TE) was calculated as RPKM (from polysome-seq) divided by RPKM (from RNA-seq). Differentially translated genes were identified with cutoff p< 0.05, |log2(TE fold change)| ≥1.
Assembly: hg38
Supplementary files format and content: "MOLM13_DMSO_vs_FP54.DEresults.RNAseq.xlsx"  and "NB4_DMSO_vs_FP54.DEresults.RNAseq.xlsx" show the differentially expression levels of mRNA with and without FP54 treatment; "MOLM13-DMSO-FP54.m6A.FC.single_peak.xlsx" shows the differentially changed m6A levels of mRNA with and without FP54 treatment; "Polysome_seq_data_FP54_vs_DMSO.xlsx" shows the differentially translated genes with and without FP54 treatment.
Library strategy: Polysome-seq


title: NB4-RNAseq-DMSO-rp1

description: Library name: NB4-RNAseq-1


title: MOLM13-Polysome-seq-FP54-rp1

description: Library name: MOLM13-Polysome-seq-3


title: ChIP_E13.5_M_H3K36me3_rep2


title: scATAC_E13_5_F_S1


title: NB4-RNAseq-FP54-rp2

description: Library name: NB4-RNAseq-5


title: 147CR_rep1

description: Library name: 147CR_rep1


title: 145_2

description: Library name: 145_2


title: MOLM13-Polysome-seq-DMSO-rp2

description: Library name: MOLM13-Polysome-seq-2


title: ChIP_E13.5_M_H3K36me3_rep1


title: scATAC_E13_5_F_S5


title: scATAC_E13_5_F7


title: MOLM13-Polysome-seq-DMSO-rp1

description: Library name: MOLM13-Polysome-seq-1


title: scATAC_E13_5_F8


title: scATAC_E13_5_M1


title: ChIP_E13.5_M_H3K27ac_rep2


title: 145.2_rep1

description: Library name: 145.2_rep1


title: scATAC_E13_5_F6


title: MOLM13-m6Aseq-FP54-rp3

description: Library name: MOLM13-m6Aseq-6


title: ChIP_E13.5_M_H3K27ac_rep1


title: scATAC_E13_5_F5


title: ChIP_E13.5_F_H3K9me3_rep2


title: MOLM13-m6Aseq-FP54-rp2

description: Library name: MOLM13-m6Aseq-5


title: 145_1_2X

description: Library name: 145_1_2X


title: scATAC_E13_5_F4


title: ChIP_E13.5_F_H3K9me3_rep1


title: MOLM13-m6Aseq-FP54-rp1

description: Library name: MOLM13-m6Aseq-4


title: MOLM13-m6Aseq-DMSO-rp3

description: Library name: MOLM13-m6Aseq-3


title: scATAC_E13_5_F3


title: 145_1_1X

description: Library name: 145_1_1X


title: ChIP_E13.5_F_H3K4me3_rep4


title: 141_rep1

description: Library name: 141_rep1


title: ChIP_E13.5_F_H3K4me3_rep3


title: 145.1_rep2

description: Library name: 145.1_rep2


title: MOLM13-m6Aseq-DMSO-rp2

description: Library name: MOLM13-m6Aseq-2


title: 136_rep1

description: Library name: 136_rep1


title: MOLM13-RNAseq-FP54-rp3

description: Library name: MOLM13-RNAseq-6


title: 145.1_rep1

description: Library name: 145.1_rep1


title: MG1655relA, CNMA, 60min, rep2

city: Gdansk

first: Dariusz

last: Nowicki

state: pomorskie

address: Wita Stwosza 59

department: Bacterial Molecular Genetics

country: Poland

institute: University of Gdansk

description: Library name: Sample 11

data_processing:
Galaxy platform v 23.0
Sequence trimming after FastQC v0.11.9 was performed using Trimmomatic v0.38.1 (adapter sequence: TruSeq2, paired-ended, for Illumina GAII). Reads were mapped to eschColi_K12 reference genome using HISAT2 (Forward (FR); Spliced alignment options:Penalty for canonical/non-canonical - 0/3, Penaulty function - Constant [f(x) = B] where constant term B=0
Rstudio R-4.3.1 environment was employed to DEGs (DESEq 1.40.2) analysis using BAM files from HISAT2
Assembly: GCA_000005845, Ensembl July 2023
Supplementary files format and content: .xlsx file includes raw count data and DEGs analysis (p ≤ 0.05 and log2FC ≥ 2.0) for each sample

organism: Escherichia coli

growth_protocol: Escherichia coli MG1655 or its relA- isogenic strain cultured in fresh LB, aerobically with shaking at 37°C

extract_protocol:
RNA was harvested using RNase Mini Kit  (Qiagen) followed by additional pufification step with DNAse I (Qiagen). Samples where then validated using Bioanalyzer 2100
RNA-seq. TruSeq total RNA stranded with NebNext Ribodepletion kit (bacteria)

treatment_protocol: CNMA (Sigma) was added to treated samples (OD=0.1) from 1M stock solution in DMSO to final concantration 0.94mM. Then, cultures were incubated in aerobic contitions by 30 and 60 min. Untreated bacteria were used as a control.

value: relA konockdown

value: CNMA


title: MOLM13-m6Aseq-DMSO-rp1

description: Library name: MOLM13-m6Aseq-1


title: MG1655relA, CNMA, 60min, rep1

description: Library name: Sample 10


title: scATAC_E13_5_F1

city: Beijing


title: ChIP_E13.5_F_H3K36me3_rep1


title: MOLM13-RNAseq-FP54-rp1

description: Library name: MOLM13-RNAseq-4


title: 136CR_rep1

description: Library name: 136CR_rep1


title: MG1655relA, CNMA, 60min, rep3

description: Library name: Sample 12


title: 136CR2_rep1

description: Library name: 136CR2_rep1


title: ChIP_E13.5_F_H3K4me1_rep1


title: MOLM13-RNAseq-FP54-rp2

description: Library name: MOLM13-RNAseq-5


title: 105_rep1

description: Library name: 105_rep1


title: ChIP_E13.5_F_H3K27ac_rep2


title: scATAC_E13_5_F2


title: 105CR_rep2

description: Library name: 105CR_rep2


title: MG1655relA, CNMA, 30min, rep1

description: Library name: Sample 7


title: MG1655relA, CNMA, 30min, rep3

description: Library name: Sample 9


title: MOLM13-RNAseq-DMSO-rp3

description: Library name: MOLM13-RNAseq-3


title: 105CR_rep1

description: Library name: 105CR_rep1


title: mESCs withdrawal LIF for four days, Hnrnpf KO_1

city: tianjin

first: Duan

middle: Xiao

last: wei

address: China

institute: Nankai

description:
Library name: F_HKO_1
Column name in raw_counts_All_Samples.txt: F_HKO_1

data_processing:
The raw reads were trimmed to remove adapters and then aligned to mouse reference genome mm10 using STAR software with the default parameter.
Expression level of individual genes was quantified as fragments per kilobase of transcript per million mapped reads (FPKM) using Cufflinks software.
Differentially expressed genes (DEGs) were defined by the Cufflinks software with fold change >2 and p-value < 0.05.
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

growth_protocol: ESCs were cultured in 85% Dulbecco’s Modified Eagle Medium (DMEM) (Gibco, 12800-082), 15% fetal bovine serum (Hyclone, SH30395.03), 2 mM L-glutamine (Invitrogen, 25030-081), 100 units/ml penicillin and 100 µg/ml streptomycin (Invitrogen, 15140122), 0.1 mM nonessential amino acids (Sigma-Aldrich, M-7145), 0.1 mM β-Mercaptoethanol (Sigma-Aldrich, M-3148), and 1000 units/mL LIF. The medium was changed every day, and ESCs were passaged every 2-3 days. Cells were incubated in a humidiﬁed 37°C incubator with 5% CO2. All ESC lines were routinely tested for mycoplasma contamination.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104) following the manufacturer's protocol.
Library construction and sequencing were conducted by Novogene in Tianjin, China. Libraries were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: mouse embryonic stem cells

value: Hnrnpf KO

value: LIF removal for 4 days


title: MG1655relA, CNMA, 30min, rep2

description: Library name: Sample 8


title: MG1655relA, control, 0min, rep3

description: Library name: Sample 6


title: MOLM13-RNAseq-DMSO-rp2

description: Library name: MOLM13-RNAseq-2

value: blood


title: ChIP_E13.5_F_H3K27ac_rep1


title: mESCs withdrawal LIF for four days, Hnrnpf KO_2

description:
Library name: F_HKO_2
Column name in raw_counts_All_Samples.txt: F_HKO_2


title: ChIP_E13.5_F_H3K4me3_rep2


title: mESCs, Hnrnpf KO_2

description:
Library name: HKO_2
Column name in raw_counts_All_Samples.txt: HKO_2


title: AQCA rep2

city: Shenzhen

first: Shanshan

last: Xu

address: Xueyuan Avenue, No. 1066

institute: Shenzhen University

description:
Library name: Sample 5
B. subtilis biofilm + AQCA, 24h, rep5

data_processing:
Illumina Casava1.7 software used for base-calling.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
Gene expression quantification in this analysis was performed using RSEM software.
Assembly: acession number: CP020102
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Bacillus subtilis

source_name: strain

growth_protocol: The samples were cultured in MSgg medium for 48 hours to allow biofilm formation.

extract_protocol:
After 24 hours of treatment, the cells were harvested, and total RNA was extracted using the Total RNA Kit (OMEGA).
RNA libraries were prepared using NEBNextő Ultra II Directional RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: When the mature biofilms was formed, DMSO or AQCA (25 μg/mL,sigma) was added.

value: strain

value: NCIB 3610

value: biofilm and planktonic bacteria

value: wild-type

value: treated with AQCA


title: ChIP_E13.5_F_H3K4me3_rep1

value: fetal germ cell

value: female


title: MOLM13-RNAseq-DMSO-rp1

description: Library name: MOLM13-RNAseq-1

value: AML

value: WT


title: AQCA rep3

description:
Library name: Sample 6
B. subtilis biofilm + AQCA, 24h, rep6


title: MG1655relA, control, 0min, rep2

description: Library name: Sample 5


title: MG1655, control, 0min, biol rep2

description: Library name: Sample 2


title: mESCs withdrawal LIF for four days, E14

description:
Library name: F_E14
Column name in raw_counts_All_Samples.txt: F_E14


title: GLP2-1 6M (demultiplex ID0)

city: Yokohama

last: Moody

address: 1-7-22 Suehiro-cho

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description:
Library name: TFHS000718
10x genomics 5' single-cell

data_processing:
Sequence reads from all samples were processed by Cell Ranger (10X Genomics). Seurat (v 5.1.0) was used to aggregate and analyze the processed data following the official vignettes (https://satijalab.org/seurat/articles/sctransform_vignette.html). Specifically, PCA analysis was performed to identify clusters, and 20 gene clusters (0–20) were projected on Uniform Manifold Approximation and Projection (UMAP) space with the normalized gene expression. Gene ontogeny analysis was performed using clusterProfiler (v4.12.6)
Samples were identified using freemuxlet v0.1 against a list of 1000genomes SNPs and matched to patient genotypes.
Assembly: hg38
Supplementary files format and content: Tab separated values and matrix files

source_name: intestinal mucosa

extract_protocol:
balloon-assisted enteroscopy to obtain intestinal mucosa biopsy. The intestinal tissue was washed with Ca2+, Mg2+-free Hank’s balanced salt solution (HBSS) (Nacalai Tesque, 17460-15) to remove fecal content. After washing, the intestinal tissue was incubated with HBSS containing 1 mM dithiothreitol (Invitrogen, 15508-013) and 1 mM EDTA (Nacalai Tesque, 06894-85) for 15 min at 37°C. The supernatant of the solution was harvested for epithelial cells by passing through a 100-μm cell strainer into a 50-mL Falcon tube. At the same time, the tissues without the epithelial cells were washed with HBSS and dissolved into solutions by incubation with HBSS containing 2.5% fetal bovine serum (FBS) (Thermo Fisher Scientific, 10270-106) and penicillin/streptomycin (Nacalai Tesque, 26253-84), 1.0 mg/mL collagenase Type3 (Worthington, 032-22364), and 0.1 mg/mL DNase (Sigma-Aldrich, DN25) for 60 min at 37 °C. The dissolved solution and digested tissues were homogenized by vigorous shaking and passed through a 100-m cell strainer into a 50-mL Falcon tube. The solution was centrifuged at 1,700 rpm for 5 min at 4°C , the supernatant was removed, and resuspended in RPMI-1640 (Nacalai Tesque, 00-5523-02) containing 10% FBS and penicillin/streptomycin (Nacalai Tesque, 26253-84) (16, 17).
Isolated single cell suspensions of IE and LP cells were pooled and incubated with a Fixable Viability Dye eFluor (eBioscience, 65-0865-14) for 15 min at 4 °C. Live cells were sorted using BD FACS Aria-II (BD Bioscience) and loaded into Chromium Controller (10X Genomics). RNA-seq libraries were prepared using Chromium single-cell 5’ gene expression library preparation (human) according to the manufacturer’s instructions (10X Genomics). The libraries were then sequenced using a DNBSEQ (MGI Tech).

value: intestinal mucosa


title: GLP2-1 0M (demultiplex ID0)

description:
Library name: TFHS000717
10x genomics 5' single-cell


title: GLP2-3 12M (demultiplex ID2)

description:
Library name: TFHS000630
10x genomics 5' single-cell


title: GLP2-5 6M (demultiplex ID0)

description:
Library name: TFHS000459
10x genomics 5' single-cell


title: DMSO rep2

description:
Library name: Sample 2
B. subtilis biofilm + DMSO control, 24h, rep2

value: treated with DMSO


title: MG1655, control, 0min, biol rep1

description: Library name: Sample 1


title: mESCs, IP

description: Library name: IP_H17

data_processing:
The raw reads were trimmed to remove adapters and then aligned to mouse reference genome mm10 using STAR software with the default parameter.
Assembly: mm10
Supplementary files format and content: BigWig

extract_protocol:
Cells were harvested and cross-linked with 1% formaldehyde at room temperature for 10 minutes. The reaction was quenched by adding 1ml of 1.25 M glycine and incubated at room temperature for 5 min, and then resuspended with RIP lysis buffer (50 mM HEPES (pH 7.5), 0.4 M NaCl, 1 mM EDTA, 1 mM DTT, 0.5% TritonX-100,10% Glycerol, 0.1 M PMSF, 1.52 mg/ml protease inhibitor cocktail, 40 U/μl RNase inhibitor). Anti-FLAG M2 magnetic beads (Sigma-Aldrich, M8823 were used for immunoprecipitation.
Library construction and sequencing were conducted by Novogene in Tianjin, China.

value: FLAG-tagged HNRNPF overexpressed (OE)

value: IP


title: mESCs, Hnrnpf KO_1

description:
Library name: HKO_1
Column name in raw_counts_All_Samples.txt: HKO_1

value: mouse embryonic stem cells


title: AQCA rep1

description:
Library name: Sample 4
B. subtilis biofilm + AQCA, 24h, rep4


title: MSC_6

status: Public on Jul 07 2025

city: Rochester

first: Sanjay

last: Misra

state: MN

address: 200 First Street SW

department: Radiology

institute: Mayo Clinic

description:
Treatment
MSC_P33P942GV.FCHHCGKBBXY_L7_R1_IAGCTCGCT-GCAGAATC

data_processing:
Libraries were sequenced at four samples per lane following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cell was sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit and HD 3.4.0.38 collection software. Base-calling was performed using Illumina’s RTA version 2.7.7.
BAM files were imported into the RNA-Seq pipeline of mm10. Exclusions included a minimum RPKM value of 0.01.
Genome_build: susScr11
Supplementary_files_format_and_content: The average RPKMs of each group (C or MSC) were calculated and MSC/C was considered as fold change.  The genes that were >1.5 or <0.75 were considered as differentially expressed genes and the genes that were <1.5 or > 0. 75 were excluded. A simple t-test was performed to determine the P value and P<0.05 was considered as significant different compared to KI-V and the genes that were >0.05 were excluded.

organism: Sus scrofa

source_name: Vein

extract_protocol: Extraction protocol 0.5 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.

treatment_protocol: Chronic Kidney disease created to pigs as described in methods. 28days later an arteriovenous fistula was clreated by ligation of carotid artery and jugular vein and adipose derived MSCs in ringer lactate were layred on the adventia of the AVF outflow vein (MSC) immidatly after AVF creation or  untreated vessels (C) . 28 days after AVF creation, animals were euthanized and the outflow veins of AVFs were harvested.

value: AVF outflow veins

tag: disease state

value: chronic kidney disease model

value: MSC Treatment


title: GLP2-5 0M (demultiplex ID2)

description:
Library name: TFHS000460
10x genomics 5' single-cell


title: DMSO rep3

description:
Library name: Sample 3
B. subtilis biofilm + DMSO control, 24h, rep3

value: strain

tag: treatment


title: mESCs, E14

description:
Library name: E14
Column name in raw_counts_All_Samples.txt: E14


title: MSC_4

description:
Treatment
MSC_P33P910GV.FCHHCGKBBXY_L6_R1_ICATAATAC-TTCTAACG


title: GLP2-2 6M (demultiplex ID0) and GLP2-3 6M (demultiplex ID1)

description:
Library name: TFHS000458
10x genomics 5' single-cell


title: MSC_3

description:
Treatment
MSC_P33P861GV.FCHHCGKBBXY_L6_R1_IGCCACAGG-CATGCCAT


title: GLP2-2 0M (demultiplex ID1) and GLP2-3 0M (demultiplex ID0)

description:
Library name: TFHS000457
10x genomics 5' single-cell


title: C_1

description:
Control
C_P33P750GV.FCHHCGKBBXY_L5_R1_ICCTTCACC-GACGCTCC

value: Control


title: DMSO rep1

description:
Library name: Sample 1
B. subtilis biofilm + DMSO control, 24h, rep1, Sample abnormality, Excluded from downstream analysis

value: NCIB 3610

value: biofilm and planktonic bacteria


title: Pig_MSC_3

data_processing:
Libraries were sequenced at four samples per lane following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cell was sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit and HD 3.4.0.38 collection software. Base-calling was performed using Illumina’s RTA version 2.7.7.
BAM files were imported into the RNA-Seq pipeline of susScr11. Exclusions included a minimum RPKM value of 0.01.
Genome_build: susScr11

source_name: Adipose derived mesenchymal stem cells (MSC)

growth_protocol: MSCs isolated from adult pigs and cultured in advanced MEM supplimented with human platlet lysat as described in methods.

extract_protocol:
RNA was isolated using miRNeasy kit (qiagen).
0.5 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.


title: C_3

description:
Control
C_P33P767GV.FCHHCGKBBXY_L6_R1_ITGCGGCGT-CCTCGGTA


title: mESCs, Input

description: Library name: Input_H17

value: input


title: Pig_MSC_2

value: Adipose derived mesenchymal stem cells (MSC)


title: Dhx16_CKO3

city: Chongqing

first: Zhigang

last: Li

state: China

address: NO.30 GaotanYan  Street, Shapingba District

institute: Southwest Hospital, Army Medical University

data_processing:
The raw sequencing data was preprocessed using SMRT Link software, and the full-length transcript sequences were obtained using the Iso-Seq analysis pipeline.
The single-molecule sequencing polymerase reads were split to obtain subreads. The subreads from the same polymerase read were self-corrected to form Circular Consensus Sequences (CCS).
By detecting concatemers (chimeric sequences) and 5' and 3' end primers (sequencing primers), the CCS sequences were classified to identify Full-Length Non-Concatemer (FLNC) sequences for subsequent analysis.
The FLNC sequences, both pre- and post-correction, are aligned to the reference genome using GMAP software.
Assembly: GRCm39
Supplementary files format and content: Summary of Differential Alternative Splicing Genes

source_name: Bone marrow

extract_protocol:
Total RNA was isolated using TRIzol reagent (Takara).
The full length transcripts were prepared using a custom protocol based on Smart-seq2. VN-anchored oligo-dT primers and TSO were used for reverse transcription (RT) of total RNA. The resulting full-length double-stranded cDNA was pre-amplified using ISPCR primers and purified with AMPure XP beads to remove primer dimers.The full-length cDNA was end-repaired, and SMRTbell adapters were ligated.Unligated fragments were digested with exonuclease, and the library was purified again using magnetic beads to obtain the sequencing library.After the library construction was completed, the quality of the library was checked. Sequencing was performed only after the quality was confirmed to meet the requirements.

value: Bone marrow

value: primary cell

value: Hematopoietic stem cells (HSC)

value: CKO


title: Pig_MSC_1


title: MG1655relA, control, 0min, rep1

description: Library name: Sample 4

value: relA konockdown


title: MSC_1

description:
Treatment
MSC_P33P940GV__Allo__M.FCHHCGKBBXY_L5_R1_IGTGTCGGA-GCTTGCGC


title: MG1655, control, 0min, biol rep3

description: Library name: Sample 3

value: WT


title: C_2

description:
Control
C_P33P755GV__NT__F.FCHHCGKBBXY_L5_R1_IACACTAAG-ATCCATAT


title: C17

first: Hisashi

last: Sawada

state: KY

address: 741 South Limestone BBSRB B251

institute: University of Kentucky

description: Library name: C17

data_processing:
Raw read data in FASTQ format were processed through fastp to remove adaptor sequences and low-quality sequences.
Trimmed sequence reads were mapped to mouse genome mm10 using STAR (v2.6.1d, mismatch=2).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including read counts of genes for each sample

source_name: Aorta

extract_protocol:
RNA was extracted using Rneasy fibrous tissue mini kits (Qiagen, #74704). 1 ug of total RNA was used for the construction of sequencing libraries.
cDNA libraries for RNA-seq were prepared using NEBNext UltraTM RNA library prep kits for Illumina (NEB) following manufacturer's protocols.

treatment_protocol: Aortic samples were harvested from male Fbn1 C1041G/+ mice administered control ASO or AGT-ASO, and from wild type littermates.

value: Aorta

tag: region

value: Ascending

value: Control-ASO


title: Dhx16_fl1


title: Dhx16_CKO2


title: C16

description: Library name: C16


title: Dhx16_CKO1