title: hiPSC-derived ExpLBM cells

city: Okayama

first: Takeshi

last: Takarada

country: Japan

institute: Okayama University

description: Library name: set2-230926-ExpLBM8-noTP

data_processing:
To obtain count matrices, reads were aligned to the human genome GRCh38 using Cell Ranger (v7.0.1) with default parameters. Downstream analysis was performed using the R package Seurat (v5.0.3) 40. For quality control, cells with more than five detected genes, a UMI count higher than 5, and <10% mitochondrial genes were kept as high-quality cells. Doublets were detected using DoubletFinder (v2.0.4) 41 and removed. Counts were normalized, and then the top 3000 highly variable genes were detected via the SCTransform and FindVariableFeatures functions of Seurat. For data integration, the batch effect was removed by the LeverageScore method via SketchData in Seurat. After scaling gene expression and performing dimensional reduction, cells were visualized using UMAP embedding. Cluster annotations were labeled with canonical markers. Transcriptome similarity was compared with published developing human limb [5–9 postconceptional weeks (PCW)] scRNA-seq data using anchor-based label transfer implemented in Seurat. To this end, anchors between the query and reference dataset were identified and filtered using the FindTransferAnchors function with the top 14 dimensions. Then, the prediction score was calculated using the TransferData function. The cell type and region similarity (defined as the mean prediction score of each cell type) were visualized in a heatmap. Trajectory analysis was performed using the monocle3 package (v1.3.7) 42 with default parameters, and the Mes1 cluster was chosen as the root node to order cells. A pseudotime heatmap was plotted using the ComplexHeatmap (v2.18.0) package.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix of cell ranger output

organism: Homo sapiens

source_name: hiPSC-derived ExpLBM cells

extract_protocol:
ExpLBM cells were washed with PBS (−) and dissociated with accutase at 37°C for 5 min, while IZ/ACP and GPC organoids were washed with PBS (−) and then treated with 900 U/mL collagenase (type II) (Gibco) for 60 min at 37°C, followed by gentle pipetting using a serological pipette to dislodge and dissociate aggregates. Cells were sorted on a FACSAria III Cell Sorter (BD Biosciences) to remove dead cells and debris via forward scatter, side scatter, and DAPI/calcein-AM staining. A total of 10,000 cells were analyzed.
A Chromium Next GEM Single Cell 3′ GEM Kit v3.1 (10x Genomics) was used for library preparation. Dissociated cells were separated into single droplets with unique molecular barcodes and then processed following the manufacturer’s protocol. Quality checks of the samples were performed using high sensitivity D5000 screen tape (Agilent) and the Agilent 4150 TapeStation system (Agilent). Sequencing was performed using DNBseq (MGI).

value: hiPSC-derived ExpLBM cells


title: G14.5_p300KO_rep2_23 (ACSS2 dataset)

status: Public on Jan 26 2025

type: SRA

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

description:
pancreatic Beta cell, G14.5p300KO, biol rep2, scRNAseq
scRNA-seq
Smart-seq3xpress

library_source: transcriptomic single cell

data_processing:
For smart-seq3xpress scRNA-seq, the index, primer and adaptor sequences in the paired-end reads were trimmed with Trimmomatic (v0.39). The trimmed reads were aligned to the Mus musculus reference genome (GRCm38/mm10) using Hisat242 (V2.1.0) with the default parameters. The reads were assigned to genes using featureCounts (v2.0.1) with default parameters.
For 10x Genomics scRNA-seq, the demultiplexing, barcoded processing, gene counting and aggregation were made using the Cellranger toolkit (v3.1.0; https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) with default settings
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Smart-seq3xpress output files: Tab-separated rexpression values matrix files

molecule: total RNA

organism: Mus musculus

source_name: pancreas

extract_protocol:
Pancreatic tissue was perfused with 0.5mg/mL collagenase P (Roche, 11213873001) dissolved in 1×HBSS buffer containing 10mM HEPES (pH 7.4), 1mM MgCl2 and 5mM glucose. Digestion was terminated by adding cold PBS. Islets were manually picked up and dissociated into single cell suspension with 0.25% trypsin (Thermo Fisher Scientific, 25200114) and incubated for 3-5min at 37℃. Fetal bovine serum (FBS) was used to terminate the digestion (40% vol/vol). After centrifugation at 1000rpm for 5min at 4℃, the supernatant was removed and the cell pellet was resuspended with HBSS buffer. Cells were directly sorted using a BD Aria SORP flow cytometer.
Smart-seq3xpress scRNA-seq was performed following a published procedure. Briefly, single cells were sorted into 384-well plates containing 0.3μL lysis. The mRNA was reverse transcribed into cDNA using 0.1μL dispensed RT mix. The libraries were constructed using TruePrep DNA Library Prep Kit (Vazyme, TD501).
10x Genomics scRNA-seq library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
smart-seq3xpress scRNA-seq,10x Genomics scRNA-seq

treatment_protocol: Mouse islets were manually harvested and cultured in RIPM1640 (Gibco, 21870076) medium supplemented with 20% human serum and 1% Penicillin/Streptomycin containing 5μM A485 (Selleck, S8740) or 20μM Nifuroxazide (Selleck, S4182) or vehicle DMSO, and incubated at 37℃ with 5% CO2 for 4 days. Approximately 40 mouse islets were seeded per well in low adhesion plates. The medium was changed every 2 days.

tag: tissue

value: pancreas

tag: cell type

value: Beta cell

tag: strain

tag: Sex

value: female

tag: diet

value: standard diet

tag: genotype

value: p300 knockout


title: G0_Acss2WT_rep1_68 (ACSS2 dataset)

description:
pancreatic Beta cell, G0Acss2WT, biol rep1, scRNAseq
scRNA-seq
Smart-seq3xpress

value: Acss2 WT


title: G0_Acss2WT_rep1_75 (ACSS2 dataset)


title: G0_Acss2WT_rep1_66 (ACSS2 dataset)


title: IZ/ACP organoids from hiPSCs (no TP)

description: Library name: set2-230926-8Step3PD-2wk-noTP

source_name: IZ/ACP organoids from hiPSCs

value: IZ/ACP organoids from hiPSCs


title: G0_Acss2WT_rep1_65 (ACSS2 dataset)


title: G0_Acss2WT_rep1_67 (ACSS2 dataset)


title: G14.5_p300KO_rep2_21 (ACSS2 dataset)


title: LPM_H3K27ac_rep2

description: Library name: LPM_325_rep2

library_source: genomic

data_processing:
Sequencing was performed using HiSeq1500 (Illumina) with a pair-read sequencing length of 150 bp. Sequences were aligned to human genome sequences (hg38) using Bowtie2 (parameters: --end-to-end, --very-sensitive, --no-mixed, --no-discordant, --phred33, -I 10, -X 700). For peak calling, gopeaks and bedtools were utilized as described in the previous section. BAM files were converted to bigwig format using deeptools with the command “bamCoverage -binSize 1 -normalizeUsing RPGC --extendReads”. A heatmap was created using the “computeMatrix” and “plotHeatmap” functions of deeptools. To separate promoter and non-promoter regions, the “annotatePeaks.pl” function of Homer was utilized, and a promoter was defined as one that was annotated as a promoter-TSS in the default setting.
Assembly: hg38
Supplementary files format and content: bigwig of mapping result
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: hiPSC-derived LPM

extract_protocol:
A total of 20,000 cells were collected as input.
Libraries were prepared using a CUT&Tag-IT Assay Kit (Active Motif) following the manufacturer’s protocol. Anti-H3K27ac (Active Motif) and anti-H3K27me3 (Active Motif) antibodies were used for reactions.

value: hiPSC-derived LPM


title: GPC organoids from hiPSCs (no TP)

description: Library name: set2-230926-8Step3BTplus-2wk-noTP

source_name: GPC organoids from hiPSCs

value: GPC organoids from hiPSCs


title: G0_Acss2WT_rep1_64 (ACSS2 dataset)


title: G0_Acss2WT_rep1_62 (ACSS2 dataset)


title: LPM_H3K27me3_rep2

description: Library name: LPM_322_rep2


title: G0_Acss2WT_rep1_61 (ACSS2 dataset)


title: G0_Acss2WT_rep1_60 (ACSS2 dataset)


title: G14.5_p300KO_rep2_2 (ACSS2 dataset)


title: G0_Acss2WT_rep1_63 (ACSS2 dataset)


title: G0_Acss2WT_rep1_6 (ACSS2 dataset)


title: LBM_H3K27ac_rep2

description: Library name: LBM_325_rep2

source_name: hiPSC-derived LBM

value: hiPSC-derived LBM


title: G0_Acss2WT_rep1_59 (ACSS2 dataset)


title: G14.5_p300KO_rep2_19 (ACSS2 dataset)


title: G0_Acss2WT_rep1_58 (ACSS2 dataset)


title: G0_Acss2WT_rep1_57 (ACSS2 dataset)


title: G14.5_p300KO_rep2_18 (ACSS2 dataset)


title: G14.5_p300KO_rep2_22 (ACSS2 dataset)


title: 414C2day0_H3K27ac_rep2

description: Library name: 414C2day0_325_rep2

source_name: hiPSC

value: hiPSC


title: G0_Acss2WT_rep1_56 (ACSS2 dataset)


title: G0_Acss2WT_rep1_54 (ACSS2 dataset)


title: 414C2day0_H3K27me3_rep2

description: Library name: 414C2day0_322_rep2


title: G14.5_p300KO_rep2_20 (ACSS2 dataset)


title: G0_Acss2WT_rep1_55 (ACSS2 dataset)


title: G14.5_p300KO_rep2_17 (ACSS2 dataset)


title: G14.5_p300KO_rep2_16 (ACSS2 dataset)


title: ExpLBM_325_rep2

description: Library name: 8-ExpLBM-325


title: LBM_H3K27me3_rep2

description: Library name: LBM_322_rep2


title: G0_Acss2WT_rep1_52 (ACSS2 dataset)


title: G0_Acss2WT_rep1_50 (ACSS2 dataset)


title: G14.5_p300KO_rep2_14 (ACSS2 dataset)


title: G0_Acss2WT_rep1_5 (ACSS2 dataset)


title: G0_Acss2WT_rep1_49 (ACSS2 dataset)


title: G0_Acss2WT_rep1_48 (ACSS2 dataset)


title: G0_Acss2WT_rep1_51 (ACSS2 dataset)


title: G14.5_p300KO_rep2_13 (ACSS2 dataset)


title: G14.5_p300KO_rep2_15 (ACSS2 dataset)


title: LPM_H3K27ac_rep1

description: Library name: 8-LPM-325


title: G0_Acss2WT_rep1_47 (ACSS2 dataset)


title: LPM_H3K27me3_rep1

description: Library name: 8-LPM-322


title: G0_Acss2WT_rep1_46 (ACSS2 dataset)


title: G0_Acss2WT_rep1_45 (ACSS2 dataset)


title: G14.5_p300KO_rep2_12 (ACSS2 dataset)


title: LBM_H3K27ac_rep1

description: Library name: 8-LBM-325


title: G0_Acss2WT_rep1_44 (ACSS2 dataset)


title: G14.5_p300KO_rep2_11 (ACSS2 dataset)


title: G0_Acss2WT_rep1_53 (ACSS2 dataset)


title: G0_Acss2WT_rep1_43 (ACSS2 dataset)


title: G14.5_p300KO_rep2_10 (ACSS2 dataset)


title: G0_Acss2WT_rep1_41 (ACSS2 dataset)


title: ExpLBM_H3K27me3_rep2

description: Library name: 8-ExpLBM-322


title: LBM_H3K27me3_rep1

description: Library name: 8-LBM-322


title: 414C2day0_H3K27me3_rep1

description: Library name: 8-414C2-322


title: G14.5_p300KO_rep1_99 (ACSS2 dataset)

description:
pancreatic Beta cell, G14.5p300KO, biol rep1, scRNAseq
scRNA-seq
Smart-seq3xpress


title: 414C2day0_H3K27ac_rep1

description: Library name: 8-414C2-325


title: G14.5_p300KO_rep2_1 (ACSS2 dataset)


title: G0_Acss2WT_rep1_40 (ACSS2 dataset)


title: G0_Acss2WT_rep1_39 (ACSS2 dataset)


title: G0_Acss2WT_rep1_38 (ACSS2 dataset)


title: G0_Acss2WT_rep1_4 (ACSS2 dataset)


title: ExpLBM_H3K27ac_rep1

description: Library name: 8ExpLBM-5-325


title: G0_Acss2WT_rep1_37 (ACSS2 dataset)


title: G0_Acss2WT_rep1_36 (ACSS2 dataset)


title: ExpLBM_H3K27me3_rep1

description: Library name: 8ExpLBM-5-322


title: G14.5_p300KO_rep1_97 (ACSS2 dataset)


title: G14.5_p300KO_rep1_98 (ACSS2 dataset)


title: G0_Acss2WT_rep1_35 (ACSS2 dataset)


title: G0_Acss2WT_rep1_34 (ACSS2 dataset)


title: G0_Acss2WT_rep1_33 (ACSS2 dataset)


title: LBM_rep2

description: Library name: 8-LBM-2

data_processing:
Sequencing was performed using HiSeq1500 (Illumina) with a pair-read sequencing length of 150 bp. Two or three biological replicates were analyzed. Sequences were aligned to human genome sequences (hg38) using Bowtie2 with default parameters. Gopeaks was used to call peaks using default parameters. Regions where overlapping peaks were identified by Bedtools that intersected between biological replicates were designated as high-confidence peaks. The read count matrix of each sample was used to detect differentially accessible peaks using edgeR. To generate a heatmap, normalized read counts obtained using edgeR were z-score-scaled and plotted. For motif analysis, findMotifsGenome.pl of Homer was used with the -size200-mask option. For annotation of peaks, annotatePeaks.pl of Homer was used with default settings. For visualization, BAM files were converted to bigwig format using deeptools with the command “bamCoverage -binSize 1 -normalizeUsing RPGC -extendReads”.
Assembly: hg38
Supplementary files format and content: bigwig of mapping result

extract_protocol:
ATAC-seq was conducted following a previously described method 39. In brief, 4000 cells were collected
Cells were lysed using lysis buffer containing 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630. The Tn5 transposase reaction using Illumina Tagment DNA Enzyme and Buffer (Illumina) was performed at 37°C for 30 min. The reacted DNA was purified using a MinElute PCR Purification Kit (QIAGEN) and amplified for 8–15 cycles using a Nextera Index Kit (Illumina) to produce libraries for sequencing.


title: G14.5_p300KO_rep1_96 (ACSS2 dataset)


title: LBM_rep1

description: Library name: 8-LBM-1


title: G0_Acss2WT_rep1_32 (ACSS2 dataset)


title: G0_Acss2WT_rep1_31 (ACSS2 dataset)


title: G14.5_p300KO_rep1_95 (ACSS2 dataset)


title: G0_Acss2WT_rep1_30 (ACSS2 dataset)


title: LPM_rep2

description: Library name: 8-LPM-2


title: G0_Acss2WT_rep1_42 (ACSS2 dataset)


title: G0_Acss2WT_rep1_3 (ACSS2 dataset)


title: G14.5_p300KO_rep1_94 (ACSS2 dataset)


title: G0_Acss2WT_rep1_29 (ACSS2 dataset)


title: LPM_rep1

description: Library name: 8-LPM-1


title: G0_Acss2WT_rep1_28 (ACSS2 dataset)


title: G0_Acss2WT_rep1_27 (ACSS2 dataset)


title: 414C2day0_rep2

description: Library name: 8-414C2-2


title: G0_Acss2WT_rep1_26 (ACSS2 dataset)


title: G0_Acss2WT_rep1_24 (ACSS2 dataset)


title: G14.5_p300KO_rep1_91 (ACSS2 dataset)


title: G0_Acss2WT_rep1_25 (ACSS2 dataset)


title: G0_Acss2WT_rep1_23 (ACSS2 dataset)


title: G0_Acss2WT_rep1_22 (ACSS2 dataset)


title: ExpLBM_rep3

description: Library name: ExpLBM8-3


title: G14.5_p300KO_rep1_92 (ACSS2 dataset)


title: 414C2day0_rep1

description: Library name: 8-414C2-1


title: G14.5_p300KO_rep1_90 (ACSS2 dataset)


title: G0_Acss2WT_rep1_21 (ACSS2 dataset)


title: G0_Acss2WT_rep1_20 (ACSS2 dataset)


title: ExpLBM_rep2

description: Library name: ExpLBM8-2


title: G0_Acss2WT_rep1_18 (ACSS2 dataset)


title: G0_Acss2WT_rep1_2 (ACSS2 dataset)


title: G0_Acss2WT_rep1_19 (ACSS2 dataset)


title: G14.5_p300KO_rep1_89 (ACSS2 dataset)


title: IAA-2-3

city: Suzhou

first: Peng

state: Jiangsu

address: Office3625 Building703, RENAI ROAD No.199, INDUSTRIAL PARK DISTRICT

department: Suzhou Medical College

institute: Soochow University

data_processing:
Raw sequence data were mapped and processed using Juicer v1.5 with default parameters.
The Hi-C data and MboI cut sites were mapped to hg19.
Replicates data were first processed separately.
After confirmation of good reproducibility by HiCRep(Yang, et.al Genome Res. 2017), we merged the replicates and re-processed as combined results.
TAD called by Arrowhead, Loops were called by HiCCUPS both from Juicer.
Assembly: hg19
Supplementary files format and content: hic

source_name: Human bone marrow

growth_protocol: HEL cells were maintained in RPMI-1640 medium (Corning, 10-040-CV) supplemented with 10% fetal bovine serum (FBS) (HyClone).

extract_protocol:
Briefly, five million CTCF-AID knock-in HEL cells without or with IAA treatment for 24 hours were crosslinked with 1% formaldehyde for 10 min at room temperature, digested with 125 units of MboI, labeled with biotinylated nucleotides and ligated for proximity ligation. After de-crosslinking, the ligated DNA was purified and sheared to 300–500 bps. Ligation junctions were pulled down with streptavidin beads and prepared as a standard Illumina library.
Each library underwent 75 cycles of paired-end sequencing on the Illumina HiSeq 4000 system.Each sample had two replicates, and we merged the replicates after confirming reproducibility. Each sample contained > 250 million paired-end fragments, > 60% ligation motif present, and > 200 million contacts.

value: Human bone marrow

tag: cell line

value: HEL, Human erythroleukemia cell

value: Erythroblast

tag: treatment

value: 500uM IAA (indole-3-acetic acid)


title: G14.5_p300KO_rep1_88 (ACSS2 dataset)


title: G0_Acss2WT_rep1_17 (ACSS2 dataset)


title: G0_Acss2WT_rep1_16 (ACSS2 dataset)


title: G14.5_p300KO_rep1_93 (ACSS2 dataset)


title: G0_Acss2WT_rep1_15 (ACSS2 dataset)


title: G0_Acss2WT_rep1_14 (ACSS2 dataset)


title: IAA-2-2


title: G14.5_p300KO_rep1_87 (ACSS2 dataset)


title: G0_Acss2WT_rep1_13 (ACSS2 dataset)


title: G0_Acss2WT_rep1_12 (ACSS2 dataset)


title: IAA-2-1


title: DMSO-1-2-2

value: DMSO


title: IAA-1-3


title: G0_Acss2WT_rep1_10 (ACSS2 dataset)


title: G0_Acss2WT_rep1_1 (ACSS2 dataset)


title: G14.5_p300KO_rep1_9 (ACSS2 dataset)


title: G14.5_p300KO_rep1_84 (ACSS2 dataset)


title: G14.5_p300KO_rep1_85 (ACSS2 dataset)


title: G0_Acss2WT_rep1_11 (ACSS2 dataset)


title: ExpLBM_rep1

description: Library name: ExpLBM8-1

value: hiPSC-derived ExpLBM cells


title: G14.5_p300KO_rep1_83 (ACSS2 dataset)

value: pancreas


title: DMSO-1-2-1


title: G0_Acss2KO_rep2_84 (ACSS2 dataset)

description:
pancreatic Beta cell, G0Acss2KO, biol rep2, scRNAseq
scRNA-seq
Smart-seq3xpress

value: Beta cell

value: Acss2 knockout


title: G0_Acss2KO_rep2_85 (ACSS2 dataset)

value: female

value: standard diet


title: DMSO-1-1-2


title: G0_Acss2KO_rep2_83 (ACSS2 dataset)


title: G0_Acss2KO_rep2_82 (ACSS2 dataset)


title: DMSO-1-1-1


title: G14.5_p300KO_rep1_81 (ACSS2 dataset)

value: p300 knockout


title: G0_Acss2KO_rep2_80 (ACSS2 dataset)


title: G0_Acss2KO_rep2_81 (ACSS2 dataset)


title: G14.5_p300KO_rep1_86 (ACSS2 dataset)


title: HEL cells, IAA treated_rep2,GATA1,ChIP

data_processing:
Paired-end reads were trimmed for index adapter by cutadapt (paired-end mode, default parameter with ‘-m 6 -O 20’) and aligned to human genome hg19 by bowtie2). Duplicated reads were then marked with Picard (version 2.6.0-SNAPSHOT) and only non-duplicated proper paired reads were kept by samtools (parameter ‘-q 1 -F 1804’ version 1.2) . To evaluate the ChIP assay quality, we first separated reads by fragment size <120 bp, or fragment size >150 bp and <2,000 bp and generated bigwig files for visualization. We observed a clear pattern that peaks in tracks with <120 bp were sharper and surrounded by peaks in tracks with >150 bp on IGV (version 2.17.14), which was consistent to the description from the original ChIP protocol paper. We then generated bigwig files using all reads that fragment size <2,000 bp.
Assembly: hg19
Supplementary files format and content: bigWig

source_name: Human blood

extract_protocol: 4 μg GATA1 antibody were added to the sonication samples, followed with gentle rotation for 16 hours at 4°C, Beads added after that,followed with gentle rotation for 6 hours at 4°C. beads transfered to a new tube. Using wash buffer to wash beads, then, samples were incubated in SDS elution buffer for 6 hours. separate beads and supernatant, DNA was in supernatant and then extracted by the phenol/chloroform/isopropanol protocol. Library construction was performed using the DNA Library Prep Kit.

value: HEL

value: Human blood

value: IAA

tag: chip antibody


title: G0_Acss2KO_rep2_8 (ACSS2 dataset)


title: G0_Acss2KO_rep2_79 (ACSS2 dataset)


title: G14.5_p300KO_rep1_80 (ACSS2 dataset)


title: G14.5_p300KO_rep1_8 (ACSS2 dataset)


title: G0_Acss2KO_rep2_78 (ACSS2 dataset)


title: G0_Acss2KO_rep2_9 (ACSS2 dataset)


title: G0_Acss2KO_rep2_75 (ACSS2 dataset)


title: HEL cells, DMSO treated_rep1,GATA1,ChIP


title: G0_Acss2KO_rep2_76 (ACSS2 dataset)


title: G0_Acss2KO_rep2_74 (ACSS2 dataset)


title: G14.5_p300KO_rep1_79 (ACSS2 dataset)


title: G14.5_p300KO_rep1_78 (ACSS2 dataset)


title: G0_Acss2KO_rep2_73 (ACSS2 dataset)


title: HUDEP-2 cells, IAA treated_rep2,GATA1,ChIP


title: G0_Acss2KO_rep2_70 (ACSS2 dataset)


title: G14.5_p300KO_rep1_77 (ACSS2 dataset)


title: G0_Acss2KO_rep2_69 (ACSS2 dataset)


title: G0_Acss2KO_rep2_71 (ACSS2 dataset)


title: HUDEP-2 cells, IAA treated_rep1,GATA1,ChIP


title: HEL cells, IAA treated_rep1,GATA1,ChIP


title: G14.5_p300KO_rep1_82 (ACSS2 dataset)


title: G14.5_p300KO_rep1_75 (ACSS2 dataset)


title: G0_Acss2KO_rep2_7 (ACSS2 dataset)


title: G14.5_p300KO_rep1_76 (ACSS2 dataset)


title: G0_Acss2KO_rep2_68 (ACSS2 dataset)


title: HEL cells, IAA treated_rep2,CTCF,ChIP

extract_protocol: 4 μg CTCF antibody were added to the sonication samples, followed with gentle rotation for 16 hours at 4°C, Beads added after that,followed with gentle rotation for 6 hours at 4°C. beads transfered to a new tube. Using wash buffer to wash beads, then, samples were incubated in SDS elution buffer for 6 hours. separate beads and supernatant, DNA was in supernatant and then extracted by the phenol/chloroform/isopropanol protocol. Library construction was performed using the DNA Library Prep Kit.

value: CTCF (Diagenode,c15410210-50)


title: HUDEP-2 cells, DMSO treated_rep2,GATA1,ChIP


title: G0_Acss2KO_rep2_65 (ACSS2 dataset)


title: HUDEP-2 cells, DMSO treated_rep1,GATA1,ChIP


title: G14.5_p300KO_rep1_73 (ACSS2 dataset)


title: G0_Acss2KO_rep2_77 (ACSS2 dataset)


title: G0_Acss2KO_rep2_64 (ACSS2 dataset)


title: G14.5_p300KO_rep1_72 (ACSS2 dataset)


title: G0_Acss2KO_rep2_72 (ACSS2 dataset)


title: G14.5_p300KO_rep1_74 (ACSS2 dataset)


title: G0_Acss2KO_rep2_66 (ACSS2 dataset)


title: HEL cells, DMSO treated_rep2,GATA1,ChIP


title: G14.5_p300KO_rep1_71 (ACSS2 dataset)


title: G0_Acss2KO_rep2_63 (ACSS2 dataset)


title: G0_Acss2KO_rep2_67 (ACSS2 dataset)


title: G0_Acss2KO_rep2_61 (ACSS2 dataset)


title: G0_Acss2KO_rep2_59 (ACSS2 dataset)


title: HUDEP-2 cells, IAA treated_rep2,CTCF,ChIP


title: G0_Acss2KO_rep2_60 (ACSS2 dataset)


title: G14.5_p300KO_rep1_70 (ACSS2 dataset)


title: G0_Acss2KO_rep2_6 (ACSS2 dataset)


title: HEL cells, DMSO treated_rep1,CTCF,ChIP


title: HUDEP-2 cells, IAA treated_rep1,CTCF,ChIP


title: G0_Acss2KO_rep2_56 (ACSS2 dataset)


title: HEL cells, IAA treated_rep1,CTCF,ChIP


title: G0_Acss2KO_rep2_55 (ACSS2 dataset)


title: G0_Acss2KO_rep2_58 (ACSS2 dataset)


title: HEL cells, DMSO treated_rep2,CTCF,ChIP


title: HUDEP-2  cells, DMSO treated_rep2,CTCF,ChIP


title: G14.5_p300KO_rep1_7 (ACSS2 dataset)


title: G0_Acss2KO_rep2_54 (ACSS2 dataset)


title: G14.5_p300KO_rep1_67 (ACSS2 dataset)


title: G0_Acss2KO_rep2_62 (ACSS2 dataset)


title: G0_Acss2KO_rep2_53 (ACSS2 dataset)


title: G14.5_p300KO_rep1_68 (ACSS2 dataset)


title: G0_Acss2KO_rep2_50 (ACSS2 dataset)


title: HUDEP2 cells, IAA treated_12h_rep3

library_source: transcriptomic

data_processing:
Raw counts of gene transcripts were derived from raw fastq files using the alignment-independent quantification tool, Salmon (https://combine- lab.github.io/salmon/), with standard settings. The raw count matrix was then imported into R-studio and utilized as input for Limma_voom analysis following the vignette of the package for normalization, differential gene expression analysis, and unbiased clustering analysis, including principal component analysis. The output of Limma_voom was used as the input for pre-ranked-based GSEA to enrich functional pathways and gene signatures (https://www.gsea-msigdb.org/gsea/index.jsp).
Assembly: hg19
Supplementary files format and content: Tab-delimited text file includes Row counts for each sample

extract_protocol:
RNA samples of three biological replicates were extracted from cultured cells, using TRIzol (Ambion by Life technologies, 343,911), following the manufacturer’s instructions. RNA was then sent out for library preparation and next-generation sequencing to a commercial company, Novogene (CA, USA).
According to the manufacturer's instructions, three biologically duplicated RNA samples were extracted from cultured cells using TRIZOL (Ambion by Life technologies, 343911). RNA sample quality was analyzed, and library were prepared and next-generation sequenced by a commercial company, Novogene (California, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly- T oligo- attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M- MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: GFP-miniAID-CTCF

value: 500uM IAA

tag: time


title: G0_Acss2KO_rep2_52 (ACSS2 dataset)


title: G0_Acss2KO_rep2_51 (ACSS2 dataset)


title: G14.5_p300KO_rep1_66 (ACSS2 dataset)


title: HUDEP-2 cells, DMSO treated_rep1,CTCF,ChIP


title: G0_Acss2KO_rep2_49 (ACSS2 dataset)


title: G0_Acss2KO_rep2_5 (ACSS2 dataset)


title: HUDEP2 cells, IAA treated_12h_rep2


title: G0_Acss2KO_rep2_57 (ACSS2 dataset)


title: G14.5_p300KO_rep1_65 (ACSS2 dataset)


title: G0_Acss2KO_rep2_48 (ACSS2 dataset)


title: HUDEP2 cells, IAA treated_12h_rep1


title: G14.5_p300KO_rep1_69 (ACSS2 dataset)


title: G0_Acss2KO_rep2_45 (ACSS2 dataset)


title: HUDEP2 cells, IAA treated_6h_rep3


title: G0_Acss2KO_rep2_46 (ACSS2 dataset)


title: G14.5_p300KO_rep1_63 (ACSS2 dataset)


title: HUDEP2 cells, IAA treated_6h_rep2


title: G0_Acss2KO_rep2_43 (ACSS2 dataset)


title: G0_Acss2KO_rep2_42 (ACSS2 dataset)


title: G14.5_p300KO_rep1_61 (ACSS2 dataset)


title: G14.5_p300KO_rep1_64 (ACSS2 dataset)


title: G0_Acss2KO_rep2_41 (ACSS2 dataset)


title: G0_Acss2KO_rep2_44 (ACSS2 dataset)


title: HUDEP2 cells, IAA treated_6h_rep1


title: G14.5_p300KO_rep1_62 (ACSS2 dataset)


title: G0_Acss2KO_rep2_4 (ACSS2 dataset)


title: G0_Acss2KO_rep2_40 (ACSS2 dataset)


title: G14.5_p300KO_rep1_60 (ACSS2 dataset)


title: G0_Acss2KO_rep2_38 (ACSS2 dataset)


title: G14.5_p300KO_rep1_6 (ACSS2 dataset)


title: HUDEP2 cells, DMSO treated_rep3


title: HUDEP2 cells, DMSO treated_rep2


title: G0_Acss2KO_rep2_37 (ACSS2 dataset)


title: HUDEP2 cells, DMSO treated_rep1


title: G0_Acss2KO_rep2_36 (ACSS2 dataset)


title: G14.5_p300KO_rep1_59 (ACSS2 dataset)


title: G0_Acss2KO_rep2_47 (ACSS2 dataset)


title: G14.5_p300KO_rep1_58 (ACSS2 dataset)


title: G0_Acss2KO_rep2_33 (ACSS2 dataset)


title: G0_Acss2KO_rep2_35 (ACSS2 dataset)


title: HEL cells, IAA treated_12h_rep3


title: HEL cells, IAA treated_12h_rep2


title: G0_Acss2KO_rep2_32 (ACSS2 dataset)


title: G14.5_p300KO_rep1_57 (ACSS2 dataset)


title: G0_Acss2KO_rep2_31 (ACSS2 dataset)


title: HEL cells, IAA  treated_12h_rep1


title: G0_Acss2KO_rep2_3 (ACSS2 dataset)


title: G14.5_p300KO_rep1_56 (ACSS2 dataset)


title: HEL cells, IAA treated_6h_rep3


title: G0_Acss2KO_rep2_39 (ACSS2 dataset)


title: G14.5_p300KO_rep1_55 (ACSS2 dataset)


title: G0_Acss2KO_rep2_29 (ACSS2 dataset)


title: G0_Acss2KO_rep2_27 (ACSS2 dataset)


title: G0_Acss2KO_rep2_30 (ACSS2 dataset)


title: HEL cells, IAA treated_6h_rep2


title: HEL cells, IAA treated_6h_rep1


title: G0_Acss2KO_rep2_25 (ACSS2 dataset)


title: G0_Acss2KO_rep2_26 (ACSS2 dataset)


title: G0_Acss2KO_rep2_24 (ACSS2 dataset)


title: G0_Acss2KO_rep2_34 (ACSS2 dataset)


title: G14.5_p300KO_rep1_54 (ACSS2 dataset)


title: G0_Acss2KO_rep2_22 (ACSS2 dataset)


title: G0_Acss2KO_rep2_23 (ACSS2 dataset)


title: G14.5_p300KO_rep1_52 (ACSS2 dataset)


title: G0_Acss2KO_rep2_21 (ACSS2 dataset)


title: G0_Acss2KO_rep2_20 (ACSS2 dataset)


title: G0_Acss2KO_rep2_2 (ACSS2 dataset)


title: HEL cells, DMSO treated_rep1


title: HEL cells, DMSO treated_rep2


title: G0_Acss2KO_rep2_28 (ACSS2 dataset)


title: G0_Acss2KO_rep2_19 (ACSS2 dataset)


title: Smoke_CNV

city: Tianjin

first: 钰云

last: 王

address: Tianjin

institute: 天津医科大学

description:
Library name: Sample 2
10x Genomics

data_processing:
Raw data were input and filtered with the Cell Ranger pipeline (10× Genomics)
Unique molecular identifier (UMI) count tables from control and CNV mice were loaded into R and processed using the Seurat R package (version 4.1.1).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: retina+choroid

extract_protocol:
Choroid-sclera and retina were digested separately in a papain solution (40U papain / 10mL DPBS) for 45 minutes. Papain was then neutralized in a trypsin inhibitor solution (0.15% ovomucoid in DPBS) and the tissue was triturated to generate a single-cell suspension. Following trituration, the cells were pelleted, resuspended, and filtered through a 40μm Nitex mesh filter to eliminate any clumped cells. Dissociated cells from retinas were finally incubated with PE anti-mouse CD73 (127206, Biolegend, US) followed by anti-PE microbeads (130-048-801, Miltenyi Biotec, US) to deplete rods. Single cell suspensions from retina and choroid-sclera were mixed and diluted at a concentration of 200 cells/μL in 0.2% BSA/DPBS for loading into 10x Genomics Chromium.
Droplet generation and cDNA libraries were completed by Novogene company (Beijing,China).

treatment_protocol: Adult C57BL/6J mice were subjected to nose exposure to the mainstream smoke of commercial cigarettes (Hongyun, China Tobacco, China) containing 1.2 mg of nicotine, 13 mg of CO, and 13 mg of tar oil per cigarette. This smoke exposure was generated using a smoke generator (BUXCO, NC, US), and induced CNV with laser photocoagulation (532 nm, 200 mW, 0.150 s, 100 μm; Vovus Spectra, Lumenis, US) using a slit lamp delivery system and a cover glass as a contact lens.

value: retina+choroid

value: WT


title: G14.5_p300KO_rep1_50 (ACSS2 dataset)


title: G0_Acss2KO_rep2_17 (ACSS2 dataset)


title: Smoke

description:
Library name: Sample 1
10x Genomics


title: G0_Acss2KO_rep2_16 (ACSS2 dataset)


title: G0_Acss2KO_rep2_18 (ACSS2 dataset)


title: G14.5_p300KO_rep1_49 (ACSS2 dataset)


title: G14.5_p300KO_rep1_53 (ACSS2 dataset)


title: G14.5_p300KO_rep1_5 (ACSS2 dataset)


title: G0_Acss2KO_rep2_14 (ACSS2 dataset)


title: G0_Acss2KO_rep2_15 (ACSS2 dataset)


title: G0_Acss2KO_rep2_13 (ACSS2 dataset)


title: HEL cells, DMSO treated_rep3


title: G14.5_p300KO_rep1_48 (ACSS2 dataset)


title: G0_Acss2KO_rep2_11 (ACSS2 dataset)


title: G14.5_p300KO_rep1_47 (ACSS2 dataset)


title: G14.5_p300KO_rep1_51 (ACSS2 dataset)


title: G0_Acss2KO_rep2_12 (ACSS2 dataset)


title: G14.5_p300KO_rep1_46 (ACSS2 dataset)


title: G0_Acss2KO_rep2_10 (ACSS2 dataset)


title: G0_Acss2KO_rep1_9 (ACSS2 dataset)

description:
pancreatic Beta cell, G0Acss2KO, biol rep1, scRNAseq
scRNA-seq
Smart-seq3xpress


title: G0_Acss2KO_rep2_1 (ACSS2 dataset)


title: G14.5_p300KO_rep1_45 (ACSS2 dataset)


title: G0_Acss2KO_rep1_8 (ACSS2 dataset)


title: G14.5_p300KO_rep1_44 (ACSS2 dataset)


title: G0_Acss2KO_rep1_78 (ACSS2 dataset)


title: G0_Acss2KO_rep1_77 (ACSS2 dataset)


title: Leaves from plants exposed to drought stress for 12 days after treated the water for 5 days [W5D12_2]

type: RNA

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: CSRS

institute: RIKEN

description: Gene expression data of W5D12_2

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacture's instructions. Then Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent microarray (GPL22197) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with package limma version 3.48.3.

organism: Manihot esculenta

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacture's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The cassava plants used in this study were grown under a greenhouse condition (50% relative humidity, 28°C, and 16-h supplemental lighting).

extract_protocol: The total RNA was extracted from the leaves using Plant RNA reagenet according to manufacture’s instruction. Furthermore, total RNA was purified using RNeasy Plant Mini kit (QIAGEN) according to manufacture’s instruction.

treatment_protocol: The plants were watered with ethanol or water (control) for 5 days, and then exposed to a drought for 12 days under a greenhouse condition after plastic pot was covered by plastic wrap to avoid the loss of water from surface.

value: Leaves

value: Water pretreatment for 5 days and drought treatement for 12 days


title: Leaves from plants exposed to drought stress for 12 days after treated the water for 5 days [W5D12_1]

description: Gene expression data of W5D12_1


title: G14.5_p300KO_rep1_42 (ACSS2 dataset)


title: G14.5_p300KO_rep1_43 (ACSS2 dataset)


title: HCT cells, DNA-PK KO, with hypoxicstress, rep3

city: Cheonan

first: Jihye

last: Park

address: 119 Dan-daero, Dongnam-gu

country: South Korea

institute: Dankook University

description:
Library name: DNA-PK KO HCT cell, hypoxic stresss rep3
C5_S66

data_processing:
Sequenced reads (paired-end) in FASTQ format were trimmed using Trim Galore (version 0.6.6) with Cutadapt (version 3.4) and their quality was assured using FastQC (version 0.11.9).
Quality-assured trimmed reads were then aligned to the reference genome (hg38 assembly) using STAR (version 2.7.9a) with the following parameters: --outSAMtype BAM SortedByCoordinate, --quantMode TranscriptomeSAM, and --outFilterMultimapNmax 1.
The integrity of transcripts was evaluated by means of transcript integrity number (TIN) scores using RseQC (tin.py, version 4.0.0).
Gene expression levels were quantified using StringTie (version 2.1.7b), and differential gene expression analysis was conducted using DESeq2 (version 1.36.0) to identify genes with significant changes between conditions.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample

source_name: HCT116 cells

growth_protocol: WT and DNA-PK KO HCT116 cells were grown in DMEM-high glucose (Cytiva Hyclone, SH30243.01) medium to approximately 60% confluence.

extract_protocol:
Total RNAs were extracted and purified from cells using the RNeasy kit (Qiagen).
RNA was converted into cDNA and sequenced by Omega Bioservices according to previously described protocols.

treatment_protocol: Cells were treated with CoCl2 at a final concentration of 200 µM for 12 hours to induce hypoxia. Control cells were treated with the same amount of H2O.

value: HCT116 cells

value: human colon cancer

value: DNA-PK knockout

value: CoCl2 treatment


title: G0_Acss2KO_rep1_76 (ACSS2 dataset)

value: pancreas

value: Beta cell

value: female

value: Acss2 knockout


title: Leaves from plants exposed to drought stress for 12 days after treated the water for 5 days [W5D12_4]

description: Gene expression data of W5D12_4


title: G0_Acss2KO_rep1_75 (ACSS2 dataset)

value: standard diet


title: Leaves from plants exposed to drought stress for 12 days after treated the 1.0% ethanol for 5 days  [E5D12_4]

description: Gene expression data of E5D12_4

value: Ethanol pretreatment for 5 days and drought treatement for 12 days


title: Leaves from plants exposed to drought stress for 12 days after treated the water for 5 days [W5D12_3]

description: Gene expression data of W5D12_3


title: G0_Acss2KO_rep1_73 (ACSS2 dataset)


title: G0_Acss2KO_rep1_74 (ACSS2 dataset)


title: HCT cells, WT, with hypoxicstress, rep3

description:
Library name: WT HCT cells, hypoxic stress rep3
C4_S65


title: HCT cells, DNA-PK KO, with hypoxicstress, rep2

description:
Library name: DNA-PK KO HCT cells, hypoxic stress rep2
B5_S60


title: G14.5_p300KO_rep1_41 (ACSS2 dataset)

value: p300 knockout


title: Leaves from plants exposed to drought stress for 12 days after treated the 1.0% ethanol for 5 days  [E5D12_2]

description: Gene expression data of E5D12_2


title: G14.5_p300KO_rep1_39 (ACSS2 dataset)


title: HCT cells, WT, with hypoxicstress, rep2

description:
Library name: WT HCT cells, hypoxic stress rep2
B4_S59


title: HCT cells, DNA-PK KO, with hypoxicstress, rep1

description:
Library name: DNA-PK KO HCT cells, hypoxic stress rep1
A5_S54


title: G14.5_p300KO_rep1_40 (ACSS2 dataset)


title: Leaves from plants exposed to drought stress for 6 days after treated the water for 5 days [W5D6_5]

description: Gene expression data of W5D6_5

value: Water pretreatment for 5 days and drought treatement for 6 days


title: G0_Acss2KO_rep1_72 (ACSS2 dataset)


title: G14.5_p300KO_rep1_38 (ACSS2 dataset)


title: Leaves from plants exposed to drought stress for 12 days after treated the 1.0% ethanol for 5 days  [E5D12_1]

description: Gene expression data of E5D12_1


title: Leaves from plants exposed to drought stress for 12 days after treated the 1.0% ethanol for 5 days  [E5D12_3]

description: Gene expression data of E5D12_3


title: G0_Acss2KO_rep1_70 (ACSS2 dataset)


title: G0_Acss2KO_rep1_71 (ACSS2 dataset)


title: HCT cells, WT, with hypoxicstress, rep1

description:
Library name: WT HCT cells, hypoxic stress rep1
A4_S53


title: G0_Acss2KO_rep1_7 (ACSS2 dataset)


title: G0_Acss2KO_rep1_68 (ACSS2 dataset)


title: Leaves from plants exposed to drought stress for 12 days after treated the 1.0% ethanol for 5 days  [E5D12_5]

description: Gene expression data of E5D12_5


title: G14.5_p300KO_rep1_4 (ACSS2 dataset)


title: Leaves from plants exposed to drought stress for 6 days after treated the water for 5 days [W5D6_1]

description: Gene expression data of W5D6_1


title: G0_Acss2KO_rep1_69 (ACSS2 dataset)


title: Leaves from plants exposed to drought stress for 6 days after treated the water for 5 days [W5D6_3]

description: Gene expression data of W5D6_3


title: Leaves from plants exposed to drought stress for 6 days after treated the water for 5 days [W5D6_4]

description: Gene expression data of W5D6_4


title: HCT cells, DNA-PK KO, without hypoxicstress, rep2

description:
Library name: DNA-PK KO HCT cells rep2
B2_S57

value: H2O treatment instead of CoCl2


title: G14.5_p300KO_rep1_37 (ACSS2 dataset)


title: Leaves from plants exposed to drought stress for 6 days after treated the water for 5 days [W5D6_2]

description: Gene expression data of W5D6_2


title: G14.5_p300KO_rep1_36 (ACSS2 dataset)


title: HCT cells, WT, without hypoxicstress, rep3

description:
Library name: WT HCT cells rep3
C1_S62


title: HCT cells, DNA-PK KO, without hypoxicstress, rep3

description:
Library name: DNA-PK KO HCT cells rep3
C2_S63


title: G14.5_p300KO_rep1_35 (ACSS2 dataset)


title: G0_Acss2KO_rep1_65 (ACSS2 dataset)


title: G0_Acss2KO_rep1_67 (ACSS2 dataset)


title: Leaves from plants exposed to drought stress for 6 days after treated the 1.0% ethanol for 5 days  [E5D6_4]

description: Gene expression data of E5D6_4

value: Ethanol pretreatment for 5 days and drought treatement for 6 days


title: G14.5_p300KO_rep1_32 (ACSS2 dataset)


title: HCT cells, DNA-PK KO, without hypoxicstress, rep1

description:
Library name: DNA-PK KO HCT cells rep1
A2_S51


title: G14.5_p300KO_rep1_34 (ACSS2 dataset)


title: G0_Acss2KO_rep1_66 (ACSS2 dataset)


title: Leaves from plants exposed to drought stress for 6 days after treated the 1.0% ethanol for 5 days  [E5D6_3]

description: Gene expression data of E5D6_3


title: HCT cells, WT, without hypoxicstress, rep2

description:
Library name: WT HCT cells rep2
B1_S56

value: WT


title: HCT cells, WT, without hypoxicstress, rep1

description:
Library name: WT HCT cells rep1
A1_S50


title: Leaves from plants exposed to drought stress for 6 days after treated the 1.0% ethanol for 5 days  [E5D6_2]

description: Gene expression data of E5D6_2

value: Leaves


title: G14.5_p300KO_rep1_33 (ACSS2 dataset)


title: Os infected +Fe 3

city: Cerdanyola del Vallès

first: ANTONI

last: GARCIA-MOLINA

state: Barcelona

address: Campus UAB - CRAG Building

department: Plant Development and Signal Transduction

country: Spain

institute: Centre for Research in Agrigenomics

description: replicate 3

data_processing:
RNA-Seq datasets were analysed on Galaxy (https://usegalaxy.org/).
Assembly: Briefly, reads were cleaned from adapters using Trimmomatic and mapped to the Arabidopsis reference genome (TAIR10) or rice reference genome (IRGSP-1.0) with STAR. Read counts were computed with featureCounts and transcriptional changes were calculated according to Likelihood ratio test hypothesis testing (adjusted P  ≤ 0.05) in DESeq2.
Supplementary files format and content: Arabidopsis reference genome (TAIR10) and rice reference genome (IRGSP-1.0)
Supplementary files format and content: csv files containing normalised counts obtained with featureCounts.

organism: Oryza sativa Japonica Group

source_name: shoots

growth_protocol: Arabidopsis thaliana ecotype Col0 and Oyrza sativa subsp. japonica cv. nipponbare were used as wild types. Arabidopsis seeds were stratified at 4 ºC for 2 day and rice seeds germinated  at 30 ºC for 2 days on dark. Seeds were sown on a 1:1 mixture of inert substrate ( 33% vermiculite +  66% turbe supplemented with 1g/L CaCO3 ) and washed dorsolite (0.6 to 1.2 mm diameter) and cultivated under a 12 h light (22 ºC and 120 µmols m-2 s-1) / 12h dark (18 ºC) cycle with relative humidity of 65% in FitoClima 1200 PLH LED cabinets (Aralab, Rio de Mouro, Portugal).

extract_protocol:
Total RNA from 18-day-old rosettes was extracted with the Maxwell® RSC Plant RNA kit (Promega, Wisconsin, USA) according to manufacturer’s indications. RNA quality and integrity was checked in gel.
RNA-Seq libraries were prepared and pair-end sequenced (2x150 bp) at Sistemas Genómicos (València, Spain) with standard Illumina protocols.

treatment_protocol: Plants were regularly irrigated with 1/10 Hoagland media adapted for low (20 µM Fe-EDTA, -Fe), sufficient (20 µM Fe-EDTA, suf) and high (200 µM Fe-EDTA, +Fe) iron availability. For pathogen infections, plants were either mock treated or infected with Colletotrichum higgisianum (Arabidopsis) or Magnaporthe oryzae (rice) suspensions at 10^6 or 10^5 spores/mL, respectively.

value: shoots

tag: cultivar

value: Nipponbare

value: inf +Fe


title: G0_Acss2KO_rep1_63 (ACSS2 dataset)


title: Os infected +Fe 2

description: replicate 2


title: G14.5_p300KO_rep1_30 (ACSS2 dataset)


title: Leaves from plants pretreated with the water for 5 days [W5_4]

description: Gene expression data of W5_4

value: Water pretreatment for 5 days


title: G0_Acss2KO_rep1_64 (ACSS2 dataset)


title: Os infected +Fe 1

description: replicate 1


title: G0_Acss2KO_rep1_62 (ACSS2 dataset)


title: G14.5_p300KO_rep1_31 (ACSS2 dataset)


title: G14.5_p300KO_rep1_3 (ACSS2 dataset)


title: Os infected suf 3

description: replicate 3

value: inf suf


title: G14.5_p300KO_rep1_29 (ACSS2 dataset)

value: pancreas


title: Leaves from plants pretreated with the water for 5 days [W5_3]

description: Gene expression data of W5_3


title: Leaves from plants exposed to drought stress for 6 days after treated the 1.0% ethanol for 5 days  [E5D6_1]

description: Gene expression data of E5D6_1


title: Leaves from plants pretreated with the water for 5 days [W5_1]

description: Gene expression data of W5_1


title: Leaves from plants pretreated with 1.0% ethanol for 5 days [E5_4]

description: Gene expression data of E5_4

value: Ethanol pretreatment for 5 days


title: G14.5_p300KO_rep1_27 (ACSS2 dataset)

value: Beta cell

value: female


title: G14.5_p300KO_rep1_28 (ACSS2 dataset)

value: standard diet


title: G0_Acss2KO_rep1_6 (ACSS2 dataset)

value: Acss2 knockout


title: Os infected suf 2

description: replicate 2


title: Os infected suf 1

description: replicate 1


title: G0_Acss2KO_rep1_59 (ACSS2 dataset)


title: G0_Acss2KO_rep1_60 (ACSS2 dataset)


title: G0_Acss2KO_rep1_57 (ACSS2 dataset)


title: Leaves from plants pretreated with 1.0% ethanol for 5 days [E5_3]

description: Gene expression data of E5_3


title: Os infected -Fe 3

description: replicate 3

value: inf -Fe


title: Os infected -Fe 2

description: replicate 2


title: Os infected -Fe 1

description: replicate 1


title: Leaves from plants pretreated with the water for 5 days [W5_2]

description: Gene expression data of W5_2


title: G0_Acss2KO_rep1_61 (ACSS2 dataset)


title: G0_Acss2KO_rep1_58 (ACSS2 dataset)


title: Leaves from plants pretreated with 1.0% ethanol for 5 days [E5_2]

description: Gene expression data of E5_2


title: G14.5_p300KO_rep1_26 (ACSS2 dataset)

value: p300 knockout


title: SH-SY5Y cells, TOP2B KO, WT TOP2B expressed, hypoxia rep2

description: Library name: TOP2B KO_WT TOP2B expressed rep2

data_processing:
Sequenced reads (paired-end) in FASTQ format were trimmed using Trim Galore (version 0.6.6) with Cutadapt (version 3.4) and their quality was assured using FastQC (version 0.11.9).
Quality-assured trimmed reads were then aligned to the reference genome (hg38 assembly) using STAR (version 2.7.9a) with the following parameters: --outSAMtype BAM SortedByCoordinate, --quantMode TranscriptomeSAM, and --outFilterMultimapNmax 1.
Normalized coverage profiles were generated from the aligned reads (BAM files) using bamCoverage in deepTools (version 3.5.3). The reads per kilobase per million mapped reads (RPKM) method was used for normalization. To merge replicates, bigwigCompare in deepTools was used with the mean operation to calculate the average signal across replicates.
Assembly: hg38
Supplementary files format and content: BigWig files, a binary format designed for efficient storage and visualization of genomic data, contain genome-wide coverage data normalized using the RPKM method.

source_name: SH-SY5Y cells

growth_protocol: Cell culture of SH-SY5Y cells were carried out as recommended by ATCC guidelines, maintaining the cells in DMEM-high glucose (Cytiva Hyclone, SH30243.01) and MEM alpha modification (Hyclone, SH30265.01), respectively, supplemented with 10% fetal bovine serum (FBS, Gibco) and 1% penicillin/streptomycin (P/S, Thermo Fisher). WT, TOP2B KO, and TOP2B mutant-expressing TOP2B KO cells were grown to approximately 80% confluence. For the transfection of WT or mutant TOP2B variants, SH-SY5Y cells were grown to 60–70% confluence in a complete medium.

extract_protocol:
Genomic DNA was extracted from WT, TOP2B KO, and TOP2B mutant-expressing TOP2B KO SH-SY5Y cells after TMP treatment and UV cross-linking. The cells were lysed in PBS containing 0.5% SDS, and protein digestion was performed using Proteinase K at 55°C for 1 hour. The lysates were sonicated to fragment the genomic DNA into 300–700 bp fragments. The DNA was purified through phenol-chloroform-isoamyl alcohol (PCI) extraction followed by ethanol precipitation. RNA contamination was removed using RNase A digestion, and the DNA was re-purified via PCI extraction and ethanol precipitation. To enrich for cross-linked DNA, samples underwent boiling and chilling cycles followed by E. coli exonuclease I digestion. Cross-links were reversed with 0.1 M KOH at 90°C for 30 minutes, and the DNA was neutralized using 3 M sodium acetate, pH 7.0. The resultant DNA was purified using PCR purification kit (Qiagen), visualized on agarose gels, and analyzed by next generation sequencing (NGS) and bioinformatics.
The library construction for TMP-seq was performed using the xGen ssDNA & Low-Input DNA Library Prep Kit (Integrated DNA Technologies) according to the manufacturer’s instructions. Briefly, 100 ng of single-stranded DNA (ssDNA) was sheared using adaptive focused acoustic technology (Covaris) to achieve a target fragment size of approximately 350 bp. The denatured ssDNA fragments underwent tailing and ligation with R2 stubby adapter to the 3’ end. After the initial ligation, the ssDNA was converted into double-stranded DNA through an extension process, and R1 stubby adapters were ligated to the 5' end. The indexed libraries were prepared through PCR amplification and quantified using qPCR with the KAPA Library Quantification Kit for Illumina platforms. Library quality was assessed using the Agilent Technologies 4200 TapeStation with HSD1000 ScreenTape. Paired-end sequencing was performed on the Illumina NovaSeq X platform.

treatment_protocol: CoCl2 (Cat. 60818, Sigma, USA), or H2O as the control (–CoCl2), was treated at a final concentration of 200µM for 12–24 h. For TMP-seq, trimethylpsoralen (TMP; Sigma, T6137), an intercalating agent, was added to the culture medium at a final concentration of 2 µg/mL for 10 minutes. DNA cross-linking was then performed using 360 nm ultraviolet light at a dose of 1.2 kJ/m²/min for 2 minutes. Cells were washed twice with cold PBS and scraped for subsequent DNA extraction and library preparation.

value: SH-SY5Y cells

value: Human nueronal cells

value: TOP2B knockout

value: Transfecting cells with pcDNA6.2/N-YFPDest expressing WT TOP2B, CoCl2 treatment


title: SH-SY5Y cells, TOP2B KO, TOP2B T1403A expressed, hypoxia, rep2

description: Library name: TOP2B KO_TOP2B mut 2 expressed rep2

value: Transfecting cells with pcDNA6.2/N-YFPDest expressing T1403A TOP2B, CoCl2 treatment


title: G14.5_p300KO_rep1_25 (ACSS2 dataset)


title: Leaves from plants pretreated with 1.0% ethanol for 5 days [E5_1]

description: Gene expression data of E5_1

value: Leaves


title: SH-SY5Y cells, TOP2B KO, TOP2B T1403A expressed, hypoxia, rep1

description: Library name: TOP2B KO_TOP2B mut 2 expressed rep1


title: G0_Acss2KO_rep1_56 (ACSS2 dataset)


title: G14.5_p300KO_rep1_24 (ACSS2 dataset)


title: Os mock +Fe 3

description: replicate 3

value: shoots

value: Nipponbare

value: WT

value: mock +Fe


title: G14.5_p300KO_rep1_22 (ACSS2 dataset)

value: pancreas


title: G14.5_p300KO_rep1_23 (ACSS2 dataset)

value: Beta cell


title: G0_Acss2KO_rep1_54 (ACSS2 dataset)

value: female


title: G0_Acss2KO_rep1_55 (ACSS2 dataset)

value: standard diet


title: Os mock +Fe 2

description: replicate 2


title: SH-SY5Y cells, TOP2B KO, WT TOP2B expressed, hypoxia, rep1

description: Library name: TOP2B KO_WT TOP2B expressed rep1


title: G14.5_p300KO_rep1_2 (ACSS2 dataset)


title: G14.5_p300KO_rep1_21 (ACSS2 dataset)


title: Os mock suf 2

description: replicate 2

value: mock suf


title: G0_Acss2KO_rep1_53 (ACSS2 dataset)

value: Acss2 knockout


title: G14.5_p300KO_rep1_19 (ACSS2 dataset)

value: p300 knockout


title: Os mock suf 3

description: replicate 3


title: G0_Acss2KO_rep1_52 (ACSS2 dataset)


title: Os mock +Fe 1

description: replicate 1


title: G14.5_p300KO_rep1_20 (ACSS2 dataset)


title: G14.5_p300KO_rep1_18 (ACSS2 dataset)


title: SH-SY5Y cells, WT, rep2

description: Library name: WT rep2

value: SH-SY5Y cells

value: H2O treatment


title: SH-SY5Y cells, TOP2B KO, hypoxia, rep2

description: Library name: TOP2B KO hypoxia rep2

value: Human nueronal cells

value: TOP2B knockout

value: CoCl2 treatment


title: SH-SY5Y cells, TOP2B KO, rep2

description: Library name: TOP2B KO rep2


title: G0_Acss2KO_rep1_51 (ACSS2 dataset)


title: G0_Acss2KO_rep1_50 (ACSS2 dataset)


title: SH-SY5Y cells, TOP2B KO, hypoxia, rep1

description: Library name: TOP2B KO hypoxia rep1


title: SH-SY5Y cells, WT, hypoxia, rep2

description: Library name: WT hypoxia rep2


title: Os mock suf 1

description: replicate 1


title: SH-SY5Y cells, TOP2B KO, rep1

description: Library name: TOP2B KO rep1


title: Os mock -Fe 1

description: replicate 1

value: mock -Fe


title: G14.5_p300KO_rep1_17 (ACSS2 dataset)


title: G0_Acss2KO_rep1_49 (ACSS2 dataset)


title: G14.5_p300KO_rep1_16 (ACSS2 dataset)


title: Os mock -Fe 2

description: replicate 2

value: shoots


title: SH-SY5Y cells, WT, hypoxia, rep1

description: Library name: WT hypoxia rep1


title: G0_Acss2KO_rep1_48 (ACSS2 dataset)


title: Ath infected +Fe 3

description: replicate 3

organism: Arabidopsis thaliana

tag: ecotype

value: inf +Fe


title: G0_Acss2KO_rep1_47 (ACSS2 dataset)


title: G14.5_p300KO_rep1_15 (ACSS2 dataset)


title: G14.5_p300KO_rep1_14 (ACSS2 dataset)


title: Os mock -Fe 3

description: replicate 3

value: Nipponbare

value: WT


title: Ath infected +Fe 2

description: replicate 2


title: SH-SY5Y cells, WT, rep1

description: Library name: WT rep1


title: CTC, M3, LPS, 6 h

city: Manila

first: Ryan

last: Lintao

address: 547 Pedro Gil Street

department: College of Medicine

country: Philippines

institute: University of the Philippines Manila

description: Library name: M3_LPS_6

data_processing:
Data cleaned via cutadapt, LC Sciences in house perl script, quality verigied using FastQC
Reads mapped to the genome via HISAT2
Mapped reads of each sample assembled using StringTie
All assemblies merged using perl scripts and gffcompare
mRNA expression profiling via StringTie
Assembly: GRCh38.p9
Supplementary files format and content: Spreadsheet files includes raw and normalized counts per sample

molecule: polyA RNA

extract_protocol:
RNeasy Mini Plus kit (Qiagen)
Illumina TruSeq-stranded-mRNA sample preparation

value: Immortalized chorion trophoblast cells from term not in labor placenta

value: wild-type

value: male

value: LPS

tag: treatment duration_(h)


title: CTC, M2, LPS, 6 h

description: Library name: M2_LPS_6


title: Ath infected +Fe 1

description: replicate 1


title: G14.5_p300KO_rep1_12 (ACSS2 dataset)

value: pancreas

value: Beta cell

value: female

value: standard diet


title: G0_Acss2KO_rep1_44 (ACSS2 dataset)

value: Acss2 knockout


title: Ath infected suf 3

description: replicate 3

value: inf suf


title: G14.5_p300KO_rep1_13 (ACSS2 dataset)

value: p300 knockout


title: G0_Acss2KO_rep1_5 (ACSS2 dataset)


title: G0_Acss2KO_rep1_45 (ACSS2 dataset)


title: CTC, M3, LPS, 24 h

description: Library name: M3_LPS_24


title: G0_Acss2KO_rep1_42 (ACSS2 dataset)


title: Ath infected suf 2

description: replicate 2


title: Ath infected suf 1

description: replicate 1


title: G14.5_p300KO_rep1_114 (ACSS2 dataset)


title: G0_Acss2KO_rep1_43 (ACSS2 dataset)


title: G14.5_p300KO_rep1_115 (ACSS2 dataset)


title: Ath infected -Fe 3

description: replicate 3

value: inf -Fe


title: CTC, M2, LPS, 24 h

description: Library name: M2_LPS_24


title: G14.5_p300KO_rep1_113 (ACSS2 dataset)


title: G0_Acss2KO_rep1_41 (ACSS2 dataset)


title: Ath infected -Fe 2

description: replicate 2


title: G14.5_p300KO_rep1_112 (ACSS2 dataset)


title: CTC, M3, control, 6 h

description: Library name: M3_ctrl_6

value: control


title: Ath infected -Fe 1

description: replicate 1

value: shoots


title: CTC, M2, control, 6 h

description: Library name: M2_ctrl_6


title: CTC, M1, LPS, 6 h

description: Library name: M1_LPS_6


title: Ath mock +Fe 3

description: replicate 3

value: mock +Fe


title: G14.5_p300KO_rep1_110 (ACSS2 dataset)


title: G0_Acss2KO_rep1_39 (ACSS2 dataset)


title: CTC, M1, control, 6 h

description: Library name: M1_ctrl_6


title: G0_Acss2KO_rep1_38 (ACSS2 dataset)


title: G0_Acss2KO_rep1_46 (ACSS2 dataset)


title: G14.5_p300KO_rep1_11 (ACSS2 dataset)


title: Ath mock +Fe 2

description: replicate 2


title: Ath mock +Fe 1

description: replicate 1


title: G14.5_p300KO_rep1_109 (ACSS2 dataset)


title: CTC, M2, control, 24 h

description: Library name: M2_ctrl_24


title: G0_Acss2KO_rep1_37 (ACSS2 dataset)


title: G0_Acss2KO_rep1_40 (ACSS2 dataset)


title: CTC, M1, LPS, 24 h

description: Library name: M1_LPS_24


title: Ath mock suf 3

description: replicate 3

value: mock suf


title: G14.5_p300KO_rep1_108 (ACSS2 dataset)


title: G0_Acss2KO_rep1_36 (ACSS2 dataset)


title: G14.5_p300KO_rep1_111 (ACSS2 dataset)


title: G0_Acss2KO_rep1_35 (ACSS2 dataset)


title: G14.5_p300KO_rep1_107 (ACSS2 dataset)


title: CTC, F3, LPS, 6 h

description: Library name: F3_LPS_6


title: G0_Acss2KO_rep1_4 (ACSS2 dataset)


title: G14.5_p300KO_rep1_106 (ACSS2 dataset)


title: Ath mock suf 1

description: replicate 1

value: WT


title: G0_Acss2KO_rep1_34 (ACSS2 dataset)


title: CTC, M3, control, 24 h

description: Library name: M3_ctrl_24

value: Immortalized chorion trophoblast cells from term not in labor placenta


title: Ath mock -Fe 3

description: replicate 3

value: mock -Fe


title: G0_Acss2KO_rep1_33 (ACSS2 dataset)


title: G14.5_p300KO_rep1_104 (ACSS2 dataset)


title: G0_Acss2KO_rep1_32 (ACSS2 dataset)


title: G14.5_p300KO_rep1_105 (ACSS2 dataset)


title: CTC, F1, LPS, 6 h

description: Library name: F1_LPS_6

value: wild-type


title: G14.5_p300KO_rep1_103 (ACSS2 dataset)


title: CTC, M1, control, 24 h

description: Library name: M1_ctrl_24

value: male


title: CTC, F2, LPS, 24 h

description: Library name: F2_LPS_24

value: LPS


title: Ath mock -Fe 1

description: replicate 1


title: Ath mock suf 2

description: replicate 2


title: Control RNA (Smart-Seq v4 Ultra Low Input RNA Kit)

city: Dunedin

first: Michael

last: Pankhurst

state: Otago

address: 270 Great King St

department: Department of Anatomy

country: New Zealand

institute: University of Otago

description: Library name: RNA control

data_processing:
FASTQ sequencing files were trimmed with Trim Galore, followed by FASTQC quality control checks
Trimmed reads were mapped with HISAT2
Assembly: mouse reference genome GRCm39 (mm39)
Supplementary files format and content: .csv file with log2 transformed RPKM values

extract_protocol:
Denuded oocytes were pipetted into 10.5 µL of Lysis buffer from the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio). Performed under a stero microscope to confirm lysis of the oocyte occurred. Amplification was performed according to manufacturer instructions.
Libraries were prepared with the ThruPLEX® DNA-seq Kit (Rubicon Genomics) according to manufacturer instructions

treatment_protocol: Adult female mice underwent daily vaginal lavage to determine the day of ovulation. Cumulus oocyte complexes were dissected from oviducts. Cumulus cells were removed with hyaluronidase and the zona pellucida was removed with Acid Tyrode's solution.

tag: batch

value: Sequencing Lane 4


title: Negative control (water-only control)

description: Library name: Negative control


title: CTC, F1, LPS, 24 h

description: Library name: F1_LPS_24

value: female


title: G0_Acss2KO_rep1_30 (ACSS2 dataset)

value: pancreas

value: Beta cell

value: standard diet


title: Wild-type female 12138, Oocyte B

description: Library name: 22_12138_12138B_Neg

source_name: Ovary

value: Ovary

value: Thy1.2-AMH0/0 mouse

value: Oocyte

value: Wild-type (Thy1.2-AMH0/0)

value: Naturally ovulated


title: G14.5_p300KO_rep1_102 (ACSS2 dataset)

value: p300 knockout


title: G0_Acss2KO_rep1_3 (ACSS2 dataset)

value: Acss2 knockout


title: CTC, F3, control, 6 h

description: Library name: F3_ctrl_6

value: Immortalized chorion trophoblast cells from term not in labor placenta

value: control


title: CTC, F2, LPS, 6 h

description: Library name: F2_LPS_6

value: wild-type


title: G14.5_p300KO_rep1_100 (ACSS2 dataset)


title: CTC, F2, control, 6 h

description: Library name: F2_ctrl_6


title: G0_Acss2KO_rep1_29 (ACSS2 dataset)


title: Wild-type female 12138, Oocyte A

description: Library name: 21_12138_12138A_Neg


title: G0_Acss2KO_rep1_28 (ACSS2 dataset)


title: G14.5_p300KO_rep1_10 (ACSS2 dataset)


title: CTC, F1, control, 6 h

description: Library name: F1_ctrl_6


title: Transgenic (AMH-overexpressing) female 12136, Oocyte B

description: Library name: 20_12136_12136B_Tg

value: Thy1.2-AMHTg/0 mouse


title: G0_Acss2KO_rep1_27 (ACSS2 dataset)


title: G0_Acss2KO_rep1_31 (ACSS2 dataset)


title: G14.5_p300KO_rep1_101 (ACSS2 dataset)


title: G0_Acss2KO_rep1_26 (ACSS2 dataset)


title: Wild-type female 12142, Oocyte B

description: Library name: 17_12142_12142B_Neg

value: Sequencing Lane 3


title: mixed sample of MOC1 shNT with doxycycline and MOC1 shKmt2d with doxycyclin [NTdox_KDdox]

city: Madison

first: Scot

middle: Carson

last: Callahan

state: WI

address: 600 highland ave

country: USA

institute: UW Health

data_processing:
Reads were initially trimmed to 75bp by Novogene for compatibility with the manufacturer-provided pipeline. Reads were then aligned to GRCm38 and further processed using the manufacturer-provided WTA processing pipeline.
Cells, having less than 200 unique genes, were filtered.  Low-quality cells, where >10% of the counts were derived from the mitochondrial genome, were also discarded. Cells with detected genes >5000 were discarded to remove likely doublet or multiplet captures.
SCTransform normalization was performed on the remaining high-quality gene matrix. The Uniform Manifold Approximation and Projection (UMAP) was used for dimensionality reduction and 2-D visualization of the single-cell.
Genome_build: GRCm38
Supplementary_files_format_and_content: 2 comma-delimited text files: counts-per-gene and sample tags

source_name: MOC1 tumor

growth_protocol: The MOC1 cell line was cultured in a 2:1 mixture of IMDM and Ham’s F-12 nutrient mixture supplemented with 5% Tet-free FBS, 1% penicillin-streptomycin, 2.5mg insulin, 20µg hydrocortisone, and 2.5µg EGF. HEK293T cells (ATCC® CRL-3216™) were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin. All cell lines were cultured at 37 °C in an atmosphere of 5% CO2

extract_protocol: RNA was extracted and libraries prepared using the BD Rhapsody™ Whole Transcriptome Analysis (WTA) Amplification Kit per manufacturer instructions.

treatment_protocol: Knockdown experiments for the mouse MOC1 cell line were done using the SMARTvector Inducible Lentiviral shRNA system from Horizon Discovery: V3SM11253-233092640 (sh-KMT2D) and VSC11658 (sh-nontargeting). All shRNA vectors were packaged into lentivirus using HEK293T cells and transduced into target cells using 8ug/ml polybrene. After transduction, cells were selected using 1.5 ug/ml puromycin for 72 hours. To induce mouse oral cavity tumor, doxycycline inducible shKMT2D knockdown and shNT MOC1 cell lines were implanted into the tongue with subsequent supplementation of doxycycline containing water (2 mg/mL).

value: MOC1 orthotopic tumor

value: shNT or shKmt2d

value: doxycycline


title: Ath mock -Fe 2

description: replicate 2

value: shoots

value: WT

value: mock -Fe


title: CTC, F1, control, 24 h

description: Library name: F1_ctrl_24

value: female


title: CTC, F3, LPS, 24 h

description: Library name: F3_LPS_24

value: LPS


title: G14.5_p300KO_rep1_1 (ACSS2 dataset)

value: pancreas

value: Beta cell

value: standard diet


title: Wild-type female 12142, Oocyte A

description: Library name: 16_12142_12142A_Neg

value: Ovary

value: Thy1.2-AMH0/0 mouse

value: Oocyte

value: Wild-type (Thy1.2-AMH0/0)

value: Naturally ovulated


title: CTC, F3, control, 24 h

description: Library name: F3_ctrl_24

value: Immortalized chorion trophoblast cells from term not in labor placenta

value: wild-type

value: control


title: UIR_3w biological replicate 2

city: Nanjing

first: Mengqiu

last: Wu

address: Children’s Hospital of Nanjing Medical University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set then expression level of gene was calculated by RSEM (v1.2.12)
Genome_build: mm9
Supplementary_files_format_and_content: xls, include FPKM values for each Sample

source_name: kidney

extract_protocol:
Kidney tissues were harvested and rapidly frozen in liquid nitrogen. Total RNA was extracted from the tissues using Trizol (Invitrogen) according to the instruction manual.
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).

treatment_protocol: C57BL/6 mice were anesthetized using isoflurane. UIR was induced by clamping the right renal pedicle for 45 minutes and then releasing it to allow reperfusion, leaving the left kidney intact. Sham treated mice served as controls. Each mouse was located supine on a thermostatic pad (37 °C) to maintain its body temperature throughout the whole process. Mice were sacrificed at 1 day, 3 days and 21 days after surgery.

value: kidney

tag: age

value: post natal week 11

value: UIR after 3 weeks


title: UIR_3w biological replicate 1

institute: Children’s Hospital of Nanjing Medical University


title: CTC, F2, control, 24 h

description: Library name: F2_ctrl_24


title: UIR_3d biological replicate 3

value: UIR after 3 days


title: Transgenic (AMH-overexpressing) female 12007, Oocyte C

description: Library name: 15_12007_12007C_Tg

value: Thy1.2-AMHTg/0 mouse

value: Sequencing Lane 3


title: G0_Acss2KO_rep1_22 (ACSS2 dataset)

value: pancreas

value: female

value: Acss2 knockout


title: UIR_3w biological replicate 3


title: IZ/ACP organoids from hiPSCs rep2

description: Library name: 4-A11-S3PD-2wk

data_processing:
Sequencing was performed using NovaSeq 6000 (Illumina) with a pair-read sequencing length of 150 bp. All sequence reads were extracted in FASTQ format using the CASAVA 1.8.4 pipeline. Fastp (v0.23.4) was used to remove adapters and filter raw reads with < 60 bases in addition to leading and trailing bases with a read quality of less than 30. For pseudoalignment of the filtered reads to GRCh38, Kallisto (v0.48.0) was used. GeTMM normalization was performed using edgeR (v4.0.3) to account for sample variation. Differentially expressed genes were identified by NOISeq (v2.46.0) analysis with a threshold of p > 0.8 and abs(Log2FC) > 1.
Assembly: GRCh38
Supplementary files format and content: tsv of normalized counts

extract_protocol:
Total RNA was extracted using a RNeasy Mini Kit (QIAGEN)
Sequencing libraries were prepared using a KAPA RNA HyperPrep Kit with RiboErase (HMR) (Nippon Genetics) and a SeqCap Adapter Kit (Set A or Set B) (Roche) following the manufacturers’ instructions.

value: IZ/ACP organoids from hiPSCs


title: G0_Acss2KO_rep1_24 (ACSS2 dataset)

extract_protocol:
Pancreatic tissue was perfused with 0.5mg/mL collagenase P (Roche, 11213873001) dissolved in 1×HBSS buffer containing 10mM HEPES (pH 7.4), 1mM MgCl2 and 5mM glucose. Digestion was terminated by adding cold PBS. Islets were manually picked up and dissociated into single cell suspension with 0.25% trypsin (Thermo Fisher Scientific, 25200114) and incubated for 3-5min at 37℃. Fetal bovine serum (FBS) was used to terminate the digestion (40% vol/vol). After centrifugation at 1000rpm for 5min at 4℃, the supernatant was removed and the cell pellet was resuspended with HBSS buffer. Cells were directly sorted using a BD Aria SORP flow cytometer.
Smart-seq3xpress scRNA-seq was performed following a published procedure. Briefly, single cells were sorted into 384-well plates containing 0.3μL lysis. The mRNA was reverse transcribed into cDNA using 0.1μL dispensed RT mix. The libraries were constructed using TruePrep DNA Library Prep Kit (Vazyme, TD501).
10x Genomics scRNA-seq library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
smart-seq3xpress scRNA-seq,10x Genomics scRNA-seq

value: Beta cell

value: standard diet


title: G0_Acss2KO_rep1_23 (ACSS2 dataset)


title: Transgenic (AMH-overexpressing) female 12007, Oocyte B

description: Library name: 14_12007_12007B_Tg

value: Ovary

value: Oocyte


title: GPC organoids from hiPSCs rep2

description: Library name: 414C2-8-Step3B10T10-2wk-A3

value: GPC organoids from hiPSCs


title: Transgenic (AMH-overexpressing) female 12136, Oocyte A

description: Library name: 19_12136_12136A_Tg

value: Naturally ovulated

value: Sequencing Lane 4


title: IZ/ACP organoids from hiPSCs rep1

description: Library name: 3-A10-S3PD-2wk


title: Transgenic (AMH-overexpressing) female 12007, Oocyte A

description: Library name: 13_12007_12007A_Tg


title: UIR_3d biological replicate 1

value: kidney


title: G0_Acss2KO_rep1_21 (ACSS2 dataset)


title: UIR_3d biological replicate 2

value: post natal week 11


title: Wild-type female 12010, Oocyte C

description: Library name: 12_12010_12010C_Neg

value: Thy1.2-AMH0/0 mouse

value: Wild-type (Thy1.2-AMH0/0)

value: Sequencing Lane 2


title: UIR_1d biological replicate 3

value: UIR after 1 day


title: G0_Acss2KO_rep1_25 (ACSS2 dataset)

value: pancreas


title: Wild-type female 12010, Oocyte B

description: Library name: 11_12010_12010B_Neg


title: GPC organoids from hiPSCs rep1

description: Library name: 414C2-8-Step3B10T10-2wk-A1


title: G0_Acss2KO_rep1_20 (ACSS2 dataset)

value: female


title: G0_Acss2KO_rep1_2 (ACSS2 dataset)

value: Acss2 knockout


title: JWH214-C16PlusHudep-1963140

data_processing:
For ATAC-seq, reads were trimmed for Nextera adapter by cutadapt (version 1.9, paired-end mode, default parameter with “ -m 6 -O 20 ”) and aligned to human genome hg19 (GRCh37-lite) by BWA (version 0.7.12-r1039, default parameter).
The duplicated reads were then marked with biobambam2 (v2.0.87) and only non-duplicated proper paired reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2). After removing mitochondrial DNA reads, the rest of reads were classified into four groups including nucleosome free, mono-, di-, and tri-nucleosome by fragment size. The bigwig files were generated using the center 80-bp of fragments and scaled to 20 million nucleosome free reads.
We observed reasonable nucleosome free peaks and pattern of mono-, di-, tri-nucleosome peaks surrounding nucleosome free peaks on IGV.
All samples exhibited twice of ENCODE criterion. Therefore, we concluded the data show enough depth. Given all samples exhibited more than 20 million nucleosome free fragments after merging replicates, we are confidence most strong nucleosome free regions won’t be missed.
Assembly: hg19
Supplementary files format and content: bigWig files

extract_protocol: not provided

value: IAA

tag: clone


title: Wild-type female 12010, Oocyte A

description: Library name: 10_12010_12010A_Neg


title: JWH213-C16MinusHudep-1963139


title: UIR_1d biological replicate 2


title: JWH211-C3MinusHudep-1963137


title: cloneC3withIAAundiff

description: hic_merge_cloneC16_C3withIAAundiff.inter_30.hic

data_processing:
Raw sequence data were mapped and processed using Juicer v1.5 with default parameters.
The Hi-C data and MboI cut sites were mapped to hg19.
Replicates data were first processed separately. After confirmation of good reproducibility by HiC-Spector, we merged the replicates and re-processed as combined results. The data were visualized with the Juicebox.
Assembly: hg19
Supplementary files format and content: hic files

tag: differentiation status

value: Not


title: JWH212-C3PlusHudep-1963138


title: G0_Acss2KO_rep1_18 (ACSS2 dataset)

description:
pancreatic Beta cell, G0Acss2KO, biol rep1, scRNAseq
scRNA-seq
Smart-seq3xpress

data_processing:
For smart-seq3xpress scRNA-seq, the index, primer and adaptor sequences in the paired-end reads were trimmed with Trimmomatic (v0.39). The trimmed reads were aligned to the Mus musculus reference genome (GRCm38/mm10) using Hisat242 (V2.1.0) with the default parameters. The reads were assigned to genes using featureCounts (v2.0.1) with default parameters.
For 10x Genomics scRNA-seq, the demultiplexing, barcoded processing, gene counting and aggregation were made using the Cellranger toolkit (v3.1.0; https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) with default settings
Assembly: mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Smart-seq3xpress output files: Tab-separated rexpression values matrix files

tag: tissue

value: Beta cell

value: standard diet


title: G0_Acss2KO_rep1_17 (ACSS2 dataset)

tag: cell type


title: Sham_3w biological replicate 3

tag: strain

value: Sham after 3 weeks


title: Transgenic (AMH-overexpressing) female 10238, Oocyte C

description: Library name: 09_12038_12038C_Tg

value: Ovary

value: Thy1.2-AMHTg/0 mouse

value: Oocyte


title: Transgenic (AMH-overexpressing) female 10238, Oocyte B

description: Library name: 08_12038_12038B_Tg

value: Naturally ovulated


title: Sham_3w biological replicate 2

value: kidney

value: post natal week 11


title: Transgenic (AMH-overexpressing) female 10238, Oocyte A

description: Library name: 07_12038_12038A_Tg


title: Sham_3w biological replicate 1


title: cloneC3noIAAundiff

description: hic_merge_cloneC16_C3noIAAundiff.inter_30.hic


title: G0_Acss2KO_rep1_16 (ACSS2 dataset)

tag: Sex


title: G0_Acss2KO_rep1_15 (ACSS2 dataset)

tag: diet


title: G0_Acss2KO_rep1_19 (ACSS2 dataset)

tag: genotype


title: cloneC3withIAAdiff

description: hic_merge_cloneC16_C3withIAAdiff.inter_30.hic

tag: cell line

value: Erythroid differentiation


title: Wild-type female 12009, Oocyte C

description: Library name: 06_12009_12009C_Neg

value: Thy1.2-AMH0/0 mouse

value: Wild-type (Thy1.2-AMH0/0)

tag: treatment

value: Sequencing Lane 1


title: G0_Acss2KO_rep1_14 (ACSS2 dataset)

value: pancreas

value: female


title: Sham_3d biological replicate 3

value: Sham after 3 days


title: cloneC16withIAAundiff

value: IAA

value: Not


title: Sham_3d biological replicate 2


title: cloneC3noIAAdiff

description: hic_merge_cloneC16_C3noIAAdiff.inter_30.hic


title: Wild-type female 12142, Oocyte C

description: Library name: 18_12142_12142C_Neg

value: Sequencing Lane 3


title: G0_Acss2KO_rep1_13 (ACSS2 dataset)

value: Beta cell

value: standard diet

value: Acss2 knockout


title: Wild-type female 12009, Oocyte B

description: Library name: 05_12009_12009B_Neg

value: Ovary

value: Oocyte


title: UIR_1d biological replicate 1

value: kidney

value: UIR after 1 day


title: G0_Acss2KO_rep1_12 (ACSS2 dataset)


title: Wild-type female 12009, Oocyte A

description: Library name: 04_12009_12009A_Neg

value: Naturally ovulated


title: cloneC16withIAAdiff

value: Erythroid differentiation


title: cloneC16noIAAundiff


title: Transgenic (AMH-overexpressing) female 10237, Oocyte B

description: Library name: 02_12037_10237B_Tg

value: Thy1.2-AMHTg/0 mouse


title: Sham_1d biological replicate 3

value: post natal week 11

value: Sham after 1 day


title: G0_Acss2KO_rep1_10 (ACSS2 dataset)

value: pancreas

value: female


title: G0_Acss2KO_rep1_11 (ACSS2 dataset)


title: Sham_1d biological replicate 2


title: Transgenic (AMH-overexpressing) female 10237, Oocyte A

description: Library name: 01_12037_10237A_Tg

value: Sequencing Lane 1


title: cloneC16noIAAdiff


title: G0_Acss2KO_rep1_1 (ACSS2 dataset)


title: explant_20dcvc_m_p8_38

status: Public on Jan 25 2025

city: San Diego

first: Elana

middle: R

last: Elkin

state: CA

address: 5500 Campanile Drive

department: School of Public Health

institute: San Diego State University

description: Library name: Sample_38

data_processing:
Reads were aligned to the human genome using STAR, with the options "outFilterMultimapNmax 10" and "sjdbScore 2".
Aligned reads were assigned to GRCh38 genes using featureCounts.
Genes with mean read counts-per-million less than four across all samples were filtered out and excluded from the analysis.
Gene counts were normalized for each sample using the counts() function in the DESeq2 R package
Differential gene expression testing was performed using the DESeq2 R package statistical computing which uses a negative binomial statistical model
Assembly: hg38
Supplementary files format and content: txt files

source_name: placenta villous explants

growth_protocol: Cells were cultured between passages 78–84 in RPMI 1640 medium supplemented with 10% FBS and 1% P/S at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
miRNeasy Mini Kit
Stranded sequencing libraries for HTR-8/SVneo cells were prepared using the TruSeq Stranded mRNA Library Prep Kit with poly A enrichment (Illumina).

treatment_protocol: Two or three individual placental cotyledons at varying distances from the umbilical cord were randomly selected and dissected, and non-villous placental tissue was cut away. The remaining villous placental tissue from the cotyledon was repeatedly washed in PBS to remove excess blood and cut into multiple samples weighing approximately 5-8 mg each, such that each well in a 6-well plate would receive around 30 mg of tissue. 30 mg isolated villous tissue was incubated for 24 hours at 37 degrees Celsius at 5% CO2 in 0 μM, 10 μM, or 20 μM concentration of either DCVC or TCVC dissolved in cell culture media (RPMI 1640 with 10% FBS and pen/strep) per well in a 6-well plate

value: placenta villous explants

tag: trimester

value: third

tag: placenta id_number

value: Male

tag: exposure time

value: 24 hours

value: 20 µM DCVC


title: explant_10dcvc_m_p8_37

description: Library name: Sample_37

value: 10 µM DCVC


title: explant_control_m_p8_36

description: Library name: Sample_36

value: Control


title: Sham_3d biological replicate 1

value: kidney

value: Sham after 3 days


title: explant_20tcvc_f_p7_35

description: Library name: Sample_35

value: Female

value: 20 µM TCVC


title: explant_10tcvc_f_p7_34

description: Library name: Sample_34

value: 10 µM TCVC


title: explant_20dcvc_f_p7_33

description: Library name: Sample_33


title: explant_10dcvc_f_p7_32

description: Library name: Sample_32


title: explant_20tcvc_m_p6_30

description: Library name: Sample_30


title: Sham_1d biological replicate 1

value: post natal week 11


title: explant_10tcvc_m_p6_29

description: Library name: Sample_29


title: explant_control_f_p7_31

description: Library name: Sample_31


title: explant_10dcvc_m_p6_27

description: Library name: Sample_27


title: explant_20dcvc_m_p6_28

description: Library name: Sample_28


title: explant_20tcvc_m_p5_25

description: Library name: Sample_25


title: Transgenic (AMH-overexpressing) female 10237, Oocyte C

description: Library name: 03_12037_10237C_Tg

value: Ovary

value: Thy1.2-AMHTg/0 mouse

value: Oocyte

value: Naturally ovulated


title: explant_20dcvc_m_p5_23

description: Library name: Sample_23

value: placenta villous explants


title: explant_control_m_p6_26

description: Library name: Sample_26

value: third


title: explant_control_m_p5_21

description: Library name: Sample_21

value: Male


title: explant_10dcvc_m_p5_22

description: Library name: Sample_22

value: 24 hours


title: explant_20dcvc_f_p4_18

description: Library name: Sample_18

value: 20 µM DCVC


title: explant_10dcvc_f_p4_17

description: Library name: Sample_17

value: 10 µM DCVC


title: explant_20tcvc_f_p4_20

description: Library name: Sample_20


title: explant_10tcvc_m_p8_39

description: Library name: Sample_39


title: explant_20tcvc_m_p8_40

description: Library name: Sample_40


title: explant_control_f_p4_16

description: Library name: Sample_16

value: Control


title: explant_20tcvc_f_p3_15

description: Library name: Sample_15


title: explant_10tcvc_m_p2_9

description: Library name: Sample_9


title: explant_control_m_p2_6

description: Library name: Sample_6


title: explant_10dcvc_f_p3_12

description: Library name: Sample_12


title: explant_20dcvc_f_p3_13

description: Library name: Sample_13


title: explant_20tcvc_f_p1_5

description: Library name: Sample_5


title: explant_10dcvc_m_p2_7

description: Library name: Sample_7


title: explant_10tcvc_f_p1_4

description: Library name: Sample_4


title: explant_20dcvc_f_p1_3

description: Library name: Sample_3


title: Evaluation of the editing specificity of hpAsCas12f1 in the MCF7 cells, repeat 3

city: Guangzhou

first: Kechen

last: Chen

state: Guangdong

address: Shatai South Road

institute: Southern Medical University

description: Library name: hpAsCas12f1_Tag-seq_Rep3

data_processing:
The analysis pipeline can be accessed at https://github.com/zhoujj2013/Tag-seq
Assembly: hg38
Supplementary files format and content: Bed file for all cutting sites

source_name: MCF7 cell line

growth_protocol: MCF7 cells were maintained inRPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
The MCF7 transfected cells were washed with 1x PBS, and harvested. The gDNA purified using the TIANamp Genomic DNA Kit.
The gDNA was fragmented, end-repaired, and ligated by dA-tail.

treatment_protocol: In 24-well plates, MCF7 cells were transfected with 490ng gRNA plasmids and 10ng CasMINI or hpCasMINI or SpCas9 or LbCas12a plasmids.

value: MCF7 cell line

value: epithelial cell


title: explant_control_f_p3_11

description: Library name: Sample_11

value: Female


title: explant_10dcvc_f_p1_2

description: Library name: Sample_2


title: explant_20dcvc_m_p2_8

description: Library name: Sample_8


title: Evaluation of the editing specificity of hpAsCas12f1 in the MCF7 cells, repeat 1

description: Library name: hpAsCas12f1_Tag-seq_Rep1


title: explant_10tcvc_f_p3_14

description: Library name: Sample_14


title: explant_20tcvc_m_p2_10

description: Library name: Sample_10

value: 20 µM TCVC


title: explant_control_f_p1_1

description: Library name: Sample_1


title: The DNA cleavage efficiency in the MCF7 cells transfected without the AsCas12f1 or hpAsCas12f1 system, repeat 3

description: Library name: Ctrl_Deep-seq_AsCas12f1_Rep3

data_processing:
Raw paired-end reads were subjected to sublibrary barcode removal (first 6 bp) using cutadapt.
Reads were then aligned to their respective reference sequences using Bowtie 2.
Editing events were quantified using CRISPResso2.
Assembly: hg38
Supplementary files format and content: txt file for deletion rate around the gRNA target sites.
Supplementary files format and content: txt file for indel rate for gRNA taget sites.

extract_protocol:
The MCF7 transfected cells were washed with 1x PBS, and harvested. The gDNA purified using the TIANamp Genomic DNA Kit.
Two round PCR were performed, the forward and reverse primers were used to amplify the target site of the first round of PCR, and then an equal amount of the first PCR product was mixed with primers containing P5 and p7 for a second round of PCR to generate the library.


title: Evaluation of the editing specificity of AsCas12f1 in the MCF7 cells, repeat 2

description: Library name: AsCas12f1_Tag-seq_Rep2


title: Evaluation of the editing specificity of hpAsCas12f1 in the MCF7 cells, repeat 2

description: Library name: hpAsCas12f1_Tag-seq_Rep2


title: The DNA cleavage efficiency in the MCF7 cells transfected without the AsCas12f1 or hpAsCas12f1 system, repeat 2

description: Library name: Ctrl_Deep-seq_AsCas12f1_Rep2


title: The DNA cleavage efficiency in the MCF7 cells transfected without the AsCas12f1 or hpAsCas12f1 system, repeat 1

description: Library name: Ctrl_Deep-seq_AsCas12f1_Rep1


title: Evaluation of the editing specificity of AsCas12f1 in the MCF7 cells, repeat 1

description: Library name: AsCas12f1_Tag-seq_Rep1


title: explant_10tcvc_f_p4_19

description: Library name: Sample_19

value: 10 µM TCVC


title: explant_10tcvc_m_p5_24

description: Library name: Sample_24


title: The DNA cleavage efficiency in the MCF7 cells transfected with the hpAsCas12f1 system, repeat 2

description: Library name: hpAsCas12f1_Deep-seq_Rep2


title: The DNA cleavage efficiency in the MCF7 cells transfected with the AsCas12f1 system, repeat 3

description: Library name: AsCas12f1_Deep-seq_Rep3


title: The DNA cleavage efficiency in the MCF7 cells transfected with the AsCas12f1 system, repeat 2

description: Library name: AsCas12f1_Deep-seq_Rep2


title: The DNA cleavage efficiency in the MCF7 cells transfected with the hpAsCas12f1 system, repeat 1

description: Library name: hpAsCas12f1_Deep-seq_Rep1


title: Evaluation of the editing specificity of AsCas12f1 in the MCF7 cells, repeat 3

description: Library name: AsCas12f1_Tag-seq_Rep3


title: The DNA cleavage efficiency in the MCF7 cells transfected with the AsCas12f1 system, repeat 1

description: Library name: AsCas12f1_Deep-seq_Rep1


title: RNA-seq - LIS1+/- MMP9 Treated organoid day 18, repeat #3

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

data_processing:
True SEQ Long RNA libraries were trimmed from their adapter with cutadapt and aligned to hg38 with STAR v2.5.2b
DEseq2 was applied to test for the differential expression between the conditions.
smallRNA libraries were also trimmed from the adapter with cutadapt, and ligned to the genome with STAR
using outFilterMatchNmin=16, alignSJDBoverhangMin=1000, alignIntronMax=1, alignEndsType EndToEnd, and outFilterMismatchNmax 3
The number of read count per gene was calculated with bedtools. The read count for mirRNAs that appear more than once in the genome was divided by the number of their copies in the genome.
Assembly: hg38
Supplementary files format and content: Supplementary_Table_2_RNAseq_CorticOs_D_105.xlsx,Supplementary_Table_3_SmallRNAseq_CorticOs_D105.xlsx,Supplementary_Table_5_RNAseq_brainOs_D_18_mmp9_treat.xlsx
Supplementary files format and content: raw read counts, normalized read count, DEseq2 statistics

source_name: Brain organoid

growth_protocol: hESCs were cultured in naïve media and then dissociated and aggregated in V-shaped low-adhesion wells. Days 0 -17: Dulbecco's Modified Eagle's Medium (DMEM), 20% KSR, 1mM sodium pyruvate, 0.1mM beta-mercaptoethanol, non-essential amino acids (NEAA) and Perstrep. 3uM SB-431542 and 5uM IWR-1 were freshly added. Days 18-35: aggregates moved to 10cm bacterial plates. The media used was DMEM-F12, Penstrep, Glutamax, and chemically defined lipid concentrate (CDLC). Days 35-70: B27 without vitamin A, 5ug/ml heparin, and N2 supplement were added to the media. Media was changed once in three days

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep Plus kit (Zymo Research) following the manufacturer's protocols
Libraries were prepared using TrueSeq standard mRNA library kit NOVASeq6000, 100PE, 40~50m for mRNA and NEBNext Small RNA Prep Kit for small RNA

treatment_protocol: Control and LIS1+/- brain organoids were either treated with MMP9 Catalytic domain for 10min at 37'c or with an equa volume of PBS (sham). RNA extraction followed the treatment.

value: Brain organoid

value: NIHhESC-10-0079 WIBR3

value: hESC

value: 10min Treatment with MMP9 Catalytic domain at concentration of 500nM, added to the media


title: RNA-seq - LIS1+/- MMP9 Treated organoid day 18, repeat #1


title: RNA-seq - LIS1+/- MMP9 Treated organoid day 18, repeat #4


title: RNA-seq - LIS1+/- Cntrl organoid day 18, repeat #4

value: 10min sham treatment with PBS+base medium


title: RNA-seq - LIS1+/- Cntrl organoid day 18, repeat #3


title: RNA-seq - Wild type MMP9 Treated organoid day 18, repeat #3

value: Wild type


title: RNA-seq - LIS1+/- Cntrl organoid day 18, repeat #1


title: RNA-seq - Wild type MMP9 Treated organoid day 18, repeat #2


title: RNA-seq - LIS1+/- Cntrl organoid day 18, repeat #2


title: RNA-seq - LIS1+/- MMP9 Treated organoid day 18, repeat #2


title: The DNA cleavage efficiency in the MCF7 cells transfected with the hpAsCas12f1 system, repeat 3

description: Library name: hpAsCas12f1_Deep-seq_Rep3


title: small RNA-seq - LIS1+/- organoid day 105, repeat #4

source_name: Cortical organoids

value: Cortical organoids


title: RNA-seq - Wild type Cntrl organoid day 18, repeat #1


title: small RNA-seq - Wild type organoid day 105, repeat #4


title: RNA-seq - Wild type Cntrl organoid day 18, repeat #4


title: RNA-seq - Wild type Cntrl organoid day 18, repeat #3


title: small RNA-seq - LIS1+/- organoid day 105, repeat #3


title: small RNA-seq - LIS1+/- organoid day 105, repeat #2


title: RNA-seq - Wild type Cntrl organoid day 18, repeat #2


title: small RNA-seq - LIS1+/- organoid day 105, repeat #1


title: small RNA-seq - Wild type organoid day 105, repeat #2


title: RNA-seq - LIS1+/- organoid day 105, repeat #4


title: small RNA-seq - Wild type organoid day 105, repeat #3


title: RNA-seq - LIS1+/- organoid day 105, repeat #2


title: small RNA-seq - Wild type organoid day 105, repeat #1


title: RNA-seq - LIS1+/- organoid day 105, repeat #1


title: RNA-seq - LIS1+/- organoid day 105, repeat #3


title: RNA-seq - Wild type MMP9 Treated organoid day 18, repeat #1


title: RNA-seq - Wild type organoid day 105, repeat #3


title: RNA-seq - Wild type organoid day 105, repeat #2


title: RNA-seq - Wild type organoid day 105, repeat #4


title: Jurkat cells, A694T-2

city: Jinan

first: Maoxiao

last: Feng

address: Beiyuan Street 247

institute: Department of Clinical Laboratory

data_processing:
Qualified reads were then mapped to reference genome using STAR. SAM files were converted to BAM format using samtools. Gene expression matrix is generated with HTSeq software. Differential analysis of gene expression was performed by using DESeq2 package.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

source_name: Jurkat

extract_protocol:
RNA was extracted using TRIzol from the Jurkat cells recombinantly expressing EV (Empty Vector), KDM6AWT or KDM6AA694T.
RNA-seq libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, #E7775) and sequenced on an Illumina platform with 125bp/150bp paired-end reads. FastQC was used to perform quality control, and then adapter sequences and poor-quality reads were removed.

value: Jurkat

value: human T lymphocyte cell line

value: KDM6A A694T overexpression

value: PMA+Ionomycin


title: Jurkat cells, A694T-3


title: Jurkat cells, KDM6A-3

value: KDM6A overexpression


title: Rx-GFP d6-1

city: ANN ARBOR

first: Yuanhao

last: Huang

state: MI

address: 1418 McIntyre st

institute: University of Michigan

description:
Library name: XUY9572-1
FLO-MIN106D flow cell

data_processing:
Data was base-called with Guppy v4.0.11 base callers. Total reads (in millions) were 1.3 and 0.81 respectively. Detected m6A modification loci with MINES (m6A Identification using Nanopore Sequencing) uses a compilation of the four random models, each corresponding to a DRACH motif, AGACT, GGACA, GGACC, and GGACT. MINES uses Tombo's fraction-modified values and coverage files as inputs and outputs a bed file of predicted sites.
Assembly: mm10
Supplementary files format and content: called m6a sites on different strands

source_name: Organoids

growth_protocol: Rx:GFP cells were differentiatied with GMEM supplemented with 5% KSR, 1% NEAA, 1% β-ME, 1% Sodium Pyruvate) and AGN (0.1µM) at 37°C.

extract_protocol:
RNA extraction was performed by combination of Trizol reagent (ThermoFisher Scientific) and RNeasy mini kit (QIAGEN).
One microgram of poly(A)-selected RNA of Rx:GFP mRO (day 6) with replicates were subjected to the Nanopore direct RNA sequencing using kit (SQK-RNA002). Sequencing was carried out on a GridION Nanopore FLO-MIN106D flow cell for each library for ∼48h.

treatment_protocol: AGN (0.1µM) treated for 6 days.

value: Organoids

value: WT

value: AGN treatnent


title: Rx-GFP d6-2

description:
Library name: XUY9572-2
FLO-MIN106D flow cell


title: Jurkat cells, KDM6A-1


title: Jurkat cells, EV-2

value: EV


title: Jurkat cells, EV-3


title: Jurkat cells, KDM6A-2


title: SMC3-AID-5min-S4-R1-NA-SPnaA

city: Worcester

first: Johan

middle: Harmen

last: Gibcus

state: MA

address: 368 Plantation Street, Dekker Lab HHMI, AS5.1015,

department: Department of Systems Biology

institute: UMass Chan Medical School

description: DT-40-CDK1 knockout , transfected with Xenops laevis CDK1as and TIR1, has a CRISPR derived mAID-clover knockin at SMC3. These cells will synchronize at mitotic entrance after addition of 1NM-PP1. Addition of auxin will deplete SMC3-clover via TIR1 proteasome degradation.

data_processing:
Fastq files were processed with the distiller pipeline (https://github.com/mirnylab/distiller-nf)
Reads were mapped to bGalGal1.mat.broiler.GRCg7b (GCA_016699485.1) using bwa mem with flags-SP.
To get pairs files, mapped reads were parsed and classified using  pairtools (https://github.com/mirnylab/pairtools).
PCR and optical duplicates were removed by matching the positions of aligned reads with 2bp flexibility.
Pairs were filtered using mapping quality scores (MAPQ > 30) on each side of aligned chimeric reads and binned into multiple resolutions before low coverage bins were removed.
Multiresolution cooler files were created with the cooler package (https://github.com/mirnylab/cooler.git)
Assembly: bGalGal1.mat.broiler.GRCg7b (GCA_016699485.1)
Supplementary files format and content: HDF5, Multiresolution cooler files (https://github.com/open2c/cooltools)
Supplementary files format and content: Mapping statistics for cooler files generated by pairtools (https://github.com/mirnylab/pairtools)
Supplementary files format and content: Compartment EV1 track (https://github.com/open2c/cooltools)
Supplementary files format and content: Eigen vectors (https://github.com/open2c/cooltools)
Supplementary files format and content: Insulation track (https://github.com/open2c/cooltools)
Supplementary files format and content: Insulation boundaries (https://github.com/open2c/cooltools)

organism: Gallus gallus

source_name: Bursa

growth_protocol: Chicken DT40 cells were cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum and 1% chicken serum at 39°C in 5% CO2 in air.

extract_protocol:
Following Hi-C 2.0 protocol steps 2.1 - 2.12 from supplemental material of Belaghzal et al., Methods 2017 Jul 1:123:56-65; PMID: 28435001
Following Hi-C 2.0 protocol steps 3.1 - 16.3 from supplemental material of Belaghzal et al., Methods 2017 Jul 1:123:56-65; PMID: 28435001

treatment_protocol: 1% formaldehyde for 10 minutes before glycine quenching (128 mM final) for 5 minutes at room temperature followed by 15 minutes on ice and wash with PBS before storing at -80°C

value: Bursa

value: lymphoblast

value: Palbociclib 11+3 h (No auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (auxin), washed (10 min), release for 5 min, after cross-linking, cells were GFP sorted (negative)


title: Jurkat cells, EV-1


title: SMC3-AID-30min-S4-R1-AN-SPnAa

value: Palbociclib 11+3 h (auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (No auxin), washed (10 min), release for 30 min, after cross-linking, cells were GFP sorted (negative)


title: SMC3-AID-G2-S4-R1-NA-SPnaA

value: Palbociclib 11+3 h (No auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (auxin), washed (10 min) and cross-linking, cells were GFP sorted (negative)


title: SMC3-AID-5min-S4-R1-AN-SPnAa

value: Palbociclib 11+3 h (auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (No auxin), washed (10 min), release for 5 min, after cross-linking, cells were GFP sorted (negative)


title: SMC3-AID-15min-S4-R1-NA-SPnaA

value: Palbociclib 11+3 h (No auxin), washed  (10 min). Release 7h. 1NMPP1 for 5 + 9 h (auxin), washed (10 min), release for 15 min, after cross-linking, cells were GFP sorted (negative)