title: lung.uninf.d0.1

city: Seattle

first: Urdahl

last: Lab

state: WA

address: 307 Westlake Ave North, Suite 500

institute: Seattle Childrens Research Institute

description:
Library name: UninfectedLung
300m reads per sample

data_processing:
10X Chromium 3’ derived single-cell RNAseq sequence reads were aligned to the 10X Genomics pre-built mouse reference genome mm10-2020-A, assigned to cells by barcodes, and UMI summarized using the 10X Cell Ranger 7.1.0 software package.
Data was annotated and transferred into R for analysis, and merged into a single Seurat object to be analyzed by Seurat through unbiased analysis (UMAP)
After initial clustering, extraneous adaptive and stromal cells were removed (T, B, NK, Endo) and allCell.rds Seurat object was saved.
Annotations were intially generated by ImmGen.Fine clusters using the ImmGen database, then adjusted based on TopMarker analysis to the ImmGenGroup annotation found in the meta.data of the allCells.rds object
Differential expression was performed using Seurat v4.4.0 (FindMarkers) on cell groups with ≥10 cells per condition. Genes with adjusted p-value < 0.05 were ranked by average log2 fold change for GSEA using fgseaMultilevel (fgsea v1.26.0) against GO:Biological Process terms. The top 200 pathways (by absolute NES) with FDR < 0.05 were reduced using rrvgo v1.20.0 (Rel semantic similarity; org.Mm.eg.db v3.18.0), and representative terms were visualized as bubble plots.
Assembly: mm10-2020-A
Supplementary files format and content: allCells.rds (found in ~/ondemand/scRNAseq/EAS_run_DEG_GSEA_All)

source_name: lung

extract_protocol:
Single cell suspensions were generated from medLN, blood, and lung samples as described above prior to Mtb infection and at days 0, 15 and 28 post-Mtb infection from pools of 8-10 mice for each suspension/condition. Cells were resuspended in 200 μl MACS buffer (PBS containing 2.5% FBS plus 1 mM EDTA), filtered through a 70 μm filter, and run on a FACS AriaII (BD) sorter. To collect parenchymal cells for single-cell RNA sequencing, alveolar macrophages (AM, SiglecF+ Autofluorescence+) were sorted separately into one collection tube to account for autofluorescence in the IV label channel, and all other IV-negative cells were sorted into another collection tube. After sorting AMs were included in respective lung samples (Mtb-infected or uninfected). Mtb-infected and uninfected bystander (mCherry+ and mCherry -) samples were harvested separately. After one round of washing with ice-cold DPBS, cells were resuspended to 1000 cells/μl in DPBS, and 8000 cells were inputted into the 10X Genomics pipeline following the manufacturer’s recommendations.
After the generation of cDNA following the manufacturer’s protocol, samples were centrifuged through two sequential rounds of 0.2 μm SpinX (Costar) columns to sterilize the sample for removal from the BSL3 facility and subsequent library generation. Libraries were submitted to Psomagen (Rockville, MD) for NovaSeq sequencing, with 300M reads per sample

value: lung

value: Myeloid

tag: genotype

value: Uninfected


title: YST-1 cells, control

status: Public on Jun 19 2026

type: SRA

city: Shinjuku-ku

first: Masahiro

last: Yo

state: TOKYO

address: 35 Shinanomachi

country: Japan

institute: Keio University

description:
Library name: Samlpe 4
Y0

library_source: transcriptomic

data_processing:
Raw FASTQ files were trimmed for adapters by Cutadapt and Salmon was used to generate the Transcripts Per Million (TPM) and estimated counts using the transcript index from GRCh38 (Gencode v33). Heatmaps of gene expression were drawn on the log2(TPM + 1) value.
Assembly: hg38
Supplementary files format and content: tab-separated text file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: right arm

extract_protocol:
We extracted RNA from patient samples of schwannoma and cultured cell lines (YST-1 and TIG-1) before and after adding of PER using the ISOGEN (Nippon Gene, Japan).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

tag: tissue

value: right arm

tag: cell line

tag: cell type

value: schwannoma

tag: treatment

value: control


title: 22531-59

type: genomic

city: North Brunswick Township

first: Jia

last: Xu

state: NJ

address: 675 US Highway One

country: USA

institute: Genomic Prediction, Inc.

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #9 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5

data_processing:
Affymetrix UK Biobank Axiom Array Manufacturer's Protocol
Primary data description: DNA copy number and genotyping

label: biotin

molecule: genomic DNA

source_name: Blastomere from ABE-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D4

growth_protocol: Thawing of human 2PN zygotes was performed using the Qinn's Advantage warming kit or using a one-step protocol with GMOPS-plus depending on the method of cryopreservation. Donated oocytes were warmed using the Cryotech warming kit. Embryos were cultured in Global total.

extract_protocol: Single cells, single polar bodies, or cytoplasmic fragments were placed into single PCR tubes containing 2 ul of Genomic Prediction's loading Buffer. Genomic DNA amplification was performed using amplification kit as indicated for each sample.

treatment_protocol: Cas9 or ABE ribonucleoprotein complex was assembled in vitro and injected at fertilization or at the 1-cell stage of embryo development. Zygotes were either at the 2PN stage or at the entry into the first mitosis.

value: Preimplantation embryo


title: blood.uninf.d0.1

description:
Library name: UninfectedBlood
300m reads per sample

library_source: transcriptomic single cell

organism: Mus musculus

source_name: blood

value: blood


title: control, muscle, patient 5

city: Gainesville

first: Darius

last: Ramkhalawan

address: 1200 Newell Drive

institute: University of Florida

description: Library name: DR154

data_processing:
For processing the sequenced fastq files, we utilized nf-core’s standardized RNA-seq pipeline (Version 3.12.0)47 with the following additional parameters. Sequencing reads were trimmed using TrimGalore with the following parameters: –trim-n to remove trailing N’s on either side of the read; –length 40 to remove reads with a trimmed size less than 40 bases; –quality 20 to remove ends of reads with below 20 phred scores; –clip_R1 5 and clip_R2 5 to trim the the first 5 bases off of the 5’ and 3’ end of the reads. Additionally, we include –min_trimmed_reads 5000 to remove any samples with below 5000 reads after trimming. We then include –skip_alignment,–skip_deseq2_qc, and –psuedo_aligner salmon with an igenomes reference fileset to call transcript quantification files for each replicate.
Assembly: hg19
Supplementary files format and content: TPM matrix of all samples

source_name: muscle

extract_protocol:
Frozen tissues were pulverized in the presence of liquid nitrogen using a mortar and pestle, followed by homogenization in TRIzol (ThermoFisher Scientific, cat no. 15596026) using a bead beater (TissueLyser LT, Qiagen, cat no. 69980) at 50 Hz for 1 min with 1/8” stainless steel beads (MP Biomedicals, cat no. 1169250-CF), followed by RNA isolation, per the TRIzol manufacturer’s protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. Paired-end RNA sequencing was carried out on an Illumina NovaSeq6000.

value: muscle


title: TIG-1 cells, 30uM PER, day7

description:
Library name: Samlpe 3
T30

value: fibroblast

value: 30uM PER, day7


title: 22531-58

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #8 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5

hyb_protocol: Affymetrix UK Biobank Axiom Array Manufacturer's Protocol


title: mln.pos.d28.2

description:
Library name: D28medLNpos2
300m reads per sample

source_name: mediastinal LN

value: mediastinal LN

value: Infection Day 28


title: control, muscle, patient 4

description: Library name: DR152


title: TIG-1 cells, 10uM PER, day7

description:
Library name: Samlpe 2
T10

value: 10uM PER, day7


title: 22531-57

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #7 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5

scan_protocol: Affymetrix UK Biobank Axiom Array Manufacturer's Protocol


title: mln.pos.d28.1

description:
Library name: D28medLNpos1
300m reads per sample


title: control, muscle, patient 3

description: Library name: DR112


title: TIG-1 cells, control

description:
Library name: Samlpe 1
T0


title: 22531-54

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #4 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5

label_protocol: Affymetrix UK Biobank Axiom Array Manufacturer's Protocol


title: mln.neg.d28.2

description:
Library name: D28medLNneg2
300m reads per sample


title: HLF ARID1B-KO IgG CUT&RUN, Sorafenib, rep2

city: Chapel Hill

first: Jacqueline

last: Brinkman

address: 120 Mason Farm Rd

department: Genetics

institute: Unversity of North Carolina-Chapel Holl

description: Library name: HLF_ARID1B-KO_Sorafenib_IgG_rep2

library_source: genomic

data_processing:
Bowtie2 alignment to GRCh38. MACS2 peak calling (-f BAMPE). MSPC consensus peaks. csaw normalization. DESeq2 differential occupancy. deepTools bigWig generation.
Assembly: GRCh38 / hg38
Supplementary files format and content: RPKM-normalized bigWig (*_rpkm.bw), csaw-scaled bigWig (*_scaled.bw), MACS2 narrowPeak (*_peaks.narrowPeak; absent for IgG controls). Note: scaled bigWig absent for HepG2_ARID1B-KO_Sorafenib_IgG_rep1 and rep2.
Library strategy: CUT&Run

source_name: HLF

growth_protocol: HepG2 (CVCL_0027) and HLF (CVCL_2947) maintained at 37°C, 5% CO2 in DMEM/10% FBS/1% P-S.

extract_protocol:
CUT&RUN adapted from EpiCypher protocol. 200,000-500,000 cells, Concanavalin A beads, overnight primary antibody at 4°C (H3K4me3 CST #3076423; H3K27ac CST #2561016; ARID1B CST #65747 clone E1U7D; FOXA1; FOXA2; IgG CST #550038), guinea pig anti-rabbit secondary (Novus NBP1-72763 1:100), pAG-MNase 700 ng/ml 1 h 4°C, CaCl2 digestion on ice 30 min, stop buffer quench, Zymo D4014 cleanup.
KAPA HyperPrep Kit (Roche #07962363001). 14 PCR cycles. Paired-end 50 bp or 150 bp reads on Illumina NextSeq 1000 (HepG2) or NovaSeq X Plus 10B (HLF).

treatment_protocol: Sorafenib: 5 µM (Selleckchem S1040) 48 h. Vehicle: equivalent DMSO. ARID1B-KO by CRISPR/Cas9.

value: HLF

value: sorafenib 5 µM, 48 h

tag: antibody

value: IgG

tag: biological replicate


title: control, muscle, patient 2

description: Library name: DR111


title: mln.uninf.d0.1

description:
Library name: UninfectedmedLN
300m reads per sample


title: 22531-53

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: YST-1 cells, 10uM PER, day7

description:
Library name: Samlpe 5
Y10


title: 22531-60

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #10 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: mln.neg.d28.1

description:
Library name: D28medLNneg1
300m reads per sample

source_name: mln

value: mln


title: control, muscle, patient 1

description: Library name: DR51


title: Tumor, Diffuse Sclerosing Variant

city: Los Angeles

first: Anthony

last: Nguyen

address: 8700 Beverly Blvd, Department of Radiation Oncology

institute: Cedars-Sinai Medical Center

description: Library name: 11A

data_processing:
Demultiplexed fastq files for gene expression libraries were processed by Cellranger (v4.0.0)
Assembly: GRCh38-3.0.0
Supplementary files format and content: Cell Ranger output files : filtered_feature_bc_matrix.h5

source_name: Tumor

extract_protocol:
Following CD45-positive selection, samples were diluted to 1000 cells/uL and processed according to the Single Cell 3’ v1 assay (10x Genomics) with a targeted 10,000 cell recovery.
Gene expression libraries were prepared according to the Single Cell 3’ v1 protocol (10x Genomics) and were sequenced using paired-end 150bp reads on the Novaseq 6000 (Illumina) through the CSMC Applied Genomics, Computation & Translational Core

value: Tumor


title: HLF ARID1B-KO IgG CUT&RUN, Sorafenib, rep1

description: Library name: HLF_ARID1B-KO_Sorafenib_IgG_rep1


title: AIS, muscle, convex, patient 10

description: Library name: DR100


title: lung.pos.d28.1

description:
Library name: D28Lungpos
300m reads per sample

value: lung

value: Myeloid


title: HLF ARID1B-KO FOXA2 CUT&RUN, Sorafenib, rep2

description: Library name: HLF_ARID1B-KO_Sorafenib_FOXA2_rep2


title: 22531-51

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: lung.neg.d28.2

description:
Library name: D28Lungneg2
300m reads per sample


title: AIS, muscle, convex, patient 9

description: Library name: DR81


title: HLF ARID1B-KO FOXA2 CUT&RUN, Sorafenib, rep1

description: Library name: HLF_ARID1B-KO_Sorafenib_FOXA2_rep1


title: 22531-52

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 24-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: 22531-48

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #5 from 6-C human embryo #2 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: female, high fat diet, replicate 4

city: Bronx

first: Ronald

last: Cutler

state: NY

address: 1300 Morris Park Ave

department: Genetics & Biochemistry

institute: Albert Einstein College of Medicine

description: Library name: FHF4

data_processing:
Raw sequence data were processed using the nf-core RNA-Seq pipeline (version 3.19.0). Reads were aligned to the GRCm39 mouse reference genome using the STAR aligner and gene quantification was performed against the GENCODE vM37 primary assembly annotation with RSEM to obtain gene expression counts.
Assembly: GRCm39
Supplementary files format and content: tab delimited text file that includes counts/TPM for each gene and sample

molecule: polyA RNA

source_name: liver

extract_protocol:
Total RNA was isolated from approximately 20 mg of homogenized whole-liver powder using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
1 µg of total RNA per sample was submitted to Azenta Life Sciences for library preparation using the NEBNext Ultra RNA Library Prep Kit (New England Biolabs) followed by sequencing on the NovaSeq platform (Illumina).

treatment_protocol: Male and female C57BL/6J mice (Jackson Laboratory, #000664) were obtained at 6 weeks of age and assigned to either a normal chow (NC; LabDiet 5053; 4.5% of calories from fat) or a high fat (HF; Research Diets, D12492; 60% of calories from fat) diet for 10 weeks. Mice were group-housed in a temperature-controlled room with ad libitum access to food and water under a 12 h light/12 h dark cycle (lights on at 07:00, Zeitgeber time 0).

value: liver

value: wt

value: high fat diet

tag: batch


title: lung.neg.d28.1

description:
Library name: D28Lungneg1
300m reads per sample


title: AIS, muscle, convex, patient 8

description: Library name: DR50


title: HLF ARID1B-KO FOXA1 CUT&RUN, Sorafenib, rep2

description: Library name: HLF_ARID1B-KO_Sorafenib_FOXA1_rep2


title: p300 CUT&Tag, OCI-AML3 cells, siControl, Day9, rep2

city: XIAMEN

first: Lanfen

last: Chen

state: Fujian Province

address: No.4221, Xiang'an South Roa

department: School of Life Sciences

country: China

institute: XIAMEN UNIVERSITY

description:
Library name: C4
cut-tag antibody: anti-p300 (Abcam, ab10483)

data_processing:
Raw sequencing reads were trimmed and filtered for quality using CutAdapt (v.2.6). Paired-end reads were aligned using Bowtie2 (v.2.3.5.1) (PMID: 22388286) against hg38 genome.
Aligned reads were sorted and non-uniquely mapping reads were marked using Picard (v.2.9.5) (http://broadinstitute.github.io/picard/). PCR duplicates, reads mapped to mitochondria or of low mapping quality were filtered using Samtools (v.1.9) (PMID: 19505943).
To correct for the fact that the Tn5 transposase binds as a dimer and inserts two adapters in the Tn5 tagmentation step, all positive-strand reads were shifted 4 bp downstream and all negative-strand reads were shifted 5 bp upstream to center the reads on the transposon binding event.
We then pooled the shifted reads by sample type and identified peaks using MACS2 (v.2.2.6) (PMID: 18798982) with a threshold of FDR-corrected p < 0.001 using the Benjamini-Hochberg procedure for multiple hypothesis correction. A union peak list for each experiment was created by combining all peaks in all samples; overlapping peaks were merged with minimum overlap > 0.5. The number of reads in each peak was determined with Diffbind (v.3.16.0) (PMID: 22217937).
Differentially expressed peaks were identified after edgeR normalization using a FDR cut-off of 0.05. Peaks were annotated using R package ChIPseeker (v.1.18.0) (PMID: 25765347).
Assembly: hg38
Supplementary files format and content: Supplementary files format and content: BigWig Track Format of each CUT&Tag sample.
Library strategy: CUT&Tag

source_name: Bone marrow

growth_protocol: OCI-AML3 cells were maintained in RPMI1640 complete medium with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
1 × 10^5 OCI-AML3 cells were collected and washed once with 500 μl wash buffer before they were bound to ConA beads for 10 min at 25 °C.
Cells were incubated with 1 mg of respective targeting antibodies at 4 °C overnight. 0.5 mg secondary antibody was added and incubated for 1 h at 25 °C. Then cells were washed three times with DIG wash buffer and incubated with 0.04 μM pA/G–Tnp for 1 h at 25 °C. Similarly, cells were washed three times with DIG 300 buffer, resuspended in tagmentation buffer and incubated at 37 °C for 1 h. Tagmentation was stopped by adding proteinase K, buffer LB and DNA extract beads. After incubation at 55 °C for 10 min, cells were plated on a magnet and unbound liquid was removed. Beads were gently rinsed twice with 80% ethanol and DNA was eluted with double-distilled water. libraries were barcoded using TruePrep™ Index Kit V2 for lllumina (Vazyme TD202) and amplified for 14 cycles. Final product was cleaned by VAHTS DNA Clean Beads at a 2 × ratio. Libraries were sequenced on a Novaseq 6000 in a 150 bp/150 bp Paired end run. An average of 20 × 106 paired reads was generated per sample.

treatment_protocol: OCI-AML3 cells were transfected at 1 × 105 cells/ ml using Lipofectamine RNAi MAX (Invitrogen) following the manufacturer's recommendations. The final concentration of the siRNA molecules is 10 nM. Collect the cells and extract total RNA after 3 days.

value: Bone marrow

value: acute myeloid leukemia blast

value: WT

value: siControl


title: blood.inf.d28.2

description:
Library name: D28Blood2
300m reads per sample

value: blood


title: 22531-47

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #4 from 6-C human embryo #2 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5

value: Preimplantation embryo


title: WT_1_2%

city: Houston

first: Jeanine

middle: L

last: Van Nostrand

state: TX

address: One Baylor Plaza M502C Van Nostrand

department: Molecular and Cellular Biology

institute: Baylor College of Medicine, Houston

description:
Library name: WT_1_2_
WT_1_2%

data_processing:
FastQ generation and demux with BCL Convert v4.3.6 and fqtk v0.3.1.
Read-filtering using FastP v0.24.0: poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp.
Alignment to the appropriate reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads.
Coordinate sorting of BAM files using samtools v1.22.1.
UMI based de-duplication: Removal of PCR and optical duplicates using UMICollapse v1.1.0.
Mapping QC: Alignment quality metrics, strand specificity, and read distribution across genomic features using RSeQC v5.0.4 and Qualimap v2.3.
Generation of comprehensive QC report using MultiQC v1.32.
Gene-expression quantification using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.
Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts (TMM, trimmed mean of M-values) using Pearson correlation.
Assembly: GRCm39_114
Supplementary files format and content: Counts and Counts per million

source_name: T-antigen immortalized MEFs

growth_protocol: Complete media with 10% CO2 at 37C

extract_protocol:
RNA/DNA Shield (Zymo); Bead based extraction by plasmidsaurus
convert mRNA into complementary DNA (cDNA) via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification.

treatment_protocol: 10% CO2 or 2% CO2 for 24 hours

value: T-antigen immortalized MEFs

value: Mouse embryonic fibroblast

value: Wildtype


title: p300 CUT&Tag, OCI-AML3 cells, siControl, Day9, rep1

description:
Library name: C4_1
cut-tag antibody: anti-p300 (Abcam, ab10483)


title: KAT7 CUT&Tag, OCI-AML3 cells, siNPM1c-AM, Day9, rep2

description:
Library name: S13
cut-tag antibody: anti-KAT7 (Cell Signaling Technology, 8418)


title: female, normal diet, replicate 4

description: Library name: FNC4

value: normal diet


title: AIS, muscle, convex, patient 6

description: Library name: DR75

value: muscle


title: HLF ARID1B-KO FOXA1 CUT&RUN, Sorafenib, rep1

description: Library name: HLF_ARID1B-KO_Sorafenib_FOXA1_rep1

value: HLF

value: sorafenib 5 µM, 48 h


title: WT_4_10%

description:
Library name: WT_4_10_
WT_4_10%


title: p300 CUT&Tag, OCI-AML3 cells, siNPM1c-AM, Day9, rep2

description:
Library name: S4
cut-tag antibody: anti-p300 (Abcam, ab10483)


title: blood.inf.d28.1

description:
Library name: D28Blood1
300m reads per sample

value: Myeloid

value: Infection Day 28


title: AIS, muscle, convex, patient 5

description: Library name: DR148


title: 22531-45

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 6-C human embryo #2 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: HLF ARID1B-KO ARID1B CUT&RUN, Sorafenib, rep2

description: Library name: HLF_ARID1B-KO_Sorafenib_ARID1B_rep2


title: 22531-46

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 6-C human embryo #2 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: mln.pos.d15.1

description:
Library name: D15medLNpos
300m reads per sample

value: mediastinal LN

value: Infection Day 15


title: mln.neg.d15.2

description:
Library name: D15medLNneg2
300m reads per sample


title: AIS, muscle, convex, patient 3

description: Library name: DR140


title: AIS, muscle, convex, patient 4

description: Library name: DR141


title: HLF ARID1B-KO ARID1B CUT&RUN, Sorafenib, rep1

description: Library name: HLF_ARID1B-KO_Sorafenib_ARID1B_rep1


title: HLF ARID1B-KO H3K4me3 CUT&RUN, Sorafenib, rep2

description: Library name: HLF_ARID1B-KO_Sorafenib_H3K4me3_rep2


title: 22531-42

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #14 from 14-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: mln.neg.d15.1

description:
Library name: D15medLNneg1
300m reads per sample


title: AIS, muscle, convex, patient 2

description: Library name: DR73


title: 22531-44

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 6-C human embryo #2 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: HLF ARID1B-KO H3K4me3 CUT&RUN, Sorafenib, rep1

description: Library name: HLF_ARID1B-KO_Sorafenib_H3K4me3_rep1


title: lung.pos.d15.1

description:
Library name: D15Lungpos
300m reads per sample

value: lung


title: 22531-41

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #13 from 14-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: AIS, muscle, concave, patient 8

description: Library name: DR147


title: 22531-40

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #12 from 14-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: HLF ARID1B-KO H3K27ac CUT&RUN, Sorafenib, rep2

description: Library name: HLF_ARID1B-KO_Sorafenib_H3K27ac_rep2


title: lung.neg.d15.2

description:
Library name: D15Lungneg2
300m reads per sample


title: AIS, muscle, concave, patient 7

description: Library name: DR146


title: HLF ARID1B-KO H3K27ac CUT&RUN, Sorafenib, rep1

description: Library name: HLF_ARID1B-KO_Sorafenib_H3K27ac_rep1


title: AIS, muscle, concave, patient 6

description: Library name: DR145


title: lung.neg.d15.1

description:
Library name: D15Lungneg1
300m reads per sample


title: HLF ARID1B-KO IgG CUT&RUN, DMSO, rep2

description: Library name: HLF_ARID1B-KO_DMSO_IgG_rep2

value: DMSO vehicle (0.1% v/v)

value: IgG


title: 22531-38

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #10 from 14-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: 22531-39

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #11 from 14-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: blood.inf.d15.2

description:
Library name: D15Blood2
300m reads per sample


title: AIS, muscle, concave, patient 5

description: Library name: DR118


title: HLF ARID1B-KO IgG CUT&RUN, DMSO, rep1

description: Library name: HLF_ARID1B-KO_DMSO_IgG_rep1


title: blood.inf.d15.1

description:
Library name: D15Blood1
300m reads per sample


title: AIS, muscle, concave, patient 4

description: Library name: DR115


title: HLF ARID1B-KO FOXA2 CUT&RUN, DMSO, rep2

description: Library name: HLF_ARID1B-KO_DMSO_FOXA2_rep2


title: 22531-36

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #8 from 14-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: AIS, muscle, concave, patient 3

description: Library name: DR113


title: 22531-35

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #7 from 14-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: 22531-34

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #6 from 14-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: HLF ARID1B-KO FOXA1 CUT&RUN, DMSO, rep2

description: Library name: HLF_ARID1B-KO_DMSO_FOXA1_rep2


title: AIS, muscle, concave, patient 1

description: Library name: DR35


title: Whole blood, 13.08y, Female, Maltese [ET060295]

city: Jinju-si

first: Jaemin

last: Kim

state: Gyeongsangnam-do

address: 501, Jinji-daero

country: South Korea

institute: Gyeongsang National University

hyb_protocol: Bisulfite-converted genomic DNA was hybridized to the custom Infinium HorvathMammalMethylChip40 array following standard Illumina protocols

scan_protocol: Arrays were scanned using the Illumina iScan System with standard settings.

data_processing: SeSAMe package in R environment

organism: Canis lupus familiaris

source_name: Whole blood

label_protocol: Standard Illumina protocol

extract_protocol: Whole blood samples were collected from the jugular vein of companion dogs and stored in EDTA tubes. Genomic DNA was extracted using the Exgene Blood SV mini kit (GeneAll Biotechnology, Seoul, Republic of Korea) according to the manufacturer’s instructions. DNA quality and purity were assessed using Qubit fluorometer and NanoDrop spectrophotometer; integrity was confirmed by agarose gel electrophoresis.

value: Whole blood

tag: Sex

value: Female

tag: age

tag: breed

value: Maltese


title: HLF ARID1B-KO FOXA1 CUT&RUN, DMSO, rep1

description: Library name: HLF_ARID1B-KO_DMSO_FOXA1_rep1


title: 22531-18

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #4 from 14-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5

value: Preimplantation embryo


title: Whole blood, 6.58y, Male, Pomeranian [ET060293]

value: Male

value: Pomeranian


title: HLF ARID1B-KO ARID1B CUT&RUN, DMSO, rep2

description: Library name: HLF_ARID1B-KO_DMSO_ARID1B_rep2


title: 22531-17

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 14-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: Whole blood, 7.00y, Male, Beagle [ET060292]

value: Beagle


title: p300 CUT&Tag, OCI-AML3 cells, siNPM1c, Day3, rep1

description: Library name: C30015

data_processing:
Raw sequencing reads were trimmed and filtered for quality using CutAdapt (v.2.6). Paired-end reads were aligned using Bowtie2 (v.2.3.5.1) (PMID: 22388286) against hg38 genome.
Aligned reads were sorted and non-uniquely mapping reads were marked using Picard (v.2.9.5) (http://broadinstitute.github.io/picard/). PCR duplicates, reads mapped to mitochondria or of low mapping quality were filtered using Samtools (v.1.9) (PMID: 19505943).
To correct for the fact that the Tn5 transposase binds as a dimer and inserts two adapters in the Tn5 tagmentation step, all positive-strand reads were shifted 4 bp downstream and all negative-strand reads were shifted 5 bp upstream to center the reads on the transposon binding event.
We then pooled the shifted reads by sample type and identified peaks using MACS2 (v.2.2.6) (PMID: 18798982) with a threshold of FDR-corrected p < 0.001 using the Benjamini-Hochberg procedure for multiple hypothesis correction. A union peak list for each experiment was created by combining all peaks in all samples; overlapping peaks were merged with minimum overlap > 0.5. The number of reads in each peak was determined with Diffbind (v.3.16.0) (PMID: 22217937).
Differentially expressed peaks were identified after edgeR normalization using a FDR cut-off of 0.05. Peaks were annotated using R package ChIPseeker (v.1.18.0) (PMID: 25765347).
Assembly: hg38
Supplementary files format and content: BigWig Track Format of each CUT&Tag sample.
Library strategy: CUT&Tag

value: Bone marrow

value: acute myeloid leukemia blast

value: WT

tag: cut-tag antibody

value: anti-P300 (Abcam, ab10483)


title: HLF ARID1B-KO ARID1B CUT&RUN, DMSO, rep1

description: Library name: HLF_ARID1B-KO_DMSO_ARID1B_rep1

value: HLF


title: 22531-16

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 14-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: Whole blood, 5.08y, Male, German Shepherd [ET060291]

value: German Shepherd


title: p300 CUT&Tag, OCI-AML3 cells, siControl, Day3, rep2

description: Library name: C300N-2

value: siControl


title: HLF ARID1B-KO H3K4me3 CUT&RUN, DMSO, rep2

description: Library name: HLF_ARID1B-KO_DMSO_H3K4me3_rep2


title: 22531-15

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 14-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: Whole blood, 1.00y, Male, Beagle [ET060290]


title: p300 CUT&Tag, OCI-AML3 cells, siControl, Day3, rep1

description: Library name: C300N


title: HLF ARID1B-KO H3K4me3 CUT&RUN, DMSO, rep1

description: Library name: HLF_ARID1B-KO_DMSO_H3K4me3_rep1


title: 22531-11

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #4 from 5-C human embryo #5 injected with ABE mRNA and PCSK9 sgRNAs_Experiment BE4


title: KAT7 CUT&Tag, OCI-AML3 cells, siNPM1c, Day3, rep2

description: Library name: S152_1

value: anti-KAT7 (Cell Signaling Technology, 8418)


title: HLF ARID1B-KO H3K27ac CUT&RUN, DMSO, rep2

description: Library name: HLF_ARID1B-KO_DMSO_H3K27ac_rep2

value: DMSO vehicle (0.1% v/v)


title: 22531-10

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 5-C human embryo #5 injected with ABE mRNA and PCSK9 sgRNAs_Experiment BE4


title: Whole blood, 13.08y, Female, Maltese [ET060287]


title: Whole blood, 13.17y, Female, Poodle [ET060286]

value: Poodle


title: HLF ARID1B-KO H3K27ac CUT&RUN, DMSO, rep1

description: Library name: HLF_ARID1B-KO_DMSO_H3K27ac_rep1


title: KAT7 CUT&Tag, OCI-AML3 cells, siControl, Day3, rep2

description: Library name: con6_1


title: 22531-08

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 5-C human embryo #5 injected with ABE mRNA and PCSK9 sgRNAs_Experiment BE4


title: HLF WT IgG CUT&RUN, Sorafenib, rep2

description: Library name: HLF_WT_Sorafenib_IgG_rep2

value: sorafenib 5 µM, 48 h

value: IgG


title: KAT7 CUT&Tag, OCI-AML3 cells, siControl, Day3, rep1

description: Library name: con6


title: Whole blood, 5.58y, Male, Pomeranian [ET060284]

value: Whole blood


title: 22531-07

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 2-C human embryo #4 injected with ABE mRNA and PCSK9 sgRNAs_Experiment BE4

value: Preimplantation embryo


title: Whole blood, 5.33y, Male, German Shepherd [ET060283]

value: Male


title: HLF WT FOXA2 CUT&RUN, Sorafenib, rep2

description: Library name: HLF_WT_Sorafenib_FOXA2_rep2


title: 22531-06

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 2-C human embryo  #4 injected with ABE mRNA and PCSK9 sgRNAs_Experiment BE4


title: H3K27ac CUT&Tag, OCI-AML3 cells, siNPM1c, Day3, rep1

description: Library name: S3

value: anti-H3K27ac (Cell Signaling Technology, 8173S)


title: 22531-04

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 2-C human embryo #3 injected with ABE mRNA and PCSK9 sgRNAs_Experiment BE4


title: HLF WT FOXA2 CUT&RUN, Sorafenib, rep1

description: Library name: HLF_WT_Sorafenib_FOXA2_rep1


title: Whole blood, 1.00y, Male, Beagle [ET060282]

value: Beagle


title: H3K27ac CUT&Tag, OCI-AML3 cells, siControl, Day3, rep2

description: Library name: C3_1

value: Bone marrow


title: 22531-03

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 2-C human embryo #3 injected with ABE mRNA and PCSK9 sgRNAs_Experiment BE4


title: HLF WT FOXA1 CUT&RUN, Sorafenib, rep2

description: Library name: HLF_WT_Sorafenib_FOXA1_rep2


title: H3K27ac CUT&Tag, OCI-AML3 cells, siControl, Day3, rep1

description: Library name: C3

value: acute myeloid leukemia blast


title: Whole blood, 14.25y, Female, Maltese [ET060279]

value: Female

value: Maltese


title: 22531-02

description:
Other option: Treff method - Phi29 mediated amplification
1-C human embryo #2 injected with ABE mRNA and PCSK9 sgRNAs, lysed_Experiment BE4

source_name: 1-C ABE-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D4


title: HLF WT FOXA1 CUT&RUN, Sorafenib, rep1

description: Library name: HLF_WT_Sorafenib_FOXA1_rep1

value: HLF

value: WT


title: H3K14ac CUT&Tag, OCI-AML3 cells, siNPM1c, Day3, rep2

description: Library name: S2_1

value: anti-H3K14ac (Cell Signaling Technology, 7627S)


title: HLF WT ARID1B CUT&RUN, Sorafenib, rep2

description: Library name: HLF_WT_Sorafenib_ARID1B_rep2


title: Whole blood, 6.58y, Male, Shih Tzu [ET060277]

value: Shih Tzu


title: HLF WT ARID1B CUT&RUN, Sorafenib, rep1

description: Library name: HLF_WT_Sorafenib_ARID1B_rep1


title: Whole blood, 0.58y, Male, Maltese [ET060281]


title: 22537-48

description:
Other option: Treff method - Phi29 mediated amplification
Several cells and cell fragments from 20-C human embryo #6 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3

source_name: Several cells and cell fragments from ABE injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D6


title: Whole blood, 5.58y, Female, Pomeranian [ET060276]

value: Pomeranian


title: H3K14ac CUT&Tag, OCI-AML3 cells, siControl, Day3, rep2

description: Library name: C2_1

value: siControl


title: Whole blood, 13.17y, Female, Poodle [ET060278]

value: Poodle


title: 22531-01

description:
Other option: Treff method - Phi29 mediated amplification
1-C human embryo #1 injected with ABE mRNA and PCSK9 sgRNAs_Experiment BE4


title: HLF WT H3K4me3 CUT&RUN, Sorafenib, rep2

description: Library name: HLF_WT_Sorafenib_H3K4me3_rep2

value: sorafenib 5 µM, 48 h


title: 22537-47

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #9 from 20-C human embryo #6 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3

source_name: Blastomere from ABE-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D6


title: 22531-37

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #9 from 14-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE5


title: HLF ARID1B-KO FOXA2 CUT&RUN, DMSO, rep1

description: Library name: HLF_ARID1B-KO_DMSO_FOXA2_rep1

value: DMSO vehicle (0.1% v/v)


title: AIS, muscle, concave, patient 2

description: Library name: DR144

value: muscle


title: H3K14ac CUT&Tag, OCI-AML3 cells, siNPM1c, Day3, rep1

description: Library name: S2


title: Whole blood, 2.67y, Male, Belgian Malinoise [ET060275]

value: Whole blood

value: Male

value: Belgian Malinoise


title: HLF WT H3K4me3 CUT&RUN, Sorafenib, rep1

description: Library name: HLF_WT_Sorafenib_H3K4me3_rep1


title: 22537-44

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #6 from 20-C human embryo #6 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3

value: Preimplantation embryo


title: Whole blood, 13.17y, Female, Poodle [ET060294]


title: H3K14ac CUT&Tag, OCI-AML3 cells, siControl, Day3, rep1

description: Library name: C2

value: Bone marrow

value: acute myeloid leukemia blast


title: p300 CUT&Tag, OCI-AML3 cells, siNPM1c, Day3, rep2

description: Library name: C30015-2

value: anti-P300 (Abcam, ab10483)


title: Whole blood, 1.00y, Male, Beagle [ET060274]

value: Beagle


title: NPM1c CUT&Tag, OCI-AML3 cells, siNPM1c, Day3, rep2

description: Library name: S1_1

value: WT

value: anti-NPM1c (ABclonal, 8457)


title: HLF WT H3K27ac CUT&RUN, Sorafenib, rep2

description: Library name: HLF_WT_Sorafenib_H3K27ac_rep2

value: HLF


title: 22537-39

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 20-C human embryo #6 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: HLF WT H3K27ac CUT&RUN, Sorafenib, rep1

description: Library name: HLF_WT_Sorafenib_H3K27ac_rep1


title: NPM1c CUT&Tag, OCI-AML3 cells, siNPM1c, Day3, rep1

description: Library name: S1


title: 22537-40

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 20-C human embryo #6 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: Whole blood, 0.58y, Male, Maltese [ET060273]

value: Maltese


title: Whole blood, 0.58y, Male, Maltese [ET060289]


title: NPM1c CUT&Tag, OCI-AML3 cells, siControl, Day3, rep2

description: Library name: C1_1

value: siControl


title: Whole blood, 13.08y, Female, Poodle [ET060271]

value: Female

value: Poodle


title: 22537-38

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #6 from 6-C human embryo #5 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3

source_name: Blastomere from ABE-injected human embryo (at 2PN stage on day 1 of development), D1; Sample collected on day D4


title: HLF WT IgG CUT&RUN, DMSO, rep2

description: Library name: HLF_WT_DMSO_IgG_rep2

value: DMSO vehicle (0.1% v/v)

value: IgG


title: 22537-37

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #5 from 6-C human embryo #5 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: KAT7 CUT&Tag, OCI-AML3 cells, siNPM1c, Day3, rep1

description: Library name: S152

value: anti-KAT7 (Cell Signaling Technology, 8418)


title: NPM1c CUT&Tag, OCI-AML3 cells, siControl, Day3, rep1

description: Library name: C1


title: atac-seq, OCI-AML3 cells, siNPM1c, Day3, rep2

description: Library name: A_15_2

data_processing:
Raw ATAC-seq reads were trimmed and filtered for quality using CutAdapt (v.2.6). Paired-end reads were aligned using Bowtie2 (v.2.3.5.1) (PMID: 22388286) against hg38 genome.
Aligned reads were sorted and non-uniquely mapping reads were marked using Picard (v.2.9.5) (http://broadinstitute.github.io/picard/). PCR duplicates, reads mapped to mitochondria or of low mapping quality were filtered using Samtools (v.1.9) (PMID: 19505943).
To correct for the fact that the Tn5 transposase binds as a dimer and inserts two adapters in the Tn5 tagmentation step, all positive-strand reads were shifted 4 bp downstream and all negative-strand reads were shifted 5 bp upstream to center the reads on the transposon binding event.
We then pooled the shifted reads by sample type and identified peaks using MACS2 (v.2.2.6) (PMID: 18798982) with a threshold of FDR-corrected p < 0.001 using the Benjamini-Hochberg procedure for multiple hypothesis correction. A union peak list for each experiment was created by combining all peaks in all samples; overlapping peaks were merged with minimum overlap > 0.5. The number of reads in each peak was determined with Diffbind (v.3.16.0) (PMID: 22217937).
Differentially expressed peaks were identified after edgeR normalization using a FDR cut-off of 0.05. Peaks were annotated using R package ChIPseeker (v.1.18.0) (PMID: 25765347).
Assembly: hg38
Supplementary files format and content: BigWig Track Format of each ATAC-seq sample.

extract_protocol:
Nuclei from 3 × 10^5 cells were isolated using a lysis buffer composed of 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20 and 0.01% Digitonin. Immediately after cell lysis, nuclei were pelleted in low-bind 1.5-ml tubes (Eppendorf) and resuspended in transpose mix (Vazyme)
Transposition was performed at 37 °C for 30 min. After purification of the DNA with the VAHTS DNA Clean Beads (Vazyme) at a 2 × ratio, libraries were barcoded using TruePrep™ Index Kit V2 for lllumina (Vazyme TD202) and amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned and size selected by VAHTS DNA Clean Beads at a 0.6 × / 0.7 × ratio.


title: HLF WT IgG CUT&RUN, DMSO, rep1

description: Library name: HLF_WT_DMSO_IgG_rep1


title: 22531-09

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 5-C human embryo #5 injected with ABE mRNA and PCSK9 sgRNAs_Experiment BE4


title: Whole blood, 6.58y, Female, Shih Tzu [ET060269]

value: Whole blood

value: Shih Tzu


title: Whole blood, 11.92y, Female, Maltese [ET060270]


title: HLF WT FOXA2 CUT&RUN, DMSO, rep2

description: Library name: HLF_WT_DMSO_FOXA2_rep2


title: 22537-34

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 6-C human embryo #5 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3

value: Preimplantation embryo


title: atac-seq, OCI-AML3 cells, siNPM1c, Day3, rep1

description: Library name: A_15

value: Bone marrow


title: HLF WT FOXA2 CUT&RUN, DMSO, rep1

description: Library name: HLF_WT_DMSO_FOXA2_rep1


title: 22537-33

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 6-C human embryo #5 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: Whole blood, 5.58y, Male, Shih Tzu [ET060268]

value: Male


title: Whole blood, 6.58y, Female, Pomeranian [ET060285]

value: Pomeranian


title: atac-seq, OCI-AML3 cells, siControl, Day3, rep2

description: Library name: A_NC

value: acute myeloid leukemia blast


title: 22537-31

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #13 from 13-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: HLF WT FOXA1 CUT&RUN, DMSO, rep2

description: Library name: HLF_WT_DMSO_FOXA1_rep2

value: WT


title: 22537-30

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #12  from 13-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: Whole blood, 3.00y, Male, Beagle [ET060267]

value: Beagle


title: HLF WT FOXA1 CUT&RUN, DMSO, rep1

description: Library name: HLF_WT_DMSO_FOXA1_rep1

value: HLF


title: atac-seq, OCI-AML3 cells, siControl, Day3, rep1

description: Library name: A_A3


title: HLF WT IgG CUT&RUN, Sorafenib, rep1

description: Library name: HLF_WT_Sorafenib_IgG_rep1

value: sorafenib 5 µM, 48 h


title: Whole blood, 0.83y, Female, Beagle [ET060266]


title: Whole blood, 0.58y, Female, Maltese [ET060265]

value: Maltese


title: H3K27ac CUT&Tag, OCI-AML3 cells, siNPM1c, Day3, rep2

description: Library name: S3_1

value: anti-H3K27ac (Cell Signaling Technology, 8173S)


title: HLF WT ARID1B CUT&RUN, DMSO, rep2

description: Library name: HLF_WT_DMSO_ARID1B_rep2


title: OCI-AML3 cells, siNPM1c, Day3, rep3

description:
Library name: si_nc15_2
Column name in all_counts.csv: si_nc15_2

data_processing:
Basecalls were performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence and low quality bases using cutadapt(v.2.6)
Clean reads were mapped to mm10 refernece genome using STAR (v.2.7.5a) .
Read counts were obtained by mapping the aligned reads to the transcripts of known genes from UCSC by using GenomicAlignments (v.1.30.0).
Differential expression analysis was performed with methods based on the negative binomial distribution in DESeq2 (v.1.34.0), using default parameters. Benjamini and Hochberg correction were used for significance tests and multiple comparisons.
Assembly: hg38
Supplementary files format and content: csv file includes raw counts for each Sample

extract_protocol:
RNA was harvested using RaPure Total RNA Micro Kit (Magen, R4012).
Library was constructed with Fast RNA-seq Lib Prep Kit V2 （Cat.No.RK20306）


title: 22537-27

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #9 from 13-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: HLF WT ARID1B CUT&RUN, DMSO, rep1

description: Library name: HLF_WT_DMSO_ARID1B_rep1


title: OCI-AML3 cells, siNPM1c, Day3, rep2

description:
Library name: si_nc15_1
Column name in all_counts.csv: si_nc15_1


title: 22537-25

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #7 from 13-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: Whole blood, 13.08y, Female, Poodle [ET060263]

value: Female

value: Poodle


title: Whole blood, 12.25y, Female, Maltese [ET060262]


title: OCI-AML3 cells, siControl, Day3, rep3

description:
Library name: si_con_2
Column name in all_counts.csv: si_con_2

value: siControl


title: Whole blood, 6.58y, Male, Yorkshire Terrier [ET060261]

value: Yorkshire Terrier


title: HLF WT H3K4me3 CUT&RUN, DMSO, rep1

description: Library name: HLF_WT_DMSO_H3K4me3_rep1

value: DMSO vehicle (0.1% v/v)


title: 22537-22

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #4 from 13-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: HLF WT H3K27ac CUT&RUN, DMSO, rep2

description: Library name: HLF_WT_DMSO_H3K27ac_rep2


title: OCI-AML3 cells, siControl, Day3, rep2

description:
Library name: si_con_1
Column name in all_counts.csv: si_con_1


title: OCI-AML3 cells, siControl, Day3, rep1

description:
Library name: si_con
Column name in all_counts.csv: si_con


title: HLF WT H3K27ac CUT&RUN, DMSO, rep1

description: Library name: HLF_WT_DMSO_H3K27ac_rep1


title: 22537-20

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 13-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: Whole blood, 5.58y, Female, Shih Tzu [ET060260]

value: Whole blood

value: Shih Tzu


title: Whole blood, 3.00y, Male, Beagle [ET060259]


title: WaGa cells, PRMT5i treatment, rep 3

city: Cambridge

first: Camille

last: Cushman

state: MA

address: 700 Main St

institute: Viska Bio

description:
Library name: WaGa PRMT5i biol rep 3
Counts_WaGa_4d.csv column name: WaGa_4d_R3

data_processing:
To generate counts for differential expression analysis, raw reads were aligned to transcripts from human GRCh38 genome (ensGRCh38p.13_v102) concatenated with the Merkel cell polyomavirus genome (GCF_000874865.1_ViralProj28509) using Salmon (salmon quant -l A \ --writeUnmappedNames \ --seqBias \ --gcBias \ --validateMappings \).
Read count normalization was performed using DESeq. Output file names from this analysis begin with "Count".
To generate counts for alternative splicing analysis, raw reads were mapped to the human GRCh38 genome using STAR (--runMode alignReads \ --runThreadN 16 \ --sjdbOverhang 149 \ --outReadsUnmapped Fastx \ --outSAMtype BAM SortedByCoordinate \ --outFilterMultimapNmax 20 \ --outFilterMismatchNmax 999 \ --outFilterMismatchNoverLmax 0.04 \ --alignIntronMin 70 \ --alignIntronMax 500000 \ --alignMatesGapMax 500000 \ --alignSJoverhangMin 8 \ --alignSJDBoverhangMin 1 \ --outSAMstrandField intronMotif \ --outFilterType BySJout \ --twopassMode Basic) and Bowtie (-n 1 -l 30 -e 70 -t -p 4 -m 1 -X 500 -S).
Mapped reads were filtered using Bedtools to remove reads overlapping expressed repeats from the UCSC genome browser RNA repeats and Gencode hg38 and coding exons annotated in the Gencode hg38 annotations. Alternative and constitutive classifications were performed using custom Python scripts and are agnostic to existing annotations other than known gene boundaries. All three cell lines were run in parallel to ensure consistency between annotations. Alternative splicing events were quantified using DEXSeq.
Assembly: For differential expression analysis: ensGRCh38p.13_v102 and GCF_000874865.1_ViralProj28509; For alternative splicing analysis: Gencode hg38 v27
Supplementary files format and content: comma-separated file (.csv) includes counts for each sample with each cell line normalized with DESeq
Supplementary files format and content: tab-delimited file (.txt) includes counts for each sample along with transcript annotation and statistical information generated from DEXSeq. Columns containing count data begin with "countData" and contain the name of the raw file it corresponds to.

source_name: WaGa

growth_protocol: All cell lines were maintained in RPMI supplemented with 10% FBS and antibiotics in a humidified environment at 37C and 5% CO2.

extract_protocol:
RNA was extracted using TRIzol (ThermoFisher, 15596026) according to manufacturer's guidelines.
RNA libraries were prepared from total RNA with poly-A selection prior to sequencing.

treatment_protocol: Cells were treated with PRMT5i (JNJ-64619178) for 4 days or DMSO control.

value: WaGa

value: Merkel cell carcinoma cell line


title: 22537-19

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 13-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3

value: Preimplantation embryo


title: BRD4 IL-26, TNF-α, IL-1β,  and JQ1

city: Bunkyo-ku

first: Yuta

last: Hasegawa

state: Tokyo

address: Hongo 2-1-1

department: Graduate School of Medicine

institute: Juntendo University

description:
Library name: D012-Br-26-T1JQ
COLO205_BRD4_IL-26,TNF-α, IL-1β and JQ1

data_processing:
Equally pooled libraries of the samples were sequenced on a NovaSeq X Plus System (Illumina), in 151-bp paired-end reads.
Sequencing adaptors, low-quality reads, and bases were trimmed using the Trimmomatic-0.39 tool.
Sequence reads were aligned to the UCSC human reference genome (hg38) using Bowtie2 version 2.4.5.
Peaks were called using MACS2 version 2.2.7.1.
bigWig files were generated using UCSC bedGraphTobigWig program.bedGraph files were generated using MACS2 version 2.2.7.1 with default setting.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Colon

growth_protocol: RPMI-1640, 10% fetal bovine serum, 50 U/mL penicillin, and 50 µg/mL streptomycin. Cells were cultured at 37°C with 5% CO2.

extract_protocol:
COLO205 cells were crosslinked with 1% formaldehyde, quenched with glycine, harvested, and lysed. Chromatin was fragmented by sonication and immunoprecipitated using antibodies against H3K27ac or BRD4. ChIP DNA was then purified and used for library preparation.
Library preparation was performed using the TruSeq ChIP Library Preparation kit (Illumina, San Diego, CA, USA).

treatment_protocol: COLO205 Cells were untreated or stimulated with human TNF-alpha, IL-1β and/or　IL-26 for 12 h . For BET inhibition experiments, cells were treated with JQ1 together with the indicated cytokines.

value: Colon

value: Colorectal adenocarcinoma

value: parental

value: IL-26,TNF-α, IL-1βand JQ1

tag: chip antibody


title: WaGa cells, DMSO treatment, rep 3

description:
Library name: WaGa DMSO biol rep 3
Counts_WaGa_4d.csv column name: WaGa_DMSO_R3

value: DMSO


title: 22537-17

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #4 from 6-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3

source_name: Blastomere from ABE-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D4


title: Whole blood, 0.83y, Female, Beagle [ET060258]

value: Beagle


title: WaGa cells, PRMT5i treatment, rep 2

description:
Library name: WaGa PRMT5i biol rep 2
Counts_WaGa_4d.csv column name: WaGa_4d_R2


title: BRD4 IL-26, TNF-α and IL-1β

description:
Library name: D010-Br-26-T1
COLO205_BRD4_IL-26,TNF-α and IL-1β

value: IL-26,TNF-α and IL-1β


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t11hr Post-Splice BiolRep3

city: St. Louis

first: Joseph

middle: D

last: Dougherty

state: MO

address: 4370 Duncan Ave

institute: Washington University in St. Louis

description: Library name: 3UTR.ActD.Eleven.Post.3

data_processing:
Sequencing reads were aligned to reference libraries using custom scripts to identify exact matches, normalized with edgeR (TMM method) to CPM, filtered for low counts, and used to calculate log₂(RNA/DNA) expression or translational efficiency (TRAP), with variant pairs filtered to retain those with ≥4 measurements across conditions.
Assembly: hg38
Supplementary files format and content: counts.txt

source_name: kidney

growth_protocol: In Vitro: HEK cells were maintained in EMEMsupplemented with 10%FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol Reagent and Zymo Clean and Concentrator Kit. 5ug of RNA per replicate were used for Library Preparation.
RNA libraries for RNA-seq were prepared using a targeted-RNA seq library preparation approach that followed similar paradigms to a Tru-Seq library construction for Illumina Sequencing.

treatment_protocol: In Vitro: Transfection was induced on 24 hours after plating and then cells were harvested 48hours after using Trizol. In Vivo: Mice were injected with AAV virus at PND1 and allowed to age until date of harvest; PND10 for Empra/eISOMPRA, PND21 for uISOMPRA. ActinomycinD:Transfection was induced on 24 hours after plating, and then on set of cells were harvested 48hours after.  5ug/mL ActinomycinD was added to the two remaining sets of cells, and one was harvested 5 hours post addition, and the final at 11 hours post addition.

value: kidney

value: human embryonic kidney cells

value: WT

value: ISOMPRA Library Transfection


title: HepG2 ARID1B-KO H3K27ac CUT&RUN, Sorafenib, rep1

description: Library name: HepG2_ARID1B-KO_Sorafenib_H3K27ac_rep1

value: sorafenib 5 µM, 48 h


title: Whole blood, 13.08y, Female, Poodle [ET060255]

value: Whole blood

value: Female

value: Poodle


title: WaGa cells, DMSO treatment, rep 2

description:
Library name: WaGa DMSO biol rep 2
Counts_WaGa_4d.csv column name: WaGa_DMSO_R2

value: WaGa

value: Merkel cell carcinoma cell line


title: Whole blood, 0.58y, Female, Maltese [ET060257]

value: Maltese


title: BRD4 IL-26

description:
Library name: D009-Br-26-C
COLO205_BRD4_IL-26

value: Colon

value: Colorectal adenocarcinoma


title: WaGa cells, PRMT5i treatment, rep 1

description:
Library name: WaGa PRMT5i biol rep 1
Counts_WaGa_4d.csv column name: WaGa_4d_R1


title: BRD4  TNF-α and IL-1β

description:
Library name: D008-Br-T1
COLO205_BRD4_TNF-α and IL-1β

value: parental

value: TNF-α and IL-1β


title: 22537-14

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 6-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3

value: Preimplantation embryo


title: Whole blood, 6.58y, Female, Yorkshire Terrier [ET060253]

value: Yorkshire Terrier


title: Whole blood, 12.33y, Female, Maltese [ET060254]


title: WaGa cells, DMSO treatment, rep 1

description:
Library name: WaGa DMSO biol rep 1
Counts_WaGa_4d.csv column name: WaGa_DMSO_R1

value: DMSO


title: BRD4 Control

description:
Library name: D007-Br-C
COLO205_BRD4_Control


title: MS-1 cells, PRMT5i treatment, rep 3

description:
Library name: MS-1 PRMT5i biol rep 3
Counts_MS1_4d.csv column name: MS1_PRMT5i_R3


title: 22537-13

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 3-C human embryo #2 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: H3K27Ac IL-26, TNF-α, IL-1β,  and JQ1

description:
Library name: D006-H3-26-T1JQ
COLO205_H3K27Ac_IL-26,TNF-α, IL-1β and JQ1

value: IL-26,TNF-α, IL-1βand JQ1


title: MS-1 cells, DMSO treatment, rep 3

description:
Library name: MS-1 DMSO biol rep 3
Counts_MS1_4d.csv column name: MS1_DMSO_R3


title: Whole blood, 5.58y, Male, Yorkshire Terrier [ET060252]

value: Male


title: H3K27Ac  TNF-α, IL-1β and JQ1

description:
Library name: D005-H3-T1-JQ
COLO205_H3K27Ac_TNF-α, IL-1βand JQ1

value: TNF-α, IL-1β and JQ1


title: 22537-11

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 3-C human embryo #2 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: MS-1 cells, PRMT5i treatment, rep 2

description:
Library name: MS-1 PRMT5i biol rep 2
Counts_MS1_4d.csv column name: MS1_PRMT5i_R2


title: HEK293 cells, ISOMPRA 3'UTR Library Transfected, Actinomycin D t5hr Post-Splice BiolRep5

description: Library name: 3UTR.ActD.Five.Post.5

value: kidney

value: human embryonic kidney cells

value: WT

value: ISOMPRA Library Transfection


title: H3K27Ac IL-26, TNF-α and IL-1β

description:
Library name: D004-H3-26-T1
COLO205_H3K27Ac_IL-26,TNF-α and IL-1β

value: IL-26,TNF-α and IL-1β


title: Whole blood, 0.83y, Female, Beagle [ET060250]

value: Whole blood

value: Female

value: Beagle


title: OCI-AML3 cells, siNPM1c, Day3, rep1

description:
Library name: si_nc15
Column name in all_counts.csv: si_nc15

value: Bone marrow

value: acute myeloid leukemia blast


title: HLF WT H3K4me3 CUT&RUN, DMSO, rep2

description: Library name: HLF_WT_DMSO_H3K4me3_rep2

value: HLF

value: DMSO vehicle (0.1% v/v)


title: Whole blood, 0.58y, Female, Maltese [ET060249]

value: Maltese


title: 22537-24

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #6 from 13-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3

value: Preimplantation embryo


title: 22537-10

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #10 from 10-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: MS-1 cells, DMSO treatment, rep 2

description:
Library name: MS-1 DMSO biol rep 2
Counts_MS1_4d.csv column name: MS1_DMSO_R2

value: Merkel cell carcinoma cell line

value: DMSO


title: H3K27Ac IL-26

description:
Library name: D003-H3-26-C
COLO205_H3K27Ac_IL-26

value: Colon

value: Colorectal adenocarcinoma

value: parental


title: 22537-09

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #9 from 10-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: 22537-21

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 13-C human embryo #4 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: Whole blood, 12.75y, Female, Beagle [ET060247]


title: H3K27Ac  TNF-α and IL-1β

description:
Library name: D002-H3-T1
COLO205_H3K27Ac_TNF-α and IL-1β

value: TNF-α and IL-1β


title: MS-1 cells, PRMT5i treatment, rep 1

description:
Library name: MS-1 PRMT5i biol rep 1
Counts_MS1_4d.csv column name: MS1_PRMT5i_R1


title: 22537-08

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #8 from 10-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: MS-1 cells, DMSO treatment, rep 1

description:
Library name: MS-1 DMSO biol rep 1
Counts_MS1_4d.csv column name: MS1_DMSO_R1


title: H3K27Ac Control

description:
Library name: D001-H3-C
COLO205_H3K27Ac_Control


title: 22537-07

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #7 from 10-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: Whole blood, 12.17y, Female, Poodle [ET060246]

value: Poodle


title: MKL-1 cells, PRMT5i treatment, rep 3

description:
Library name: MKL-1 PRMT5i biol rep 3
Counts_MKL1_4d.csv column name: MKL1_4d_R3


title: 22537-06

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #6 from 10-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: BRD4 TNF-α, IL-1β and JQ1

description:
Library name: D011-Br-T1-JQ
COLO205_BRD4_TNF-α, IL-1βand JQ1

value: TNF-α, IL-1β and JQ1


title: 22537-04

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #4 from 10-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: MKL-1 cells, DMSO treatment, rep 3

description:
Library name: MKL-1 DMSO biol rep 3
Counts_MKL1_4d.csv column name: MKL1_DMSO_R3


title: facial, temporal region, donor 1, section D2

city: Hamburg

first: Tolga

last: Düz

address: Beiersdorfstraße 1-9

country: Germany

institute: Beiersdorf AG

description:
Library name: V2_R1_s1_D2
8 µm binned output

data_processing:
Raw sequencing data were processed with Space Ranger (v3.1.3, 10x Genomics) for demultiplexing, alignment to the GRCh38-2024-A reference genome, read trimming, de-duplication, filtering, and generation of feature-barcode matrices. Spatial data were aligned to microscopic images with Image Reorientation and Filter probes enabled, resulting in 18,085 protein-coding genes targeted by 53,504 probes for downstream spatial analysis. Sequencing was performed on a NovaSeq® X Plus (Illumina).
Assembly: GRCh38-2024-A
Supplementary files format and content: matrix.mtx.gz: Raw UMI count matrix including all barcodes across the entire capture area.
Supplementary files format and content: features.tsv.gz: List of all genes/features corresponding to the rows of matrix.mtx.gz.
Supplementary files format and content: barcodes.tsv.gz: List of all barcodes corresponding to the columns of matrix.mtx.gz.
Supplementary files format and content: filtered_feature_bc_matrix.h5: Filtered HDF5 matrix containing only barcodes/spots passing quality control.
Supplementary files format and content: tissue_hires_image.png: High-resolution tissue image used for spatial mapping.
Supplementary files format and content: tissue_lowres_image.png: Low-resolution tissue image for quick visualization.
Supplementary files format and content: scalefactors_json.json: JSON file with scaling factors to map spot coordinates to tissue image pixels.
Supplementary files format and content: tissue_positions.parquet: Table with coordinates of each spot, aligned to the tissue image.
Library strategy: Spatial Transcriptomics

source_name: Skin

extract_protocol:
Fresh frozen human skin tissue was sectioned using a cryostat. Three 5 µm sections were collected for RNA isolation and quality control, and one 5 µm section was mounted on Schott Nexterion™ 3-D Hydrogel-coated slides for spatial transcriptomics. RNA quality was assessed using the Agilent Fragment Analyzer; only samples with RNA quality number (RQN) ≥4 were used.
Spatial gene expression libraries were prepared using the 10x Genomics Visium HD Spatial Gene Expression Reagent Kits following the manufacturer’s protocols. Tissue sections were formaldehyde-fixed, H&E-stained, scanned, destained, and permeabilized. Whole-transcriptome hybridization was performed overnight using the human probe set v2.0 (18,536 protein-coding genes, 54,018 probes), followed by probe ligation, capture, extension to generate spatially barcoded ligation products, pre-amplification, purification, and library construction. All experimental steps were conducted by Crown Bioscience Germany GmbH.

value: Skin

value: Pilosebaceous Unit

tag: disease state

value: Healthy

tag: ethnicity

value: White

tag: reference


title: Whole blood, 5.33y, Male, Beagle [ET060245]

value: Whole blood

value: Male

value: Beagle


title: Whole blood, 5.58y, Female, Yorkshire Terrier [ET060244]

value: Female

value: Yorkshire Terrier


title: MKL-1 cells, PRMT5i treatment, rep 2

description:
Library name: MKL-1 PRMT5i biol rep 2
Counts_MKL1_4d.csv column name: MKL1_4d_R2

value: Merkel cell carcinoma cell line


title: 22537-03

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 10-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3

value: Preimplantation embryo


title: 22537-16

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 6-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: PA treated HepG2 cells for Cur and copper incubation_3

city: Chongqing

first: si

last: qin

state: Chongqing

institute: The Third Affiliated Hospital of Chongqing Medical University

data_processing:
Through removing low quality, ploy-N, and adapter contained reads by in-house perl scripts, high-quality clean data were used for further analysis.
After building index of the reference genome (GRCh38.p13), paired-end clean reads were aligned to the mouse genome using Hisat (v2.1.0).
For the quantification of gene expression, RSEM (v1.3.3) was used to count the clean reads numbers mapped to each gene, and the TPM (transcripts per million reads) value of each gene was obtained according to the gene length and reads count.
Assembly: GRCh38.p13
Supplementary files format and content: Text file include all TPM values for each Sample

growth_protocol: HepG2 cells were gifted by Dr. Hongmin Zhang [Department of Infectious Diseases, Institute for Viral Hepatitis, Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Chongqing, China] and cultured in Dulbecco's modified Eagle's medium (DMEM; Gibco Life Science, Grand Island, NY, USA) containing 10% fetal bovine serum and 1% penicillin-streptomycin (Beyotime, Shanghai, China), at 37°C in a 95%-O2 and 5%-CO2 atmosphere.

extract_protocol:
RNA was harvested using TRIzol (Takara, Shiga, Japan). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina® Stranded mRNA Prep, Ligation according to manufacturer’s recommendations.

treatment_protocol: For PA group, The HepG2 cells pre-treated with 750 μM for 24h. For PA-Cur group, the cells pre-treated with 750 μM for 24h, were then incubated with 20 μM Cur for 12 h. For PA-Cur-Cu group, the PA-treated HepG2 cells were co-treated with Cur (20 µM) and CuCl2 (5 µM) for 12 h.

value: liver

value: Human hepatocellular carcinomas

value: cancer cell

value: Cur-Cu + PA


title: Whole blood, 2.08y, Male, German Shepherd [ET060243]

value: German Shepherd


title: facial, temporal region, donor 1, section D1

description:
Library name: V2_R3_s3_D1
8 µm binned output


title: PA treated HepG2 cells for Cur and copper incubation_2


title: Whole blood, 0.58y, Male, Beagle [ET060242]


title: MKL-1 cells, DMSO treatment, rep 2

description:
Library name: MKL-1 DMSO biol rep 2
Counts_MKL1_4d.csv column name: MKL1_DMSO_R2

value: DMSO


title: Whole blood, 0.58y, Male, Poodle [ET060241]

value: Poodle


title: 22537-15

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 6-C human embryo #3 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: 22537-02

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 10-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: MKL-1 cells, PRMT5i treatment, rep 1

description:
Library name: MKL-1 PRMT5i biol rep 1
Counts_MKL1_4d.csv column name: MKL1_4d_R1


title: PA treated HepG2 cells for Cur and copper incubation_1


title: 22537-01

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 10-C human embryo #1 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: PA treated HepG2 cells for Cur incubation_3

value: Cur + PA


title: Whole blood, 13.67y, Female, Beagle [ET060239]


title: MKL-1 cells, DMSO treatment, rep 1

description:
Library name: MKL-1 DMSO biol rep 1
Counts_MKL1_4d.csv column name: MKL1_DMSO_R1


title: 22424-27

description:
Other option: Treff method - Phi29 mediated amplification
ES cells from the ICM outgrowth of 6AA human blastocyst; embryo #5 injected with ABE RNP with HBG1/2 & PCSK9 sgRNAs_Experiment BE2

source_name: ESCs from outgrowth of ABE-injected human embryo (at 2PN stage on day 1 of development, D1)


title: P3b_RNA

city: Pittsburgh

first: Timothy

last: Billiar

state: PA

address: 200 Lothrop Street

department: Surgery

institute: University of Pittsburgh

description:
Library name: P3b_RNA
DOGMA-seq

data_processing:
For each sample, HTO and ADT fastq files were processed by kite (https://github.com/pachterlab/kite) to get an ADT count matrix and a HTO count matrix. For multiome data (GEX and ATAC), feature-barcode count matrix was generated using cellranger-arc count (mapped to GRCh38 human reference genome) and cellranger-arc aggr. Seurat and Signac were used to create an object for the feature-barcode count matrix of multiome data, and ADT matrix and HTO matrix were added to this Seurat object.
Assembly: GRCh38
Supplementary files format and content: DOGMAseq_CD14mono.rds

source_name: PBMC

extract_protocol:
Blood samples were obtained from human study subjects. PBMCs were isolated by standard Ficoll centrifugation.
For each sample, ~ 0.5 million cells were transferred into two 1.5 mL low-binding tubes, incubated with Human TruStain FcX™ (BioLegend) for 10 min and then incubated with a unique TotalSeq™-A anti-human Hashtag antibody (BioLegend) for 30 min. After 3 times of wash (1350 rpm * 5min, PBS+2%FBS), 187500 cells/tube were pooled into one 1.5 mL low-binding tube and incubated with TotalSeq™-A Human Universal Cocktail, V1.0 (BioLegend) for 30 min. Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kits were purchased to prepare GEX and ATAC libraries.

value: PBMC


title: Whole blood, 12.17y, Female, Poodle [ET060238]


title: Whole blood, 3.00y, Male, Beagle [ET060251]


title: Whole blood, 5.25y, Male, Beagle [ET060237]


title: PA treated HepG2 cells for Cur incubation_2


title: P3b_HTO

description:
Library name: P3b_HTO
DOGMA-seq


title: 22424-25

description:
Other option: Treff method - Phi29 mediated amplification
TE cells #1 from the outgrowth of 6AA human blastocyst; embryo #5 injected with ABE RNP with HBG1/2 & PCSK9 sgRNAs_Experiment BE2

data_processing:
Affymetrix UK Biobank Axiom Array Manufacturer's Protocol
Primary data description: DNA copy number and genotyping

source_name: TE cells from outgrowth of ABE-injected human embryo (at 2PN stage on day 1 of development, D1)


title: PA treated HepG2 cells for Cur incubation_1


title: 22424-26

description:
Other option: Treff method - Phi29 mediated amplification
TE cells #2 from the outgrowth of 6AA human blastocyst; embryo #5 injected with ABE RNP with HBG1/2 & PCSK9 sgRNAs_Experiment BE2


title: P3b_ATAC

description:
Library name: P3b_ATAC
DOGMA-seq

library_source: other

molecule: other


title: PA treated HepG2 cells_3

value: PA


title: 22476-13

description:
Other option: Treff method - Phi29 mediated amplification
TE biopsy from 4BB human blastocyst; embryo #6 injected with ABE RNP with HBG1/2 & PCSK9 sgRNAs_Experiment BE2

source_name: TE biopsy from ABE-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D6


title: Whole blood, 2.00y, Female, Beagle [ET060235]

value: Whole blood


title: Whole blood, 5.33y, Male, Beagle [ET060236]

value: Male


title: 22537-12

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 3-C human embryo #2 injected with ABE RNP with PCSK9 sgRNAs_Experiment BE3


title: P3b_ADT

description:
Library name: P3b_ADT
DOGMA-seq


title: 22476-07

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 4-C human embryo #4 injected with ABE RNP with HBG1/2 & PCSK9 sgRNAs_Experiment BE2


title: P3a_RNA

description:
Library name: P3a_RNA
DOGMA-seq


title: Whole blood, 0.58y, Male, Beagle [ET060234]

value: Beagle


title: PA treated HepG2 cells_2

source_name: liver


title: 22476-05

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 3-C human embryo #3 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE2


title: PA treated HepG2 cells_1


title: CnR_merged_IgG_to_B-MYB_pT487

city: Wuerzburg

first: Stefan

last: Gaubatz

address: Am Hubland

department: Biochemistry and Cell Biology

institute: University of Wuerzburg

description: Library name: Sample 13

data_processing:
Base calling was performed using Illumina’s BaseSpace platform
Galaxy was used to analyze NGS data (https://usegalaxy.eu)
Reads were mapped to the human genome (hg38) using Bowtie2 (2.5.3)
Files were converted to bigwig with bamCoverage (3.5.4)
Assembly: hg38
Supplementary files format and content: bigWig files
Library strategy: CUT&Run

growth_protocol: A549 mAID TRRAP cells were cultured in RPMI medium supplemented with 10% FCS and 1% penicillin/streptomycin

extract_protocol:
Cells were detached, coupled to ConA-coated magnetic beads (Polysciences Europe) and permeabilized. Primary antibody (2 µg anti-HA, Abcam, ab9110 or 2 µg anti B-MYB pT487, Abcam, ab76009) was added over night at 4 °C. Cells were then washed in the presence of digitonin and Protein A-MNase was added for 1 hour at 4°C. Next, cells were washed with low-salt rinse buffer. Incubation buffer containing CaCl2 and digitonin was added for 30 min at 4°C. Mnase activity was stopped in the presence of 20 µg/ml Rnase A. DNA fragments were released at 37°C for 30 min and decrosslinking was performed for 1 hour at 50°C by adding 0.01% SDS and 10 mg/ml Proteinase K. DNA was extracted with phenol-chloroform and resuspended in TE buffer.
Libraries were prepared with NEBnext Ultra II DNA Library Prep Kit (New England Biolabs). Libraries were PCR amplified for 12-16 cycles. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq2000 Illumina platform.

treatment_protocol: For the HA CUT&RUN, TRRAP degradation was performed by addition of 1µM 5-PH-IAA for 6h. CHK1i was performed by addition of 100nM prexasertib for 4h. For the B-MYB (pT487) CUT&RUN, cells were treated with DMSO or with 1µM 5-Ph-IAA for 16 hours.

value: lung carcinoma

value: mAID-TRRAP

value: 5-Ph-IAA, 16 hours


title: Whole blood, 0.58y, Male, Poodle [ET060233]


title: P3a_HTO

description:
Library name: P3a_HTO
DOGMA-seq


title: 22476-04

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 3-C human embryo #3 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE2

extract_protocol: Single cells, single polar bodies, or cytoplasmic fragments were placed into single PCR tubes containing 2 ul of Genomic Prediction's loading Buffer. Genomic DNA amplification was performed using amplification kit as indicated for each sample.

value: Preimplantation embryo


title: P3a_ATAC

description:
Library name: P3a_ATAC
DOGMA-seq


title: 22476-03

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 3-C human embryo #3 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE2


title: CnR_B-MYB_pT487_IAA

description: Library name: Sample 12


title: P3a_ADT

description:
Library name: P3a_ADT
DOGMA-seq


title: Whole blood, 12.17y, Female, Poodle [ET060230]

value: Female


title: Whole blood, 12.83y, Female, Beagle [ET060231]


title: CnR_B-MYB_pT487_DMSO

description: Library name: Sample 11


title: 22476-01

description:
Other option: Treff method - Phi29 mediated amplification
1-C human embryo #1 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE2


title: Whole blood, 5.50y, Female, Beagle [ET060229]


title: CnR_merged_IgG_to_HA_r2

description: Library name: Sample 10

value: 5-Ph-IAA, 6 hours and CHK1i, 4 hours


title: 22424-23

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 2-C human embryo #13 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1

source_name: Blastomere from ABE-injected human embryo (at 2PN stage on day 1 of development, D1); Sample collected on day D3


title: P2b_RNA

description:
Library name: P2b_RNA
DOGMA-seq


title: P2b_HTO

description:
Library name: P2b_HTO
DOGMA-seq


title: 22424-22

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 2-C human embryo #12 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: Whole blood, 5.25y, Male, Beagle [ET060228]


title: CnR_merged_IgG_to_HA_r1

description: Library name: Sample 9


title: P2b_ATAC

description:
Library name: P2b_ATAC
DOGMA-seq


title: CnR_HA_IAA_CHK1i_r2

description: Library name: Sample 8


title: 22424-21

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 2-C human embryo #12 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: Whole blood, 2.00y, Female, Beagle [ET060227]


title: Whole blood, 0.58y, Male, Beagle [ET060226]


title: P2b_ADT

description:
Library name: P2b_ADT
DOGMA-seq


title: CnR_HA_IAA_CHK1i_r1

description: Library name: Sample 7


title: 22424-20

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 2-C human embryo #11 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: P1_RNA

description:
Library name: P1_RNA
DOGMA-seq


title: 22424-19

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 2-C human embryo #11 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: CnR_HA_IAA_r2

description: Library name: Sample 6

value: 5-Ph-IAA, 6 hours


title: P1_HTO

description:
Library name: P1_HTO
DOGMA-seq


title: 22424-18

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #4 from 4-C human embryo #10 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: CnR_HA_IAA_r1

description: Library name: Sample 5


title: CnR_HA_CHK1i_r2

description: Library name: Sample 4

value: CHK1i, 4 hours


title: 22424-17

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #3 from 4-C human embryo #10 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs _Experiment BE1


title: P1_ATAC

description:
Library name: P1_ATAC
DOGMA-seq


title: Whole blood, 13.17y, Female, Maltese [ET060223]

value: Maltese


title: Whole blood, 0.58y, Male, Poodle [ET060225]


title: Whole blood, 8.00y, Male, Beagle [ET060222]


title: Whole blood, 5.50y, Female, Beagle [ET060221]


title: CnR_HA_CHK1i_r1

description: Library name: Sample 3


title: P1_ADT

description:
Library name: P1_ADT
DOGMA-seq


title: 22424-16

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 4-C human embryo #10 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: MM5040-D7-MCSF

description:
Library name: MM5040-D7-MCSF
scRNA-seq

data_processing:
We generated feature-barcode count matrix using cellranger count (mapped to GRCh38 human reference genome) for each sample separately. The outputs of the samples from the same donor were aggregated using cellranger aggr. The feature-barcode count matrix was processed using Seurat package.
Assembly: GRCh38
Supplementary files format and content: D3D7_CD14mono.rds, Ma-healthy.rds, Ma-trauma.rds

growth_protocol: On day 0, cryopreserved PBMCs were thawed and resuspended in complete media (RPMI164+ 10%FBS + penicillin (100U/mL) + streptomycin (100U/mL)) at 5 * 10^5 cell/mL at 37° with 5%CO2 overnight.

extract_protocol:
Blood samples were obtained from human study subjects. PBMCs were isolated by standard Ficoll centrifugation.
Flow isolated monocytes were further proceeded with scRNA libraries using Chromium Single Cell 3' Reagent Kits (v3.1, CG000315)

treatment_protocol: On day 1, GM-CSF (Sigma-Aldrich, Cat# G5035; final concentration: 50 ng/mL) or M-CSF (Sigma-Aldrich, Cat# H6916; final concentration: 50 ng/mL) were added to the media. On day 4, the same amount of fresh complete media with or without cytokines correspondingly were added to the cultured cells. Cells were harvested on day 7 (Accutase: Sigma-Aldrich, Cat# A6964).

value: in vitro culture


title: CnR_HA_DMSO_r2

description: Library name: Sample 2

value: DMSO


title: Whole blood, 5.50y, Female, Beagle [ET060220]


title: 22424-15

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 4-C human embryo #10 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: MM5040-D7-GMCSF

description:
Library name: MM5040-D7-GMCSF
scRNA-seq


title: 22424-13

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 2-C human embryo #9 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: CnR_HA_DMSO_r1

description: Library name: Sample 1


title: MM5040-D7-Ctrl

description:
Library name: MM5040-D7-Ctrl
scRNA-seq


title: Whole blood, 1.25y, Male, German Shepherd [ET060219]

value: German Shepherd


title: 22424-12

description:
Other option: Treff method - Phi29 mediated amplification
1-C human embryo #8 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: Whole blood, 0.58y, Female, Beagle [ET060218]


title: IAA_CHK1i_r3

description: Library name: Sample 12

data_processing:
Galaxy was used to analyze NGS data (https://usegalaxy.eu)
Reads were mapped to the human genome (hg38) using HISTAT2 (2.2.1)
Reads were counted with featureCounts (2.0.8)
Differential expression was assed with limma (3.58.1) with the significance value q<0.05
Assembly: hg38
Supplementary files format and content: Raw counts txt file, one file for all samples

extract_protocol:
RNA was isolated with RNeasy Mini Kit (Qiagen), including an on-column DNAse digestion.
The sequencing library was prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module. 1µg RNA was used for library preparation.

treatment_protocol: Cells were synchrosied for 20h with 2mM Thymidin. Cells were washed 2 times with 1x PBS and after addition of fresh medium were cultured for 4 more hours. TRRAP degardation was  performed by addition of 1µM 5-PH-IAA for 6h. CHK1i was performed by addition of 100mM prexasertib for 3h.

value: WT

value: 4h release from thymidin block, 5-Ph-IAA-treatment and CHK1i


title: MM5040-D3-MCSF

description:
Library name: MM5040-D3-MCSF
scRNA-seq

value: PBMC


title: IAA_CHK1i_r2

description: Library name: Sample 11


title: Whole blood, 0.58y, Female, Poodle [ET060217]

value: Whole blood

value: Poodle


title: 22424-11

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 2-C human embryo #7 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: Whole blood, 13.25y, Female, Maltese [ET060215]


title: 22424-10

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 2-C human embryo #7 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: IAA_CHK1i_r1

description: Library name: Sample 10

value: lung carcinoma


title: MM5040-D3-GMCSF

description:
Library name: MM5040-D3-GMCSF
scRNA-seq


title: MM5040-D3-Ctrl

description:
Library name: MM5040-D3-Ctrl
scRNA-seq


title: IAA_r3

description: Library name: Sample 9

value: 4h release from thymidin block and 5-Ph-IAA-treatment


title: 22424-08

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 2-C human embryo #6 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: Whole blood, 8.00y, Male, Beagle [ET060214]

value: Male

value: Beagle


title: MM5027-D7-MCSF

description:
Library name: MM5027-D7-MCSF
scRNA-seq


title: 22424-07

description:
Other option: Treff method - Phi29 mediated amplification
1-C human embryo #5 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1

value: Preimplantation embryo


title: MM5027-D7-GMCSF

description:
Library name: MM5027-D7-GMCSF
scRNA-seq


title: IAA_r2

description: Library name: Sample 8


title: MM5027-D7-Ctrl

description:
Library name: MM5027-D7-Ctrl
scRNA-seq


title: IAA_r1

description: Library name: Sample 7


title: 22424-06

description:
Other option: Treff method - Phi29 mediated amplification
1-C human embryo #4 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: Whole blood, 7.00y, Male, Beagle [ET060213]


title: Whole blood, 1.50y, Male, German Shepherd [ET060211]


title: Whole blood, 5.50y, Female, Beagle [ET060212]

value: Female


title: Whole blood, 0.58y, Female, Beagle [ET060210]


title: 22424-05

description:
Other option: Treff method - Phi29 mediated amplification
1-C human embryo #3 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: CHK1i_r3

description: Library name: Sample 6

value: 4h release release from thymidin block and CHK1i


title: MM5027-D3-MCSF

description:
Library name: MM5027-D3-MCSF
scRNA-seq


title: 22424-04

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 2-C human embryo #2 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs _Experiment BE1


title: CHK1i_r2

description: Library name: Sample 5


title: 22424-01

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 2-C human embryo #1 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: 22424-02

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #2 from 2-C human embryo #1 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs_Experiment BE1


title: DMSO_r2

description: Library name: Sample 2

value: 4h release from thymidin block


title: CHK1i_r1

description: Library name: Sample 4


title: MM5027-D3-GMCSF

description:
Library name: MM5027-D3-GMCSF
scRNA-seq


title: 22424-03

description:
Other option: Treff method - Phi29 mediated amplification
Blastomere #1 from 2-C human embryo #2 injected with ABE mRNA and HBG1/2 & PCSK9 sgRNAs _Experiment BE1


title: Whole blood, 0.58y, Female, Poodle [ET06029]


title: DMSO_r3

description: Library name: Sample 3


title: MM5027-D3-Ctrl

description:
Library name: MM5027-D3-Ctrl
scRNA-seq


title: MM4035-D7

description:
Library name: MM4035-D7
scRNA-seq

value: cryoperserved cells after thawing


title: Whole blood, 13.33y, Female, Maltese [ET06027]

value: Maltese


title: Whole blood, 8.00y, Male, Beagle [ET06026]


title: Whole blood, 7.00y, Male, Beagle [ET06025]


title: DMSO_r1

description: Library name: Sample 1


title: Whole blood, 5.33y, Male, Belgian Malinoise [ET06024]

value: Belgian Malinoise


title: MM4029-D7

description:
Library name: MM4029-D7
scRNA-seq


title: MM4029-D3

description:
Library name: MM4029-D3
scRNA-seq


title: Recurrent Pregnancy Loss Patient 13

city: Varanasi

first: Ashish

last: Ashish

address: Banaras Hindu University

country: India

institute: MRU Lab

description: Genomic DNA extracted from products of conception (RPOC) samples obtained from patients with a history of recurrent pregnancy loss (RPL). Copy number variations (CNVs) were detected using high-resolution array comparative genomic hybridization (aCGH) on Agilent SurePrint G3 Human CGH 4x180K microarrays. Each test sample (Cy5-labeled) was hybridized against pooled genomic DNA from Agilent Human Reference DNA(Cy3-labeled) to identify chromosomal gains, deletions, and amplifications associated with RPL.

hyb_protocol: Equal amounts of Cy5-labeled test DNA and Cy3-labeled reference DNA were combined and hybridized onto Agilent SurePrint G3 Human CGH 4x180K microarrays according to the manufacturer's protocol (Agilent Oligo aCGH/ChIP-on-Chip Hybridization Kit). The hybridization mixture was incubated at 65°C for 24–40 hours in a rotating hybridization oven at 20 rpm. After hybridization, arrays were washed using Agilent Oligo aCGH Wash Buffer Kit and scanned using an Agilent DNA Microarray Scannerand data were processed using the Agilent Feature Extraction 12.1 Software

scan_protocol: Microarrays were scanned using the Agilent SureScan G2600D Microarray Scanner at 3 μm resolution with default laser and PMT settings for two-color arrays.

data_processing: Cytogenomics v4.0.3.003

source_name: Products of Conception (RPOC)

label_protocol: Genomic DNA (500 ng) from test and reference samples was labeled using the Agilent Genomic DNA Labeling Kit according to the manufacturer’s instructions. Test sample DNA was labeled with Cy3-dUTP and reference DNA with Cy5-dUTP. Labeled products were purified using spin columns, and dye incorporation was quantified using a NanoDrop spectrophotometer.

growth_protocol: Not applicable. DNA was extracted directly from uncultured products of conception (RPOC) tissue obtained from spontaneous pregnancy loss. No cell culture or in vitro growth was performed.

extract_protocol: Genomic DNA was extracted from products of conception (RPOC) tissue using the QIAamp DNA Mini Kit (Qiagen), following the manufacturer’s instructions. Tissue samples were homogenized and lysed with proteinase K, followed by purification through silica-membrane columns. DNA concentration and purity were assessed using NanoDrop spectrophotometry and agarose gel electrophoresis.

treatment_protocol: Not Applicable

value: products of conception (RPOC)  disease status:recurrent pregnancy loss

tag: gestational age

value: first trimester (8–12 weeks)

source_name: Agilent Human Reference DNA

value: Agilent Human Reference DNA


title: MM4027-D7

description:
Library name: MM4027-D7
scRNA-seq

value: PBMC


title: KO, Input 3

city: Calgary

first: Ankita

last: Ankita

state: AB

address: 3330 Hospital Dr NW

department: Alberta Children’s Hospital Research Institute

country: Canada

institute: University of Calgary

description:
Library name: Sample 12
NextSeq P3 100 cycle

data_processing:
FASTQ files were aligned to the mm10 genome build using Bowtie2 (v2.5.4 ). For broad peak calling, MACS2 (v2.2.6) was used with a threshold of --broad-cutoff 0.1 and then DiffBind (v3.16.0) was used to generate consensus peaks.
BAM files were processed to generate bigwig  files using bamCoverage from deepTools (v3.5.6). RPGC (reads per genome coverage) normalisation method  was implemented for conversion. We used ProfileHeatmap from deepTools  to visualize the signal intensity  around consensus peaks of  ChIP and Input samples.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Trophoblast Stem Cells

growth_protocol: TSCs were cultured in Full Medium consisting of 20% fetal bovine serum (FBS) (Wisent 098-150), 1mM sodium pyruvate (ThermoFisher Scientific 11360070), 1x Antibiotic-Antimycotic (Wisent 450-115-EL), 55 μM 2-mercaptoethanol (Gibco 21985023), 37.5 ng/ml bFGF (Cambridge Stem Cell Institute), and 1μg/ml heparin (Sigma H3149) in RPMI 1640 with L-Glutamine (Wisent 350-000-CL), with 70% of the medium pre-conditioned on mouse embryonic fibroblasts.

extract_protocol:
Native ChIP-seq was performed on approximately 250,000 cells per reaction, resuspended to a concentration of ~5,000 cells/µl inl nuclear isolation buffer (Sigma, NUC-101). MNase digestion was carreid out at 21 ◦C for 8 min. Digested chromatin was then suspended in Complete IP buffer [20 mM Tris–HCl (pH 8), 2 mM EDTA, 150 mM NaCl, 0.1% Triton-X100, 1 ×Protease inhibitor cocktail, and 1 mM phenylmethanesulfonyl fluoride (PMSF)]. Following pre-clearing the chromatin on a mix of protein A / protein G beads, and after 10% was set aside for input, IP was performed overnight rotating at 30 rpm, at 4 ◦C, using 250 ng antibodies against H3K9me3 (Abcam, ab8898) and on a subset of samples also for H3K4me3 (Diagenode, C15200152). DNA was washed in low salt and then high salt washes, before eluting in ChIP elution buffer (100 mM NaHCO 3 and 1% SDS).
Libraries were generated with the NEB Ultra II kit and quantitated using a Agilent Bioanalyzer. Libraries were paired-end sequenced on a NextSeq2000 using the P3 100 cycle program.

value: Trophoblast Stem Cells

tag: genotype

value: Peg3 KO

value: NEB ultra II DNA library prep


title: KO, Input 2

description:
Library name: Sample 11
NextSeq P3 100 cycle


title: KO, Input 1

description:
Library name: Sample 10
NextSeq P3 100 cycle


title: Whole blood, 1.83y, Male, Belgian Malinoise [ET06023]

source_name: Whole blood

tag: tissue

value: Whole blood