title: OD600 0.5 ompR mutant rep1

first: Lijun

last: Wang

state: Beijing Shi

address: Shuangqing Road 30#

department: Department of Basic Medical Science

institute: Tsinghua University

description:
ompR mutant rep1
OD600 0.5

data_processing:
Illumina Casava1.7 software used for basecalling.
High quality reads in each sample were mapped to the reference genome using Bowtie2.
RSEM computes maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model.
TPM method is used to calculated expression level.
We identified differentially expressed genes by using the DESeq2 package.
Assembly: K. pneumoniae ATCC43816 (CP009208)  as reference genome
Supplementary files format and content: An excel file include TPM, counts, fold change, P values for each Sample.

organism: Klebsiella pneumoniae ATCC 43816

source_name: bacteria culture

extract_protocol:
Total RNA was extracted from culture grown on LB at OD600 of 0.5 using RNAprep pure Cell / Bacteria Kit according the manufacturer’s instructions (Tiangen Biotech, China) and further purified with a RNeasy Mini Kit (QIAGEN, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: ompR knockout

tag: medium

value: LB

tag: temperature

tag: condition

value: ambient air


title: OD600 0.5 WT rep2

status: Public on Apr 01 2024

type: SRA

city: Beijing

country: China

description:
WT rep2
OD600 0.5

library_source: transcriptomic

molecule: total RNA

tag: genotype

value: wide type


title: RAW264.7 cells, LPS-stimulated and treated with 10 μM GRd, sample 2

city: Harbin

first: Hui

last: Li

address: No.246 Xuefu Road

institute: 2nd affiliated hospital of Harbin Medical University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary files format and content: excel,expression profiles

organism: Mus musculus

growth_protocol: RAW264.7 cells were cultured in DMEM supplemented with 10% fetal bovine serum and incubated at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: RAW264.7 cells were stimulated with LPS for 6h, then GRd (20 μmol/L) at different concentration (0, 1, 5, 10, and 20 μmol/L) was added and the cells were incubated for 24 h.

tag: cell line

tag: cell type

value: Macrophages

value: WT

tag: treatment

value: LPS and 10 uM GRd

tag: time

value: LPS for 6h, then GRd for 24 h


title: OD600 0.5 WT rep1

description:
WT rep1
OD600 0.5


title: RAW264.7 cells, LPS-stimulated and treated with 10 μM GRd, sample 3


title: RAW264.7 cells, miRNA, control 2

value: no LPS or GRd


title: RAW264.7 cells, miRNA, control 3


title: retinal organoid, Isogenic Control, D260, Multiome (ATAC)

city: Iowa City

first: Nathaniel

middle: Kevin

last: Mullin

state: IA

address: 375 Newton Road

country: USA

institute: University of Iowa

library_source: genomic

data_processing:
Single-cell gene expression data integration and processing: scRNA libraries were pooled and sequenced using the NovaSeq 6000 instrument (Illumina) generating 100-bp paired end reads. FASTQ files were generated from base calls with the bcl2fastq software (Illumina). For the ESCS Patient 2 experiment, reads were mapped to the pre-built GRCh38 reference (refdata-gex-GRCh38-2020-A) with Cell Ranger v7.0.0 (10X Genomics) using the ‘count’ function with the following parameters: --expect-cells=8000 --localcores=56. Only cells passing the default Cell Ranger call were analyzed further. For the AAV experiment, custom reference genomes were built to allow mapping of EGFP and associated 3’UTR regions originating from AAV cargo. For AAV- NR2E3-T2A-EGFP transduced and untransduced samples, reads were mapped to a reference genome containing T2A-EGFP-BGHpolyA sequence. For AAV-EGFP transduced samples, reads were mapped to a reference genome containing EGFP-WPRE-BGHpolyA sequence. Data from all samples was integrated using CCA. The top 2000 variable features as determined by vst method were used. For AAV-transduced samples, the transgene feature was not included as a variable feature. Only cells with between 1,000 and 7,000 unique genes (features) were included in the analysis. Only cells with < 10% of reads mapping to mtDNA-encoded genes and < 20% of reading mapping to ribosomal genes were included. Counts data were normalized using the NormalizeData function (Seurat) with the following parameters: normalization.method = "LogNormalize", scale.factor = 10000. 2000 variable features were identified with the FindVariableFeatures function using the vst selection method. Integration anchors were identified using the FindIntegrationAnchors function using 25 dimensions. An assay “Integrated” was generated for the 2000 variable features using the IntegrateData function using 25 dimensions. The integrated data were then used in principal component analysis (PCA).
Single-nucleus multimodal data integration and processing: Single-nucleus multimodal libraries were sequenced using the NovaSeq 6000 instrument (Illumina). Sequencing was performed by the Genomics Division of the Iowa Institute of Human Genetics. FASTQ files were generated from base calls with the bcl2fastq software (Illumina). Reads were mapped to the pre-built GRCh38 reference (GRCh38-2020-A-2.0.0, 10X Genomics) using Cell Ranger ARC (v.2.0.0, 10X Genomics) with default parameters. Resulting cell-by-peak and cell-by-gene matrices (ATAC and Gene Expression assays respectively) from the four samples were integrated separately using latent semantic indexing (ATAC) and canonical correlation analysis (gene expression) respectively. For CCA, only cells with between 500 and 4,000 unique genes (features) were included in the analysis. Only cells with < 10% of reads mapping to mtDNA-encoded genes and < 8% of reading mapping to ribosomal genes were included. For LSI, only cells with between 2,000 and 15,000 peak region fragments and less than 1,000 mtDNA depth were included in analysis. Cells passing both ATAC and Gene Expression QC cutoffs were retained and used to generate a UMAP following Weighted Nearest Neighbor (WNN) analysis. MultiModal Neighbors were identified using dimensions 1:30 from the PCA resulting from CCA (GEX) and 2:50 from the LSI reduction (ATAC). Clusters were identified using FindClusters (Seurat) based on the "wsnn" graph using the SLM algorithm with a resolution of 0.5. Clusters were annotted for cell type manually. ATAC peaks to be used downstream (i.e. motif enrichment analysis) were called using MACS2 (Feng et al., 2012; Zhang et al., 2008) with the CallPeaks function in Signac.
Dimensionality reduction with UMAP and cell type annotation: 30 principal components were identified out of the integrated dataset described above using the RunPCA function (Seurat) (Stuart et al., 2019). Uniform manifold approximation and projection (UMAP) was performed using the RunUMAP function using 25 principal components. Cells were annotated with the using the D40-D160 organoid dataset from this publication (Mullin, Bohrer et al., 2024) as a reference.
Assembly: GRCh38
Supplementary files format and content: For scRNAseq data, raw and log normalzied counts are provided for each library (*_counts.csv and *_normalized.csv, respectively). Counts were accessed from the filtered Seurat object via seurat_obj@assays$RNA@counts. Normalized counts were accessed from the filtered Seurat object via seurat_obj@assays$RNA@data. Count matrices are appended with the following metadata: "barcode", 10X cell barcode; "donor", iPSC line of origin; "timepoint", differentiation day of sample collection; "library", unique library identifier; "celltype", initial cell type annotation; "umap_dim_1"/"umap_dim_2", UMAP coordinates.
Supplementary files format and content: For multimodal sequencing data, raw and log normalzied gene expression (GEX) counts and raw peak counts (from MACS2 calls) are provided for each library (*_gex_counts.csv and *_gex_normalized.csv, and *_peaks_counts.csv respectively).  Raw gene expression counts were accessed from the filtered Seurat object via seurat_obj@assays$RNA@counts. Normalized gene expression counts were accessed from the filtered Seurat object via seurat_obj@assays$RNA@data. Raw peak  counts were accessed from the filtered Seurat object via seurat_obj@assays$macs2_peaks@counts. Count matrices are appended with the following metadata: "barcode", 10X cell barcode; "donor", iPSC line of origin; "timepoint", differentiation day of sample collection; "library", unique library identifier; "celltype", initial cell type annotation; "umap_dim_1"/"umap_dim_2", UMAP coordinates.
Library strategy: Multiome (ATAC)

molecule: genomic DNA

organism: Homo sapiens

source_name: Isogenic Control

growth_protocol: Retinal differentiation was performed as described previously with minor modifications (Bohrer 2023). Briefly, iPSCs were cultured on laminin 521 coated plates in E8 medium. Embryoid bodies (EBs) were lifted with ReLeSR (STEMCELL Technologies, Cambridge, MA) and transitioned from E8 to neural induction medium (NIM- DMEM/F12 (1:1), 1% N2 supplement, 1% non-essential amino acids, 1% Glutamax (Thermo Fisher Scientific), 2 µg/mL heparin (Sigma-Aldrich, St. Louis MO) and Primocin (InvivoGen, San Diego, CA)) over a four-day period. On day 6, NIM was supplemented with 1.5 nM BMP4 (R&D Systems, Minneapolis, MN). On day 7, EBs were adhered to Matrigel coated plates (Corning). BMP4 was gradually transitioned out of the NIM over seven days. On day 16, the media was changed to retinal differentiation medium (RDM - DMEM/F12 (3:1), 2% B27 supplement (Thermo Fisher Scientific), 1% non-essential amino acids, 1% Glutamax and 0.2% Primocin). On day 25-30 the entire EB outgrowth was mechanically lifted using a cell scraper and transferred to ultra-low attachment flasks in 3D-RDM (RDM plus 10% Fetal bovine serum (FBS)); Thermo Fisher Scientific), 100 µM taurine (Sigma-Aldrich), 1:1000 chemically defined lipid concentrate (Thermo Fisher Scientific), and 1 µM all-trans retinoic acid (until day 100; Sigma-Aldrich). The cells were fed three times per week with 3D-RDM until harvest.

extract_protocol:
Organoid dissociation for single-cell RNAseq: For Day 40-260 scRNAseq samples, approximately ten organoids displaying morphology of successful retinal differentiation were selected for each of the three lines. Organoids were allowed to settle by gravity in a 1.5mL tube and culture medium was removed. Organoids were dissociated in a solution of 20U/mL papain (Worthington) and 120U/mL DNase (Worthington) in Earle’s balanced salt solution (EBSS) (Worthington). Samples were incubated in 300µL of above papain solution at 37˚C with continuous shaking (500rpm) until all organoids were completely dissociated (approximately 1 hour). Samples were triturated with a pipette every 15 minutes. Following dissociation, cells were pelleted at 500 x g for 5 minutes and resuspended in 8µg/mL recombinant albumin (New England Biolabs) in dPBS-/-. Cells were passed through a 70µm filter to encapsulation with the Chromium Controller instrument (10X Genomics). Approximately 8,000 cells were targeted for encapsulation per sample.   Nucleus isolation for single-nucleus multimodal sequencing: Nuclei were isolated from differentiation day 160 and 260 organoids from an independent batch of differentiation (i.e., completely different round initiated on a separate day) than single-cell gene expression samples. Nuclei were isolated following a protocol based on 10X Genomics’ demonstrated protocol CG000366. Briefly, approximately ten organoids were selected as described above. Medium was aspirated and 500µL of chilled 0.1X Lysis Buffer (Tris-HCl, NaCl, MgCl2, Tween-20, NP40, Digitonin, BSA, DTT, RNase Inhibitor) was added to each sample. Samples were homogenized with 15 strokes of a sterile pestle in a 1.5mL tube on ice. Samples were then incubated on ice for 5 minutes. Following incubation, samples were mixed with a P1000 pipette 10 times on ice and incubated for 8.5 minutes on ice. 500µL of Wash Buffer (Tris-HCl, NaCl, MgCl2, Tween-20, BSA, DTT, RNase Inhibitor) was added and lysed cells were mixed 5 times with pipetting. Cells were pelleted at 500 x g for 5 minutes in a refrigerated (4˚C) centrifuge and resuspended in 500µL chilled wash buffer. This process was repeated for three total washes. Nuclei were resuspended in Diluted Nuclei Buffer (Nuclei Buffer (10X Genomics), DTT, RNase Inhibitor) and passed through a 70µm strainer. Nuclei were counted on a hemocytometer with DAPI to visualize intact nuclei. Approximately 9,000 nuclei were targeted for encapsulation per sample using the Chromium X instrument (10X Genomics).
Single-cell gene expression library preparation and sequencing: Single cells were partitioned and barcoded with the Chromium Controller instrument (10X Genomics) and Single Cell 3' Reagent (v3.1 chemistry) kit (10X Genomics) according to the manufacturer’s specifications with no modification (Rev C). Final libraries were quantified using the Qubit dsDNA HS Assay Kit (Life Technologies) and diluted to 3ng/µL in buffer EB (Qiagen). Library quality was confirmed using the Bioanalyzer High Sensitivity DNA Assay (Agilent) prior to sequencing.  Single-nucleus multimodal library preparation and sequencing: Nuclei were processed following the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (Rev. E) without modification. Final libraries were quantified using the Qubit dsDNA HS Assay Kit and diluted to 3ng/µL. Library quality was checked using the Bioanalyzer or Tapestation (Agilent).

tag: sample type

value: retinal organoid

value: Isogenic Control

tag: differentiation day


title: del(4)(p16)_4

type: genomic

city: Setagaya

first: Tomoko

last: Kawai

state: Tokyo

department: Department of Maternal-Fetal Biology

country: Japan

institute: National Research Institute for Child Health and Development

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

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

data_processing:
R package minfi and ChAMP were used. We removed probes with detection P values of >0.01 in at least one sample and a bead count <3 in at least 5% of samples, and non-CpG targeting probes. We also filtered single-nucleotide polymorphism-related probes, multi-hit probes, probes located on either X or Y chromosome.
Normalized Average Beta: Background was corrected using the NOOB method in the minfi package, then NOOB-corrected data were normalised by BMIQ in the ChAMP package.

label: Cy5 and Cy3

source_name: disease peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from peripheral blood using QIAsymphony DNA Midi Kit (96) according to standard instructions

tag: gender

value: Male

tag: age

tag: disease state

tag: genetic variants inheritance

value: NR

value: peripheral blood cells


title: m169

city: Jerusalem

first: Batia

last: Azria

state: Israel

address: Jerusalem

country: Israel

institute: Hebrew university of Jerusalem

data_processing:
Quality control applied with trim_galore V0.6.0 deploying cutadapt V1.18 and fastqc v0.11.7. Paired-end bisulfite treated FASTQ files were aligned by Bismark V0.13.1 deploying Bowtie2 aligner to mm10 assembly. Methylation calling performed with bismark_methylation_extractor followed by Bismark cov2cytp and a custom AWK script transforming files to methylKit input format. Differential methylated regions were obtain with methylKit R-package V1.10.0 and earlier consistent versions. Genome_build: mm10.
Assembly: mm10
Supplementary files format and content: all processed data are in methkit format

source_name: Liver

growth_protocol: All animal experiments were performed in accordance with the guidelines of the Hebrew University Institutional Committee for the Use of Animals for Research. Female C57BL mice aged 10-12 weeks, were maintained in a Specific Pathogen-Free (SPF) animal facility (Hebrew University-Hadassah Medical School Jerusalem, Israel), housed under regular 12h light-dark cycle.  Tet2/Tet3 DKO mice were generated by injecting 1,000 genome-equivalent copies of AAV8 carrying the gene for Cre under the hepatocyte-specific Tbg promoter (Penn vector) into the jugular vein of three-month-old Tet2F/Tet3F mice.

extract_protocol: Partial hepatectomy was carried out on 12 weeks old mice by removing 2/3 of the liver, including resection of the left lower, upper lobes and the right upper lobe.  Mice were anaesthetized and subjected to liver perfusion. Whole liver was then digested by collagenase (Roche) and hepatocytes removed and isolated by means of a Percoll gradient. Cells were then sorted by FACS according to size. Hepatoblasts were prepared from E11.5 and E16.5 mouse embryos by collecting fetal liver samples from littermate siblings which were then minced and digested for 30 min at 37°C with 0.025% collagenase IV (Sigma-Aldrich, C4-22-1G). After gentle pipetting, the cell suspension was filtered through a 40-mm cell strainer and washed twice with RPMI medium containing 10% FBS. The cells were then stained for 40 minutes at 4°C with moderate agitation with Liv2 (mouse) mAb (MBL, D118-3) for E11.5 hepatoblast, and Dlk1-APC-conjugated mouse Pref-1/DLK1/FA1 antibody (R&D Systems, FAB8634A-100) for E16.5 hepatoblast. Positive hepatoblast cells were then isolated by Flow cytometry. DNA was isolated from purified cells, incubated in lysis buffer (25 mM Tris-HCl (pH  8), 2 mM EDTA, 0.2% SDS, 200 mM NaCl) supplemented with 300 μg/ml proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation. The methylation profile was checked using the RRBS assay [Boyle, 2012]. Briefly, the DNA was digested with the MspI enzyme to yield CpG enriched fragments. Adapter sequences were ligated at both ends, and DNA fragments were then treated with sodium-bisulfite, allowing for easy distinction between methylated and unmethylated bases. The DNA was then amplified by PCR to produce the final libraries.

tag: tissue

value: Liver

value: hepatoblast from E11.5 embryo

value: Liv2+ hepatoblast of E11.5 liver embryo


title: RAW264.7 cells, LPS-stimulated and treated with 1 μM GRd, sample 1

value: LPS and 1 uM GRd


title: m170

treatment_protocol: Partial hepatectomy was carried out on 12 weeks old mice by removing 2/3 of the liver, including resection of the left lower, upper lobes and the right upper lobe.


title: RAW264.7 cells, miRNA, control 1


title: RAW264.7 cells, LPS-stimulated and treated with 10 μM GRd, sample 1


title: RAW264.7 cells, LPS-stimulated and treated with 1 μM GRd, sample 2


title: OD600 0.5 ompR mutant rep2

description:
ompR mutant rep2
OD600 0.5

value: ompR knockout

value: LB


title: RAW264.7 cells, LPS-stimulated and treated with 1 μM GRd, sample 3


title: retinal organoid, NR2E3-null, D260, Multiome (ATAC)


title: m168


title: retinal organoid, Isogenic Control, D260, Multiome (GEX)

data_processing:
Single-cell gene expression data integration and processing: scRNA libraries were pooled and sequenced using the NovaSeq 6000 instrument (Illumina) generating 100-bp paired end reads. FASTQ files were generated from base calls with the bcl2fastq software (Illumina). For the ESCS Patient 2 experiment, reads were mapped to the pre-built GRCh38 reference (refdata-gex-GRCh38-2020-A) with Cell Ranger v7.0.0 (10X Genomics) using the ‘count’ function with the following parameters: --expect-cells=8000 --localcores=56. Only cells passing the default Cell Ranger call were analyzed further. For the AAV experiment, custom reference genomes were built to allow mapping of EGFP and associated 3’UTR regions originating from AAV cargo. For AAV- NR2E3-T2A-EGFP transduced and untransduced samples, reads were mapped to a reference genome containing T2A-EGFP-BGHpolyA sequence. For AAV-EGFP transduced samples, reads were mapped to a reference genome containing EGFP-WPRE-BGHpolyA sequence. Data from all samples was integrated using CCA. The top 2000 variable features as determined by vst method were used. For AAV-transduced samples, the transgene feature was not included as a variable feature. Only cells with between 1,000 and 7,000 unique genes (features) were included in the analysis. Only cells with < 10% of reads mapping to mtDNA-encoded genes and < 20% of reading mapping to ribosomal genes were included. Counts data were normalized using the NormalizeData function (Seurat) with the following parameters: normalization.method = "LogNormalize", scale.factor = 10000. 2000 variable features were identified with the FindVariableFeatures function using the vst selection method. Integration anchors were identified using the FindIntegrationAnchors function using 25 dimensions. An assay “Integrated” was generated for the 2000 variable features using the IntegrateData function using 25 dimensions. The integrated data were then used in principal component analysis (PCA).
Single-nucleus multimodal data integration and processing: Single-nucleus multimodal libraries were sequenced using the NovaSeq 6000 instrument (Illumina). Sequencing was performed by the Genomics Division of the Iowa Institute of Human Genetics. FASTQ files were generated from base calls with the bcl2fastq software (Illumina). Reads were mapped to the pre-built GRCh38 reference (GRCh38-2020-A-2.0.0, 10X Genomics) using Cell Ranger ARC (v.2.0.0, 10X Genomics) with default parameters. Resulting cell-by-peak and cell-by-gene matrices (ATAC and Gene Expression assays respectively) from the four samples were integrated separately using latent semantic indexing (ATAC) and canonical correlation analysis (gene expression) respectively. For CCA, only cells with between 500 and 4,000 unique genes (features) were included in the analysis. Only cells with < 10% of reads mapping to mtDNA-encoded genes and < 8% of reading mapping to ribosomal genes were included. For LSI, only cells with between 2,000 and 15,000 peak region fragments and less than 1,000 mtDNA depth were included in analysis. Cells passing both ATAC and Gene Expression QC cutoffs were retained and used to generate a UMAP following Weighted Nearest Neighbor (WNN) analysis. MultiModal Neighbors were identified using dimensions 1:30 from the PCA resulting from CCA (GEX) and 2:50 from the LSI reduction (ATAC). Clusters were identified using FindClusters (Seurat) based on the "wsnn" graph using the SLM algorithm with a resolution of 0.5. Clusters were annotted for cell type manually. ATAC peaks to be used downstream (i.e. motif enrichment analysis) were called using MACS2 (Feng et al., 2012; Zhang et al., 2008) with the CallPeaks function in Signac.
Dimensionality reduction with UMAP and cell type annotation: 30 principal components were identified out of the integrated dataset described above using the RunPCA function (Seurat) (Stuart et al., 2019). Uniform manifold approximation and projection (UMAP) was performed using the RunUMAP function using 25 principal components. Cells were annotated with the using the D40-D160 organoid dataset from this publication (Mullin, Bohrer et al., 2024) as a reference.
Assembly: GRCh38
Supplementary files format and content: For scRNAseq data, raw and log normalzied counts are provided for each library (*_counts.csv and *_normalized.csv, respectively). Counts were accessed from the filtered Seurat object via seurat_obj@assays$RNA@counts. Normalized counts were accessed from the filtered Seurat object via seurat_obj@assays$RNA@data. Count matrices are appended with the following metadata: "barcode", 10X cell barcode; "donor", iPSC line of origin; "timepoint", differentiation day of sample collection; "library", unique library identifier; "celltype", initial cell type annotation; "umap_dim_1"/"umap_dim_2", UMAP coordinates.
Supplementary files format and content: For multimodal sequencing data, raw and log normalzied gene expression (GEX) counts and raw peak counts (from MACS2 calls) are provided for each library (*_gex_counts.csv and *_gex_normalized.csv, and *_peaks_counts.csv respectively).  Raw gene expression counts were accessed from the filtered Seurat object via seurat_obj@assays$RNA@counts. Normalized gene expression counts were accessed from the filtered Seurat object via seurat_obj@assays$RNA@data. Raw peak  counts were accessed from the filtered Seurat object via seurat_obj@assays$macs2_peaks@counts. Count matrices are appended with the following metadata: "barcode", 10X cell barcode; "donor", iPSC line of origin; "timepoint", differentiation day of sample collection; "library", unique library identifier; "celltype", initial cell type annotation; "umap_dim_1"/"umap_dim_2", UMAP coordinates.
Library strategy: Multiome (GEX)

molecule: polyA RNA


title: retinal organoid, NR2E3-null, D260, Multiome (GEX)


title: m150

value: hepatocyte

value: C57BL Tet2/Tet3 DKO

value: liver 7 d after Phx of 10-12w old female Tet2/Tet3 mice


title: del(4)(p16)_2

value: 6 years

value: WHS


title: m149


title: retinal organoid, NR2E3-null, D160, Multiome (ATAC)


title: del(4)(p16)_3

value: Female

value: 8 years


title: m147

value: liver 7 d after Phx of 10-12w old male Tet2/Tet3 mice


title: retinal organoid, NR2E3-null, D160, Multiome (GEX)

value: retinal organoid


title: m132

value: liver 2 mounth after Phx of 10-12w old femal


title: retinal organoid, Isogenic Control, D260, scRNAseq

library_source: transcriptomic single cell

data_processing:
Single-cell gene expression data integration and processing: scRNA libraries were pooled and sequenced using the NovaSeq 6000 instrument (Illumina) generating 100-bp paired end reads. FASTQ files were generated from base calls with the bcl2fastq software (Illumina). For the ESCS Patient 2 experiment, reads were mapped to the pre-built GRCh38 reference (refdata-gex-GRCh38-2020-A) with Cell Ranger v7.0.0 (10X Genomics) using the ‘count’ function with the following parameters: --expect-cells=8000 --localcores=56. Only cells passing the default Cell Ranger call were analyzed further. For the AAV experiment, custom reference genomes were built to allow mapping of EGFP and associated 3’UTR regions originating from AAV cargo. For AAV- NR2E3-T2A-EGFP transduced and untransduced samples, reads were mapped to a reference genome containing T2A-EGFP-BGHpolyA sequence. For AAV-EGFP transduced samples, reads were mapped to a reference genome containing EGFP-WPRE-BGHpolyA sequence. Data from all samples was integrated using CCA. The top 2000 variable features as determined by vst method were used. For AAV-transduced samples, the transgene feature was not included as a variable feature. Only cells with between 1,000 and 7,000 unique genes (features) were included in the analysis. Only cells with < 10% of reads mapping to mtDNA-encoded genes and < 20% of reading mapping to ribosomal genes were included. Counts data were normalized using the NormalizeData function (Seurat) with the following parameters: normalization.method = "LogNormalize", scale.factor = 10000. 2000 variable features were identified with the FindVariableFeatures function using the vst selection method. Integration anchors were identified using the FindIntegrationAnchors function using 25 dimensions. An assay “Integrated” was generated for the 2000 variable features using the IntegrateData function using 25 dimensions. The integrated data were then used in principal component analysis (PCA).
Single-nucleus multimodal data integration and processing: Single-nucleus multimodal libraries were sequenced using the NovaSeq 6000 instrument (Illumina). Sequencing was performed by the Genomics Division of the Iowa Institute of Human Genetics. FASTQ files were generated from base calls with the bcl2fastq software (Illumina). Reads were mapped to the pre-built GRCh38 reference (GRCh38-2020-A-2.0.0, 10X Genomics) using Cell Ranger ARC (v.2.0.0, 10X Genomics) with default parameters. Resulting cell-by-peak and cell-by-gene matrices (ATAC and Gene Expression assays respectively) from the four samples were integrated separately using latent semantic indexing (ATAC) and canonical correlation analysis (gene expression) respectively. For CCA, only cells with between 500 and 4,000 unique genes (features) were included in the analysis. Only cells with < 10% of reads mapping to mtDNA-encoded genes and < 8% of reading mapping to ribosomal genes were included. For LSI, only cells with between 2,000 and 15,000 peak region fragments and less than 1,000 mtDNA depth were included in analysis. Cells passing both ATAC and Gene Expression QC cutoffs were retained and used to generate a UMAP following Weighted Nearest Neighbor (WNN) analysis. MultiModal Neighbors were identified using dimensions 1:30 from the PCA resulting from CCA (GEX) and 2:50 from the LSI reduction (ATAC). Clusters were identified using FindClusters (Seurat) based on the "wsnn" graph using the SLM algorithm with a resolution of 0.5. Clusters were annotted for cell type manually. ATAC peaks to be used downstream (i.e. motif enrichment analysis) were called using MACS2 (Feng et al., 2012; Zhang et al., 2008) with the CallPeaks function in Signac.
Dimensionality reduction with UMAP and cell type annotation: 30 principal components were identified out of the integrated dataset described above using the RunPCA function (Seurat) (Stuart et al., 2019). Uniform manifold approximation and projection (UMAP) was performed using the RunUMAP function using 25 principal components. Cells were annotated with the using the D40-D160 organoid dataset from this publication (Mullin, Bohrer et al., 2024) as a reference.
Assembly: GRCh38
Supplementary files format and content: For scRNAseq data, raw and log normalzied counts are provided for each library (*_counts.csv and *_normalized.csv, respectively). Counts were accessed from the filtered Seurat object via seurat_obj@assays$RNA@counts. Normalized counts were accessed from the filtered Seurat object via seurat_obj@assays$RNA@data. Count matrices are appended with the following metadata: "barcode", 10X cell barcode; "donor", iPSC line of origin; "timepoint", differentiation day of sample collection; "library", unique library identifier; "celltype", initial cell type annotation; "umap_dim_1"/"umap_dim_2", UMAP coordinates.
Supplementary files format and content: For multimodal sequencing data, raw and log normalzied gene expression (GEX) counts and raw peak counts (from MACS2 calls) are provided for each library (*_gex_counts.csv and *_gex_normalized.csv, and *_peaks_counts.csv respectively).  Raw gene expression counts were accessed from the filtered Seurat object via seurat_obj@assays$RNA@counts. Normalized gene expression counts were accessed from the filtered Seurat object via seurat_obj@assays$RNA@data. Raw peak  counts were accessed from the filtered Seurat object via seurat_obj@assays$macs2_peaks@counts. Count matrices are appended with the following metadata: "barcode", 10X cell barcode; "donor", iPSC line of origin; "timepoint", differentiation day of sample collection; "library", unique library identifier; "celltype", initial cell type annotation; "umap_dim_1"/"umap_dim_2", UMAP coordinates.

value: Isogenic Control


title: retinal organoid, Isogenic Control, D160, Multiome (GEX)


title: m129

value: Liver


title: m113

value: liver 7 d after Phx of 10-12w old femal


title: retinal organoid, Isogenic Control, D160, Multiome (ATAC)


title: m130


title: m112


title: retinal organoid, NR2E3-null, D160, scRNAseq


title: retinal organoid, ND Control, D260, scRNAseq

source_name: ND Control

value: ND Control


title: Nsd2_KI_homo_1_thymocytes_DNAme

description: SAMPLE 4

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Mouse Methylation Beadchip using standard Illumina protocol

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

data_processing: GenomeStudio software used for normalization

source_name: Thymocytes

extract_protocol: genomic DNA was extracted and purified from thymocytes using Qiagen AllPrep DNA/RNA Mini Kit.

value: Thymocytes

value: Male

value: 90 days

tag: strain

value: Thymocytes isolated from thymus


title: m111

value: hepatocyte


title: SI-WT-4

city: Oberschleißheim

first: Caspar

last: Ohnmacht

address: Ingolstädter Landstraße 1

department: Institute for Allergy Research

country: Germany

institute: Helmholtz Munich

description:
GEX4
10X Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Small intestine lamina propria

extract_protocol:
Small intestine was extracted from mice and Peyer's patches were removed. Then intestine was opened longitudinally, washed in PBS and cut into 0.5-1 cm pieces. The pieces were then incubated in ice cold PBS with 30 mM EDTA for 30 min and thoroughly washed in PBS. Afterwards they were cut into smaller pieces and digested three times for 10 min, 20 min and 30 min in RPMI 1640 containing 25 mM HEPES, 0.5 mg/ml Collagenase D and 10 µg/ml DNaseI. Disintegrated supernatants were collected in RPMI1640 + 10% FCS in between digestion steps. Cells were then filtered to remove clumps and Percoll density gradient centrifugation (40%/80%) was performed to purify lymphocytes. Cells were stained with antibodies against CD45, CD3 and CD4 and before sorting 7AAD was added to label dead cells. They were then sorted for CD45+CD3+CD4+7AAD- using the FACS Aria III and collected in PBS with 0.04% BSA.
Library was prepared according to manufacturer's instructions (Chromium Single Cell 5' Library; 10X Genomics).

value: Small intestine lamina propria

value: CD4+ T cells

value: Wildtype


title: m148

value: C57BL Tet2/Tet3 DKO


title: retinal organoid, Isogenic Control, D160, scRNAseq


title: Nsd2_KO_hetero_2_thymocytes_DNAme

description: SAMPLE 6

value: 107 days


title: retinal organoid, Isogenic Control, D120, scRNAseq


title: m104


title: m103


title: m110


title: retinal organoid, ND Control, D160, scRNAseq


title: retinal organoid, Isogenic Control, D80, scRNAseq


title: retinal organoid, NR2E3-null, D80, scRNAseq


title: Nsd2_KI_hetero_1_thymocytes_DNAme

description: SAMPLE 3


title: m83

value: liver control of 10-12w old femal


title: WT_2_thymocytes_DNAme

description: SAMPLE 2

value: wild type


title: retinal organoid, ND Control, D80, scRNAseq

value: retinal organoid


title: retinal organoid, Isogenic Control, D40, scRNAseq

value: Isogenic Control


title: retinal organoid, NR2E3-null, D40, scRNAseq


title: Nsd2_KO_hetero_thymo_1_H3K36me2

data_processing:
The Illumina HiSeq 2500 generates raw images and base calling through an integrated primary analysis software called RTA v 1.16.66.3 (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ using illumina package bcl2fastq2-v1.8.4.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using BWA-MEM v0.7.17.
Created Bam files were put into deepTools to generate a coverage track bigwig. The coverage was calculatied as the number of reads per 100 bp bin using the reads per kilobase per million mapped reads (RPKM) normalization.
Assembly: mm10
Supplementary files format and content: Big wig files include RPKM values for each Sample.

extract_protocol:
Thymi were loosened in PBS by making a cut. Thymocytes were collected after cell suspensions were passed through a 70-μm cell strainer. Collected thymocytes (1×10^6) were fixed with 1% formaldehyde for 5 min. The cells were resuspended in SDS lysis buffer, and the lysate was sonicated to fragment chromatin using the Covaris S220 system (Covaris). The chromatin was purified by centrifugation and immunoprecipitated with Dynabeads M-280 Sheep anti-mouse IgG (Veritas Life Sciences, PA, USA) conjugated to anti-H3K36me2 antibodies ab176921 (Abcam, Cambridge, UK) in 1xRIPA (150 mM) buffer with protease inhibitors for 2 h at 4 °C. The chromatin-bound beads were washed sequentially with 1xRIPA (150 mM) buffer, 1xRIPA (500 mM) buffer and TE buffer. After washing, the chromatin-bound beads were incubated in ChIP direct elution buffer with proteinase K (200 µg/ml) overnight at 65 °C. DNA was purified using AMPure XP beads (Beckman Coulter, CA, USA) according to the manufacturer’s instructions.
Libraries were prepared using prepared with NEBNext ChIP-Seq Library Prep Master Mix Set and Multiplex Oligos from Illumina (New England BioLabs) according to manufacture’s protocol.

value: Thymocytes from thymus

tag: chip antibody


title: Nsd2_KI_hetero_thymo_2_H3K36me2

value: 110 days


title: del(4)(p16)_1

value: Female

value: 16 years

value: WHS

value: NR

value: peripheral blood cells


title: Nsd2_KO_hetero_thymo_2_H3K36me2


title: m84

value: Liver

value: hepatocyte


title: Nsd2_KI_homo_thymo_H3K36me2

value: 90 days


title: retinal organoid, ND Control, D40, scRNAseq

value: ND Control


title: Nsd2_KI_hetero_thymo_1_H3K36me2


title: retinal organoid, escs_patient_2, D160, scRNAseq


title: WT_thymo_2_H3K36me2


title: retinal organoid, NR2E3-null, D160, untransduced, scRNAseq

value: untransduced


title: WT_thymo_1_H3K36me2


title: WT_1_thymocytes_DNAme

description: SAMPLE 1

value: Thymocytes

value: Male

value: Thymocytes isolated from thymus


title: Nsd2_KO_hetero_1_thymocytes_DNAme

description: SAMPLE 5

value: 107 days


title: retinal organoid, NR2E3-null, D160, aav-nr2e3-gfp, scRNAseq

value: retinal organoid


title: retinal organoid, NR2E3-null, D160, aav-gfp, scRNAseq

value: aav-gfp


title: Input

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Raw reads were aligned to the mouse reference (GRCm38) using GSNAP (with parameters -M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap). Reads were filtered to include only uniquely mapped reads. MACS2 was used to call peaks.
Assembly: GRCm38
Supplementary files format and content: Peak calls in bed format relative to the input per sample

source_name: Bone Marrow Derived Macrophages

extract_protocol: Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

value: AbFlex® RNA Pol II antibody, Cat#91151, lot number 26520003

value: WT

value: Bone Marrow Derived Macrophages

value: No treatment


title: KO-R837-6h-rep2 [RNA Pol II ChIP-seq]

value: N4bp1 KO


title: retinal organoid, NR2E3-null, D130, untransduced, scRNAseq


title: A363-20

city: Jiaxing

first: Wanqi

last: Shao

address: 2468 Central Road East

department: Jiaxing University Master Degree Cultivation Base

institute: Zhejiang Chinese Medical University

data_processing:
A 1 ul miRNA sequencing library was used for detection and detected on an Agilent Bioanalyzer using a High Sensitivity DNA chip according to the manufacturer's instructions. The qualified libraries were sequenced by Illumina NovaSeq sequencing platform, and the original sequencing data were obtained.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: non-adenomyosis patients plasma exosomes

extract_protocol:
Total RNA was extracted and purified from plasma exosome using miRNeasy Serum/Plasma Advanced Kit (Qiagen, cat. No. 217204) according to the kit instruction.
RNA concentration and purity were evaluated using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 System (Agilent Technologies, CA, USA).


title: A363-18

value: non-adenomyosis patients plasma exosomes


title: KO-R837-6h-rep1 [RNA Pol II ChIP-seq]


title: retinal organoid, escs_patient_2, D80, scRNAseq


title: WT-R837-6h-rep2 [RNA Pol II ChIP-seq]


title: WT-R837-6h-rep1 [RNA Pol II ChIP-seq]


title: KO-R837-4h-rep2 [RNA Pol II ChIP-seq]


title: KO-R837-4h-rep1 [RNA Pol II ChIP-seq]


title: A363-14


title: WT-R837-4h-rep2 [RNA Pol II ChIP-seq]


title: A363-16


title: A363-17


title: KO-R837-2h-rep2 [RNA Pol II ChIP-seq]


title: A363-15


title: A363-12


title: WT-R837-4h-rep1 [RNA Pol II ChIP-seq]


title: A363-11


title: KO-R837-2h-rep1 [RNA Pol II ChIP-seq]


title: A363-10

source_name: adenomyosis patients plasma exosomes

value: adenomyosis patients plasma exosomes


title: retinal organoid, NR2E3-null, D120, scRNAseq


title: WT-R837-2h-rep2 [RNA Pol II ChIP-seq]


title: A363-08


title: A363-07


title: KO-unstim-rep2 [RNA Pol II ChIP-seq]


title: WT-R837-2h-rep1 [RNA Pol II ChIP-seq]


title: A363-06


title: KO-unstim-rep1 [RNA Pol II ChIP-seq]


title: retinal organoid, NR2E3-null, D260, scRNAseq


title: A363-03


title: WT-unstim-rep1 [RNA Pol II ChIP-seq]


title: LuCaP 23.1 empty vector, rep4

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

data_processing:
RNA sequencing data was aligned to grch37 using the nextflow core RNAseq pipeline (https://github.com/nf-core/rnaseq).
Transcripts were quantified using featureCounts from the subread package (http://bioconductor.org/packages/release/bioc/html/Rsubread.html).
The R bioconductor package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) was used for performing differential gene expression analysis
Assembly: GRCh37
Supplementary files format and content: raw counts file

source_name: prostate cancer

growth_protocol: PDX tumors were passaged in NOD scid gamma (NSG) mice at the NCI and propagated in vitro as 3-dimensional organoid cultures. PDXs were enzymatically degraded using the MACS human Tumor Dissociation Kit

extract_protocol:
RNA was extracted from first generation organoids using RNeasy kit according to manufacturer’s instructions, and profiled for quality using a Bioanalyzer.
Poly-A–enriched and Illumina–barcoded libraries were prepared using the TruSeq kit.
Libraries were sequenced on a NextSeq 500 to a depth of 75 million base pairs (150 bp paired end) at the NCI Sequencing Facility.

treatment_protocol: LuCaP 23.1 cells were transduced with generated lentivirus via centrifugation and LentiBOOST.

value: prostate cancer

value: LuCaP 23.1

value: Empty Vector

tag: Sex

value: male


title: LuCaP 23.1 empty vector, rep3


title: EPC2_hTERT_lane1

city: Philadelphia

first: Sydney

middle: M.

last: Shaffer

state: PA

address: 421 Curie Blvd

department: Department of Pathology

institute: University of Pennsylvania

data_processing:
For scRNA-seq we processed the data using 10X Cell Ranger software.
Assembly: hg38
Supplementary files format and content: Tab-separated values and matrix files.

extract_protocol:
For scRNA-seq we followed protocols from 10X genomics for cell lines.
For scRNA-seq library construction we followed protocols from 10X genomics.

value: Esophageal epithelium


title: LuCaP 23.1 empty vector, rep2


title: LuCaP 23.1 empty vector, rep1


title: A363-04


title: LuCaP 23.1 ectopically expressing HNF1A, rep4

value: HNF1A expressing


title: hSMC-sinrf2-2-1

city: Yangling

first: Xia

last: Zhou

state: Shannxi

address: No.3 Taicheng Road, Yangling Shaanxi, China

institute: northwest a&f university

data_processing:
Cleaned raw data were aligned to the human reference genome (NCBI: GCF_000001405.40) using Hisat2 (v2.0.5). FeatureCounts (v2.0.3) was used to count the reads numbers mapped to each gene.
Assembly: GCF_000001405.40
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: lung

extract_protocol:
Total RNA was extract by using Trizol, 1 μg was used for library construction.
To prepared the RNA libraries for RNA-seq，mRNA was  purified from total RNA using poly-T  oligo-attached magnetic beads, Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random  hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted  into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments  of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent bioanalyzer 2100 system.

value: lung

value: PASMC


title: hSMC-sinrf2-1-3


title: hSMC-sinrf2-2-3


title: hSMC-sinrf2-2-2


title: hSMC-sinrf2-1-2


title: LuCaP 23.1 ectopically expressing HNF1A, rep3


title: hSMC-sinrf2-1-1


title: LuCaP 23.1 ectopically expressing HNF1A, rep2


title: hSMC-NC-3

value: Control siRNA


title: A363-05


title: WT-unstim-rep2 [RNA Pol II ChIP-seq]


title: hSMC-NC-2


title: H2170_CRISPRi_MYCp1_HiChIP_rep2

city: Salt Lake City

first: Xiaoyang

last: Zhang

state: Utah

address: 1950 Circle of Hope Drive

department: Oncological Sciences

institute: University of Utah

data_processing:
HiC-Pro to align sequencing reads
hichipper to identify chromatin loops connecting H3K27ac anchors
Assembly: hg19
Supplementary files format and content: intra-chromosomal interaction counts text file in bedpe format. Rows are interactions (loops). Columns are chromosome1, start1, end1, chromosome2, start2, end2, FDR (blank), PETs
Supplementary files format and content: inter-chromosomal interaction counts text file in bedpe format. Rows are interactions (loops). Columns are chromosome1, start1, end1, chromosome2, start2, end2, FDR (blank), PETs
Library strategy: HiChIP

extract_protocol:
HiChIP protocol (Mumbach et al., 2016, Nature Methods) to enrich DNA fragments that are in proximity with each other
Illumina Tagment DNA Enzyme and Buffer Kit (Illumina 20034197)

value: Lung squamous cancer cell line

tag: hichip antibody

value: H3K27ac (Abcam ab4729)


title: A363-01


title: H2170_CRISPRi_MYCp1_HiChIP_rep1


title: hSMC-NC-1


title: hEC-sinrf2-2-3

value: PAEC


title: hEC-sinrf2-2-1


title: IMR9_control_Rep3

city: new york city

first: Carmen

last: Argmann

state: NY

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine

data_processing:
RNA-seq reads were aligned to the GRCh38 primary assembly with Gencode release annotation by STAR (v2.7.3a).
Quantification was done with featureCounts
Raw count data was pre-filtered to keep genes with CPM>1.0 for at least 30% of the samples.  After filtering, count data was normalized via the weighted trimmed mean of M-values(Robinson and Oshlack, 2010), where the weights originate from the delta method on the binomial data.  Normalized counts were further transformed into normally distributed expression values via the voom-transformation and was the final input for statistical modeling. Statistical analysis was carried out using Limma framework (Ritchie et al., 2015) in R language version 3.0.3 and its available packages.
Assembly: GRCh38
Supplementary files format and content: tab delimited text file containing count data for each sample

source_name: Control sample

growth_protocol: COL6A3 gene expression was depleted by transducing IMR90 cells (incubated at 37oC, 5% CO2, and 20% O2) with COL6A3 shRNA lentiviral particles (Santa Cruz sc-94560-V), and control IMR90 cells with control shRNA lentiviral particles (Santa Cruz sc-108080) according to manufacturer’s instructions with following adaptations: only lentiviral particles (without polybrene) were used, multiplicity of infection was 1, and concentration of puromycin (ThermoFisher A1113803) was 2 mg/mL.Validation of knockdown was confirmed by qPCR.

extract_protocol:
RNA was extracted using the RNeasy® Mini Kit (74104, Qiagen) and manufacturer's instructions and included a genomic DNA digestion step (RNase-free DNase Set 79254, Qiagen).
Illumina TruSeq Stranded mRNA library prep kit was selected to specifically investigate mRNAs. Polyadenylated RNA molecules are enriched by using oligo-dT beads. Strand information is preserved. Sequencing was performed using an Illumina NextSeq instrument to achieve 30 million reads per sample (triplicates) with 100nt paired end reads.

tag: shRNA

value: Control


title: IMR9_control_Rep2


title: IMR9_control_Rep1


title: hEC-sinrf2-1-3


title: hEC-sinrf2-1-1


title: hEC-NC-3


title: IMR90 COL6A3shRNA_Knockdown_Rep3

value: COL6A3 shRNA lentiviral particles (Santa Cruz sc-94560-V),


title: IMR90 COL6A3shRNA_Knockdown_Rep2


title: hEC-NC-2


title: hEC-NC-1


title: IMR90 COL6A3shRNA_Knockdown_Rep1


title: IMR90_control_shRNA_Rep3

source_name: shRNA_Control sample

value: control shRNA lentiviral particles (Santa Cruz sc-108080)


title: LuCaP 23.1 ectopically expressing HNF1A, rep1

tag: genotype


title: IMR90_control_shRNA_Rep2


title: venule, day 6, aged serum exposure, round 2

city: Baltimore

first: Peter

middle: C

last: Searson

address: 3400 North Charles Street

institute: Johns Hopkins University

data_processing:
alignment and quantification to GRCh38 using Rsubread
Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) was calculated for each gene as outlined in Trapnell et al., Nature Biotechnology, 2010.
Normalization using variance stabilizing regularized logarithm transformation (rlog) using DESeq2
Assembly: hg38
Supplementary files format and content: .txt file containing averaged FPKM values for all of the above conditions across three biological replicates each

source_name: WTC iEC

growth_protocol: Cell culture was conducted at 5% CO2 and 37 °C.  iECs were differentiated using ETV2 modified RNA from induced pluripotent stem cells. In control microvessels, iECs were seeded into a 150 µm diameter cylinder suspended in a bulk collagen I hydrogel at a density of 20 million cells/mL and maintained in EBM-2 basal media supplemented with 5% FBS, 0.4% hFGF-B, 0.1% VEGF, 0.1% R3-IGF-1, 0.1% ascorbic acid, 0.1% hEGF, and 0.1% GA-1000. Venule models included iPCs differentiated from the same induced pluripotent stem cells and sequentially seeded: iPCs were seeded at a density of 6 million cells/mL in the 150 µm diameter cylinder, then allowed to mature for 24 hours in E6 media supplemented with 10% fetal bovine serum, then iECs were seeded at the same density and conditions as above, and maintained in iEC media.

extract_protocol:
Microvascular models were washed with 1x PBS and perfused with RLT buffer; downstream lysate was collected and supplemented with β-mercaptoethanol, before isolating RNA using a RNeasy Mini Kit (Qiagen) with DNase I digestion (Qiagen).
RNA libraries were prepared with the Takara SMART-seq v4 kit following QC of purified lysates.

treatment_protocol: When supplemented with young or aged human serum, the 5% FBS volume in iEC maintenance media was replaced with a 5% volume of human serum pooled equally from 50 male donors with an average age of 25 (young) or 65 (aged).

tag: cell line

value: WTC iEC

value: IPSC-derived endothelial cell

tag: model

value: venule

value: aged serum


title: venule, day 6, aged serum exposure, round 3

tag: cell type

tag: treatment


title: venule, day 6, aged serum exposure, round 1


title: IMR90_control_shRNA_Rep1


title: venule, day 6, young serum exposure, round 3

value: young serum


title: hEC-sinrf2-2-2


title: venule, day 6, young serum exposure, round 2


title: venule, day 6, young serum exposure, round 1


title: HT29_H3K27ac_HiChIP

value: Colorectal adenocarcinoma cell line


title: DOHH2_H3K27ac_HiChIP_rep1

value: Non-Hodgkin lymphoma cell line (B-cell)


title: hEC-sinrf2-1-2


title: venule, day 6, media exposure, round 2

value: media


title: venule, day 6, media exposure, round 3


title: venule, day 6, media exposure, round 1


title: REC1_H3K27ac_HiChIP_rep2

value: Non-Hodgkin lymphoma cell line


title: REC1_H3K27ac_HiChIP_rep1


title: control microvessel, day 6, aged serum exposure, round 5

value: control microvessel


title: CUTLL1_H3K27ac_HiChIP_rep1

value: Non-Hodgkin lymphoma cell line (T-cell)


title: control microvessel, day 6, aged serum exposure, round 4


title: control microvessel, day 6, aged serum exposure, round 2


title: control microvessel, day 6, young serum exposure, round 5


title: MCF7_H3K27ac_HiChIP_rep2

value: Breast carcinoma cell line


title: MCF7_H3K27ac_HiChIP_rep1

value: H3K27ac (Abcam ab4729)


title: control microvessel, day 6, young serum exposure, round 4


title: ZR751_H3K27ac_HiChIP_rep2


title: ZR751_H3K27ac_HiChIP_rep1


title: control microvessel, day 6, young serum exposure, round 2


title: DOHH2_H3K27ac_HiChIP_rep2


title: H2170_H3K27ac_HiChIP

value: Lung squamous cancer cell line


title: control microvessel, day 6, media exposure, round 4


title: control microvessel, day 6, media exposure, round 5


title: VCaP_H3K27ac_HiChIP

source_name: VCaP

value: VCaP

value: Prostate adenocarcinoma cell line


title: 22RV1_H3K27ac_HiChIP


title: MDACAP2B_H3K27ac_HiChIP_rep2


title: MDACAP2B_H3K27ac_HiChIP_rep1


title: control microvessel, day 6, media exposure, round 2


title: CUTLL1_H3K27ac_HiChIP_rep2


title: HNT34_NT_3

city: Parma

first: Andrea

last: Gherli

address: Via Gramsci 14

department: Medicine and Surgery

country: Italy

institute: University of Parma

data_processing:
The raw sequence files were quality controlled using FastQC (v 1.3)
Transcripts were aligned using the STAR package
Assembly: GRCh38
Supplementary files format and content: txt files with raw counts

extract_protocol:
RNA extracted with Qiagen RNeasy Kit
TruSeq mRNA stranded sample preparation kit (Illumina, San Diego, CA, USA, #20020594)

value: control non targeting shRNA (NT)


title: HNT34_NT_2


title: HNT34_87_3

value: shRNA targeting EVI1 gene (#18)


title: RNASeq_PROLIF_G_rep1.5 (re-analyzed)

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description:
20-S2-KD5NT_S16
re-analysis of GSM5352883
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab

data_processing:
RNA-Seqpairedreads were aligned to the hg38 genome with Hisat2(v2.1.0)using theensemblannotation(v95).
Reads ingeneswere countedusingfeaturecounts, with multimapping readsfractionally assigned using --fractionand-M.
Low abundance genes were filtered out of further analysis using edgeR's function "filterByExpr".
Normalisation between library sizes to get FPKM values was done using the trimmed mean of M-values method.
Normalisationfor differential expression was bylimma-voom(Law et al. 2014)and tests calculatedbylmFitandeBayes.
Calculations of changing expression over time were done pairwiseProlifvday0,day0 vday3 andday3 vday15;first within each donor and then combined across donors.
Assembly: hg38 ensembl95
Supplementary files format and content: Bigwig RNA-Seq coverage file generated with deeptools bamCoverage (binsize 50bp)
Supplementary files format and content: Raw read counts per gene, one column per sample
Supplementary files format and content: RPKM for each gene passing the filtering threshold in each sample.  Includes Prolif, day0, 1, 3 and 9 timepoints from previous study (GSE176020; Potolitsyna et al., 2022).
Supplementary files format and content: Differential expression analysis tables including logFC and adj.P.Val.  Analysis 1) bulk day15 versus adipocytes isolated from day15.  Analysis 2) Adipogenesis timecourse analysis with Prolif, day0 and day3 timepoints from previous study (GSE176020; Potolitsyna et al,. 2022).

source_name: Human primary adipose stem cells

growth_protocol: Human normal adipose tissue-derived mesenchymal stem cells were isolated from subcutaneous liposuction material. Cells were expanded in DMEM/F12 containing 10% fetal calf serum, and 20 ng/ml basic fibroblast growth factor (FGF2; Sigma-Aldrich F5392). Cells at passage 5-8 were used in three independent differentiations into the adipocyte lineage.

extract_protocol:
For RNA-seq, total mRNA was isolated from cells at aforementioned stages of differentiation using the Qiagen RNeasy kit and processed for Illumina library preparation and sequencing.
Illumina sequencing libraries were generated as per Illumina protocols.

treatment_protocol: For adipogenic differentiation, confluent cells were cultivated for 48h in DMEM/F12/10% fetal bovine serum without growth factors. Adipogenesis was then induced by addition of 10 µg/ml insulin, 200 µM indomethacin, 0.5 µM 1-methyl-3 isobutylxanthine and 1 µM dexamethasone. Medium was renewed every 3 days until day 9. Cells were then maintained in DMEM/F12/10% fetal bovine serum and 10 µg/ml insulin until day 15. RNA from the total cell population ("bulk") was harvested by direct lysis in the well. For mature adipocyte isolation, D15 samples were trypsinized, resuspended in HBSS, 0,5% BSA, and centrifuged 200g for 5 min. Floating mature adipocytes were harvested in Trizol and processed for RNA extraction.

value: Human primary adipose stem cells

tag: time point

value: day-2 (proliferating)

tag: adipose depot

value: Gluteal

tag: culture

value: Cultured in vitro

tag: cell fraction

value: bulk


title: RNASeq_PROLIF_G_rep3.5 (re-analyzed)

description:
22-S12-KD3NT_S22
re-analysis of GSM5352885
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: RNASeq_D9_A_rep3 (re-analyzed)

description:
15-19199_S2
re-analysis of GSM5352882
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab

value: Abdominal subcutaneous


title: HNT34_NT_1


title: HNT34_87_2


title: RNASeq_PROLIF_G_rep2.5 (re-analyzed)

description:
21-S7-KD6NT_S19
re-analysis of GSM5352884
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: HNT34_87_1


title: RNASeq_D1_A_rep3 (re-analyzed)

description:
13-19197_S18
re-analysis of GSM5352880
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: RNASeq_D0_A_rep3 (re-analyzed)

description:
12-19196_S15
re-analysis of GSM5352879
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab

value: day0 (induction of differentiation)


title: HNT34_16_2

value: shRNA targeting EVI1 gene (#16)


title: RNASeq_D3_A_rep3 (re-analyzed)

description:
14-19198_S21
re-analysis of GSM5352881
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: HNT34_16_3


title: RNASeq_PROLIF_A_rep3 (re-analyzed)

description:
11-19195_S12
re-analysis of GSM5352878
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: HNT34_16_1


title: RNASeq_D9_A_rep2 (re-analyzed)

description:
10-19194_S9
re-analysis of GSM5352877
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: Post_Azacitidine-Entinostat

data_processing:
A digital expression matrix was generated for each sample using Cellranger software (10x Genomics)
Data were integrated using Harmony and analyzed using Seurat (R package)
Assembly: GRCh38
Supplementary files format and content: Tab separated values files and matrix files

source_name: Bone Marrow

extract_protocol:
Single cells were lysed, barcoded, and normalized for input onto the Chromium Single Cell A Chip Kit (10x Genomics)
Chromium Single Cell A Chip Kit (10x Genomics)

value: Bone Marrow


title: m85

data_processing:
Quality control applied with trim_galore V0.6.0 deploying cutadapt V1.18 and fastqc v0.11.7. Paired-end bisulfite treated FASTQ files were aligned by Bismark V0.13.1 deploying Bowtie2 aligner to mm10 assembly. Methylation calling performed with bismark_methylation_extractor followed by Bismark cov2cytp and a custom AWK script transforming files to methylKit input format. Differential methylated regions were obtain with methylKit R-package V1.10.0 and earlier consistent versions. Genome_build: mm10.
Assembly: mm10
Supplementary files format and content: all processed data are in methkit format

value: Liver

value: hepatocyte

value: liver control of 10-12w old femal


title: retinal organoid, ND Control, D120, scRNAseq

extract_protocol:
Organoid dissociation for single-cell RNAseq: For Day 40-260 scRNAseq samples, approximately ten organoids displaying morphology of successful retinal differentiation were selected for each of the three lines. Organoids were allowed to settle by gravity in a 1.5mL tube and culture medium was removed. Organoids were dissociated in a solution of 20U/mL papain (Worthington) and 120U/mL DNase (Worthington) in Earle’s balanced salt solution (EBSS) (Worthington). Samples were incubated in 300µL of above papain solution at 37˚C with continuous shaking (500rpm) until all organoids were completely dissociated (approximately 1 hour). Samples were triturated with a pipette every 15 minutes. Following dissociation, cells were pelleted at 500 x g for 5 minutes and resuspended in 8µg/mL recombinant albumin (New England Biolabs) in dPBS-/-. Cells were passed through a 70µm filter to encapsulation with the Chromium Controller instrument (10X Genomics). Approximately 8,000 cells were targeted for encapsulation per sample.   Nucleus isolation for single-nucleus multimodal sequencing: Nuclei were isolated from differentiation day 160 and 260 organoids from an independent batch of differentiation (i.e., completely different round initiated on a separate day) than single-cell gene expression samples. Nuclei were isolated following a protocol based on 10X Genomics’ demonstrated protocol CG000366. Briefly, approximately ten organoids were selected as described above. Medium was aspirated and 500µL of chilled 0.1X Lysis Buffer (Tris-HCl, NaCl, MgCl2, Tween-20, NP40, Digitonin, BSA, DTT, RNase Inhibitor) was added to each sample. Samples were homogenized with 15 strokes of a sterile pestle in a 1.5mL tube on ice. Samples were then incubated on ice for 5 minutes. Following incubation, samples were mixed with a P1000 pipette 10 times on ice and incubated for 8.5 minutes on ice. 500µL of Wash Buffer (Tris-HCl, NaCl, MgCl2, Tween-20, BSA, DTT, RNase Inhibitor) was added and lysed cells were mixed 5 times with pipetting. Cells were pelleted at 500 x g for 5 minutes in a refrigerated (4˚C) centrifuge and resuspended in 500µL chilled wash buffer. This process was repeated for three total washes. Nuclei were resuspended in Diluted Nuclei Buffer (Nuclei Buffer (10X Genomics), DTT, RNase Inhibitor) and passed through a 70µm strainer. Nuclei were counted on a hemocytometer with DAPI to visualize intact nuclei. Approximately 9,000 nuclei were targeted for encapsulation per sample using the Chromium X instrument (10X Genomics).
Single-cell gene expression library preparation and sequencing: Single cells were partitioned and barcoded with the Chromium Controller instrument (10X Genomics) and Single Cell 3' Reagent (v3.1 chemistry) kit (10X Genomics) according to the manufacturer’s specifications with no modification (Rev C). Final libraries were quantified using the Qubit dsDNA HS Assay Kit (Life Technologies) and diluted to 3ng/µL in buffer EB (Qiagen). Library quality was confirmed using the Bioanalyzer High Sensitivity DNA Assay (Agilent) prior to sequencing.  Single-nucleus multimodal library preparation and sequencing: Nuclei were processed following the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression (Rev. E) without modification. Final libraries were quantified using the Qubit dsDNA HS Assay Kit and diluted to 3ng/µL. Library quality was checked using the Bioanalyzer or Tapestation (Agilent).

tag: sample type

value: retinal organoid

value: ND Control

tag: differentiation day


title: ENT_Input2

data_processing:
nfcore ChIP pipeline (version 2.0.0)
MACS2 for peak calling
HOMER for annotation of peaks
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
ActiveMotif ChIP IT® Express  (ActiveMotif, Carlsbad, CA, USA, #53008)
NEBNext® Ultra™ II DNA Library Prep Kit (#E7645, New England Biolabs, Ipswich, MA)

treatment_protocol: Samples were treated for 24 hours with AR-42 0.8uM, entinostat 4uM, or DMSO vehicle

tag: antibody

value: Input

value: ENT


title: RNASeq_D3_A_rep2 (re-analyzed)

description:
9-19193_S6
re-analysis of GSM5352876
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: Pre_Azacitidine-Entinostat

tag: tissue


title: RNASeq_D1_A_rep2 (re-analyzed)

description:
8-19192_S3
re-analysis of GSM5352875
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: ENT_Input1


title: RNASeq_D0_A_rep2 (re-analyzed)

description:
7-19191_S1
re-analysis of GSM5352874
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: RNASeq_PROLIF_A_rep2 (re-analyzed)

description:
6-19190_S20
re-analysis of GSM5352873
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: ENT_EVI2

value: EVI


title: RNASeq_D9_A_rep1 (re-analyzed)

description:
5-19204_S17
re-analysis of GSM5352872
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab

value: Human primary adipose stem cells


title: ENT_EVI1


title: RNASeq_D3_A_rep1 (re-analyzed)

description:
4-19203_S14
re-analysis of GSM5352871
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: ENT_27AC2


title: DMSO_Input2

value: DMSO


title: RNASeq_D1_A_rep1 (re-analyzed)

description:
3-19202_S11
re-analysis of GSM5352870
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: RNASeq_PROLIF_A_rep1 (re-analyzed)

description:
1-19200_S5
re-analysis of GSM5352868
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab

value: day-2 (proliferating)


title: ENT_27AC1


title: DMSO_Input1


title: DMSO_EVI2


title: DMSO_EVI1


title: DMSO_27AC2


title: RNASeq_D3_G_rep3 (re-analyzed)

description:
15-P8D3_S15
re-analysis of GSM5352866
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab

value: Gluteal

value: Cultured in vitro


title: RNASeq_D1_G_rep3 (re-analyzed)

description:
14-P8D1_S14
re-analysis of GSM5352865
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab

value: bulk


title: RNASeq_D9_G_rep3 (re-analyzed)

description:
16-P8D9_S16
re-analysis of GSM5352867
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: DMSO_27AC1


title: RNASeq_D0_G_rep3 (re-analyzed)

description:
13-P8D0_S13
re-analysis of GSM5352864
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab

value: day0 (induction of differentiation)


title: RNASeq_PROLIF_G_rep3 (re-analyzed)

description:
12-KD3NT_S12
re-analysis of GSM5352863
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: AR2_Input1


title: RNASeq_D9_G_rep2 (re-analyzed)

description:
11-P6D9_S11
re-analysis of GSM5352862
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: RNASeq_D1_G_rep2 (re-analyzed)

description:
9-P6D1_S9
re-analysis of GSM5352860
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: AR2_EVI1


title: RNASeq_D0_G_rep2 (re-analyzed)

description:
8-P6D0_S8
re-analysis of GSM5352859
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: AR2_27AC2


title: AR2_27AC1


title: RNASeq_PROLIF_G_rep2 (re-analyzed)

description:
7-KD6NT_S7
re-analysis of GSM5352858
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: RNASeq_D0_A_rep1 (re-analyzed)

description:
2-19201_S8
re-analysis of GSM5352869
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab

value: Abdominal subcutaneous


title: m131

extract_protocol: Partial hepatectomy was carried out on 12 weeks old mice by removing 2/3 of the liver, including resection of the left lower, upper lobes and the right upper lobe.  Mice were anaesthetized and subjected to liver perfusion. Whole liver was then digested by collagenase (Roche) and hepatocytes removed and isolated by means of a Percoll gradient. Cells were then sorted by FACS according to size. Hepatoblasts were prepared from E11.5 and E16.5 mouse embryos by collecting fetal liver samples from littermate siblings which were then minced and digested for 30 min at 37°C with 0.025% collagenase IV (Sigma-Aldrich, C4-22-1G). After gentle pipetting, the cell suspension was filtered through a 40-mm cell strainer and washed twice with RPMI medium containing 10% FBS. The cells were then stained for 40 minutes at 4°C with moderate agitation with Liv2 (mouse) mAb (MBL, D118-3) for E11.5 hepatoblast, and Dlk1-APC-conjugated mouse Pref-1/DLK1/FA1 antibody (R&D Systems, FAB8634A-100) for E16.5 hepatoblast. Positive hepatoblast cells were then isolated by Flow cytometry. DNA was isolated from purified cells, incubated in lysis buffer (25 mM Tris-HCl (pH  8), 2 mM EDTA, 0.2% SDS, 200 mM NaCl) supplemented with 300 μg/ml proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation. The methylation profile was checked using the RRBS assay [Boyle, 2012]. Briefly, the DNA was digested with the MspI enzyme to yield CpG enriched fragments. Adapter sequences were ligated at both ends, and DNA fragments were then treated with sodium-bisulfite, allowing for easy distinction between methylated and unmethylated bases. The DNA was then amplified by PCR to produce the final libraries.

value: liver 2 mounth after Phx of 10-12w old femal


title: RNASeq_D1_G_rep1 (re-analyzed)

description:
4-P5D1_S4
re-analysis of GSM5352855
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: RNASeq_D3_G_rep1 (re-analyzed)

description:
5-P5D3_S5
re-analysis of GSM5352856
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: Aza

city: Meldola

first: Matteo

last: Marchesini

state: FC

address: via Piero Maroncelli 40

institute: IRCSS Istituto Romagnolo per lo Studio dei Tumori "Dino Amadori" (IRST)

value: Bone Marrow

value: CD45+ leukemia cells

value: azacitidine (Aza)


title: Ent_Aza

value: combination of azacitidine and entinostat (Ent_Aza)


title: RNASeq_D0_G_rep1 (re-analyzed)

description:
3-P5D0_S3
re-analysis of GSM5352854
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: RNASeq_PROLIF_G_rep1 (re-analyzed)

description:
2-KD5NT_S2
re-analysis of GSM5352853
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: VEH

first: Anna

last: Montanaro

department: Department of Medicine and Surgery


title: RNASeq_PROLIF_G_rep0 (re-analyzed)

description:
1-KD4NT_S1
re-analysis of GSM5352852
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab


title: AR2_Input2


title: Nalm-6 R cells, NU, 1

city: Rouen

first: Souleymane

last: Abdoul-Azize

state: State...

address: 22 Bd Gambetta

country: France

institute: Rouen normandy Univ

data_processing:
nf-core/rnaseq v3.1 analysis pipeline to generate multi quality control report
STAR v2.6.1d and SALMON v1.4.0 tools for alignment
Differential expression analysis, based on a model using the binomial negative distribution, was performed with DESeq2 tool to evaluate significant counts
Read count extraction and normalization were performed using DESeq2 tool
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: Nalm-6 R B cell precursor leukemia cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using NucleoSpin RNA kit  kit (Macherey‑Nagel). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Kit for Illumina following manufacturer's protocols.

treatment_protocol: PLC signaling pathway was inhibited by treatment of 16 h post confluent cells  with 1µM U73122 (Abcam),

value: B cell precursor leukemia

value: WT

tag: time


title: Nalm-6 R cells, NU, 2


title: 293T. Mock, 2

city: Suwon

first: Hyunmi

last: Kim

address: 206, World cup-ro, Yeongtong-gu

country: South Korea

institute: Ajou University School of Medicine

data_processing:
A quality control of raw sequencing data was performed using FastQC. Adapter and  low quality reads were removed using Fastp.
Then the trimmed reads were mapped to the reference genome using STAR. The quantification of reads was processed using Salmon. The Read Counts were processed based on TMM + CPM normalization method using EdgeR.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file for each sample

growth_protocol: The cells were grown in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) with 10 % fetal bovine serum (FBS; GenDepot) and 1% antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
DNA was extracted using a TaKaRa RNAiso Plus.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

value: embryonic kidney


title: Vehicle

value: Vehicle


title: AR2_EVI2

value: EVI


title: RNASeq_D3_G_rep2 (re-analyzed)

description:
10-P6D3_S10
re-analysis of GSM5352861
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab

value: Human primary adipose stem cells


title: Nalm-6 R cells, NC, 2

value: DMSO


title: 293T. Mock, 1


title: Nalm-6 R cells, NC, 1


title: 293T, stat6, 2

value: STAT6 overexpression


title: RNASeq_D9_G_rep1 (re-analyzed)

description:
6-P5D9_S6
re-analysis of GSM5352857
adipogenesis_rpkm_tmm.tab
nucleolus_adipogenesis_DE.tab

value: Gluteal

value: Cultured in vitro


title: 293T, stat6, 1


title: 003G_Mouse56_Vehicle only

city: San Francisco

first: Kristen

last: Seim

address: 201 Haskins Way

institute: GraphiteBio

description:
GCPS5566
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

data_processing:
Using CRISPResso report files, unedited reads were labeled as “WT”, whereas indels were grouped together as non-homologous end joining "NHEJ". These two groups were aggregated to %HDR from ddPCR and normalized for a total 100% sum.
Assembly: hg38
Supplementary files format and content: csv file with HDR recombination counts

source_name: bone marrow

extract_protocol:
Genomic DNA was PCR amplified using KAPA HiFi HotStart ReadyMix (2X) (Roche).
A second round of PCR with primers containing Nextera sequencing adapters enriched the target locus.
Individual samples were indexed using xGenTM UDI IDT index primers (IDT). Indexed samples were pooled and sequenced on an Illumina Miseq and analyzed.

value: bone marrow

value: HSCs

value: 003G_Mouse56_Vehicle only


title: 293T, stat6, 3


title: Ent

value: Bone Marrow

value: entinostat (Ent)


title: 003G_Mouse55_Vehicle only

description:
GCPS5565
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse55_Vehicle only


title: 003G_Mouse29_Vehicle only

description:
GCPS5564
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse29_Vehicle only


title: 003G_Mouse26_Vehicle only

description:
GCPS5563
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse26_Vehicle only


title: 293T. Mock, 3

value: WT


title: WS6


title: 003G_Mouse50_Donor2 - RNPonly

description:
GCPS5556
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse50_Donor2 - RNPonly


title: 003G_Mouse51_Donor2 - RNPonly

description:
GCPS5557
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse51_Donor2 - RNPonly


title: 003G_Mouse22_Donor2 - RNPonly

description:
GCPS5555
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse22_Donor2 - RNPonly


title: B primaryTat-Zta 6h 1

city: Villejuif

last: Schwager

state: Please Select

address: 114 Rue Edouard Vaillant

institute: Institut Gustave Roussy

description:
BcellsTatZta_counts.csv
T_Z6h1

data_processing:
The reads were trimmed with trimgalore (0.6.7) and cutadapt (3.4) to remove the Illumina adapter sequences from the 3′-ends. The trimmed reads were mapped to the GRCh38 genome from the Illumina iGenomes using Hisat2 and quantified with FeatureCounts.
Assembly: GRCh38
Supplementary files format and content: raw counts

source_name: blood

extract_protocol:
Total RNA was extracted using a NucleoSpin RNA isolation kit (Macherey-Nagel, Germany) following manufacturer’s instructions
Novogene NGS RNA Library Prep Set (PT042)

value: blood

value: Primary B cells

value: B cells

value: Tat + Zta 6h


title: B primary Tat-Zta 48h 3

description:
BcellsTatZta_counts.csv
T_Z48h3

value: Tat + Zta 48h


title: B primaryTat-Zta 6h 4

description:
BcellsTatZta_counts.csv
T_Z6h4


title: B primaryTat-Zta 6h 3

description:
BcellsTatZta_counts.csv
T_Z6h3


title: 003G_Mouse44_Donor2 - MOI 2500

description:
GCPS5543
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: bone marrow

value: 003G_Mouse44_Donor2 - MOI 2500


title: B primary Tat-Zta 48h 2

description:
BcellsTatZta_counts.csv
T_Z48h2


title: B primary Tat-Zta 48h 1

description:
BcellsTatZta_counts.csv
T_Z48h1


title: B primary Tat-Zta 48h 4

description:
BcellsTatZta_counts.csv
T_Z48h4


title: 003G_Mouse20_Donor2 - RNPonly

description:
GCPS5553
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: HSCs

value: 003G_Mouse20_Donor2 - RNPonly


title: B primary Zta 48h 4

description:
BcellsTatZta_counts.csv
Zta48h4

value: Zta 48h


title: B primary Zta 48h 3

description:
BcellsTatZta_counts.csv
Zta48h3


title: 003G_Mouse21_Donor2 - RNPonly

description:
GCPS5554
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse21_Donor2 - RNPonly


title: B primary Zta 48h 2

description:
BcellsTatZta_counts.csv
Zta48h2


title: Gene expression profiles of skeletal muscles in response to GDE5 deficiency exp1

type: RNA

city: Higashi-Hiroshima

first: Yanaka

last: Noriyuki

address: Kagamiyama 1-4-4

department: Graduate School of Biosphere Science

institute: Hiroshima University

hyb_protocol: Hybridization was performed according to manufacturer's instructions (Agilent).

scan_protocol: Scanned on an Agilent G2565BA scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 9.5).

source_name: wild-type

label_protocol: 1 µg of total RNA were primed with T7 promoter primer, then reversed transcribed in the presence of MMLV-RT. cRNAs were synthesized in the presence of each dATP, dTTP, dGTP, dCTP with Cy3-labeled or Cy5-labeled dCTP according to manufacturer's instructions (Agilent).

growth_protocol: Mice were maintained in accordance with the Hiroshima University guidelines for the care and use of laboratory animals.

extract_protocol: Total RNAs of gastrocnemius (GAS) muscles were extracted using QIAzol following manufacturer's instructions.

treatment_protocol: Male wild-type and skeletal muscle-specific GDE5 (Gpcpd1) deficient mice (15 weeks) were fed normal diet.

value: wild-type

value: skeletal muscle

value: GDE5 KO


title: 003G_Mouse42_Donor2 - MOI 2500

description:
GCPS5541
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse42_Donor2 - MOI 2500


title: 003G_Mouse43_Donor2 - MOI 2500

description:
GCPS5542
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse43_Donor2 - MOI 2500


title: Gene expression profiles of skeletal muscles in response to GDE5 deficiency exp2

source_name: skeletal muscle-specific GDE5 (Gpcpd1) deficient


title: B primary Zta 48h 1

description:
BcellsTatZta_counts.csv
Zta48h1


title: 003G_Mouse41_Donor2 - MOI 2500

description:
GCPS5540
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse41_Donor2 - MOI 2500


title: B primary Zta 6h 4

description:
BcellsTatZta_counts.csv
Zta6h4

value: blood

value: Zta 6h


title: 003G_Mouse15_Donor2 - MOI 2500

description:
GCPS5539
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse15_Donor2 - MOI 2500


title: 003G_Mouse14_Donor2 - MOI 2500

description:
GCPS5538
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse14_Donor2 - MOI 2500


title: B primary Zta 6h 3

description:
BcellsTatZta_counts.csv
Zta6h3

value: Primary B cells

value: B cells


title: 003G_Mouse13_Donor2 - MOI 2500

description:
GCPS5537
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: bone marrow

value: 003G_Mouse13_Donor2 - MOI 2500


title: B primary Zta 6h 1

description:
BcellsTatZta_counts.csv
Zta6h1


title: B primaryTat-Zta 6h 2

description:
BcellsTatZta_counts.csv
T_Z6h2

value: Tat + Zta 6h


title: 003G_Mouse12_Donor2 - MOI 2500

description:
GCPS5536
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: HSCs

value: 003G_Mouse12_Donor2 - MOI 2500


title: B primary Tat 48h 4

description:
BcellsTatZta_counts.csv
Tat48h4

value: Tat 48h


title: B primary Tat 48h 1

description:
BcellsTatZta_counts.csv
Tat48h1


title: 003G_Mouse38_Donor1 - RNPonly

description:
GCPS5532
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse38_Donor1 - RNPonly


title: 003G_Mouse9_Donor1 - RNPonly

description:
GCPS5530
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse9_Donor1 - RNPonly


title: B primary Tat 48h 3

description:
BcellsTatZta_counts.csv
Tat48h3


title: 003G_Mouse40_Donor1 - RNPonly

description:
GCPS5534
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse40_Donor1 - RNPonly


title: B primary Tat 48h 2

description:
BcellsTatZta_counts.csv
Tat48h2


title: 003G_Mouse32_Donor1 - MOI 2500

description:
GCPS5520
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse32_Donor1 - MOI 2500


title: B primary Tat 6h 2

description:
BcellsTatZta_counts.csv
Tat6h2

value: Tat 6h


title: 003G_Mouse10_Donor1 - RNPonly

description:
GCPS5531
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse10_Donor1 - RNPonly


title: B primary Tat 6h 3

description:
BcellsTatZta_counts.csv
Tat6h3

value: blood


title: 003G_Mouse33_Donor1 - MOI 2500

description:
GCPS5521
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse33_Donor1 - MOI 2500


title: B primary c 48h 3

description:
BcellsTatZta_counts.csv
BC48hr3

value: no


title: B primary Tat 6h 4

description:
BcellsTatZta_counts.csv
Tat6h4

value: Primary B cells


title: 003G_Mouse3_Donor1 - MOI 2500

description:
GCPS5517
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse3_Donor1 - MOI 2500


title: 003G_Mouse4_Donor1 - MOI 2500

description:
GCPS5518
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: bone marrow

value: 003G_Mouse4_Donor1 - MOI 2500


title: 003G_Mouse2_Donor1 - MOI 2500

description:
GCPS5516
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse2_Donor1 - MOI 2500


title: 003G_Mouse31_Donor1 - MOI 2500

description:
GCPS5519
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: HSCs

value: 003G_Mouse31_Donor1 - MOI 2500


title: 003G_Mouse39_Donor1 - RNPonly

description:
GCPS5533
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: 003G_Mouse39_Donor1 - RNPonly


title: B primary Zta 6h 2

description:
BcellsTatZta_counts.csv
Zta6h2

value: B cells

value: Zta 6h


title: B primary c 48h 2

description:
BcellsTatZta_counts.csv
BC48hr2


title: B primary c 48h 4

description:
BcellsTatZta_counts.csv
BC48hr4


title: B primary c 6h 4

description:
BcellsTatZta_counts.csv
BC6hr4


title: B primary c 48h 1

description:
BcellsTatZta_counts.csv
BC48hr1


title: B primary c 6h 3

description:
BcellsTatZta_counts.csv
BC6hr3


title: KW-152-D2-328-HBB-i2v2-bgh-2500

description:
GCPS1447
Amplicon sequencing of the HBB editing locus for pooled human HSCs after editing (pre-mouse injection)
Mouse_OnTarget_Summary_Table_2.csv
HDR counts


title: KW-152-D2-328-HBB-RNP only

description:
GCPS1445
Amplicon sequencing of the HBB editing locus for pooled human HSCs after editing (pre-mouse injection)
Mouse_OnTarget_Summary_Table_2.csv
HDR counts

value: KW-152-D2-328-HBB-RNP only


title: KW-152-D029-1125-HBB-i2v2-bgh-2500

description:
GCPS1442
Amplicon sequencing of the HBB editing locus for pooled human HSCs after editing (pre-mouse injection)
Mouse_OnTarget_Summary_Table_2.csv
HDR counts


title: KW-152-D029-1125-Untreated

description:
GCPS1439
Amplicon sequencing of the HBB editing locus for pooled human HSCs after editing (pre-mouse injection)
Mouse_OnTarget_Summary_Table_2.csv
HDR counts


title: BLAS Tat-Zta 48h 2

value: BLAS

value: Tat + Zta 48h


title: B primary Tat 6h 1

description:
BcellsTatZta_counts.csv
Tat6h1

value: Tat 6h


title: KW-152-D029-1125-HBB-RNP only

description:
GCPS1440
Amplicon sequencing of the HBB editing locus for pooled human HSCs after editing (pre-mouse injection)
Mouse_OnTarget_Summary_Table_2.csv
HDR counts


title: BLAS Tat-Zta 6h 3

value: blood

value: Tat + Zta 6h


title: BLAS Tat-Zta 48h 3


title: p320_RuDDR_Taq_Rep2

city: Stanford

first: Jinglong

last: Wang

state: CA California

address: 1291 Welch Rd, CCSR Room 1240

department: Radiation Oncology

institute: Stanford University

library_source: other

data_processing:
PCR-mediated template switching, involved the extraction and merging of barcodes from the paired-end sequencing library based on sequencing identification (ID). Paired barcodes underwent pairwise alignment and were compared with a reference barcode list to determine matched, switched, and randomly occurring errors.
The mapping of each paired library to the reference DNA template was executed using CRISPResso2 and stored in BAM files.
The ID and Cigar information were extracted and generated into TXT files, which were then merged with the matched file containing barcodes identified by ID.
Gene information was incorporated based on the sgRNA spacer sequence.
For the analysis of repair outcomes, it was assumed that the Double-Strand Breaks (DSB) occurred within ±10bps of the ideal break site. This implies that the deletion window must overlap with the DSB window, and all insertions must reside within this DSB window.
Assembly: hg19, pMCB320-DDR, pMCB320-RuDDR
Supplementary files format and content: tab delimited text files contain the pairwise alignment information including: the index, the barcode 1 (sequence_x), sequence identity (ID), length of barcode 1 (len_x), the barcode 2 or the spacer (sequence_y), length of barcode 2 (len_y), the reverse complement of barcode 2 (sequence_y_rcp) and the alignment score between barcode 1 and the barcode 2 (Align_score).
Supplementary files format and content: tab delimited text files contain the filtered, annotated mapping information including: the Index, the sequencing identity (ID), the barcode 1 (barcode), the barcode 2 or sgRNA spacer (seq_exp), the alignment score between barcode 1 and barcode 2 (Align_score), the gene name (Symbol), the mapping to a 362bp region of interest in the reference template (Cigar), the length of deletion (D_length),  the position of deletion (D_location), the length of insertion (I_insertion), the position of insertion (I_location).
Library strategy: Dual-barcode Repair-Seq

molecule: other

organism: Escherichia coli

source_name: Endura Electrocompetent cells

growth_protocol: K562-iCas9-DDR cell line was cultured at 37 °C and 5% CO2 in RPMI supplemented with 10% (vol/vol) FBS, 50 U/mL penicillin/streptomycin, 2 mM L-glutamine , 1× MEM-NEAA, 1 mM sodium pyruvate , 50 μM 2-mercap- toethanol and 20 mM Hepes (pH 7.4).

extract_protocol:
Genomic DNA was isolated using protocol described in Hu et al., 2016 Nature Protocols (PMC4895203)
DDR libraries were constructed through a two-step PCR process. In the initial PCR, outer layer primers (DDR-lib-F1 and DDR-lib-R1) were employed to amplify the regions of interest. Subsequently, in the second PCR, I5-DDR and I7-DDR primers were used to tag the libraries, which were then purified through electrophoresis and a gel-extraction kit.

treatment_protocol: G1/G0-arrested K562-iCas9-DDR cell lines were treated by 50 μM Palbociclib. The cycling and G1/G0-arrested cells were transduced with Cas12a plus DDR1-crRNA nucleoproteins to generated twined  DSBs in different compound-treated conditions.

value: Endura Electrocompetent cells

value: Bacteria

value: recA13 supE44 ara-14 galK2 lacY1 proA2 rpsL20(StrR) xyl-5[lambda]- leu mtl-1 F- mcrB mrr hsdS20(rB-, mB-)

value: Transformation

tag: polymerase

value: Taq


title: B primary c 6h 1

description:
BcellsTatZta_counts.csv
BC6hr1

value: Primary B cells

value: no


title: p320_RuDDR_Taq_Rep3


title: BLAS Tat-Zta 6h 2


title: BLAS Tat-Zta 48h 1


title: 003G_Mouse1_Donor1 - MOI 2500

description:
GCPS5515
Amplicon sequencing of the HBB editing locus for human HSCs extracted from mouse bone marrow (engraftment study)
Mouse_OnTarget_Summary_Table_1csv.csv
HDR counts

value: bone marrow

value: HSCs

value: 003G_Mouse1_Donor1 - MOI 2500


title: p320_RuDDR_Plat_Rep3

value: Platinum


title: p320_RuDDR_Plat_Rep2


title: BLAS Zta 48h 2

value: B cells

value: Zta 48h


title: BLAS Zta 48h 1

value: BLAS


title: p320_RuDDR_Ph_Rep3

value: Phusion


title: BLAS Zta 6h 3

value: blood

value: Zta 6h


title: p320_RuDDR_Ph_Rep2

value: Endura Electrocompetent cells


title: BLAS Zta 6h 2


title: BLAS Zta 6h 1


title: p320_RuDDR_Ph_Rep1

value: Bacteria


title: KW-152-D2-328-Untreated

description:
GCPS1444
Amplicon sequencing of the HBB editing locus for pooled human HSCs after editing (pre-mouse injection)
Mouse_OnTarget_Summary_Table_2.csv
HDR counts


title: B primary c 6h 2

description:
BcellsTatZta_counts.csv
BC6hr2


title: IDH-MUT_DMSO_3

first: Nduka

middle: M

last: Amankulor

address: 3400 Civic Center Boulevard, 15th Floor

department: Department of Neurosurgery

data_processing:
Reads were aligned to the human genome (GRCh38) using STAR aligner(v2.7.3a) with default parameters. Gene-count matrices were produced by featureCounts (v2.0.1).
Assembly: GRCh38
Supplementary files format and content: Sample by gene matrix of read counts

source_name: Astrocytes

extract_protocol:
Illumina’s TruSeq RNA Access Library Preparation protocol following the manufacturer’s instruction
Pooled libraries were then sequenced on Illumina NextSeq 500 platform with single-end 76 bp reads, to a target read count of 40 million reads per sample.

value: Astrocytes

value: IDH-MUT

value: DMSO


title: IDH-MUT_ATRA_2

value: ATRA


title: BLAS Zta 48h 3


title: BLAS Tat-Zta 6h 1

value: Tat + Zta 6h


title: p320_RuDDR_Plat_Rep1

value: recA13 supE44 ara-14 galK2 lacY1 proA2 rpsL20(StrR) xyl-5[lambda]- leu mtl-1 F- mcrB mrr hsdS20(rB-, mB-)

value: Transformation


title: BLAS Tat 6h 3

value: Tat 6h


title: BLAS Tat 6h 1


title: BLAS c 48h 2

value: no


title: BLAS Tat 48h 1

value: B cells

value: Tat 48h


title: IDH-MUT_ATRA_1


title: IDH-WT_ATRA_3

value: IDH-WT


title: IDH-MUT_DMSO_1


title: p320_RuDDR_Taq_Rep1

value: Taq


title: IDH-WT_DMSO_2


title: BLAS c 48h 3

value: blood

value: BLAS


title: BLAS Tat 48h 3


title: IDH-WT_DMSO_3


title: IDH-WT_ATRA_2


title: IDH-MUT_ATRA_3


title: BLAS Tat 6h 2


title: IDH-WT_ATRA_1


title: IDH-WT_DMSO_1


title: BLAS c 6h 3


title: BLAS c 48h 1


title: BLAS c 6h 1


title: BLAS c 6h 2


title: EDTA-K3 plasma anticoagulant tubes [9-OSA53]

city: Lleida

first: David

last: de Gonzalo-Calvo

state: Lleida

address: Rovira Roure 80

country: Spain

institute: IRBLleida

description:
HTG EdgeSeq miRNA WTA Sequencer NB551420
GEO_data HTG OSA Processed TB.txt

data_processing:
FASTQ files were processed by HTG EdgeSeq parser software. Parser produces text file of counts per target miRNA. Differential gene expression analysis based on the negative binomial distribution (DESeq package (R version 4.1.1)
biocLite("DESeq2"): 1. Quality assess and clean raw sequencing data; 2. Align reads to a reference; 3. Count the number of reads assigned to each contig/gene; 4. Extract counts and store in a matrix; 5. Create column metadata table; 6. Analyze count data using DESEQ2
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RAW data (total counts) and analyzed count data for each sample

source_name: Plasma samples were collected in the early morning and after 10-14 h of overnight fasting and after sleep test.

extract_protocol:
HTG EdgeSeq extraction-free chemistry can detect miRNA targets without the requirement for RNA extraction, adaptor ligation, cDNA synthesis or pre-amplification of the sample by PCR.  Plasma samples were thawed and 15µl of each sample was plated in 24 wells and loaded onto the HTG EdgeSeq instrument.
HTG EdgeSeq miRNA following manufacture's protocols. Set of 2083 targets used, plus 5 negative controls, 1 positive control and 13 housekeeping genes - total of 2102 observations per sample

tag: Sex

value: Male

tag: age

tag: body mass_index

tag: apnea hypoapnea_index


title: IDH-MUT_DMSO_2

tag: genotype