title: HDM-specific, anti-IL4Ra-treated, Plasma cells,  Bone Marrow, biol. repl. 6, scRNAseq

city: Tarrytown

first: Joseph

middle: Cooper

last: Devlin

state: NY

address: 777 Old Saw Mill River Rd

department: Molecular Profiling and Data Science

institute: Regeneron Pharmaceuticals

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The single cell-count matrix was filtered for by calculating the ratio of the total number of annotated genes divided by the log10 of the total number of UMIs counted. Cells with a gene to UMI ratio below about 0.1 were filtered out. Cells with more than four times the interquartile range of the total number of UMIs were filtered out. Cells with more than about 80% of reads map to a mitochondrial gene were filtered out. High quality cells with a gene to UMI ratio above about 0.1, with less than about four times the interquartile range of the total number of UMIs counted, and with less than 80% of reads mapping to a mitochondrial gene were retained. The count matrices from each individual sample capture were normalized to a total count of 10,000 and batch corrected using the Harmony algorithm to generate a combined uniform manifold approximation and projection (UMAP). Unsupervised clustering by the Leiden algorithm was then used to determine cell type clusters and a Wilcox test was used to identify specific cell type and cluster marker genes.
Assembly: GRCm38, GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
The IgE-secretion trap method and single cell preparation is described in detail in our recent work. In brief, the IgE-secretion trap was performed with an StAv-ectoFcepsilon to specifically capture IgE-secreting plasma cells. Cells were sorted and submitted for scRNA-seq gene expression. We sequenced PCs from dLN and BM of mice exposed to HDM for 15 weeks, and from BM of mice exposed to HDM for 19 weeks with the last 8 weeks with anti-IL4Ra. At the end of the experiment, bone marrow and lung draining lymph nodes were collected and processed. Draining lymph nodes were mashed on 12-well, 70-mm filter plates (Corning Costar) in RPMI 1640 media to generate single cell suspensions. For BM extraction, femurs were cut at both ends, placed in a PCR plate with holes punched at the bottom, and spun down for 3 min at 500g. RBC lysis was performed on single cell suspensions from draining lymph nodes and bone marrow. B cells and plasma cells were isolated using EasySep mouse pan-B cell isolation kit (STEMCELL, cat: 19844) by negative selection to remove unwanted cells (CD4, CD8, CD11c, CD49b, CD90.2, Ly-6C/G (Gr-1), TER119). Purified cells were processed and secretion trap was assembled as described in the previous paragraph. Secreted IgE was captured using StAv-ectoFceRIa for 1 h at 37C with shaking at 400 rpm. Following IgE secretion trap, cells were washed and stained with an antibody mix containing B220 (RA3-6B2), CD138 (281-2), IgG1 (A85-1), IgE (R35-72), DUMP (IgM (II/41), IgD (11-26c.2a), TCRb (H57-597), Ly6G (1A8-Ly6g), CD49b (DX5), and CD11b (M1/70)) along with barcoded antigens (Der p1, Der p2, Der f1, and Ole e1). Finally, cells were labeled with DAPI before they were sorted on a BD Symphony S6.
Human allergic donor BM and matching donor sera were obtained from StemCell Technologies. Allergy status of each donor sera was checked by ImmunoCAP test (Phadia, Thermo Fisher Scientific) following the manufacturer’s instructions. To obtain mononuclear cells fresh BM aspirate was diluted 7:1 with PBS and 2mM EDTA and loaded onto 15mL of Ficoll in SepMate tube (Stem Cell Technologies). Samples were spun in SepMate tubes at 1200g for 20 minutes. Top layer of cells was removed, and cells were washed twice with autoMacs rinsing solution at 300g for 8 minutes (StemCell Technologies). B and antibody secreting cells were isolated using magnetic bead depletion (EasySep Human Pan-B Cell Isolation Kit, StemCell Technologies, Inc., Vancouver, CA, Cat: 19554) from single cell suspensions of allergic BM cells according to manufacturer’s protocol.
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Cells captured by secretion trap were suspended in PBS with 0.04% w/v BSA and loaded onto a Chromium® Controller device (10x Genomics) at 15,000 cells per lane. Partitions of the cells in barcoded beads were formed and the cells lysed. Reverse transcription was performed followed by breakdown of the partition. RNA-seq, Feature Barcode, and V(D)J libraries were prepared using a Chromium® Next GEM Single Cell 5’ Kit, v.2 (10x Genomics). After amplification of the libraries, cDNA was split into separate RNA-seq, Feature Barcode, and V(D)J aliquots. To enrich the V(D)J aliquot for BCR sequences, the Chromium® Automated Single Cell Mouse and Human BCR Amplification & Library Construction Kit (10x Genomics) was used. Feature Barcode libraries for DNA-barcoded Antigens or DNA-barcoded cell surface proteins were prepared using a Chromium® 5’ Feature Barcode Library Construction kit (10x Genomics). Paired-end sequencing was performed on an Illumina NovaSeq® 6000 sequencing system for RNA-seq, feature barcode, and V(D)J libraries. For RNA-seq and Feature Barcode libraries, the Cell Ranger Single-Cell Software Suite, version 6.1.1 (10x Genomics) was used to perform sample de-multiplexing, alignment, filtering, and UMI counting.

value: Plasma cells

value: bone marrow

tag: age

value: 25 weeks


title: 15349

status: Public on Nov 27 2024

type: genomic

city: Newcastle upon Tyne

first: Sarah

last: Rice

address: Central Parkway

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

description: Articular cartilage from human foetal femur

hyb_protocol: Genomic DNA was bisulfite converted using the standard protocol for the Illumina methylation EPIC 850k (v1.0) array.

scan_protocol: Scanning was performed as standard with the iScan N0660 (#4498).

data_processing:
R v4.2.2 & minfi
Quantile-normalised Average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Genomic DNA methylation profile of articular cartilage from human foetal femur

label_protocol: Illumina

extract_protocol: Genomic DNA was extracted using Qiagen Allprep kit.

tag: Sex

value: female


title: 15347


title: 344_3

type: SRA

city: Köln

first: Jens

middle: C

last: Brüning

address: Gleueler Str. 50

department: Neuronal Control of Metabolism

country: Germany

institute: Max Planck Institute for Metabolism Research

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were demultiplexed, aligned to the mouse reference genome GRCm38 and counted using cellranger (version 7.0.0; 10x Genomics).
Ambient RNA molecules were removed from cellranger raw count matrix files with cellbender:remove-background (v0.3). Filtered count matrices were analyzed in R with Seurat (v4.3.0). Nuclei with at least 1000 detectable genes were retained. Genes expressed in at least 10 nuclei were retained. ScDblFinder (v1.15.4) with standard parameters was run on individual 10x lanes to remove doublets. The count data were normalized with NormalizeData and scaled with ScaleData function. Genes were then defined as variable using FindVariableFeatures and used as input into PCA with RunPCA. The top 30 PC were retained and used for further dimensionality reduction using RunUMAP and clustered using a resolution of 0.8 with FindClusters.
To perform cell-type specific quality control, the nuclei were split into two broad categories, neuronal and nonneuronal, using CellAnnotatorR(v) based on the expression of neuronal marker gene Rbfox3 or Snap25 and the absence of nonneuronal markers. Neuronal data was further filtered by removing nuclei with UMI in the first and 99th percentile. Library complexity was calculated by dividing the log of the total genes detected per nuclei by the log of the total UMI per nuclei. Nuclei in the first percentile of this metric were removed. Add_Mito_Ribo_Seurat was used to identify and remove nuclei with >1% mitochondria and ribosomal genes. We finally removed outliers by isOutlier with nmads=5 run on individual 10x lanes from the package SingleCellExperiment70. After all quality control, a total of 23664 neurons remained. Neuronal cell types were labeled by projecting labels from a previously published data set (GSE166649) using Seurat FindtransferAnchors and TransferData function.
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-separated files for barcodes(cells), genes and matrix file for processed counts corresponding to the data set used in the analysis. Matrix contains data in format genes x cells. Comma-separated metadata file with annotations from processing pipeline. barcodes correspond to first column of metadata file.

molecule: nuclear RNA

organism: Mus musculus

source_name: hindbrain

extract_protocol:
After decapitation, the brain was removed, and the DVCs were isolated from the brainstem under a surgical microscope. A 1 mm coronal section of the hindbrain from bregma -7.0 to -8.0 mm was cut with a razor blade. From the coronal section, a 1.4 mm square containing the DVC was snap-frozen. Samples from the same experimental condition were pooled (n = 5 mice per sample) and nuclei were extracted. Sorting of 2n nuclei was performed by flow cytometry using a BD FACSAria IIIu Influx cell sorter (BD Biosciences). The gating was set according to size and granularity using FSC and SSC to capture singlets and remove debris. To detect DraQ5-positive nuclei fluorescence was set at 647 nm and 670 nm. Each sample was sorted into separate tubes, each with a total of 20,000 nuclei per 40 µl.
Sequencing libraries were generated using 10x Genomics Chromium Single-Cell 3′ Reagent kit according to the standardized protocol. Paired-end sequencing was performed using an Illumina NovaSeq 6000.

treatment_protocol: All experiments were performed in adult C57BL/6 diet-induced obesity mice with an of age 24 weeks. Mice were housed in solid bottom cages with environmental enrichment at 22°C (± 2°C) in 55% (± 10%) humidity and a 12-hour light/dark cycle (light: 6:00 to 18:00). Mice were s.c. injected with vehicle or 325 nmol/kg EB1002 2 hours prior to euthanasia. Samples from the same experimental condition were pooled together (n = 5 mice/group) for a total of 3 samples per condition.

tag: tissue

value: hindbrain

tag: treatment

value: Agonist


title: 2_CT2A, all-in-one, 72 hrs, rep2

city: Charlestow

first: Lisa

last: Nieland

state: Massachusetts

address: 149 13th street

department: Neurology

country: USA

institute: Massachusetts General Hospital

description: 300-cycle v2 kit (Illumina)

library_source: genomic

data_processing:
CRISPR screen was performed using CRISPResso2 analysis (http://www.crispresso2.pinellolab.org). Percentages of Unmodified and Modified reads were used to plot data (CRISPResso2 output: quantification_of_editing_frequency.txt)
mmu-miR21a primer set designed with: https://www.ncbi.nlm.nih.gov/tools/primer-blast/
Fw: TTGACTGCAAACCATGATGCTG-mir21-1-mmu-86584000-fw
Rv: TGCTTTAAACCCTGCCTGAGC-mir21-1-mmu-86584221-rv
amplicon (222bp):
TTGACTGCAAACCATGATGCTgggtaatgtttgaatgaaaacatttgata
tggatggtcagatgaaagataccaaaatgtcagacagcccatcgactgct
gttgccatgagattcaacagtcaacatcagtctgataagctatccgacaa
ggtggtacagccatgcgatgtcacgaccacgacagggggcaagcacgagg
tGCTCAGGCAGGGTTTAAAGCA
sgRNA sequence (without PAM):
GACTGTTGAATCTCATGGCAAC
CRISPR screen was used to check the the top 5 potential murine off-targets of sgRNA3. Mouse genome was amplified with the following primer sets and amplicons designed with: https://www.ncbi.nlm.nih.gov/tools/primer-blast/
Off-target 1; Chr4, location 153280201.
FW: CACTGCCCCAGCTGTAAGAT
RV: CCCTTCATCCACTTTGGCTT
Amplicon (248bp):
CACTGCCCCAGCTGTAAGATcaatctttctccaaagccattgcctctcaa
cagtcttgttacttccagacaattcatgacagggagaaatctgtagctgc
ccctctatccaagaccaccaggcctagtaactcacagggacttggagaac
tctaccaaccaagtctttagtataactgtggcatctcatgacaacagaaa
tggattggtgaaaaatcagcagaaagaaAAGCCAAAGTGGATGAAGGG
Off-target 2; Chr 11, location 112908309.
FW: TAGAAAAGGTCGGCGCTGG
RV: CTCTTGAAGTATGGCCGTGGT
Amplicon (243bp):
TAGAAAAGGTCGGCGCTGGctgctgaaccttatacacccatagtttttaa
cgagaaatagatagcatttactgagctaatgacttgtgcaattaagctct
gatgggctgactataattgccatgaggtttaacagtggggagatgcaggg
ggagatgcagggggagatgcagggagatgcagggggaggatgccaagaca
gttgaccaatcgtgaaggtattACCACGGCCATACTTCAAGAG
Off-target 3; Chr 11, location 119227215.
FW: CCCACACATGGTGATCCGA
RV: GGCCGGCTAAGATTCACCC
Amplicon (247bp):
CCCACACATGGTGATCCGAggctgttaacagacaccgtgattgccaggag
agtcaacagttcccaagaagaacttcctagctatactcaagacattccac
tcaccagaaagctatgggggggggggggggacaaaacaaacaaacagaga
aaaaacccataagtactgctcagctaagagatccatccccagcaaccagc
taagaaccaactctggtaaattcccaatGGGTGAATCTTAGCCGGCC
Off-target 4; Chr 10, location 36314200.
FW: ACAGCCAGGAAATATAGGATCATTC
RV: TTTTGGTGCAGCAGTTGGGT
Amplicon (236bp):
ACAGCCAGGAAATATAGGATCATTCcagattatataattagaattctctt
ttgaagctcatggcaacttaaatacagctagaattttgttttgaatggac
acagggtatgcaaatttatattgcaaaggtaatcaattatgtctgccata
cttgttttaatttattaagtgagttaataaaatcataacagtaaaatgca
ttgcgtgtagtaagtcACCCAACTGCTGCACCAAAA
Off-target 5; Chr 15, location  45517500.
FW: GTGGGGCTCAGATGCAGTAT
RV: TGACTAGGACACACAGCAAATGT
Amplicon (227bp):
GTGGGGCTCAGATGCAGTATacacaaccatctcagataaaataatacaaa
taaaatattaaatagtaaatgaattttaatatacattgaaatatactgga
taactctatatttatttcattgacattgcaaatttacgttgccatgatca
tcaacattgattatgacacacatagattatagcatagtatcttatttttg
aaaaACATTTGCTGTGTGTCCTAGTCA
Library strategy: CRISPR screen

growth_protocol: CT2A cells were cultured in DMEM (10% Fet Bone Serum and 1% penstrep) and maintained in 5% CO2 in 37C

extract_protocol:
1-2-4) genomic DNA was extracted using DNAeasy DNA isolation kit (Qiagen) and quantified using a NanoDrop (Wilmington, DE) ND-1000. 3) genomic DNA was extracted using the adapted TRIzol™ Reagent Experimental protocol for DNA isolation (Invitrogen, 15596026) from FACS sorted mCherryPOS (tumor cells) and mCherryNEG (non-tumor cells) by utilizing the remaining sample post-removal of the aqueous layer of the in Qiazol lysed RNA (Qiagen).
1-2-4) mmu-miR-21a or off-targets were amplified, using the Phusion High Fidelity PCR kit (New England Biolabs), for Next Generation Sequencing (NGS) analysis primers amplified a 222 bp at a Tm of 67°C DNA fragment of the mouse miR-21. The PCR products were purified using the Qiagen PCR purification kit. Next, the PCR products were loaded on a 2% agarose gel (Bio-Research, Worcester, MA), and DNA fragments were resolved by gel electrophoresis. The purified PCR products were sequenced at the MGH CCIB DNA Core and CRISPR efficiency was determined based on CRISPResso2 analysis 3) Genome modified reads were determined by NGS using a two-step PCR-based Illumina library construction method. The first PCR reaction was done with approximately 100 ng of gDNA using Q5 High-fidelity DNA Polymerase (NEB) and the respective primers, with cycling conditions of one cycle at 98 °C for 2 min; 35 cycles of 98 °C for 10 s, 65 °C for 10 s, 72 °C for 20 s; and one cycle of 72°C for 1 min. PCR-1 products were purified using paramagnetic beads at a ratio of 1.8×. Approximately 20 ng of purified PCR-1 product was used as a template for a second PCR (PCR-2) to add Illumina barcodes with adaptor sequences using Q5 (cycling conditions of one cycle at 98°C for 2 min; 10 cycles at 98°C for 10 s, 65°C for 30 s, 72°C 30 s; and one cycle at 72°C for 5 min). PCR-2 products were pooled based on concentrations from capillary electrophoresis (QIAxcel, QIAGEN). Final libraries were quantified by Qubit dsDNA High Sensitivity assay (Thermo Fisher) and sequenced on a MiSeq sequencer using a 300-cycle v2 kit (Illumina). On-target genome editing activities were determined from amplicon sequencing data using CRISPResso2.

treatment_protocol: 1) cells were transfected with lipofectamine 2000 and saCas9:sgRNA 3:1 ratio incubated for 72hrs. 2) cells were transfected with lipofectamine 2000 and 400ng all-in-one plasmid DNA and incubated for 37 hrs, genomic DNA was extracted from cell pellets. 3) mice were implanted with 25,000 CT2A cells and treated intracranially with 2ul AAV8-control or AAV8-CRISPR at day 3 and day 6 post-tumor implantation. Mice were sacked at day 15 post-tumor implantation and brain tissue was FACS sorted for mcherry+ CT2A cells, genomic DNA was extracted immediately after FACS. 4) cells were transfected with lipofectamine 2000 and 400ng all-in-one plasmid DNA and incubated for 37 hrs, genomic DNA was extracted from cell pellets.

tag: cell line

tag: cell type

value: mouse glioma

tag: genotype

value: wild-type

value: all-in-one

tag: endpoint

value: 72 hours


title: HDM-specific, Plasma cells,  Bone Marrow, biol. repl. 6, scRNAseq

description: 10x Genomics

molecule: total RNA

tag: strain


title: 2_CT2A, all-in-one, 72 hrs, rep1

description: 300-cycle v2 kit (Illumina)


title: 2_CT2A, SaCas9 only control, 72 hrs, rep3

description: 300-cycle v2 kit (Illumina)

value: transfected SaCas9


title: HDM-specific, Plasma cells,  Bone Marrow, biol. repl. 5, scRNAseq

description: 10x Genomics


title: 2_CT2A, SaCas9 only control, 72 hrs, rep2

description: 300-cycle v2 kit (Illumina)


title: 15342


title: 2_CT2A, SaCas9 only control, 72 hrs, rep1

description: 300-cycle v2 kit (Illumina)


title: HDM-specific, Plasma cells,  Bone Marrow, biol. repl. 4, scRNAseq

description: 10x Genomics


title: 15337


title: 2_CT2A wildtype, nonedited control, 72 hrs, rep4

description: 300-cycle v2 kit (Illumina)

value: non-transfected


title: HDM-specific, Plasma cells,  Bone Marrow, biol. repl. 3, scRNAseq

description: 10x Genomics


title: 2_CT2A wildtype, nonedited control, 72 hrs, rep3

description: 300-cycle v2 kit (Illumina)


title: 15336

value: male


title: 3_mousebrain, CT2Amcherry+, AAV8-Control, day 15, rep1

description: 300-cycle v2 kit (Illumina)

source_name: Tumor implanted brain tissue

value: Tumor implanted brain tissue

tag: time of_treatment

value: day 3 and day 6 post-tumor implant

value: Day 15 post-tumor implant


title: 2_CT2A wildtype, nonedited control, 72 hrs, rep1

description: 300-cycle v2 kit (Illumina)


title: 2_CT2A, all-in-one, 72 hrs, rep3

description: 300-cycle v2 kit (Illumina)


title: HDM-specific, Plasma cells,  Bone Marrow, biol. repl. 2, scRNAseq

description: 10x Genomics


title: 15334


title: 2_CT2A wildtype, nonedited control, 72 hrs, rep2

description: 300-cycle v2 kit (Illumina)


title: 15332


title: HDM-specific, Plasma cells,  Bone Marrow, biol. repl. 1, scRNAseq

description: 10x Genomics


title: 1_CT2A, SaCas9 + sgRNA3, CRISPR-edited, 72 hrs, rep2

description: 300-cycle v2 kit (Illumina)

value: transfected SaCas9 + sgRNA


title: 1_CT2A, SaCas9 only control, 72 hrs, rep3

description: 300-cycle v2 kit (Illumina)


title: 15330


title: 1_CT2A, SaCas9 only control, 72 hrs, rep2

description: 300-cycle v2 kit (Illumina)


title: 1_CT2A, SaCas9 only control, 72 hrs, rep1

description: 300-cycle v2 kit (Illumina)


title: 1_CT2A, SaCas9 + sgRNA3, CRISPR-edited, 72 hrs, rep1

description: 300-cycle v2 kit (Illumina)


title: 1_CT2A wildtype, nonedited control, 72 hrs, rep3

description: 300-cycle v2 kit (Illumina)


title: 2_CT2A, SaCas9 only control, 72 hrs, rep4

description: 300-cycle v2 kit (Illumina)


title: 15346


title: HDM-specific, IgE sorted, Plasma cells,  Lymph Node, biol. repl. 3, scRNAseq

description: 10x Genomics

source_name: lymph node

value: Plasma cells

value: lymph node


title: 1_CT2A wildtype, nonedited control, 72 hrs, rep1

description: 300-cycle v2 kit (Illumina)


title: HDM-specific, IgE sorted, Plasma cells,  Lymph Node, biol. repl. 2, scRNAseq

description: 10x Genomics

value: 25 weeks


title: 15325


title: HDM-specific, IgE sorted, Plasma cells,  Lymph Node, biol. repl. 1, scRNAseq

description: 10x Genomics


title: 15305


title: 1_CT2A, SaCas9 + sgRNA3, CRISPR-edited, 72 hrs, rep3

description: 300-cycle v2 kit (Illumina)


title: 15300


title: HDM-specific, IgE sorted, Plasma cells,  Bone Marrow, biol. repl. 4, scRNAseq

description: 10x Genomics

value: bone marrow


title: HDM-specific, IgE sorted, Plasma cells,  Lymph Node, biol. repl. 4, scRNAseq

description: 10x Genomics


title: HDM-specific, IgE sorted, Plasma cells,  Bone Marrow, biol. repl. 3, scRNAseq

description: 10x Genomics


title: 15296


title: HDM-specific, IgE sorted, Plasma cells,  Bone Marrow, biol. repl. 2, scRNAseq

description: 10x Genomics


title: 15295

value: female


title: 15328


title: HDM-specific, IgE sorted, Plasma cells,  Bone Marrow, biol. repl. 1, scRNAseq

description: 10x Genomics


title: 1_CT2A wildtype, nonedited control, 72 hrs, rep2

description: 300-cycle v2 kit (Illumina)


title: 15294


title: 15293


title: 15282


title: Rep4, mRNA

city: Warsaw

first: Patrycja

last: Rosa

address: Ludwika Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology, Polish Academy of Sciences

description: polyA RNA

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1. (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

source_name: brain

extract_protocol:
Mice were sacrificed and subsequently brains were collected, placed in cold HBSS (without Ca2+ and Mg2+), and transferred into 30 % sucrose (w/v) in PBS for 48 h and frozen in Tissue Freezing Medium (Leica) at -80°C. The tissue was minced, transferred onto c-tubes containing 1,950 µl DMEM, and supplemented with 50 µl of Deoxyribonuclease I (Sigma Aldrich). Dissociation was performed with the MACS dissociator with heaters (Militenyi Biotec) for 22 minutes and later the samples were passed through 70 nm and 40 nm strainers into 50 ml cold HBSS with ions to stop the enzymatic reaction (EasyStrainer™, BioOne).
For flow cytometry, cells were suspended in the Stain Buffer (BD Pharmingen) with anti-mouse CD16/CD32 Fc Block™ 1:200 (BD Pharmigen) for 10 min. Next, anti-mouse CD11b antibody 1:250 (M1/70, BD Pharmigen) was added and cells were incubated for 20 min at 4 °C, then washed with Stain Buffer. Cells were sorted using purity precision mode on FACS Aria (BD FACSAria Cell sorter BD-Biosciences), into 200 μL of sterile PBS.
Preparation of gel beads in emulsion andlibraries were performed with Chromium Controller and Single-Cell Gene Expression v2 Chemistry (10X Genomics). Libraries’ quality and quantity were verified with a High-Sensitivity DNA Kit (Agilent Technologies, USA) on a 2100 Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: Mice were fed with BLZ-945 (MedChemExpress, HY-12768) at a dose of 200 mg/kg b.w. daily in 100 µl PB (Peanut butter, GoOn, Santé); controls received orally PB. BLZ-945 was delivered for 14 or 21 days to establish the kinetics of depletion; repopulation was allowed for 7 days without any treatment.

value: brain

value: microglia

tag: library type

value: mRNA


title: Rep4, HTO

description: Hashtag-derived oligonucleotide (HTO)

library_source: other

molecule: protein

value: HTO


title: Rep3, HTO

description: Hashtag-derived oligonucleotide (HTO)


title: 15278


title: Rep3, mRNA

description: polyA RNA


title: mRNA_HAYW_rep4

type: RNA

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

institute: Warsaw University of Life Sciences - SGGW

description: Biological replicate_HAYW 4 of 8

hyb_protocol: For hybridization, Microarray Hybridization Chamber (Agilent, USA) and Hyb-Buffer (Agilent, USA) were used according to manufacturer protocol.

scan_protocol: Microarray Scanner (model G2565CA) with SureScan High-Resolution Technology (Agilent, USA). Microarray data were extracted, the background subtracted and LOWESS normalisation performed using the standard procedures contained in the Agilent Feature Extraction (FE) Software Version 10.7.3.1.

data_processing: The statistical analysis was performed using Gene Spring 13 software default protocol (Agilent Technologies, USA). The statistical significance of the differences was evaluated using student test (p<0.05) and fold change FC>1.3. A multiple testing correction was performed using Benjamini and Hochberg False Discovery Rate (FDR) ≤0.05.

organism: Rattus norvegicus

source_name: (HAYW) Liver samples from rats fed with standard diet with 1% cholesterol addition and supplemented with Hayward kiwi fruit lyophilisate

label_protocol: MiRNA Complete Labeling and Hyb Kit (Version 2.3, December 2010) (Agilent) was used for labeling, according to manufacturer protocol.

extract_protocol: Total RNA was isolated according to the protocol supplied with the miRNeasy Mini Kit (Qiagen, USA). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 9,2 were included into the analysis.

treatment_protocol: Experiments were done on male Wistar rats. All animals from control group (CHOL) were fed a diet with 1% cholesterol. Rats from test groups were fed diet with 1% cholesterol supplemented with 5% Geneva kiwifruit (GENE) or 5% Hayward kiwifruit (HAYW) lyophilisate. Rats were dissected after 42 day experiment and samples of liver were taken immediately, stored overnight in 4oC and then in -80oC until analyzed.

tag: diet

value: anti-atherogenic diet

value: liver

value: Wistar

tag: gender


title: 15272


title: mRNA_CHOL_rep8

description: Biological replicate_CHOL 8 of 8

source_name: (CHOL) Liver samples from rats fed with standard diet with 1% cholesterol addition

value: atherogenic diet

value: male


title: Rep2, HTO

description: Hashtag-derived oligonucleotide (HTO)


title: mRNA_CHOL_rep7

description: Biological replicate_CHOL 7 of 8


title: mRNA_CHOL_rep3

description: Biological replicate_CHOL 3 of 8


title: mRNA_HAYW_rep8

description: Biological replicate_HAYW 8 of 8


title: 15271


title: mRNA_HAYW_rep2

description: Biological replicate_HAYW 2 of 8


title: mRNA_HAYW_rep7

description: Biological replicate_HAYW 7 of 8


title: mRNA_HAYW_rep3

description: Biological replicate_HAYW 3 of 8


title: mRNA_HAYW_rep5

description: Biological replicate_HAYW 5 of 8


title: mRNA_CHOL_rep4

description: Biological replicate_CHOL 4 of 8


title: Rep2, mRNA

description: polyA RNA


title: mRNA_GENE_rep8

description: Biological replicate_GENE 8 of 8

source_name: (GENE) Liver samples from rats fed with standard diet with 1% cholesterol addition and supplemented with Geneva kiwi fruit lyophilisate


title: mRNA_HAYW_rep1

description: Biological replicate_HAYW 1 of 8


title: 15257


title: mRNA_HAYW_rep6

description: Biological replicate_HAYW 6 of 8


title: mRNA_CHOL_rep5

description: Biological replicate_CHOL 5 of 8


title: mRNA_CHOL_rep6

description: Biological replicate_CHOL 6 of 8


title: mRNA_CHOL_rep1

description: Biological replicate_CHOL 1 of 8


title: mRNA_GENE_rep5

description: Biological replicate_GENE 5 of 8


title: mRNA_GENE_rep6

description: Biological replicate_GENE 6 of 8


title: mRNA_GENE_rep7

description: Biological replicate_GENE 7 of 8


title: Rep1, HTO

description: Hashtag-derived oligonucleotide (HTO)


title: mRNA_CHOL_rep2

description: Biological replicate_CHOL 2 of 8


title: 15254


title: HUVEC, BRG1 CUT&RUN, siMIR100HG + overexpression MIR100HG

city: Frankfurt am Main

first: Timothy

last: Warwick

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

institute: Goethe Universität Frankfurt am Main

data_processing:
Resulting reads were aligned to the GRCh38 genome assembly using Bowtie2 (v2.4.5) (https://doi.org/10.1038/nmeth.1923) with the parameters –local and –very-sensitive.
Mates were fixed with samtools (v1.1.0) (10.1093/gigascience/giab008) fixmate with the parameter –m set, and duplicate alignments were subsequently removed using samtools markdup with the –r flag set. Reads aligning to blacklisted regions as defined by ENCODE were removed using bedtools (2.27.1) (https://doi.org/10.1093/bioinformatics/btq033) intersect with the –v flag set.
Resulting BAM files were indexed using samtools index. Peaks were called using MACS3 (v3.0.0) (https://doi.org/10.1186/gb-2008-9-9-r137) with the parameters –scale-to-small –f BAMPE and –g hs.
Assembly: hg38
Supplementary files format and content: BigWig files of genomic coverage per condition normalized by CPM.
Library strategy: CUT&RUN

source_name: HUVEC

growth_protocol: Pooled human umbilical vein endothelial cells (HUVEC) were purchased from PromoCell (C-12203, Lot No. 405Z013, 408Z014, 416Z042, Heidelberg, Germany) and cultured at 37 °C with 5 % CO2 in a humidified incubator.

extract_protocol:
5X volume of binding buffer (20 mM HEPES pH 7.9, 20 mM KCl, 1 mM CaCl2, 1 mM MnCl2) was added to the samples and the pH adjusted with sodium acetate before being transferred to a purification column (ActiveMotif, 58002) and centrifuged at 11,000 xg for 30 sec. The column was then washed with 750 µl wash buffer and dried by centrifugation for 2 min. DNA was eluted with 25 µl elution buffer and the DNA concentration measured with a Qubit 3.0 Fluorometer (Life Technologies).
Samples were brought to 50 µl with 0.1X TE buffer and DNA end preparation performed as instructed but with incubation at 20 °C for 20 min and then 58 °C for 45 min. Adaptor ligation was performed with a 1:10 dilution of adaptor (NEB, E6440S). For DNA purification, 0.9X Volume AMPure XP beads (Beckman Coulter, A63881) was added to the samples and incubated for 5 min at RT. Beads were washed twice with 200 µl 80 % ethanol and DNA eluted with 17 µl 0.1X TE buffer for 2 min at RT. PCR amplification of the eluted DNA was performed as described in the manufacturer’s protocol but with the addition of 2.5 µl Evagreen (20X) for visualization of the amplification curves on an AriaMx Real-time PCR system (Agilent Aria 1.7). The denaturation and annealing/extension steps of the PCR amplification were performed for around 12 cycles and stopped before the curves plateaued. A cleanup of the PCR reaction was performed twice with 1.1X Ampure beads and eluted each time in 33 µl 0.1X TE buffer. DNA concentrations were measured with a Qubit (Thermo Fisher) and size distributions measured on a Bioanalyzer (Agilent).

treatment_protocol: For small interfering RNA (siRNA) treatments, HUVEC (80–90 % confluent) were transfected with GeneTrans II according to the instructions provided by MoBiTec (Göttingen, Germany). A Stealth siRNA was used for siRNA-mediated knockdown of BRG1 (Thermo Fisher Scientific, siRNA ID HSS110006, Cat. No. 1299001). As control, Stealth RNAi™ negative control Med GC (Life technologies) was used. All siRNA experiments were performed for 48 h. 500,000 HUVEC were washed with wash buffer (20 mM HEPES pH 7.9, 150 mM NaCl, 500 nM spermidine, 1X Roche Protein Inhibitor Cocktail) at RT. Cells were resuspended in wash buffer and 10 µl BioMag®Plus Concanavalin A (ConA) beads (Polysciences, 86057-3) were added for 10 min at RT. Beads were separated on a magnetic rack and washed once before being resuspended in 100 µl antibody buffer (wash buffer, 0.25 % Digitonin and 2 mM EDTA) and 1 µl BRG1 antibody (Abcam, ab110641). Beads were incubated with the antibody over night with gentle shaking at 4 °C. The next day, beads were washed twice with 200 µl 0.25 % Digitonin wash buffer and resuspended in Digitonin wash buffer containing 2 µl CUTANA™ pAG-MNase (15-1016, EpiCypher, 15-1016) and incubated on ice for 30 min. Samples were washed twice and then resuspended in 100 µl Digitonin wash buffer containing 2 µl CaCl2 at a final concentration of 100 mM and incubated for 2 h at 4 °C with gentle shaking. 33 µl of 2X “stop solution” (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.25 % Digitonin, 100 µg/ml RNase A, 50 µg/ml Glycoblue) was added to the beads and incubated at 37 °C for 10 min. Samples were placed on a magnetic rack and the supernatant removed and kept for DNA purification. For rescue experiments, plasmid overexpression (full length pcDNA3.1+JPX (NR_024582.1) or pcDNA3.1+MIR100HG (isoform NR_137194.1 missing the last 1035nt) in HUVECs was performed 24h after siRNA knockdown. Therefore, the Neon electroporation system (Invitrogen) was used according to the instructions of the manufacturer. The overexpression was done for 24h. Full length pcDNA3.1+JPX and pcDNA3.1+MIR100HG were obtained from Biomatik (Canada ).

value: HUVEC

value: siMIR100HG, overexpression MIR100HG


title: Rep1, mRNA

description: polyA RNA


title: mRNA_GENE_rep4

description: Biological replicate_GENE 4 of 8


title: HUVEC, BRG1 CUT&RUN, siJPX + overexpression JPX

value: siJPX, overexpression JPX


title: HUVEC, BRG1 CUT&RUN, siMIR100HG


title: Repopulated, rep3

library_source: transcriptomic

data_processing:
We used rna-seq-star-deseq2 workbench v 2.0.0.
Sequence reads were trimmed using for adaptor sequence/ low quality reads using Cutadapt 3.0.
Trimmed sequence reads were mapped to GRCm38/mm10 genome assembly using STAR v. 2.7.10b
Read count extraction and normalization were done using edgeR v4.2.0.
Assembly: mm10
Supplementary files format and content: all.csv

molecule: polyA RNA

extract_protocol:
Mice were sacrificed and subsequently brains were collected, placed in cold HBSS (without Ca2+ and Mg2+), and transferred into 30 % sucrose (w/v) in PBS for 48 h and frozen in Tissue Freezing Medium (Leica) at -80°C. The tissue was minced, transferred onto c-tubes containing 1,950 µl DMEM, and supplemented with 50 µl of Deoxyribonuclease I (Sigma Aldrich). Dissociation was performed with the MACS dissociator with heaters (Militenyi Biotec) for 22 minutes and later the samples were passed through 70 nm and 40 nm strainers into 50 ml cold HBSS with ions to stop the enzymatic reaction (EasyStrainer™, BioOne).
For flow cytometry, cells were suspended in the Stain Buffer (BD Pharmingen) with anti-mouse CD16/CD32 Fc Block™ 1:200 (BD Pharmigen) for 10 min. Next, anti-mouse CD11b antibody 1:250 (M1/70, BD Pharmigen) was added and cells were incubated for 20 min at 4 °C, then washed with Stain Buffer. Cells were sorted using purity precision mode on FACS Aria (BD FACSAria Cell sorter BD-Biosciences), into 200 μL of sterile PBS.
For RNA isolation, sorted CD11b+ cells were stored in the -80°C freezer. The samples were thawed on ice and total RNA was isolated with the RNAeasy Plus Mini kit (Qiagen) according to the manual. RNA concentration was immediately determined using a spectrophotometer.
For bulk RNA-seq strand-specific polyA-enriched RNA libraries were prepared using the KAPA Stranded mRNA Sample Preparation Kit according to the manufacturer’s protocol (Kapa Biosystems, MA, USA). Library evaluation was done with Agilent 2100 Bioanalyzer using the Agilent DNA High Sensitivity chip (Agilent Technologies, Ltd.)

value: BLZ-945 depletion


title: mRNA_GENE_rep3

description: Biological replicate_GENE 3 of 8


title: HUVEC, BRG1 CUT&RUN, siJPX

value: siJPX


title: Repopulated, rep2


title: 15237


title: mRNA_GENE_rep2

description: Biological replicate_GENE 2 of 8


title: HUVEC, BRG1 CUT&RUN, siScr

value: siScr


title: HUVEC, ATAC-seq, siJPX, 2

data_processing:
Reads were aligned to the GRCh38 genome assembly using Bowtie2 (v2.4.5) (https://doi.org/10.1038/nmeth.1923) with the parameters –local –very-sensitive.
Duplicates and multi-mapping reads were removed using samtools (v1.10) (10.1093/gigascience/giab008) rmdup and samtools view.
Peaks were called using MACS3 (v3.0.0) (https://doi.org/10.1186/gb-2008-9-9-r137) with the parameters –nomodel, -B, --SPMR and –format BAMPE.
Differential peaks were also called using MACS3 by comparing read pileups between conditions using macs3 bdgdiff, normalized with the requisite total sequencing depths per condition. Peaks with a log likelihood greater than 3.84 were considered as differential.
Assembly: hg38
Supplementary files format and content: BigWig files of genomic coverage per replicate normalized by CPM.

extract_protocol:
5X volume of binding buffer (20 mM HEPES pH 7.9, 20 mM KCl, 1 mM CaCl2, 1 mM MnCl2) was added to the samples and the pH adjusted with sodium acetate before being transferred to a purification column (ActiveMotif, 58002) and centrifuged at 11,000 xg for 30 sec. The column was then washed with 750 µl wash buffer and dried by centrifugation for 2 min. DNA was eluted with 25 µl elution buffer and the DNA concentration measured with a Qubit 3.0 Fluorometer (Life Technologies).
As described in detail at: doi: 10.1002/0471142727.mb2129s109

treatment_protocol: For small interfering RNA (siRNA) treatments, HUVEC (80–90 % confluent) were transfected with GeneTrans II according to the instructions provided by MoBiTec (Göttingen, Germany). A Stealth siRNA was used for siRNA-mediated knockdown of BRG1 (Thermo Fisher Scientific, siRNA ID HSS110006, Cat. No. 1299001). As control, Stealth RNAi™ negative control Med GC (Life technologies) was used. All siRNA experiments were performed for 48 h. 500,000 HUVEC were washed with wash buffer (20 mM HEPES pH 7.9, 150 mM NaCl, 500 nM spermidine, 1X Roche Protein Inhibitor Cocktail) at RT. Cells were resuspended in wash buffer and 10 µl BioMag®Plus Concanavalin A (ConA) beads (Polysciences, 86057-3) were added for 10 min at RT. Beads were separated on a magnetic rack and washed once before being resuspended in 100 µl antibody buffer (wash buffer, 0.25 % Digitonin and 2 mM EDTA) and 1 µl BRG1 antibody (Abcam, ab110641). Beads were incubated with the antibody over night with gentle shaking at 4 °C. The next day, beads were washed twice with 200 µl 0.25 % Digitonin wash buffer and resuspended in Digitonin wash buffer containing 2 µl CUTANA™ pAG-MNase (15-1016, EpiCypher, 15-1016) and incubated on ice for 30 min. Samples were washed twice and then resuspended in 100 µl Digitonin wash buffer containing 2 µl CaCl2 at a final concentration of 100 mM and incubated for 2 h at 4 °C with gentle shaking. 33 µl of 2X “stop solution” (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.25 % Digitonin, 100 µg/ml RNase A, 50 µg/ml Glycoblue) was added to the beads and incubated at 37 °C for 10 min. Samples were placed on a magnetic rack and the supernatant removed and kept for DNA purification.


title: HUVEC, ATAC-seq, siMIR100HG, 3


title: Repopulated, rep1


title: 15232


title: HUVEC, ATAC-seq, siMIR100HG, 2


title: Control, repl3

value: control


title: HUVEC, ATAC-seq, siJPX, 1


title: 15225


title: 15216

value: female


title: 15213


title: Control, repl2

value: brain


title: HUVEC, ATAC-seq, siScr, 3


title: HUVEC, ATAC-seq, siMIR100HG, 1


title: 15240


title: HUVEC, ATAC-seq, siScr, 1


title: Control, repl1

value: microglia


title: RNA-seq_HT29 PTENKD_EZH2i _R3

city: Bloomington

first: Ahmed

middle: H

last: Ghobashi

state: IN

institute: Indiana University

data_processing:
Sequencing read quality control for all samples was assessed with FastQC (v0.11.9)
An index of the hg38 genome was created, and reads were aligned with STAR (v2.7.10a) with the additional parameter --quantMode GeneCounts to generate count matrix
Deseq2 (v3.24.0) was used for differential expression analysis. Gene Set Enrichment Analysis using the Molecular Signatures Database collections and database were run with clusterProfiler (v1.38.3) and volcanoplot was visualized with EnhancedVolcano.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene count values for all samples

source_name: Cell line

growth_protocol: HT29 cells were maintained in McCoy 5A media supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEB NextUltra DNA Library following the manufacturer's protocol.

treatment_protocol: Cells were treated with 2 μM EZH2 inhibitor (GSK503 (Sigma, SML2718) ) for 72 hours

value: Cell line

value: Primary colorectal cancer cells

value: PTEN knockdown

value: EZH2 inhibitor


title: mRNA_GENE_rep1

description: Biological replicate_GENE 1 of 8

value: anti-atherogenic diet

value: liver

value: Wistar


title: 15210


title: HUVEC, ATAC-seq, siScr, 2

value: HUVEC


title: 15199


title: RNA-seq_HT29 PTENKD _R3

value: Untreated


title: RNA-seq_HT29 PTENKD_EZH2i _R1


title: RNA-seq_HT29 PTENKD _R2


title: RNA-seq_HT29 PTENKD _R1


title: RNA-seq_HT29 PTENKD_EZH2i _R2


title: 15191

value: male


title: BV2-T2-1

city: Beijing

first: Xuan

last: Zhao

address: 45 Changchun Street, Xicheng District, Beijing

country: China

institute: xuanwu hospital capital medical university

data_processing:
The sequencing data was filtered with DESeq2
The clean reads were mapped to the rn6 genome using HISAT2.
Then expression level of gene was calculated by STRING TIE. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: BMDM

extract_protocol:
Total RNA was extracted using the RNAfast200 kit according to the manufacturer’s protocol.
The strand-specific RNA-seq libraries were prepared using a NEBNext® Ultra™ I RNA Library Prep Kit for Illumina (NEB, MA, USA) following the manufacturer’s instructions.

treatment_protocol: BMDMs were treated with or without NETs

value: BMDM

value: WT

value: NETs-treated


title: 15176


title: RNA-seq_HT29 EV KD_EZH2i_R3


title: RNA-seq_HT29 EV KD_EZH2i_R1


title: RNA-seq_HT29 EV KD_EZH2i_R2


title: 15123


title: RNA-seq_HT29 EV KD_R3


title: BV2-NC-2

value: Normal


title: 15058

value: female


title: RNA-seq_HT29 EV KD_R2


title: RNA-seq_HT29 EV KD_R1


title: BV2-NC-1


title: 14965


title: HT29 PTENKD_EZH2i _R1

data_processing:
read alignment was performed using Bowtie2 (52)(v2.4.2) against the hg38 reference genome, peaks were called with MACS (53)(v2.2.7.1), and differentially accessible peaks were calculated using DiffBind (54).
Assembly: hg38
Supplementary files format and content: NarrowPeaks

extract_protocol:
Transposase-accessible chromatin with sequencing (ATAC-seq) was performed using an ATAC-seq kit according to the manufacturer’s protocol (Active motif, #53150).
Purified DNA was used to prepare Illumina library using the NEBNext Ultra II DNA Library Prep kit (NEB, #E7645) as per the manufacturer's protocol, followed by sequencing.


title: HT29 PTENKD_EZH2i _R2


title: 14902


title: BV2-T2-3


title: HT29 EV KD_EZH2i_R2


title: RNA, SA ASCL1 05, d3 NE, rep3

city: London

first: Roberta

last: Azzarelli

address: 29-39 Brunswick square

department: School of Pharmacy

institute: University College London

data_processing:
fastp for adapter and quality trimming
alignment with STAR
read counts obtained with featureCounts
Differential expression analysis with DESeq2
Assembly: mm39
Supplementary files format and content: csv file of raw counts
Supplementary files format and content: csv file of CPM (counts per million)
Supplementary files format and content: csv file of differential expression analysis results

source_name: mouse embryonic stem cell

growth_protocol: 2 days differentiation towards neuroectoderm before treatment

extract_protocol:
RNA was extracted using the RNeasy mini kit
300ng RNA poly(A) selected with NEBNext poly(A) mRNA magnetic isolation module and libraries constructed with NEBNext Ultra II Directional RNA Library Prep kit

treatment_protocol: doxocycline treatment (0.1 or 0.5 ug/ml) for 24 hours

value: mouse embryonic stem cell

value: neuroectoderm media + dox


title: HT29 EV KD_EZH2i_R1

value: Cell line


title: BV2-T2-2


title: HT29 PTENKD _R2

value: Primary colorectal cancer cells


title: 14849


title: RNA, SA ASCL1 05, d3 NE, rep1


title: HT29 EV KD_R1


title: BV2-NC-3


title: HT29 EV KD_R2


title: HUVEC, iCLIP, BRG1, 500 nm UV, N2

description: HUVEC__BRG1_iCLIP__BRG1__binding_sites.bed

data_processing:
Basic quality controls were performed using FastQC (version 0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The FASTX-Toolkit (version 0.0.14) (http://hannonlab.cshl.edu/fastx_toolkit/) and seqtk (version 1.3) (https://github.com/lh3/seqtk/) were used to filter reads based on sequencing qualities (Phred score) in the barcode and UMI regions.
Read were de-multiplexed according to the sample barcode on positions 6 to 11 of the reads using Flexbar (version 3.4.0, using non-default parameter --barcode-keep) (Roehr et al., 2017). Flexbar was also used to trim UMI and barcode regions as well as adapter sequences from read ends requiring a minimal overlap of 1 nt of read and adapter. UMIs were added to the read names and reads shorter than 15 nt were removed from further analysis.
The downstream analysis was done as described in Chapters 3.4 and 4 of (Busch et al., 2020) with an additional step to remove reads directly mapped to the chromosome ends using Samtools (version 1.9) (Danecek et al., 2021) and bedtools (version 2.27.1) (Quinlan and Hall, 2010). Those reads do not have an upstream position and, thus, no crosslink position can be extracted. Genome assembly and annotation of GENCODE (release 31) (Frankish et al., 2019) were used during mapping with STAR (version 2.7.3a) (Dobin et al., 2013).
Processed reads from five replicates were merged prior to peak calling with PureCLIP (version 1.3.1)(Krakau et al., 2017) using a minimum transition probability of 1%. Significant crosslink sites (1 nt) were filtered by their PureCLIP score, removing the lowest 2% of crosslink sites. The remaining sites were merged into 7-nt wide binding sites using the R/Bioconductor package BindingSiteFinder (version 1.0.0), filtering for sites with atleast 3 positions covered by crosslink events. Only reproducible binding sites were considered for further analyses, which had to be supported by four out of five replicates. Binding sites were overlapped with gene and transcript annotations obtained from GENCODE (release 29).
iCLIP coverage per gene was computed using bedtools (v2.27.1) coverage with GENCODE (10.1093/nar/gkaa1087) annotated genes as input regions. The same procedure was performed for RNA-sequencing data in order to compare iCLIP and RNA-sequencing coverages. Gene biotype annotations were taken from the GENCODE v43 gene annotations to facilitate comparisons between lncRNAs and protein-coding RNAs. The enrichment in number of iCLIP binding sites per biotype was computed using a Fisher’s exact test, where the expected number of binding sites was established by computing the proportions of gene biotypes which were expressed in the RNA-sequencing dataset (counts per million > 5).
Assembly: hg38
Supplementary files format and content: BED files of BRG1-RNA binding sites.

extract_protocol:
RNA was purified using neutral phenol/chloroform/isoamylalcohol (Ambion, AM9722) followed by chloroform (Serva, 39554.02) extraction, and reverse transcribed using SuperScript III™ (Life Technologies, 18080-044). cDNA was cleaned up using MyONE Silane beads (Life Technologies, 37002D) followed by ligation of a second adapter containing a bipartite (5-nt + 4-nt) unique molecular identifier (UMI) as well as a 6-nt experimental barcode (Buchbender et al., 2020).
iCLIP2 libraries were pre-amplified with 6 PCR cycles using short primers (P5Solexa_short and P3Solexa_short) and then size-selected using the ProNex Size-Selective Purification System (Promega, NG2001) in a 1:2.95 (v/v) sample:bead ratio to eliminate products originating from short cDNAs or primer dimers. The size-selected library was amplified using P5Solexa and P3Solexa primers, and primers were removed using the ProNex Size-Selective Purification System (Promega, NG2001) in a 1:2.4 (v/v) sample:bead ratio.

treatment_protocol: For each replicate, cells were grown near confluence on two 150 mm culture dishes, washed with ice-cold PBS, irradiated with 150 mJ/cm2 UV light at 254 nm (CL-1000, UVP), harvested by scraping and centrifugation and stored at -80 °C until lysis.

value: 500 nm UV


title: 14826


title: 14812


title: RNA, SA ASCL1 01, d3 NE, rep3


title: HUVEC, iCLIP, BRG1, 500 nm UV, N1


title: HUVEC, iCLIP, BRG1, 300 nm UV, N2

value: 300 nm UV


title: HUVEC, iCLIP, BRG1, 300 nm UV, N1


title: 14784


title: HUVEC, iCLIP, control

description: HUVEC__BRG1_iCLIP__Control__binding_sites.bed

value: control


title: RNA, SA ASCL1 01, d3 NE, rep2


title: RNA, SA ASCL1 01, d3 NE, rep1


title: HUVEC BRG1 RedChIP

data_processing:
RedC and RedChIP reads were deduplicated using FastUniq (v1.1) (https://doi.org/10.1371/journal.pone.0052249) and subsequently trimmed for quality using Trimmomatic (v0.39) (10.1093/bioinformatics/btu170) with the flag –phred33 and setting SLIDINGWINDOW:5:26 MINLEN:0.
Reads with the appropriate linker oligonucleotide AGTCGGAGCGTTGCCTATCGCATTGATGGTGCTAGGA were identified using SeqKit (v2.7.0) (10.1371/journal.pone.0163962)  grep to select reads with either the forward or reverse bridging oligonucleotide, permitting up to four mismatches. Valid 3’ RNA reads were also identified using seqkit grep and searching for either the pattern “^GGG” or “CCC$”. DNA and 5’ RNA sequences were split from reads containing the bridging oligonucleotide sequence using cutadapt (v2.8) (https://doi.org/10.14806/ej.17.1.200) with either –g or –a set to the sequence of the bridging oligonucleotide. Additionally, the –m flag was set to 14, and the –O to 37, with –e set to 0.11 to permit the mismatches allowed in the previous step.
DNA reads, 5’ RNA reads and 3’ RNA reads were each aligned separately to the GRCh38 genome assembly using STAR (2.7.10) (10.1093/bioinformatics/bts635). In the case of the DNA, the parameters –alignIntronMax 1 --alignMatesGapMax 1 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0 were all set, whereas for alignment of the RNA reads, --alignIntronMax 20000 --alignMatesGapMax 20000 were both used.
For all of the alignments, uniquely mapping reads were selected using samtools (v1.1.0) (10.1093/gigascience/giab008) view with –q set to 255. DNA alignments were mapped onto 5 kilobase genomic bins which were computed using bedtools (v2.27.1) (https://doi.org/10.1093/bioinformatics/btq033) makewindows with GRCh38 chromosome sizes and –w 5000. RNA alignments were mapped to GRCh38 gene regions which were taken from GENCODE v43 gene annotations (10.1093/nar/gkaa1087). Only interactions where both RNA alignments uniquely mapped to the same gene were kept for analysis.
RNA-bin interaction counts were then computed, and could be compared between Red-C and BRG1 RedChIP. Interaction counts per sample were normalized based on the total number of valid interacting reads obtained per sample.
Assembly: GRCh38
Supplementary files format and content: Text file containing RNA-bin interaction counts
Library strategy: RedChIP

molecule: other

extract_protocol:
After DNA restriction, RNA 3’ ends were dephosphorylated using T4 PNK (NEB, M0201). DNA ends were then blunted using T4 DNA polymerase (NEB, M0203L) and Klenow (NEB, M0210M) and then A-tailed using Klenow (exo-) (NEB, M0212M). RNA 3’ OH ends were ligated with the 5’ rApp ends of the bridge adapter (IDT, /rApp/TCCTAGCACCATCAATGCGATAGGCAACGCTCCGACT* and /Phos/GTCGGAGCGTTGCC/T-Biotin/ATCG) and unligated bridge adapter was washed away with multiple wash steps before ligation of the bridge adapter to DNA. Nuclei were lysed, sonicated and centrifuged and the supernatant passed through Amicon 30K Ultra-0.5 mL Centrifugal Filters (Merck Millipore, UFC503008) by centrifugation. 5% of the concentrated supernatant was used as input (Red-C) and the remaining supernatant divided into aliquots and made up to 1 mL with RIPA buffer (50 mM Tris pH 7.5, 150 mM NaCl, 2 mM EDTA, 0.5% SDC, 0.1% SDS, 1% NP-40, 1× protease inhibitors, 100 U SUPERase.In RNase inhibitor (Invitrogen, AM2696)). 4 µL anti-BRG1 antibody (Abcam, ab110641) was added to the supernatant aliquots overnight. Washed protein A/G beads were added to the IP reactions for 6 h. Proteinase K digestion was performed and RNA-DNA chimeras precipitated from IP and input fractions before purification with AMPure XP beads (Beckman Coulter, A63882). RNA-DNA chimeras were digested with MmeI (NEB, R0637L) in a reaction containing a double-stranded oligonucleotide with an MmeI site (IDT, CTGTCCGTTCCGACTACCCTCCCGAC and GTCGGGAGGGTAGTCGGAACGGACAG). Biotinylated bridge adapter and RNA-DNA chimeras were then pulled down using streptavidin beads (Thermo Fisher, 65002) and a switch template oligonucleotide (IDT, iCiGiCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTrGrGrG**) added to permit reverse transcription (SMART technology).
Illumina adapters (AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT and AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNN***) were ligated and DNA-cDNA chimeras were then amplified with the KAPA HiFi kit (Roche, Cat. No. 07958838001). PCR products were enriched for fragments >200 bp and sequenced on a NextSeq2000 instrument (Illumina) using v2 chemistry, resulting in 90 million reads for the Red-C sample and 145 million reads for the BRG1 RedChIP sample, with a 2x100bp paired-end setup.

treatment_protocol: 5x10^7 HUVEC were crosslinked with formaldehyde and lysed for nuclear extraction. RNA that was not crosslinked to DNA was washed away with nuclease-free water followed by the addition of SDS. Nuclei were pelleted and DNA integrity tested by loading DNA on an agarose gel after incubation with the N1aIII restriction enzyme (NEB, R0125L).

tag: fraction

value: IP


title: 14726


title: RNA, WT ASCL1 05, d3 NE, rep3


title: RNA, SA ASCL1 05, d3 NE, rep2


title: HUVEC RedChIP Input

value: input


title: 14682


title: RNA, WT ASCL1 05, d3 NE, rep2


title: 14718


title: HUVEC, RIP-seq, BRG1, 3

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC. Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (release 99) using STAR 2.7.3a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10 %. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package.
Resulting BAM files were merged using samtools (v1.1.0).
Genomic coverage of merged BAM files was computed using bamCoverage (v3.5.3) (10.1093/nar/gkw257).
Assembly: hg38
Supplementary files format and content: BigWig files of genomic coverage per condition.

extract_protocol:
For elution of RNA, the remaining wash buffer was removed and 1 ml QIAzol (Qiagen) was added to the beads and incubated at RT for 10 min. 400 µl chloroform was added to the samples and vortexed for 10 sec followed by incubation for a further 10 min at RT. Samples were then centrifuged at 12,000 xg for 15 min at 4 °C. 500 µl of the upper aqueous phase was transferred to a new tube and 2 µl glycogen (GlycoBlue Coprecipitant, ThermoFisher, AM9515) and 500 µl isopropanol added. Samples were inverted multiple times and incubated at RT for 10 min before being centrifuged again at 12,000 xg for 10 min. The supernatant was removed and the pellet washed with 1 ml 75 % ethanol by vortexing. The pellet was centrifuged at 7,500 xg for 5 min at 4 °C, dried and resuspended in 30 µl nuclease-free water.
900 ng of total RNA isolated from HUVEC was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio).

treatment_protocol: Cells were grown to 80 % confluence (~3 million cells) and washed with Hanks buffer. Hanks buffer was added to the cells on ice for irradiation with 0.150 J/cm2 254 nm UV light (BLX-254, Vilber). Cells were scraped in Hanks buffer and centrifuged at 1,000 xg at 4 °C for 4min. For nuclear protein isolation, cells were resuspended in hypotonic buffer (10 mM HEPES pH 7.6, 10 mM KCl, 0.1 mM EDTA pH 8.0, 0.1 mM EGTA pH 8.0, 1 mM DTT, 40 µg/ml PMSF) and incubated on ice for 15 min. Nonidet was added to a final concentration of 0.75 % and cells were centrifuged (1 min, 4 °C, 16000 xg). The nuclear-pellet was washed twice in hypotonic buffer, lysed in high salt buffer (20 mM HEPES pH 7.6, 400 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1 mM DTT, 40 µg/ml PMSF) and centrifuged (5 min, 4 °C, 16000 xg). 10% of the nuclear lysate was taken as input. 4 µg of antibody (Anti-BRG1, A303-877A , Bethyl) was pre-coupled to 30 µl protein G magnetic beads in wash buffer (20 mM HEPES pH 7.6, 200 mM NaCl, 1 mM EDTA pH 8.0, 1 mM EGTA pH 8.0, 1 mM DTT, 40 µg/ml PMSF) for 1 h at RT, then washed once with high salt buffer and twice with bead wash buffer. The antibody-coupled beads were added to the nuclear lysate and rotated for 1 h at 4 °C. Samples were placed on a magnetic bar and the lysate discarded. Beads were washed three times in high salt buffer (50 mM Tris/HCl, 1 M NaCl, 1 mM EDTA, 0.1 % SDS, 0.5 % Na-Deoxycholate, 1 % NP-40, 1 mM DTT, 40 µg/ml PMSF) at 4 °C for 10 min per wash. Beads were then washed twice in wash buffer 2 (20 mM Tris/HCl, 10 mM MgCl2, 0.2 % Tween, 1 mM DTT, 40 µg/ml PMSF).

value: HUVEC

tag: rip antibody

value: Anti-BRG1, A303-877A , Bethyl


title: HUVEC, RIP-seq, Input, 2


title: HUVEC, RIP-seq, Input, 3


title: RNA, WT ASCL1 05, d3 NE, rep1


title: HUVEC, RIP-seq, BRG1, 1


title: HT29 PTENKD _R1


title: RNA, ESC, d3 NE, rep3


title: HUVEC, BRG1 CUT&RUN, PROTAC 60 minutes, 480 minutes washout, 2

data_processing:
Resulting reads were aligned to the GRCh38 genome assembly using Bowtie2 (v2.4.5) (https://doi.org/10.1038/nmeth.1923) with the parameters –local and –very-sensitive.
Mates were fixed with samtools (v1.1.0) (10.1093/gigascience/giab008) fixmate with the parameter –m set, and duplicate alignments were subsequently removed using samtools markdup with the –r flag set. Reads aligning to blacklisted regions as defined by ENCODE were removed using bedtools (2.27.1) (https://doi.org/10.1093/bioinformatics/btq033) intersect with the –v flag set.
Resulting BAM files were indexed using samtools index. Peaks were called using MACS3 (v3.0.0) (https://doi.org/10.1186/gb-2008-9-9-r137) with the parameters –scale-to-small –f BAM and –g hs.
Peaks were called using MACS3 (v3.0.0) (https://doi.org/10.1186/gb-2008-9-9-r137).
Differential peaks were also called using MACS3 by comparing read pileups between conditions using macs3 bdgdiff, normalized with the requisite total sequencing depths per condition. Peaks with a log likelihood greater than 3.84 were considered as differential.
Assembly: hg38
Supplementary files format and content: BigWig files of genomic coverage per replicate normalized by library depth.
Library strategy: CUT&RUN

treatment_protocol: Cells were treated at 70% confluence with 1 µM PROTAC AU-15330 or DMSO in full growth medium (EGM) for 60 min. For those with a wash out period, media was changed to normal growth medium for a subsequent 60, 240 or 480 minutes. 500,000 HUVEC were washed with wash buffer (20 mM HEPES pH 7.9, 150 mM NaCl, 500 nM spermidine, 1X Roche Protein Inhibitor Cocktail) at RT. Cells were resuspended in wash buffer and 10 µl BioMag®Plus Concanavalin A (ConA) beads (Polysciences, 86057-3) were added for 10 min at RT. Beads were separated on a magnetic rack and washed once before being resuspended in 100 µl antibody buffer (wash buffer, 0.25 % Digitonin and 2 mM EDTA) and 1 µl BRG1 antibody (Abcam, ab110641). Beads were incubated with the antibody over night with gentle shaking at 4 °C. The next day, beads were washed twice with 200 µl 0.25 % Digitonin wash buffer and resuspended in Digitonin wash buffer containing 2 µl CUTANA™ pAG-MNase (15-1016, EpiCypher, 15-1016) and incubated on ice for 30 min. Samples were washed twice and then resuspended in 100 µl Digitonin wash buffer containing 2 µl CaCl2 at a final concentration of 100 mM and incubated for 2 h at 4 °C with gentle shaking. 33 µl of 2X “stop solution” (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.25 % Digitonin, 100 µg/ml RNase A, 50 µg/ml Glycoblue) was added to the beads and incubated at 37 °C for 10 min. Samples were placed on a magnetic rack and the supernatant removed and kept for DNA purification.

value: BRG1 PROTAC 60 minutes, 480 minutes washout


title: RNA, ESC, d3 NE, rep2


title: HUVEC, BRG1 CUT&RUN, PROTAC 60 minutes, 480 minutes washout, 3


title: HUVEC, RIP-seq, Input, 1


title: 14369

value: male


title: RNA, ESC, d3 NE, rep1


title: HUVEC, BRG1 CUT&RUN, PROTAC 60 minutes, 240 minutes washout, 3

value: BRG1 PROTAC 60 minutes, 240 minutes washout


title: ATAC, SA ASCL1 05, d3 NE, rep4

data_processing:
adapter and quality trimming with fastp
alignment with bowtie2
sambamba for alignment filtering and selection of nucleosome free regions by insert size
peak calling with MACS2
deepTools bamCoverage to generate bigWig files per sample and average bigWig obtained using WiggleTools
Differential accessibility analysis with DiffBind
Assembly: mm39
Supplementary files format and content: bigwig files of the average of the four replicates for each condition - normalisation method reads per genomic content (RPGC)
Supplementary files format and content: Differential accessibility results obtained using DiffBind for each of the comparisons

extract_protocol:
pelleted 50,000 cells
followed the protocol in Corces et al, Nature Methods, 2017


title: HUVEC, BRG1 CUT&RUN, PROTAC 60 minutes, 240 minutes washout, 1


title: HUVEC, BRG1 CUT&RUN, PROTAC 60 minutes, 480 minutes washout, 1


title: HUVEC, BRG1 CUT&RUN, PROTAC 60 minutes, 240 minutes washout, 2


title: HUVEC, BRG1 CUT&RUN, PROTAC 60 minutes, 60 minutes washout, 3

value: BRG1 PROTAC 60 minutes, 60 minutes washout


title: ATAC, SA ASCL1 05, d3 NE, rep3


title: HUVEC, BRG1 CUT&RUN, PROTAC 60 minutes, 60 minutes washout, 2


title: dpMSC rep2

city: Nanjing

first: Dandan

last: Wang

address: 321 Zhongshan Road

institute: Nanjin Drum Tower Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
samtools used for calculating FPKM
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: mesenchymal stem cell

growth_protocol: Fresh thymus tissues were collected from mice for enzymatic digestion. After removal of blood vessels, the thymus was washed extensively with Dulbecco’s Modified Eagle Medium with Nutrient Mixture F-12. Then, the thymic fragments were incubated for 40 min at 37°C with DF12 medium containing 4 mg/mL collagenase II and 4 mg/mL neutral protease. Fetal bovine serum was added to the mesenchymal tissues to neutralize the excess digesting. The digested mixture was then passed through a 100 mm filter to obtain cell suspensions. Finally, the cells were plated on 60-mm culture dishes and allowed to proliferate in DF12 medium, supplemented with 20% FBS plus 100 U penicillin/streptomycin (Sigma) and cultured at 37°C in a 5% CO2 humidified incubator. After 2 days of culture, nonadherent cells were removed, and adherent cells were washed and incubated until confluence in DF12 medium. Medium was then changed every 3 days and serially expanded. For dental pump MSCs isolation, we firstly extracted the lower incisors from mandibles of the mouse under stereomicroscope. Then we removed the dentin from the apical roots to expose the dental pulps. Next we pull out the dental pulps very carefully and put them into a tube with c-DMEM on ice for future use. Dental pulp tissues were digested and cultured as thymus tissues as above.

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: dental pulp

value: mesenchymal stem cell


title: dpMSC rep3


title: HUVEC, RIP-seq, BRG1, 2


title: ATAC, SA ASCL1 05, d3 NE, rep2

value: mouse embryonic stem cell


title: HUVEC, BRG1 CUT&RUN, PROTAC 60 minutes, 60 minutes washout, 1


title: dpMSC rep1


title: 14540

data_processing:
R v4.2.2 & minfi
Quantile-normalised Average Beta
Unmethylated and methylated signal intensities

extract_protocol: Genomic DNA was extracted using Qiagen Allprep kit.

value: female


title: HUVEC, BRG1 CUT&RUN, PROTAC 60 minutes, 0 minutes washout, 3

value: BRG1 PROTAC 60 minutes, 0 minutes washout


title: HUVEC, BRG1 CUT&RUN, PROTAC 60 minutes, 0 minutes washout, 1


title: ATAC, SA ASCL1 05, d3 NE, rep1

value: neuroectoderm media + dox


title: tMSC rep3

value: thymus


title: HUVEC, BRG1 CUT&RUN, Control, 0 minutes washout, 3

value: Control, no washout period


title: RatHepatocytes_Ctrl

city: Hiroshima

first: Nariaki

last: FUJIMOTO

state: Hiroshima

address: 1-2-3 Kasumi

department: RIRBM

country: Japan

institute: Hiroshima University

hyb_protocol: the standard Affymetrix protocol

scan_protocol: GeneChip 3000 Scanner

data_processing: Expression console software

label: biotin

source_name: RatHepatocytes, Ctrl

label_protocol: the standard Affymetrix protocol

growth_protocol: collagen-coated 6-well plates with Hepatocyte Basal Medium containing growth factors (Lonza Co.)

extract_protocol: NucleoSpin RNA II (Machery- Nagel GmbH)

treatment_protocol: triiodothyronine (T3) at 10-9 M for 24 hrs

tag: tag

value: male, SD, liver


title: HUVEC, BRG1 CUT&RUN, Control, 0 minutes washout, 2


title: HUVEC, BRG1 CUT&RUN, PROTAC 60 minutes, 0 minutes washout, 2


title: tMSC rep2


title: HUVEC, BRG1 CUT&RUN, Control, 0 minutes washout, 1


title: ATAC, SA ASCL1 01, d3 NE, rep3


title: HUVEC, ATAC-seq, BRG1 PROTAC, 240 minutes, 3

data_processing:
Reads were aligned to the GRCh38 genome assembly using Bowtie2 (v2.4.5) (https://doi.org/10.1038/nmeth.1923) with the parameters –local –very-sensitive.
Duplicates and multi-mapping reads were removed using samtools (v1.10) (10.1093/gigascience/giab008) rmdup and samtools view.
Genomic ATAC-seq seq coverage was computed using bamCoverage (3.5.3) (10.1093/nar/gkw257) with the parameters –normalizeUsing RPKM and –effectiveGenomeSize  2864785220.
Peaks were called using MACS3 (v3.0.0) (https://doi.org/10.1186/gb-2008-9-9-r137) with the parameters –nomodel and –format BAMPE.
Differential peaks were also called using MACS3 by comparing read pileups between conditions using macs3 bdgdiff, normalized with the requisite total sequencing depths per condition. Peaks with a log likelihood greater than 3.84 were considered as differential.
Assembly: hg38
Supplementary files format and content: BigWig files of genomic coverage per replicate normalized by RPKM.

treatment_protocol: Cells were treated at 70% confluence with 1 µM PROTAC AU-15330 or DMSO in full growth medium (EGM) for 30, 60 or 240 minutes. 50,000 HUVEC were used for ATAC library preparation using lllumina Tagment DNA Enzyme and Buffer Kit (Illumina). The cell pellet was resuspended in 50 µl of the lysis/transposition reaction mix (25 µl TD-Buffer, 2.5 µl Nextera Tn5 Transposase, 0.5 µl 10 % NP-40 and 32 µl H2O) and incubated at 37 °C for 30 min followed by immediate purification of DNA fragments with the MinElute PCR Purification Kit (Qiagen).

value: BRG1 PROTAC, 240 minutes


title: tMSC rep1


title: RatHepatocytes_T3(24h)

source_name: RatHepatocytes, T3, 24hrs


title: HUVEC, ATAC-seq, BRG1 PROTAC, 240 minutes, 2


title: HUVEC, ATAC-seq, BRG1 PROTAC, 240 minutes, 1


title: HUVEC, ATAC-seq, BRG1 PROTAC, 60 minutes, 3

value: BRG1 PROTAC, 60 minutes


title: ATAC, SA ASCL1 01, d3 NE, rep1


title: HUVEC, ATAC-seq, BRG1 PROTAC, 60 minutes, 2

value: HUVEC


title: HUVEC, ATAC-seq, BRG1 PROTAC, 30 minutes, 2

value: BRG1 PROTAC, 30 minutes


title: HUVEC, ATAC-seq, BRG1 PROTAC, 60 minutes, 1


title: HUVEC, ATAC-seq, BRG1 PROTAC, 30 minutes, 3


title: ATAC, WT ASCL1 05, d3 NE, rep4


title: ATAC, WT ASCL1 05, d3 NE, rep3


title: ATAC. SA ASCL1 01, d3 NE, rep4


title: ATAC, WT ASCL1 05, d3 NE, rep2


title: HUVEC, ATAC-seq, Control, 30 minutes, 3

value: Control


title: HUVEC, ATAC-seq, Control, 30 minutes, 2


title: HUVEC, ATAC-seq, BRG1 PROTAC, 30 minutes, 1


title: HUVEC, ATAC-seq, Control, 30 minutes, 1


title: ATAC, ESC, d3 NE, rep4


title: S-001780492

city: Boston

first: Vrushali

middle: Dipak

last: Fangal

state: MA

address: 181 Longwood Avenue

department: Brigham and Women's Hospital

institute: Harvard Medical School

description:
Library name: S-001780492
Column name in mouse_vitd_def_th2_matrix.csv: S-001780492

data_processing:
Trimmed reads were aligned to the mouse reference genome (GRCm38) using the STAR aligner (v2.7.10a). Gene expression read counts were quantified using HTSeq (v0.13.5).
Assembly: GRCm38
Supplementary files format and content: The processed data files are tab-delimited text files, containing normalized expression values (log-CPM) for each gene across all samples. Gene identifiers are based on Ensembl (GRCm38).

source_name: TH2 cells

growth_protocol: C57BL/6 mice were used to establish a vitamin D-deficient mouse model. Mice were maintained in a virus- and parasite-free animal facility under a 12-hour light/dark cycle with unrestricted access to food and water. Vitamin D-deficient mice were bred and reared in a UV-free environment and fed a diet lacking vitamin D metabolites (TD97340; Harlan Teklad). Wild-type control mice were maintained under identical conditions but fed a standard diet containing vitamin D3 (400 IU per kg of diet). The experiments were performed using second-generation offspring to ensure stable vitamin D levels.

extract_protocol:
At day 5 of polarization, cells were harvested and total RNA was isolated using the microRNeasy kit (Qiagen) according to the manufacturer's instructions. RNA quality and concentration were evaluated using a Nanodrop 8000 spectrophotometer.
RNA-seq libraries were prepared using the TruSeq® Stranded Total RNA Library Prep Globin Kit (Illumina) following the manufacturer’s protocols.

treatment_protocol: No additional treatments were applied. The dataset focuses on comparing TH2 cells derived from vitamin D-deficient mice versus wild-type controls under basal conditions.

value: TH2 cells

value: WT

value: Vit-D deficient

tag: batch


title: Rat-Rev-4

city: Detroit

first: Pooja

last: Malaviya

state: Michigan

address: 4717 St Antoine, Kresge eye institute Room#404

institute: Wayne state university

description: LncRNA/mRNA expression profiling for retina from rat diabetic for 4 months followed by good glycemic control for 4 months

hyb_protocol: The labeled cRNA was hybridized in an Agilent hybridization oven at 65˚C for 17 hours onto the Rat LncRNA Array v3.0.

scan_protocol: Hybridized samples were fixed and scanned using Agilent DNA Microarray Scanner G2505C.

data_processing: The acquired images were analyzed by Agilent Feature Extraction software.

source_name: Retina, Reversal, replicate 4

label_protocol: RNA (4 rats/group) was amplified and Cyanine-3 (Cy3) labeled cRNA was prepared from RNA using the One-Color Arraystar Flash RNA Labeling Kit utilizing a random priming method (Agilent).

extract_protocol: Total RNA was isolated from retina using RNeasy Micro Kit (Qiagen, Valencia, CA, USA) and RNA was quantified by NanoDrop ND-1000 spectrophotometer.

treatment_protocol: Wistar rats (male), made diabetic and were divided into two groups; rats in group 1 remained in poor glycemic control (Diab group) throughout the eight-month of duration, and in group 2 rats were maintained in poor glycemic control for four months followed by good glycemic control for four months (Rev group). The rats were sacrificed by carbon dioxide inhalation and their retina was isolated. Age-matched normal rats were used as controls (Norm group).

value: Wistar

value: retina

value: male

tag: group

value: Rev


title: ATAC, SA ASCL1 01, d3 NE, rep2

value: mouse embryonic stem cell


title: S-001780493

description:
Library name: S-001780493
Column name in mouse_vitd_def_th2_matrix.csv: S-001780493


title: S-001780490

description:
Library name: S-001780490
Column name in mouse_vitd_def_th2_matrix.csv: S-001780490


title: S-001780491

description:
Library name: S-001780491
Column name in mouse_vitd_def_th2_matrix.csv: S-001780491


title: S-001780489

description:
Library name: S-001780489
Column name in mouse_vitd_def_th2_matrix.csv: S-001780489


title: ATAC, ESC, d3 NE, rep3

value: neuroectoderm media + dox


title: Rat-Rev-2

source_name: Retina, Reversal, replicate 2


title: Rat-Rev-3

source_name: Retina, Reversal, replicate 3


title: Rat-Rev-1

source_name: Retina, Reversal, replicate 1


title: S-001780488

description:
Library name: S-001780488
Column name in mouse_vitd_def_th2_matrix.csv: S-001780488


title: ATAC, ESC, d3 NE, rep2


title: ATAC, ESC, d3 NE, rep1


title: Rat-Diab-4

description: LncRNA/mRNA expression profiling for retina from rat diabetic for 8 months

source_name: Retina, Diabetic, replicate 4

value: Diab


title: S-001780487

description:
Library name: S-001780487
Column name in mouse_vitd_def_th2_matrix.csv: S-001780487


title: S-001780483

description:
Library name: S-001780483
Column name in mouse_vitd_def_th2_matrix.csv: S-001780483

value: regular


title: Rat-Diab-2

source_name: Retina, Diabetic, replicate 2


title: ATAC, WT ASCL1 05, d3 NE, rep1


title: S-001780482

description:
Library name: S-001780482
Column name in mouse_vitd_def_th2_matrix.csv: S-001780482


title: ATAC, ESC, d2 NE, rep4


title: S-001780481

description:
Library name: S-001780481
Column name in mouse_vitd_def_th2_matrix.csv: S-001780481


title: Murine AML, OGDH shRNA2, clone 5, D4, rep2

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: SH24_Ogdh2081c5
SH24_IGO_09521_34_S34

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.6.1a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

growth_protocol: Murine AML cells were maintained in culture in RPMI + 10% FBS + 1% penicillin-streptomycin and stimulated with doxycycline for the indicated durations. Approximately 5x105-1x106  cells were harvested for RNA extraction for each condition.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

treatment_protocol: Prior to doxycycline induction, cells were transduced with retroviral vectors expressing the indicated doxycycline-inducible shRNAs

value: Murine AML

tag: time

value: Mll-Af9; NrasG12D

value: doxycycline


title: Rat-Diab-1

source_name: Retina, Diabetic, replicate 1

tag: tissue


title: Murine AML, OGDH shRNA2, clone 3, D4, rep1

description:
Library name: SH21_Ogdh2081c3
SH21_IGO_09521_31_S31

tag: treatment


title: ATAC, ESC, d2 NE, rep3

tag: cell line


title: Murine AML, OGDH shRNA1, clone 5, D4, rep2

description:
Library name: SH20_Ogdh346c5
SH20_IGO_09521_30_S30

tag: cell type


title: ATAC, ESC, d2 NE, rep1


title: Murine AML, OGDH shRNA1, clone 1, D4, rep2

description:
Library name: SH18_Ogdh346c1
SH18_IGO_09521_28_S28

tag: genotype


title: Murine AML, OGDH shRNA1, clone 5, D4, rep1

description:
Library name: SH19_Ogdh346c5
SH19_IGO_09521_29_S29


title: Rat-Norm-3

description: LncRNA/mRNA expression profiling for normal rat retina

source_name: Retina, normal, replicate 3

value: Norm


title: Murine AML, OGDH shRNA2, clone 3, D4, rep2

description:
Library name: SH22_Ogdh2081c3
SH22_IGO_09521_32_S32


title: Murine AML, OGDH shRNA1, clone 1, D4, rep1

description:
Library name: SH17_Ogdh346c1
SH17_IGO_09521_27_S27


title: Rat-Norm-2

source_name: Retina, normal, replicate 2


title: Rat-Norm-4

source_name: Retina, normal, replicate 4


title: Rat-Diab-3

source_name: Retina, Diabetic, replicate 3


title: G1E-ER4 LDB1-AID RCMC, Auxin 4 hr, Biological Replicate 1

city: Cambridge

first: Viraat

middle: Yogi

last: Goel

department: Biological Engineering

institute: Massachusetts Institute of Technology (MIT)

description:
sequencing also performed on Illumina NovaSeq X
Processed data file merges biological replicates 1 & 2. Raw data files from the NovaSeq 6000 contain "NovaS1" in their filename while raw data files from the NovaSeq X contain "NovaX" in their filename.

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired end reads were aligned to the UCSC mm9 genome using bowtie2 v2.2.5 with --local --reorder --very-sensitive-local. Aligned paired end reads were then parsed with pairtools (v0.3.0) parse with --add-columns mapq --walks-policy mask --min-mapq 2 --drop-sam --drop-readid.
Parsed reads were filtered for PCR duplicates and unmapped/mutiply mapping reads with pairtools dedup with --max-mismatch 1. Remaining reads were indexed (pairix v0.3.7) and filtered to retain only those reads where both read mates lie in a locus of interest. These filtered reads were subsequently converted to .cool format using cooler (v0.8.11) cload pairs, and then to .mcool format with cooler zoomify, including the --balance option.
Loops were identified using cooltools (v0.5.3)
Assembly: mm9
Supplementary files format and content: mcool:multi-resolution contact map
Library strategy: Region Capture Micro-C

extract_protocol:
Cells were fixed with 3 mM DSG for 35 minutes, followed by an additional 10 minutes with 1% formaldehyde. Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and followed by reverse crosslinking of the chromatin and Protease K digestion. DNA was purified using a DNA Clean and Concentrator kit (Zymo), and then size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments.
Size-selected DNA fragments bound to streptavidin coated beads were used to prepare Micro-C libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with 5-7 PCR cycles on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled in a 1:1 ratio to a total of 2-4 µg of DNA. 80-mer biotinylated probes were designed end-to-end to tile across regioins of interest with Twist Bioscience. Capture was performed using the custom target enrichment panels using Twist Bioscience's Standard Hybridization Target Enrichment Protocol (Twist Bioscience, 104178) with the inclusion of Mouse Cot-1 DNA (Invitrogen) blocker solution. The library pool was hybridized to custom probe panels for loci of interest and bound to streptavidin coated beads. Bead-bound fragments were pulled down, amplified with 4 PCR cycles on the thermocycler using Equinox Library Amp Mix (Twist), and purified using Twist Binding and Purification Beads (Twist). Following qPCR quantification, the target enriched library pool was submitted for sequencing.

value: proerythroblast

value: Auxin, 4hr


title: Murine AML, control shRNA, clone 7, D4, rep2

description:
Library name: SH16_Ren713c7
SH16_IGO_09521_26_S26


title: Murine AML, control shRNA, clone 7, D4, rep1

description:
Library name: SH15_Ren713c7
SH15_IGO_09521_25_S25


title: G1E-ER4 LDB1-AID RCMC, Untreated, Biological Replicate 1


title: Murine AML, control shRNA, clone 2, D4, rep2

description:
Library name: SH14_Ren713c2
SH14_IGO_09521_24_S24


title: Murine AML, control shRNA, clone 2, D4, rep1

description:
Library name: SH13_Ren713c2
SH13_IGO_09521_23_S23


title: Lpar3-/- kidney, hypoxia, 12 h,rep3

last: Yin

address: 19 Xinjiekouwaida Street

department: College of Life Science

institute: Beijing Normal University

data_processing:
Quality control: clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data
Mapping: Hisat2 v2.0.5 was used to map the reads to GRCm38.
Quantification of gene expression level: featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis: DESeq2 R package (1.20.0) was used.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: kidney

extract_protocol:
Total RNA was extracted using the CTAB method. 1 μg of total RNA was used for library construction
After being purified from total RNA by using poly-T oligo-attached magnetic beads, the mRNA was cut into fragments using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). Random hexamer primer and M-MuLV Reverse Transcriptase were used to synthesize the first strand cDNA. PCR was performed to synthesize the second strand cDNA. Then the remaining overhangs were converted into blunt ends. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure was ligated to prepare for hybridization. AMPure XP system (Beckman Coulter, Beverly, USA) was used to select 370~420 bp cDNA fragments, which were then amplified by PCR and purified by AMPure XP beads again to get the library.

value: kidney

value: systemic hypoxia


title: Murine AML, OGDH shRNA2, clone 5, D0, rep1

description:
Library name: SH11_Ogdh2081c5
SH11_IGO_09521_21_S21

value: untreated


title: Lpar3-/- kidney, hypoxia, 12 h,rep2


title: Murine AML, OGDH shRNA2, clone 3, D0, rep2

description:
Library name: SH10_Ogdh2081c3
SH10_IGO_09521_20_S20


title: Murine AML, OGDH shRNA2, clone 5, D4, rep1

description:
Library name: SH23_Ogdh2081c5
SH23_IGO_09521_33_S33


title: Rat-Norm-1

source_name: Retina, normal, replicate 1

value: Wistar


title: Lpar3-/- kidney, hypoxia, 12 h,rep1


title: Murine AML, OGDH shRNA2, clone 5, D0, rep2

description:
Library name: SH12_Ogdh2081c5
SH12_IGO_09521_22_S22


title: ATAC, ESC, d2 NE, rep2

source_name: mouse embryonic stem cell


title: Murine AML, OGDH shRNA2, clone 3, D0, rep1

description:
Library name: SH9_Ogdh2081c3
SH9_IGO_09521_19_S19


title: Murine AML, OGDH shRNA1, clone 5, D0, rep2

description:
Library name: SH8_Ogdh346c5
SH8_IGO_09521_18_S18


title: WT kidney, hypoxia, 12 h,rep3

value: WT


title: Murine AML, OGDH shRNA1, clone 1, D0, rep2

description:
Library name: SH6_Ogdh346c1
SH6_IGO_09521_16_S16


title: Murine AML, OGDH shRNA1, clone 5, D0, rep1

description:
Library name: SH7_Ogdh346c5
SH7_IGO_09521_17_S17


title: Murine AML, OGDH shRNA1, clone 1, D0, rep1

description:
Library name: SH5_Ogdh346c1
SH5_IGO_09521_15_S15


title: Murine AML, control shRNA, clone 7, D0, rep2

description:
Library name: SH4_Ren713c7
SH4_IGO_09521_14_S14


title: Murine AML, control shRNA, clone 7, D0, rep1

description:
Library name: SH3_Ren713c7
SH3_IGO_09521_13_S13


title: WT kidney, hypoxia, 12 h,rep1


title: Murine AML, control shRNA, clone 2, D0, rep2

description:
Library name: SH2_Ren713c2
SH2_IGO_09521_12_S12


title: PG-C3

city: Rangsit

first: Sasin

last: Charoensuksira

state: Pathum Thani

address: 99 Moo 18 Klong Luang

country: Thailand

institute: Thammasat University

description:
Library name: D2C1_1CD1_PG-C3
FFPE sample, Whole Transcriptome Atlas

data_processing:
save-interim-files = false, quality-trim-score = 20, 2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10, adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1, stitching-max-mismatch = 2, dedup-hd = 1, threads = 4
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_v1.0.pkc)
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: xlsx file includes normalized counts for each Sample. The final list of detectable genes was obtained by dropping genes with a limit of quantification (LOQ) of 1% coverage within replicates. Analyzed counts represent the upper quartile normalized collapsed counts across the study after removing QC flagged segments and features.
Library strategy: Spatial Transcriptomics

source_name: Scalp tissue

extract_protocol:
Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with flourescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: Scalp tissue

value: CD34+ hair follicle progenitor cells

value: Normal scalp


title: PG-C1

description:
Library name: D2C1_1CD1_PG-C1
FFPE sample, Whole Transcriptome Atlas


title: 12mpf_Sox10CreUbiswitch_ear

city: Los Angeles

first: Tuo

last: Shi

state: California

address: 1425 San Pablo St BCC 403

institute: University of Southern California

description: 10x Genomics multiome snATAC library

data_processing:
Base calling and sample were demultiplexed by bcl2fastq performed by the single cell sequencing and CyTOF core at Chilren's Hospital Los Angeles
Zebrafish sequences were alinged to danRer11 and UMI counts were created using cellranger-atac count v2 (14dpf) or cellranger-arc count v2.0.0 (12mpf). Lizard sequences were aligned to AnoCar2.0v2 and UMI counts were created using cellranger-arc count v2.0.0
Downstream analysis was performed in R using Seurat v5.0.1 and Signac v1.12.0 and in Unix Shell using deepTools
Assembly: danRer11/GRCz11 and AnoCar2.0v2
Supplementary files format and content: .h5 files of filtered barcode feature count matrix for each individual library
Supplementary files format and content: .bigwig files of 14 dpf and 12 mpf zebrafish hair and supporting cell pseudo-bulk ATAC tracks
Supplementary files format and content: .tsv and .tbi files of snATAC fragments required to visualize ATAC coverage in R
Library strategy: snATAC-seq (14dpf zebrafish) and Single Cell Multiome ATAC + Gene Expression (12 mpf zebrafish and adult lizard)

organism: Danio rerio

source_name: inner ear

extract_protocol:
For 14 dpf zebrafish, heads from converted Sox10:Cre; ubb:LOXP-EGFP-LOXP-mCherry fish were decapitated at the level of the pectoral fin with eyes and brains removed. For 12 mpf zebrafish, utricle, saccule, and lagena were extracted from converted Sox10:Cre; ubb:LOXP-EGFP-LOXP-mCherry fish after brains and otolith crystals were removed. For adult lizard, saccules were extracted from lizard heads and otoconia crystals were removed. Dissected heads and otic sensory patches were then incubated in fresh Ringer’s solution for 5–10 min, followed by mechanical and enzymatic dissociation by pipetting every 5 min in protease solution (0.25% trypsin (Life Technologies, 15090-046), 1 mM EDTA, and 400 mg/mL Collagenase D (Sigma, 11088882001) in PBS) and incubated at 28.5 °C for 20–30 min or until full dissociation. Reaction was stopped by adding 6× stop solution (6 mM CaCl2 and 30% fetal bovine serum (FBS) in PBS). Cells were pelleted (376 × g, 5 min, 4 °C) and resuspended in suspension media (1% FBS, 0.8 mM CaCl2, 50 U/mL penicillin, and 0.05 mg/mL streptomycin (Sigma-Aldrich, St. Louis, MO) in phenol red-free Leibovitz’s L15 medium (Life Technologies)) twice. Final volumes of 500 μL resuspended cells were placed on ice and fluorescence-activated cell sorted (FACS) to isolate live cells that excluded the nuclear stain DAPI
10X Genomics Chromium Next GEM Single Cell ATAC Library and Gel Bead Kit v1.1 (14 dpf zebrafish) or Single Cell Multiome ATAC + Gene Expression kit (12 mpf zebrafish and adult lizard)

value: inner ear

value: mixed

value: Sox10:Cre; ubb:LOXP-EGFP-LOXP-mCherry


title: Murine AML, control shRNA, clone 2, D0, rep1

description:
Library name: SH1_Ren713c2
SH1_IGO_09521_11_S11

value: Murine AML


title: PG-A5

description:
Library name: D2C1_1AGA2_PG-A5
FFPE sample, Whole Transcriptome Atlas

value: Androgenetic alopecia


title: PFC_WT4

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

description:
PFC
Experinced Socail defeat stress
PFC_Counts.txt

data_processing:
Bulk RNA-seq reads were aligned with STAR 2.7.1a to the reference sequence (mm10 from UCSC). Mouse reference was used for gene annotation and counting (gencode M27). Uniquely mapped reads were quantified using featureCounts using protein coding genes by gene.
Assembly: Mouse mm10
Supplementary files format and content: tab-delimited text files raw counts for each sample

source_name: C57Bl6J male mice, medial Prefrontal cortex

extract_protocol:
RNAs were isolated with QIAGEN miRNseasy Kits.
Total RNA library

value: medial Prefrontal cortex

tag: Sex

value: male

value: SocialDefeat


title: 14dpf_Sox10CreUbiswitch_ear

description: 10x Genomics snATAC library


title: PG-A4

description:
Library name: D1D3C2_1_AGA1_PG-A4
FFPE sample, Whole Transcriptome Atlas


title: Murine AML, OGDH shRNA2, D4, induced sorted, rep2

description: Library name: KL30_E06_shOgdh2081_D4BFPplus

growth_protocol: Murine AML cells were maintained in culture in RPMI + 10% FBS + 1% penicillin-streptomycin + murine IL3/IL6/SCF and stimulated with doxycycline for the indicated durations. BFP negative (min; uninduced) and BFP positive (plus;induced) cells were isolated by FACS. Approximately 5x105-1x106  cells were harvested for RNA extraction for each condition.

treatment_protocol: Prior to doxycycline induction, cells were transduced with lentiviral vectors expressing the indicated BFP-linked, doxycycline-inducible shRNAs

value: doxycycline


title: PFC_WT3

tag: strain


title: Murine AML, OGDH shRNA1, D4, induced sorted, rep2

description: Library name: KL10_C10_shOgdh346_D4BFPplus


title: PFC_WT2

description:
PFC
Staying Homecage
PFC_Counts.txt

value: Homecage


title: PG-A3

description:
Library name: D1D3C2_1_AGA1_PG-A3
FFPE sample, Whole Transcriptome Atlas


title: Murine AML, OGDH shRNA1, D4, induced sorted, rep1

description: Library name: KL25_E01_shOgdh346_D4BFPplus


title: PG-C2

description:
Library name: D2C1_1CD1_PG-C2
FFPE sample, Whole Transcriptome Atlas


title: PG-A2

description:
Library name: D1D3C2_1_AGA3_PG-A2
FFPE sample, Whole Transcriptome Atlas


title: Murine AML, control shRNA, D4, induced sorted, rep2

description: Library name: KL20_E07_shRen713_D4BFPplus


title: Murine AML, control shRNA, D4, uninduced sorted, rep2

description: Library name: KL19_D07_shRen713_D4BFPmin


title: Murine AML, control shRNA, D2, induced sorted, rep2

description: Library name: KL18_D06_shRen713_D2BFPplus


title: WT kidney, hypoxia, 12 h,rep2

value: kidney

value: systemic hypoxia


title: Murine AML, control shRNA, D0, rep2

description: Library name: KL16_D04_shRen713_D0

value: untreated


title: Lipid Oligo Barcode library of WT and E0 deletion CMs

first: Seong Won

last: Kim

address: 77 Ave Louis Pasteur

department: Genetics

description:
Library name: CP48_multiplex
Pooled snRNAseq

data_processing:
Fastq files were demultiplexed and aligned to hg38 using CellRanger commands. Background reads were removed using CellBender. DropletUtils package was used to convert processed files to CellRanger output format.
Assembly: hg38
Supplementary files format and content: Processed files include gene expression matrix after CellBender in the CellRanger output format. Sample deconvolution information and sample metadata are in the assignment table.

growth_protocol: hiPSCs used in this study were derived from the male parent hiPSC line PGP1. The cells were cultured on Matrigel-coated plates in mTeSR1 media. The hiPSC-CMs were generated from hiPSCs using a small molecule-mediated differentiation method, which modulates the Wnt signaling pathway and cardiomyocytes were metabolically selected by glucose deprivation as previously described.

extract_protocol:
Cells were lysed, and the isolated nuclei were incubated with the commercially available lipid-oligo barcodes (3’ CellPlex Kit from 10X Genomics). Nuclei were washed, counted, and pooled at equal number. Intact single nuclei were sorted with FACS.
The standard 10X Genomics sequencing was performed according to the manufacturer’s instructions.

treatment_protocol: Cardiomyocytes were lifted with TrypLE and cells were frozen down.

value: hiPSC-CM


title: Murine AML, control shRNA, D4, induced sorted, rep1

description: Library name: KL5_C05_shRen713_D4BFPplus


title: Murine AML, control shRNA, D4, uninduced sorted, rep1

description: Library name: KL4_C04_shRen713_D4BFPmin


title: NAc_Ctrl1

description:
Nac
Staying Homecage
NAc_Counts.txt

source_name: C57Bl6J male mice, Nucleus Accumbens

value: Nucleus Accumbens


title: Lipid Oligo Barcode library of WT and E1 deletion CMs

description:
Library name: CP43_multiplex
Pooled snRNAseq


title: Murine AML, control shRNA, D2, induced sorted, rep1

description: Library name: KL3_C03_shRen713_D2BFPplus


title: Murine AML, OGDH shRNA2, D4, induced sorted, rep1

description: Library name: KL15_D03_shOgdh2081_D4BFPplus


title: NAc_Coca2

description:
Nac
Exploration in conditioned place preference chamber with cocaine (7.5 mg/kg, i.p.) administraion
NAc_Counts.txt

value: Cocaine CPP


title: Murine AML, control shRNA, D2, uninduced sorted, rep1

description: Library name: KL2_C02_shRen713_D2BFPmin


title: Lipid Oligo Barcode library of WT and MEF2_T>C CMs 2

description:
Library name: CP10_multiplex
Pooled snRNAseq


title: Murine AML, control shRNA, D0, rep1

description: Library name: KL1_C01_shRen713_D0


title: NAc_Coca1


title: Lipid Oligo Barcode library of WT and MEF2_T>C CMs 1

description:
Library name: CP6_multiplex
Pooled snRNAseq


title: S-001656721

description:
Library name: S-001656721
Column name in mouse_calcitriol_th2_matrix.csv: S-001656721

source_name: TH2 cells

growth_protocol: Mice were maintained in a virus- and parasite-free animal facility under a 12-hour light/dark cycle with unrestricted access to food and water. Male and female Balb/c mice (aged 6–8 weeks) were obtained from Charles River Laboratories. The mice were bred on diets with varying vitamin D3 concentrations (400 IU, 1000 IU, or 4000 IU per kg of diet) for two generations to establish vitamin D equilibrium.

treatment_protocol: To assess the effects of vitamin D, calcitriol stimulation was applied to TH2 cells at a final concentration of 100 nM during the last 24 hours of culture. The vehicle control group was treated with 2% ethanol as a solvent control for calcitriol.

value: TH2 cells

value: WT

value: control


title: S-001656723

description:
Library name: S-001656723
Column name in mouse_calcitriol_th2_matrix.csv: S-001656723

value: Vitamin D


title: NAc_Ctrl2

description:
Nac
Staying Homecage
NAc_Counts.txt


title: Pooled snRNAseq of WT and E0 deletion CMs

description:
Library name: CP48
Pooled snRNAseq


title: Pooled snRNAseq of WT and E1 deletion CMs

description:
Library name: CP43
Pooled snRNAseq


title: PFC_WT1

description:
PFC
Staying Homecage
PFC_Counts.txt


title: Murine AML, control shRNA, D2, uninduced sorted, rep2

description: Library name: KL17_D05_shRen713_D2BFPmin

value: Murine AML


title: PG-A1

description:
Library name: D1D3C2_1_AGA3_PG-A1
FFPE sample, Whole Transcriptome Atlas

value: Scalp tissue

value: CD34+ hair follicle progenitor cells

value: Androgenetic alopecia


title: S-001656718

description:
Library name: S-001656718
Column name in mouse_calcitriol_th2_matrix.csv: S-001656718