title: Genomic DNA methylation from 201516310048_R05C01


title: lung adenocarcinoma cells, young KP mouse, rep 6, L003

status: Public on Nov 12 2024

type: SRA

city: New York

first: Yingqian

middle: Ada

last: Zhan

state: New York

address: 430 East 67th Street

department: EPIGENETICS RESEARCH CENTER

country: USA

institute: MSKCC

library_source: genomic

data_processing:
The Bismark pipeline was adopted to map bisulfite-treated EPIC sequencing reads and determine cytosine methylation states.
Trim Galore v0.6.4 was used to remove raw reads with low-quality (less than 20) and adapter sequences.
The trimmed sequence reads were C(G) to T(A) converted and mapped to similarly converted reference human genome (mm10) using default Bowtie 2 settings within Bismark.
Duplicated reads were discarded. The remaining alignments were then used for cytosine methylation calling by Bismark methylation extractor.
bigWig files were generated using bedGraphToBigWig from kentUtils.
Assembly: mm10
Supplementary files format and content: bigWig for cytosine read coverage and methylation rate
Supplementary files format and content: bsseq object in rds format for cytosine read counts on all samples
Library strategy: Enzymatic Methyl-seq (EM-Seq)

molecule: genomic DNA

organism: Mus musculus

source_name: Primary mouse lung tumor tissue

growth_protocol: Samples were obtained from primary mouse tissues. All mice were housed in non-pathogenic conditions, controlled temperature (20–25 °C), and a 12-hour light–dark cycle with 30-70% relative humidity. Food and water were provided ad libitum.

extract_protocol:
Genomic DNA was purified using DNeasy Blood & Tissue Kit (Qiagen, #69504), following manufacturer's protocol.
NEB Next Enzymatic Methyl-seq (EM-seq, New England Biolabs, #E7120S) was used to identify 5-methylcytosine and 5-hydroxymethylcytosine bases and sequencing libraries were constructed by NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, #E7645S), following the manufacturer’s protocol.

treatment_protocol: No treatment has been performed.

tag: tissue

value: Primary mouse lung tumor tissue

tag: cell type

value: lung tumor cells

tag: genotype

value: LSL-KrasG12D/+; Trp53fl/fl


title: lung adenocarcinoma cells, aged KP mouse, rep 1, L003


title: lung adenocarcinoma cells, young KP mouse, rep 1, L003


title: lung adenocarcinoma cells, aged KP mouse, rep 2, L003


title: Genomic DNA methylation from 201516310048_R04C01

type: genomic

city: Barcelona

first: Joan

address: Carrer del Doctor Aiguader, 88

country: Spain

institute: Hospital del Mar Research Institute

hyb_protocol: The bisulfite converted DNA was processed and hybridized to the 450K or EPIC BeadChip (Illumina, Inc.), according to the manufacturer's instructions.

scan_protocol: The BeadChip images were scanned on the iScan system and the data was extracted into GenomeStudio software v2011.1, using default analysis settings.

data_processing: Idat files were loaded with Minfi. CpGs with a detection rate lower than 99% (detection p-value > 0.05) or having a beadcount lower than 1% in at least 5% of samples were excluded. Additionally, CpGs at multi-hit or single-nucleotide polymorphism locations (MethylToSNP) were also excluded. Samples having a call-rate lower than 95% or sex mismatch were excluded. DNA methylation was expressed as beta values and we applied preprocessnoob and BMIQ normalizations

label: Cy5 and Cy3

organism: Homo sapiens

source_name: Blood DNA

label_protocol: Bisulfite conversion was performed using 500 ng genomic DNA input using the EZ DNA Methylation Gold Kit (Zymo Research)

extract_protocol: DNA was extracted from whole peripheral blood collected in 10mL EDTA tubes during the first 24h after stroke onset.

value: Blood DNA

tag: Sex

value: male

value: yes


title: Genomic DNA methylation from 201516310047_R08C01

value: female

value: no


title: Genomic DNA methylation from 201516290038_R07C01


title: Genomic DNA methylation from 201516310047_R03C01


title: Genomic DNA methylation from 201516290038_R05C01


title: lung adenocarcinoma cells, aged KP mouse, rep 4, L002


title: lung adenocarcinoma cells, young KP mouse, rep 2, L003


title: lung adenocarcinoma cells, aged KP mouse, rep 3, L002


title: Genomic DNA methylation from 201516290038_R03C01


title: lung adenocarcinoma cells, young KP mouse, rep 7, L002


title: lung adenocarcinoma cells, young KP mouse, rep 6, L002


title: Genomic DNA methylation from 201516290038_R04C01


title: Genomic DNA methylation from 201516330029_R07C01


title: Genomic DNA methylation from 201516290036_R03C01


title: lung adenocarcinoma cells, young KP mouse, rep 3, L002


title: Genomic DNA methylation from 201516290036_R04C01


title: lung adenocarcinoma cells, aged KP mouse, rep 2, L002


title: lung adenocarcinoma cells, aged KP mouse, rep 1, L002


title: lung adenocarcinoma cells, young KP mouse, rep 3, L003


title: lung adenocarcinoma cells, aged KP mouse, rep 4, L001


title: Genomic DNA methylation from 201516290036_R02C01


title: Genomic DNA methylation from 201516290036_R01C01


title: Genomic DNA methylation from 201516290012_R08C01


title: Genomic DNA methylation from 201503670103_R04C01


title: lung adenocarcinoma cells, young KP mouse, rep 1, L002


title: lung adenocarcinoma cells, young KP mouse, rep 2, L002


title: Genomic DNA methylation from 201503670088_R06C01


title: Genomic DNA methylation from 201503670103_R01C01


title: Genomic DNA methylation from 201503670103_R05C01


title: lung adenocarcinoma cells, young KP mouse, rep 3, L001


title: Genomic DNA methylation from 201503670081_R02C01


title: lung adenocarcinoma cells, aged KP mouse, rep 3, L001


title: lung adenocarcinoma cells, aged KP mouse, rep 1, L001


title: Genomic DNA methylation from 201503670079_R08C01


title: lung adenocarcinoma cells, aged KP mouse, rep 2, L001


title: Genomic DNA methylation from 201503670079_R05C01


title: Genomic DNA methylation from 201503670068_R07C01


title: lung adenocarcinoma cells, young KP mouse, rep 2, L001


title: Genomic DNA methylation from 201503670068_R04C01


title: AT2, Aged male, batch 8_12

source_name: Primary lung tissue

value: Primary lung tissue

value: type 2 alveolar cells

value: wildtype


title: Genomic DNA methylation from 201503670068_R01C01


title: Genomic DNA methylation from 201503670061_R07C01


title: AT2, Aged male, batch 8_17


title: AT2, Young male, batch 8_12


title: lung adenocarcinoma cells, young KP mouse, rep 6, L001


title: Genomic DNA methylation from 201503670061_R02C01


title: lung adenocarcinoma cells, young KP mouse, rep 1, L001


title: lung adenocarcinoma cells, young KP mouse, rep 7, L001


title: Genomic DNA methylation from 201516290012_R04C01


title: Genomic DNA methylation from 201503670057_R08C01


title: AT2, Young male, batch 8_17


title: AT2, Aged male, batch 8_13


title: Genomic DNA methylation from 201503670061_R03C01


title: Genomic DNA methylation from 201503670056_R06C01


title: Genomic DNA methylation from 201503670056_R04C01


title: AT2, Young male, batch 8_13


title: RNA Pol II 500k frozen Rep2

city: Baltimore

first: Patricia

middle: J

last: Gearhart

state: Maryland

address: 251 Bayview Blvd, Rm 06009C

department: Laboratory of Molecular Biology and Immunology

institute: NIH/NIA

data_processing:
Demultiplexing using bcl2convert
Adapter trimming using trimgalore
Alignment using bowtie2
Duplicate marking and removal using SAMtools
Peak calling using MACS2
IDR analysis using idr
Assembly: GRCm39 (mm39)
Supplementary files format and content: BED files containing all mapped and QC'd reads are provided
Supplementary files format and content: Bedgraph files containing peak data are provided for non-IgG samples (IgG used as control for peak calling within experiments)
Library strategy: CUT&RUN

source_name: Splenic

growth_protocol: Primary B cells purified from mouse spleens were stimulated in RPMI 1640 supplemented with 10% FBS, 1% GlutaMAX, 1% Pen/Strep, 50 micromolar 2-me. Cells were cultured at 37C 5% CO2 for 48 hours

extract_protocol:
Cells were fixed with 0.1% formaldehyde for 1 minute and quenched with glycine. Nuclei were isolated and used for CUT&RUN modified for primary B cells
EpiCypher Library Prep Kit

value: Splenic

value: Follicular B cells

tag: antibody

value: RNA Polymerase II

tag: treatment

value: 48 hour stim w anti-CD40 and IL-4


title: AT2, Young female, batch 8_10


title: AT2, Aged female, batch 8_10


title: Genomic DNA methylation from 201503670056_R02C01


title: Genomic DNA methylation from 201503670055_R06C01


title: IgG 500k frozen Rep2

value: IgG


title: H3K4me3 500k frozen Rep2


title: Genomic DNA methylation from 201503670048_R07C01


title: RNA Pol II 250k frozen Rep2


title: IgG 250k frozen Rep2


title: Genomic DNA methylation from 201503670048_R06C01


title: H3K4me3 250k frozen Rep2


title: Genomic DNA methylation from 201503670041_R08C01


title: RNA Pol II 100k frozen Rep2


title: Genomic DNA methylation from 201503670041_R05C01


title: Genomic DNA methylation from 201503670041_R01C01


title: Genomic DNA methylation from 201503670057_R01C01


title: H3K4me3 100k frozen Rep2


title: IgG 100k frozen Rep2


title: Genomic DNA methylation from 201503670019_R08C01


title: Genomic DNA methylation from 201503670019_R06C01


title: Genomic DNA methylation from 201503670019_R04C01


title: RNA Pol II 500k fresh Rep1


title: IgG 500k fresh Rep1


title: RNA Pol II 250k fresh Rep1


title: Genomic DNA methylation from 201503670019_R03C01


title: Genomic DNA methylation from 201503670014_R06C01


title: Genomic DNA methylation from 201503670014_R02C01


title: RNA Pol II 100k fresh Rep2


title: Genomic DNA methylation from 201503670014_R01C01


title: Genomic DNA methylation from 201503670013_R01C01


title: Genomic DNA methylation from 201503670055_R05C01


title: Genomic DNA methylation from 201496850149_R03C01


title: H3K4me3 100k fresh Rep2


title: Genomic DNA methylation from 201503670048_R03C01


title: IgG 100k fresh Rep2


title: Genomic DNA methylation from 201496850149_R01C01


title: RNA Pol II 100k fresh Rep1


title: IgG 100k fresh Rep1


title: Genomic DNA methylation from 201496850066_R03C01


title: Genomic DNA methylation from 201496850066_R08C01


title: Genomic DNA methylation from 201496850066_R01C01


title: H3K4me3 500k fresh Rep1


title: RNA Pol II 500k frozen Rep1


title: Genomic DNA methylation from 201492570171_R06C01


title: RNA Pol II 250k frozen Rep1


title: H3K4me3 250k fresh Rep1


title: Genomic DNA methylation from 201492570171_R02C01


title: IgG 250k fresh Rep1


title: IgG 500k frozen Rep1


title: Genomic DNA methylation from 201496710183_R04C01


title: H3K4me3 500k frozen Rep1


title: Genomic DNA methylation from 201490020041_R04C01


title: RNA Pol II 100k frozen Rep1


title: Genomic DNA methylation from 201490020032_R08C01


title: Genomic DNA methylation from 201490020041_R06C01


title: H3K4me3 250k frozen Rep1


title: Genomic DNA methylation from 201490020032_R06C01


title: IgG 100k frozen Rep1


title: H3K4me3 100k frozen Rep1


title: Genomic DNA methylation from 201465860031_R08C01


title: Genomic DNA methylation from 201490020032_R03C01


title: Genomic DNA methylation from 201465860031_R05C01


title: RANKL+PRDX1_rep1

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

country: South Korea

institute: Chungbuk National University

library_source: transcriptomic

data_processing:
mRNA-Seq reads were mapped to reference mouse genome (mm10 assembly) using HISAT2 with default parameters.
RNA expression was quantified using analyzeRepeats.pl command in HOMER
DEGs was assessed with DESeq2 using getDiffExpression.pl in HOMER.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

source_name: Primary cells

growth_protocol: Bone marrow (BM) cells were collected by flushing femurs and tibias from 6- to 8-week-old C57BL/6 mice. Cells were cultured in α-minimum essential medium (α-MEM) supplemented with 10% FBS and M-CSF (5 ng/ml) for 16 h.  Non-adherent cells were harvested and cultured with M-CSF (30 ng/ml) for 3 days. Floating cells were removed and adherent cells were used as bone marrow-derived macrophage (BMM) cells.

extract_protocol:
Total RNA was isolated using the TRIzol reagent according to the manufacturer's instructinos.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Osteoclast precursor cells werecultured with or without RANKL (100ng/ml) in the presence or absence of PRDX1(200nM).

value: Primary cells

tag: strain

value: cultured with RANKL and treated with PRDX1


title: RANKL+PRDX1_rep2


title: RANKL_rep2

value: cultured with RANKL


title: H3K4me3 100k fresh Rep1


title: Genomic DNA methylation from 201465860028_R03C01


title: Genomic DNA methylation from 201465860028_R01C01


title: RANKL_rep1


title: PRDX1_rep2

value: treated with PRDX1


title: Genomic DNA methylation from 201465860027_R06C01

value: Blood DNA


title: IgG 250k frozen Rep1


title: Genomic DNA methylation from 201465860026_R07C01

value: male


title: Genomic DNA methylation from 201465860026_R04C01


title: Genomic DNA methylation from 201465860026_R02C01


title: MCSF_rep1

value: cultured with M-CSF


title: Genomic DNA methylation from 201465860026_R01C01


title: MCSF_rep2


title: scRNA-Seq_Mutant_1

city: Philadelphia

first: Ernestina

last: Schipani

state: PA

address: 310A Stemmler Hall, 3450 Hamilton Walk

department: McKay Orthopaedic Research Laboratory

institute: University of Pennsylvania

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Libraries were uniquely indexed using the Chromium Dual Index Kit, pooled, and sequenced on an Illumina NovaSeq 6000 sequencer using a paired-end, dual-indexing run strategy. Sequencing for each library aimed for 20,000 mean reads per cell. The data were then processed using the Cell Ranger pipeline (10x Genomics, version 6.1.2) for demultiplexing, alignment of sequencing reads to the mm10 mouse transcriptome, and generation of feature-barcode matrices.
Assembly: mm10
Supplementary files format and content: Processed files are the raw and filtered feature-barcode matrices in Hierarchical Data Format (HDF5, or H5) that are output from Cell Ranger (raw_feature_bc_matrix.h5 and filtered_feature_bc_matrix.h5). For more information, see the Cell Ranger documentation for ‘Outputs’:https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-outputs-overview.

source_name: Bone

extract_protocol:
scRNA-seq was performed on cells from the long bones of the hindlimbs in 12-week-old mice, sorted by FACS. Femurs were dissected free of muscle and connective tissues, with the ends trimmed to access the marrow cavity. Bone marrow stromal cells were harvested using a 27-gauge needle and a 10 mL syringe filled with Dulbecco's Phosphate-Buffered Saline (DPBS) (Gibco, Thermo Fisher) supplemented with 10% FBS (Hyclone). Cells were counted and diluted to approximately 15-20 x 10^6 cells/mL in suspension buffer, and Ai14-positive cells were sorted by FACS. A fluorescent-labeled negative control (PRX1-Cre-/-; Ai14-/-; HIF2f/f) was utilized to establish the gating threshold for the positively selected population. scRNA-seq was carried out using the 10X Genomics platform.
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent Kit v3 according to the manufacturer's instructions.

value: Bone

value: Bone Marrow Stromal cell

value: PRx1-Cre+/Ai14+/-/HIF2f/f mutant


title: Genomic DNA methylation from 201465850049_R03C01

value: no


title: scRNA-Seq_Control_2

description: 10X Genomics

value: PRx1-Cre+/Ai14+/-/HIF-/- control


title: Genomic DNA methylation from 201465850049_R02C01


title: Genomic DNA methylation from 201465850048_R07C01


title: CD326-negative from skin cells_Tag

city: Tokyo

first: Yoshitaka

last: Taketomi

address: 7-3-1 Hongo, Bunkyo-ku,

department: CDBIM, Graduate School of Medicine,

country: Japan

institute: The University of Tokyo

description: Tag

data_processing:
Fastq data preprocessing and generation of the single-cell gene-expression matrix was performed as described previously (Shichino et al. Commun Biol 5, 602, 2022).
The resultant dataset was analyzed using R software package Seurat v4.2.1133 in R 4.2.1.
We first calculating metrics (percent.mito, percent,ribo) and filtered out mitochondrial gene-high cells (over 0.25), doublets, and not-hashtag-assigned cells. Next, PCA analysis was performed against 6728 of highly-variable genes identified by FindVariableFeatures (selection.method=mvp, mean.cutoff=c(0.1, Inf), dispersion.cutoff=c(1, Inf)) function in Seurat v4.0.4 in R version 4.1.3 (2022-03-10). Cell clustering was performed by using FindNeighbors and FindClusters function in Seurat v4.0.4 in R version 4.1.3 (2022-03-10). 1:113 PCs were used for clustering analysis. Clustering resolution parameters were changed sequentially (from 1.0 to 3.5) and evaluate clustering stability by using silhouette score against FIt-SNE space. We use python implementation of FIt-SNE 1.1.1 (Linderman, et al. Nat Methods 16, 243-245, 2019) through reticulate package in R version 4.1.3 (2022-03-10) for visualizaiton of clustering result, because it is better than commonly-used UMAP method in terms of calculation speed and visualization. FIt-SNE parameters are as follows: perplexity=200 df=0.9. Tag assignment and Clustering results of each resolution parameters were shown separately in tabs. Next, we find out marker genes in each cell cluster defined in resolution 1 in parallel by using parallelized version of FindAllMarkers function in Seurat (test method = wilcox, minimum expression in each cluster >= 20%, only.pos=TRUE).
Because BD Rhapsody TAS-Seq data is non-UMI data (raw count data), we perform global normalization to 1M tags and perform scaling by using Seurat ScaleData function with regressing out library size (total raw read count of each cells) as a confounding factor.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw tag-count values for each sample

source_name: Ear skin

extract_protocol:
The ear skin was minced finely with scissors and resuspended in 2 ml of Accutase followed by incubation in a shaking incubator for 10 min at 37°C. The digests were centrifuged at 800 g for 3 min and the cell pellets were resuspended in Liberase solution consisting of 250 µg/ml Liberase TM and 2,000 units/ml DNase I in RPMI-1640 supplemented with 10 mM HEPES and 5% (v/v) fetal bovine serum followed by incubation in a shaking incubator for 30 min at 37°C. Procedure for the digestion with Liberase and DNase was repeated twice. The resulting cells were isolated by 25% (v/v) Percoll density gradient, and then filtered through a 40-µm cell strainer. The cells were isolated CD326-negative fraction by autoMACS.
Preparation of the scRNA-seq library was performed as described previously (Shichino et al. Commun Biol 5, 602, 2022). In brief, cells prepared from mouse skin were stained with BD Ms Single-Cell Multiplexing Kit (anti-mouse CD45, 30-F11) or Custom BD Single-Cell Multiplexing Set (anti-mouse MHC-H2 class I, M1/42). Obtained single-cell suspensions were subjected to a BD Rhapsody system with Targeted mRNA and AbSeq Amplification Kit following the manufacture’s instructions. Resultant beads were reverse transcribed, treated with exonuclease I, and subjected to TAS-Seq workflow for cDNA and hashtag library amplification. Ligand products were purified and performed barcording PCR. Size distribution of amplified products was analyzed by a MultiNA system (MCE-202). Resultant libraries and barcorded hastag libraries were quantified using KAPA Library Quantification Kit. Pooled libraries were sequenced on an Illumina NovaSeq 6000 sequencer with an Illumina NovaSeq 6000 S4 Reagent Kit v1.5. Two billion clusters, equivalent to 400 Gb/analysis, were obtained by pair-ended analysis of 100 bp of sequencing data.
BD Rhapsody

treatment_protocol: Abhd12b-/- and Abhd12b+/+ were subjected to a HClO-induced SSc model. Hypochlorous acid mixed with 100 mM potassium dihydrogen phosphate (pH 6.2) at 110:1 were administrated subcutaneously to the back of mice at a dose of 200 µl for 5 days/week and 20 µl/one ear twice/week for 6 weeks repeatedly.

value: Ear skin

value: Skin cells (CD326-negative)


title: PRDX1_rep1


title: scRNA-Seq_Control_1

description: 10X Genomics


title: Whole skin cells_Tag

description: Tag

value: Skin cells (Whole)


title: Genomic DNA methylation from 201465850047_R03C01

value: yes


title: Genomic DNA methylation from 201465850048_R04C01

value: female


title: Whole skin cells_cDNA

description: cDNA


title: GSDMD, IL1B and IL18, replicate 3

city: Ljubljana

first: Iva

last: Hafner Bratkovič

address: Hajdrihova 19

country: Slovenia

institute: National Institute of Chemistry (Slovenia)

data_processing:
RNAlysis 3.9.2: Sequence reads were trimmed for adaptor sequences using CutAdapt and aligned to mouse genome, version GRCm38/mm10, using Kallisto.
R: DESeq2 package was used for analysis of differential expression,
WebGestalt online server was used for over-representation analysis to determine non redundant gene ontology terms, describing biological processes
Assembly: GRCm38/mm10
Supplementary files format and content: DESeq_normalizeddata.txt: tab-delimited file includes DESEq2 normalized counts for each sample

source_name: B16F10 Red F-luc melanoma tumor model, electroporated with plasmid DNA

extract_protocol:
Total RNA was extracted from the fresh tumors using TriPure Isolation Reagent (Roche), following the manufacturer's protocol.
Azenta Life Sciences (Genewiz, Leipzig) performed sample quality control, library preparation and rRNA removal by polyA selection for mRNA species.

value: C57BL/6J OlaHSd

value: electroporation with NT GSDMD and IL-1β and IL-18


title: Genomic DNA methylation from 201465850041_R07C01


title: CD326-negative from skin cells_cDNA

description: cDNA


title: Genomic DNA methylation from 201465850048_R01C01


title: GSDMD, IL1B and IL18, replicate 2

value: B16F10 Red F-luc melanoma tumor model, electroporated with plasmid DNA


title: Genomic DNA methylation from 201465850041_R01C01


title: GSDMD, IL1B and IL18, replicate 1


title: GSDMD and IL18, replicate 3

value: electroporation with NT GSDMD and IL-18


title: Genomic DNA methylation from 201465850012_R07C01

value: Blood DNA


title: scRNA-Seq_Mutant_2

description: 10X Genomics


title: Genomic DNA methylation from 201465850049_R04C01

value: male


title: Genomic DNA methylation from 201465850012_R04C01


title: Genomic DNA methylation from 201465850012_R03C01


title: GSDMD and IL18, replicate 2


title: GSDMD and IL12, replicate 3

value: electroporation with NT GSDMD and IL-12


title: Genomic DNA methylation from 201465850006_R04C01


title: GSDMD and IL18, replicate 1


title: GSDMD and IL12, replicate 2


title: Genomic DNA methylation from 201465850006_R03C01


title: Genomic DNA methylation from 201465850005_R07C01


title: GSDMD and IL1B, replicate 3

value: electroporation with NT GSDMD and IL-1β


title: GSDMD and IL12, replicate 1


title: Genomic DNA methylation from 201465850005_R03C01


title: GSDMD and IL1B, replicate 2


title: Genomic DNA methylation from 201465850005_R04C01


title: Genomic DNA methylation from 201465850004_R04C01


title: Genomic DNA methylation from 201465850041_R03C01


title: Genomic DNA methylation from 201465850004_R01C01


title: Gasdermin, replicate 3

value: electroporation with NT GSDMD


title: Genomic DNA methylation from 201465840058_R08C01


title: GSDMD and IL1B, replicate 1


title: Genomic DNA methylation from 201465840058_R07C01


title: Control, replicate 3

value: electroporation with empty vector


title: Gasdermin, replicate 2


title: Genomic DNA methylation from 201465840058_R05C01

value: no


title: Control, replicate 1


title: Control, replicate 2


title: Genomic DNA methylation from 201465840058_R04C01


title: Genomic DNA methylation from 201465840053_R07C01


title: Genomic DNA methylation from 201465840053_R04C01


title: MC38 tdLN, triplet LNP treated

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description:
10x Genomics
Metadata_Full_dataset_tdLN_triplet.LNP_ntrIL21_TBS_merged.csv
Metadata_T.subset_tdLN_triplet.LNP_ntrIL21_TBS_merged.csv
Metadata_DC.subset_tdLN_triplet.LNP_ntrIL21_TBS_merged.csv

data_processing:
Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: mm10
Supplementary files format and content: Compressed .tar.gz files containing raw UMI counts in Cellranger output format and comma-delimited text files including metadata per cell

source_name: tumor draining lymph node

extract_protocol: All methods listed in Hamouda et al. Intratumoral administration of lipid nanoparticles carrying mRNA encoding for IL-21, IL-7, and 4-1BBL induces anti-tumor immunity in preclinical tumor models.

value: tumor draining lymph node

value: CD45+ cells

value: Triplet LNP


title: MC38 tdLN, ntrIL21 LNP treated


title: MC38 tdLN, TBS treated

value: TBS


title: Genomic DNA methylation from 201465840053_R02C01


title: Genomic DNA methylation from 201465850006_R02C01


title: MC38 tumor, triplet LNP treated

description:
10x Genomics
Metadata_Full_dataset_Tumor_triplet.LNP_ntrIL21_TBS_merged.csv
Metadata_CD8T.and.CD4T.subset_Tumor_triplet.LNP_ntrIL21_TBS_merged.csv
Metadata_DC.subset_Tumor_triplet.LNP_ntrIL21_TBS_merged.csv
Metadata_Neutrophils.subset_Tumor_triplet.LNP_ntrIL21_TBS_merged.csv
Metadata_TAM.and.monocyte.subset_Tumor_triplet.LNP_ntrIL21_TBS_merged.csv

source_name: subcutaneous MC38 tumor

value: subcutaneous MC38 tumor


title: Gasdermin, replicate 1


title: Genomic DNA methylation from 201465840052_R05C01


title: MC38 tumor, ntrIL21 LNP treated

value: female


title: Genomic DNA methylation from 201465840052_R07C01


title: Basal cell P13, Duct 2

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

institute: Université Libre de Bruxelles

data_processing:
Reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR software to generate read alignments for each sample.
Annotations for Mus_musculus.GRCm38.87.gtf were obtained from ftp.Ensembl.org.
After transcripts assembling, gene level counts were obtained using HTseq and normalized to 20 millions of aligned reads.
Assembly: mm10/Grcm38.87
Supplementary files format and content: .csv / normalised gene expression

source_name: prostate

extract_protocol:
RNA extraction from FACS isolated cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer ́s recommendations.
Indexed cDNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’s recommendations.

value: prostate

value: tip, ventral lobe

tag: age

value: Male


title: MC38 tumor, TBS treated


title: Genomic DNA methylation from 201465840035_R03C01


title: Basal cell P13, Duct 1


title: Basal cell P13, Tip 2


title: Genomic DNA methylation from 201465840035_R04C01


title: Basal cell P13, Tip 1


title: Genomic DNA methylation from 201465840034_R06C01


title: Genomic DNA methylation from 201465840034_R02C01


title: MATR and SOFT, HTO

description: 10X genomics, cell hashing

data_processing:
Sequencing reads were aligned and annotated with the mm10-2020-A reference dataset as provided by 10X Genomics and demultiplexed using CellRanger (v.5.0.0)
Data was demultiplexed based on data from cell hashing, by the function HTODemux() included in Seurat R package (v.4.2.0) with parameter ‘positive.quantile = 0.99’. Further downstream analyses were carried out individually for each of the four samples (MATR, SOFT, COL1 and STIFF).
Quality control and downstream analysis were performed using the Seurat R package (v.4.2.0). For each sample, all the cells passed the following criteria: showed expression of more than 2000 and less than 7000 unique genes and had less than 10% UMI counts belonging to mitochondrial sequences.
Read counts were normalized using the NormalizeData() function of Seurat, with parameter ‘normalization.method = "LogNormalize" and scale.factor=10000’. A PCA for each sample was calculated using the scaled expression data of the 2000 most variable genes (identified as outliers on a mean/variability plot, implemented in the FindVariableGenes() function).
UMAP calculation and graph-based clustering were performed for each sample using Seurat (default parameters) with the respective 30 PCA results as input.
Assembly: mm10-2020-A
Supplementary files format and content: .mtx / gene expression matrix
Supplementary files format and content: .tsv / genes and cell barcode
Library strategy: scRNA-seq, HTO cell hashing

source_name: mammary gland

extract_protocol:
Single cells from the mammary gland organoid from Matrigel (MATR), soft (SOFT), collagen (COL1) and stiff (STIFF) condition were dissociated.
Dissociated cells were labelled with TotalSeq-A hashtag oligonucleotide (HTO) antibodies. Matrigel and soft, collagen and stiff were pooled and loaded onto each channel of the Chromium Single Cell 3′ microfluidic chips (V2- chemistry, PN-120232, 10X Genomics) and barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics). RNA from the barcoded cells was subsequently reverse transcribed, followed by amplification, shearing 5′ adaptor and sample index attachment. The libraries were prepared using the Chromium Single Cell 3′ Library Kit (V3-chemistry, PN-120233, 10X Genomics) and sequenced on an Illumina Novaseq 6000 (paired-end 100bp reads).

value: mammary gland

tag: group

value: soft


title: Genomic DNA methylation from 201465840034_R03C01

value: Blood DNA

value: male


title: COL1 and STIFF, HTO

description: 10X genomics, cell hashing

value: stiff


title: Genomic DNA methylation from 201465840027_R03C01


title: Genomic DNA methylation from 201465840021_R06C01


title: Genomic DNA methylation from 201465840020_R01C01


title: clpC6xH_+aTc_#3

city: OMaha

first: Scot

middle: P.

last: Ouellette

state: Nebraska

address: 985900 Nebraska Medical Center

department: Pathology, Microbiology, and Immunology

institute: University of Nebraska Medical Center

description: ClpC is over-expressed.

data_processing:
The original fastq format reads were trimmed by fqtirm tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30).
The trimmed fastq files were processed by FastQC (Andrews S. (2010).
FastQC: a quality control tool for high throughput sequence data; available online at http://www.bioinformatics.babraham.ac.uk/projects/fastqc for quality control.
Assembly: Chlamydia trachomatis 434/Bu bacterial reference genome and annotation files were downloaded from Ensembl (http://bacteria.ensembl.org/Chlamydia_trachomatis_434_bu/Info/Index).
Supplementary files format and content: Excel file showing fold changes and statistical significance between uninduced and induced conditions

organism: Chlamydia trachomatis

source_name: Infected human HeLa cell line

growth_protocol: HeLa cells were infected with C. trachomatis L2. Samples were collected at 18. The infected cells were grown in 1X DMEM containing 10% FBS, 10 ug gentamycin, and 500 ug/mL spectinomycin at 37 celcius degree in 5% CO2

extract_protocol:
Total RNA was collected from C. trachomatis infected cell cultures using Trizol. Total RNA was DNased then further purified to remove rRNA using MicrobEnrich, MicrobExpress.
the Illumina Stranded Total RNA Prep protocol

treatment_protocol: 20 nM inducer (Anhydrotetracycline) was treated or not at 10 hpi.

tag: cell line

value: Infected human HeLa cell line

value: Induced with 20 nM aTc for 8 h (in DMEM)


title: clpC6xH_+aTc_#1

description: ClpC is over-expressed.

value: Uninduced condition (in DMEM)


title: Genomic DNA methylation from 201465840021_R02C01

value: no


title: Genomic DNA methylation from 201465840019_R08C01


title: clpC6xH_-aTc_#3

description: Normal Developmental Cycle


title: clpC6xH_+aTc_#2

description: ClpC is over-expressed.


title: MATR and SOFT, GEX

description: 10X genomics, cell hashing


title: Genomic DNA methylation from 201465840019_R07C01


title: clpC6xH_-aTc_#2

description: Normal Developmental Cycle


title: Genomic DNA methylation from 201465840052_R04C01


title: Genomic DNA methylation from 201465840052_R02C01


title: COL1 and STIFF, GEX

description: 10X genomics, cell hashing


title: Genomic DNA methylation from 201465840019_R02C01

value: yes


title: Genomic DNA methylation from 201005080132_R06C01


title: Genomic DNA methylation from 201005080131_R08C01


title: Genomic DNA methylation from 9980102107_R06C02


title: Genomic DNA methylation from 201005080131_R03C01


title: Genomic DNA methylation from 9980102107_R05C02


title: Genomic DNA methylation from 9980102107_R05C01


title: Genomic DNA methylation from 201465840019_R06C01


title: Genomic DNA methylation from 9980102107_R04C02


title: Genomic DNA methylation from 201005080126_R06C01


title: Genomic DNA methylation from 201005080131_R01C01


title: Genomic DNA methylation from 9980102107_R04C01


title: Genomic DNA methylation from 9980102107_R03C02


title: clpC6xH_-aTc_#1

description: Normal Developmental Cycle


title: Genomic DNA methylation from 9980102107_R01C02


title: Genomic DNA methylation from 201005080126_R01C01


title: Genomic DNA methylation from 201005080123_R07C01


title: Genomic DNA methylation from 201465840014_R04C01


title: Genomic DNA methylation from 201005080123_R05C01


title: Genomic DNA methylation from 201414140048_R06C01


title: Genomic DNA methylation from 9980102107_R02C02


title: Genomic DNA methylation from 201005080123_R04C01


title: Genomic DNA methylation from 201005080132_R07C01


title: Genomic DNA methylation from 9980102075_R03C02


title: Genomic DNA methylation from 9980102075_R02C02


title: Genomic DNA methylation from 201005080123_R02C01


title: BC transplant 2

type: RNA

hyb_protocol: Affymetrix MG-430 PM array strips were hybridized with 8 mg of labeled cDNA, washed, stained and scanned according to the protocol described in GeneAtlas 3’IVT express kit User Manual.

scan_protocol: Arrays were scanned with GeneAtlasImaging station scanner (Affymetrix, Santa Clara, CA)

data_processing: All the results were normalized using the RMA normalization algorithm using R-bioconductor affy package with standard parameters. Cross experiment normalization was further performed to eliminate the batch effect using non-parametric empirical Bayes frameworks for adjusting data implemented in ComBat  function of the Surrogate Variable Analysis package (SVA) in R-bioconductor

label: Biotin

source_name: Transplanted BC

label_protocol: cDNA was labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: Mice were maintained in a certified animal house according to European guidelines

extract_protocol: Cells were sorted after 3 days of transplantation and 50 cells were used for RNA extraction. RNA extraction was performed using Absolutely RNA Nanoprep kit (Stratagene) according to the manufacturer’s recommendations.

treatment_protocol: For the transplantation of mammary gland cells, we prepared 10,000 BC cells only as multipotent condition and mixture of 8000 LC cells and 2000 BC cells as unipotent control condition.

value: Transplanted BC


title: Genomic DNA methylation from 9980102075_R01C02


title: Control 1

source_name: Transplanted BC and LC mixture

value: Transplanted BC and LC mixture


title: Genomic DNA methylation from 201005010152_R03C01


title: BC transplant 1


title: Genomic DNA methylation from 201005010152_R01C01


title: Genomic DNA methylation from 9980102044_R05C02


title: Genomic DNA methylation from 201005010152_R04C01


title: Genomic DNA methylation from 201005080126_R02C01


title: Genomic DNA methylation from 9980102044_R04C01


title: Control 2


title: Genomic DNA methylation from 9980102044_R03C01


title: Genomic DNA methylation from 201005010096_R08C01


title: Genomic DNA methylation from 9980102044_R02C02


title: Genomic DNA methylation from 201005010096_R07C01


title: Genomic DNA methylation from 201005010096_R03C01


title: Genomic DNA methylation from 9980102020_R06C01


title: Genomic DNA methylation from 9980102044_R01C02


title: Genomic DNA methylation from 201005010095_R03C01


title: Genomic DNA methylation from 201005010091_R06C01


title: Genomic DNA methylation from 201005010091_R08C01


title: Genomic DNA methylation from 201005010091_R03C01


title: Genomic DNA methylation from 201005010095_R06C01


title: Genomic DNA methylation from 9980102020_R01C01


title: Genomic DNA methylation from 9980102020_R04C02


title: Genomic DNA methylation from 9980102020_R04C01


title: Genomic DNA methylation from 9980102044_R06C02


title: Genomic DNA methylation from 9980102002_R03C02


title: Genomic DNA methylation from 9980102002_R05C02


title: Genomic DNA methylation from 201005010001_R06C01


title: Genomic DNA methylation from 201005010001_R01C01


title: Genomic DNA methylation from 9980102002_R04C02


title: Genomic DNA methylation from 201005010091_R02C01


title: Genomic DNA methylation from 201004820122_R07C01


title: Genomic DNA methylation from 9980102002_R03C01


title: Genomic DNA methylation from 9980092137_R06C02


title: Genomic DNA methylation from 9980092137_R04C01


title: Genomic DNA methylation from 201004820096_R07C01


title: Genomic DNA methylation from 201005010037_R08C01


title: Genomic DNA methylation from 9980092137_R03C01


title: Genomic DNA methylation from 9980092137_R03C02


title: Genomic DNA methylation from 201005010037_R07C01


title: Genomic DNA methylation from 201004820096_R03C01


title: Genomic DNA methylation from 9980092137_R02C02


title: Genomic DNA methylation from 9969489161_R04C02


title: Genomic DNA methylation from 201004220210_R06C01


title: Genomic DNA methylation from 9969489161_R03C02


title: Genomic DNA methylation from 201004820059_R03C01


title: Genomic DNA methylation from 9980092137_R05C02


title: Genomic DNA methylation from 9980092137_R01C02


title: Genomic DNA methylation from 201004820059_R05C01


title: Genomic DNA methylation from 201004220194_R02C01


title: Genomic DNA methylation from 201004220210_R02C01


title: Genomic DNA methylation from 201004220189_R06C01


title: Genomic DNA methylation from 201004220195_R01C01


title: Genomic DNA methylation from 201004220189_R03C01


title: Genomic DNA methylation from 201004820059_R01C01


title: Genomic DNA methylation from 9969489158_R03C01


title: Genomic DNA methylation from 9969489161_R06C02


title: Genomic DNA methylation from 9969489161_R02C02


title: Genomic DNA methylation from 201004220194_R04C01


title: Genomic DNA methylation from 9969489158_R06C02


title: Genomic DNA methylation from 9969489158_R05C02


title: Genomic DNA methylation from 9969489158_R05C01


title: Genomic DNA methylation from 201004220189_R04C01


title: Genomic DNA methylation from 201004220165_R01C01


title: Genomic DNA methylation from 9969489158_R04C02


title: Genomic DNA methylation from 201004220170_R07C01


title: Genomic DNA methylation from 9969489158_R02C01


title: Genomic DNA methylation from 9969489156_R03C02


title: Genomic DNA methylation from 9969489161_R01C02


title: Genomic DNA methylation from 9969489156_R04C02


title: Genomic DNA methylation from 201004220163_R03C01


title: Genomic DNA methylation from 9969489158_R01C02


title: Genomic DNA methylation from 201004220165_R08C01


title: Genomic DNA methylation from 201004220163_R01C01


title: Genomic DNA methylation from 201004220165_R02C01


title: Genomic DNA methylation from 9969489155_R06C02


title: Genomic DNA methylation from 201004220170_R04C01


title: Genomic DNA methylation from 9969489156_R01C02


title: Genomic DNA methylation from 9969489155_R06C01


title: Genomic DNA methylation from 9969489156_R06C01


title: Genomic DNA methylation from 201004220160_R05C01


title: Genomic DNA methylation from 9969489155_R05C02


title: Genomic DNA methylation from 201004220163_R07C01


title: Genomic DNA methylation from 201004220160_R04C01


title: Genomic DNA methylation from 201004220160_R07C01


title: Genomic DNA methylation from 201004220160_R08C01


title: Genomic DNA methylation from 201004220159_R05C01


title: Genomic DNA methylation from 9969489158_R01C01


title: Genomic DNA methylation from 9969489155_R04C01


title: Genomic DNA methylation from 9969489155_R04C02


title: Genomic DNA methylation from 9969489155_R05C01


title: Genomic DNA methylation from 9969489155_R03C02


title: Genomic DNA methylation from 201004220159_R01C01


title: Genomic DNA methylation from 9969489155_R03C01


title: Genomic DNA methylation from 201004220159_R03C01


title: Genomic DNA methylation from 9969489155_R02C01


title: Genomic DNA methylation from 201004220158_R06C01


title: Genomic DNA methylation from 201004220158_R05C01


title: Genomic DNA methylation from 9969489155_R02C02


title: Genomic DNA methylation from 9969489155_R01C02


title: Genomic DNA methylation from 201004220158_R02C01


title: Genomic DNA methylation from 9969489155_R01C01


title: Genomic DNA methylation from 201004220144_R06C01


title: Genomic DNA methylation from 9969489154_R06C02


title: Genomic DNA methylation from 9969489154_R05C01


title: Genomic DNA methylation from 9969489154_R04C01


title: Genomic DNA methylation from 9969489154_R03C01


title: Genomic DNA methylation from 9969489154_R02C02


title: Genomic DNA methylation from 9969489154_R01C02


title: Genomic DNA methylation from 9969489137_R06C02


title: Genomic DNA methylation from 9969489137_R05C02


title: Genomic DNA methylation from 9969489137_R04C02


title: Genomic DNA methylation from 201004220194_R03C01


title: Genomic DNA methylation from 9969489137_R04C01


title: Genomic DNA methylation from 201004220158_R01C01


title: Genomic DNA methylation from 201004220140_R04C01


title: Genomic DNA methylation from 201004220144_R05C01


title: Genomic DNA methylation from 201004220130_R07C01


title: Genomic DNA methylation from 201004220140_R06C01


title: Genomic DNA methylation from 201004220119_R06C01


title: Genomic DNA methylation from 201004220144_R03C01


title: Genomic DNA methylation from 201004220130_R02C01


title: Genomic DNA methylation from 201004220140_R07C01


title: Genomic DNA methylation from 201004220119_R07C01


title: Genomic DNA methylation from 201004220132_R01C01


title: Genomic DNA methylation from 9969489154_R06C01


title: Genomic DNA methylation from 9969489137_R03C02


title: Genomic DNA methylation from 9969489137_R03C01


title: Genomic DNA methylation from 201004220118_R03C01


title: Genomic DNA methylation from 201004220119_R05C01


title: Genomic DNA methylation from 201004220119_R02C01


title: Genomic DNA methylation from 9969489137_R02C02


title: Genomic DNA methylation from 201004220118_R07C01


title: Genomic DNA methylation from 201004220132_R02C01


title: Genomic DNA methylation from 9969489137_R02C01


title: Genomic DNA methylation from 201004220118_R02C01


title: Genomic DNA methylation from 9969489116_R06C01


title: Genomic DNA methylation from 9969489116_R05C01


title: Genomic DNA methylation from 9969489116_R04C01


title: Genomic DNA methylation from 201004220117_R08C01


title: Genomic DNA methylation from 201004220117_R04C01


title: Genomic DNA methylation from 9969489116_R03C01


title: Genomic DNA methylation from 9969489092_R06C01


title: Genomic DNA methylation from 9969489092_R06C02


title: Genomic DNA methylation from 201004220117_R01C01


title: Genomic DNA methylation from 9969489092_R04C02


title: Genomic DNA methylation from 201004220116_R07C01


title: Genomic DNA methylation from 9969489065_R06C02


title: Genomic DNA methylation from 201004220102_R05C01


title: Genomic DNA methylation from 201004220116_R05C01


title: Genomic DNA methylation from 9969489092_R01C02


title: Genomic DNA methylation from 201004220117_R02C01


title: Genomic DNA methylation from 201004220116_R08C01


title: Genomic DNA methylation from 9969489065_R06C01


title: Genomic DNA methylation from 201004220100_R03C01


title: Genomic DNA methylation from 201004220102_R03C01


title: Genomic DNA methylation from 201004220102_R07C01


title: Genomic DNA methylation from 9969489065_R05C02


title: Genomic DNA methylation from 201004220078_R05C01


title: Genomic DNA methylation from 9969489065_R04C02


title: Genomic DNA methylation from 201004220073_R04C01


title: Genomic DNA methylation from 201004220092_R07C01


title: Genomic DNA methylation from 9969489065_R04C01


title: Genomic DNA methylation from 9969489065_R03C02


title: Genomic DNA methylation from 9969489065_R02C02


title: Genomic DNA methylation from 200999660202_R08C01


title: Genomic DNA methylation from 200999660192_R08C01


title: Genomic DNA methylation from 9969489092_R02C01


title: Genomic DNA methylation from 9969489033_R06C02


title: Genomic DNA methylation from 200999660192_R03C01


title: Genomic DNA methylation from 200999660192_R04C01


title: Genomic DNA methylation from 9969489033_R06C01


title: Genomic DNA methylation from 200999660184_R05C01


title: Genomic DNA methylation from 9969489065_R05C01


title: Genomic DNA methylation from 200999660191_R07C01


title: Genomic DNA methylation from 9969489033_R03C02


title: Genomic DNA methylation from 9969489092_R01C01


title: Genomic DNA methylation from 9969489033_R03C01


title: Genomic DNA methylation from 200999660177_R05C01


title: Genomic DNA methylation from 9969489033_R04C02


title: Genomic DNA methylation from 9969489009_R06C02


title: Genomic DNA methylation from 9969489033_R04C01


title: Genomic DNA methylation from 9969489009_R04C01


title: Genomic DNA methylation from 9969489009_R03C02


title: Genomic DNA methylation from 200999660177_R04C01


title: Genomic DNA methylation from 9969489033_R05C01


title: Genomic DNA methylation from 200999660165_R04C01


title: Genomic DNA methylation from 200999660177_R03C01


title: Genomic DNA methylation from 200999660032_R04C01


title: Genomic DNA methylation from 200999660202_R01C01


title: Genomic DNA methylation from 9969489007_R06C01


title: Genomic DNA methylation from 9969489009_R02C01


title: Genomic DNA methylation from 9969489009_R03C01


title: Ro998 lung  FFPE slice

city: Milan

first: Filippo

last: Pietrantonio

address: Via Venezian, 1

department: Medical Oncology

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori

data_processing:
Auristone EPI-Call platform v2.0.0
Reads were trimmed and quality checked using Trim-Galore v0.6.7
Reads were aligned using STAR v2.7.10a
Read count extraction performed using RSEM v1.3.3
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: lung

extract_protocol:
RNA was harvested using RNeasy FFPE kit (Qiagen).
RNA libraries for RNA-seq were prepared using Ultra II Directional RNA Library Prep Kit (NEBNext).

value: lung


title: Ro970 sigma-rectum FFPE slice

source_name: sigma-rectum

value: sigma-rectum


title: Genomic DNA methylation from 9969489007_R05C02

value: female


title: Ro961 ileum-colon, FFPE slice

source_name: ileum-colon

value: ileum-colon


title: Genomic DNA methylation from 9969489007_R04C02

source_name: Blood DNA


title: Ro954 ileum, FFPE slice

source_name: ileum

value: ileum


title: Genomic DNA methylation from 200999660184_R04C01


title: Genomic DNA methylation from 200999660184_R02C01


title: Genomic DNA methylation from 9969489007_R03C02


title: Genomic DNA methylation from 9969489007_R03C01


title: Ro901 sigma, FFPE slice

source_name: sigma

value: sigma


title: Ro859 colon FFPE slice

source_name: colon

value: colon


title: Ro813 lung FFPE slice


title: Genomic DNA methylation from 9969489006_R06C01

value: Blood DNA


title: Genomic DNA methylation from 9969489006_R06C02

value: male


title: Ro805 liver FFPE slice

source_name: liver

value: liver


title: Genomic DNA methylation from 9969489006_R05C02


title: Ro798 colon, FFPE slice


title: Genomic DNA methylation from 9969489006_R05C01


title: Ro753 liver, FFPE slice


title: Ro774 uterine cervix, FFPE slice

source_name: uterine cervix

value: uterine cervix


title: Ro695 liver, FFPE slice


title: Genomic DNA methylation from 9969489005_R05C02


title: Ro583 colon-rectum, FFPE slice

source_name: colon-rectum

value: colon-rectum


title: Genomic DNA methylation from 9969489005_R03C02


title: Ro540 colon, FFPE slice


title: Genomic DNA methylation from 9969489005_R04C02


title: Genomic DNA methylation from 9969489005_R06C01


title: Genomic DNA methylation from 9969489007_R04C01


title: Genomic DNA methylation from 9969489005_R03C01


title: Ro511 ovary, FFPE slice

source_name: ovary

value: ovary


title: Genomic DNA methylation from 9969489005_R02C02

value: no


title: Ro406 lung  FFPE slice


title: Ro487 colon, FFPE slice


title: Ro473 lung FFPE slice


title: Genomic DNA methylation from 9969489002_R04C02


title: Genomic DNA methylation from 9969489005_R02C01


title: Ro392 rectum FFPE slice

source_name: rectum

value: rectum


title: Ro366 lung  FFPE slice


title: Genomic DNA methylation from 9969489002_R01C02


title: Ro363 ileum-colon FFPE slice


title: Genomic DNA methylation from 9969489002_R04C01


title: Genomic DNA methylation from 9969477167_R04C01


title: Genomic DNA methylation from 9969477167_R06C02


title: Genomic DNA methylation from 9969489007_R02C01


title: Genomic DNA methylation from 9969477167_R05C01


title: H1944.MPS1i.rep2

first: Shunsuke

last: Kitajima

address: 3-8-31 Ariake, Koto

institute: Japanese Foundation for Cancer Research

data_processing:
NCI-H647: Raw reads were trimmed and quality-filtered using the Trim Galore, Trimmomatic, and cutadapt software.Trimmed reads were then mapped to the human GRCh38 genome using STAR.Reads on annotated genes were counted using featureCounts.
NCI-H1944: Raw reads were trimmed using  Trimmomatic. Trimmed reads are mapped to the human GRCh38 genome with HISAT2. Transcript is assembled by StringTie with aligned reads.
Assembly: hg38
Supplementary files format and content: A tab-delimited text file includes raw read counts.

growth_protocol: NCI-H1944 and NCI-H647 cells were cultured in RPMI 1640 supplemented with 10% FBS, 1x penicillin-streptomycin, and 2.5 μg/ml plasmocin prophylactic.

extract_protocol:
RNA extraction was performed using QIAGEN RNeasy Mini Kit and RNase-Free DNase Set.
NCI-H647: Libraries were prepared using QIAseq FastSelect -rRNA HMR Kit , QIAseq Stranded RNA Lib Kit UDI, and DNBSEQ MGIEasy Universal Library Conversion Kit according to the manufacturer’s instruction. NCI-H1944: Libraries were prepared using TruSeq stranded mRNA LT Sample Prep Kit according to the manufacturer’s instruction.

treatment_protocol: Cells were treated with MPS1i (100 nM, BAY-1217389), or DMSO as a control, for 48 hr, washed out the drug, and then cultured for 24 hr.

value: WT


title: H1944.DMSO.rep2

value: DMSO


title: Genomic DNA methylation from 9969489002_R03C01


title: H1944.MPS1i.rep1


title: Ro520 lung, FFPE slice

value: lung


title: H1944.DMSO.rep1


title: Genomic DNA methylation from 9969477167_R02C01


title: Genomic DNA methylation from 9969477167_R03C01


title: Genomic DNA methylation from 9969477167_R02C02


title: Onda-11 cells, CTRL, Replicate 5

first: Nereo

last: Kalebic

address: V.le Rita Levi-Montalcini, 1

institute: Human Technopole

data_processing:
Raw fastq were processed using nf-core pipeline for RNA-Seq version 3.11.2
Assembly: GRCh38
Supplementary files format and content: salmon_merged_counts.tsv: tab delimited file containing raw counts merged with Salmon
Supplementary files format and content: rlog_normalized_counts.csv: comma separated file containing regularized log-transformed counts data
Supplementary files format and content: DESeq2_output.csv: comma separated value file output of DESeq2 analysis

source_name: Brain

growth_protocol: Glioblastoma stem cell culture

extract_protocol:
SMART-Seq® v4 Ultra® Low Input RNA Kit 860 for Sequencing (Takara)
Read configuration: 150x10x10x150

treatment_protocol: ADD3 overexpression

value: Brain

value: Onda-11 GSC

value: CTRL

value: GSC culture


title: Genomic DNA methylation from 9611518097_R05C01


title: Onda-11 cells, ADD3 OE, Replicate 4

value: ADD3 OE


title: Genomic DNA methylation from 9611518097_R04C02

value: female


title: Onda-11 cells, ADD3 OE, Replicate 5


title: Onda-11 cells, CTRL, Replicate 4


title: Ro204 ileum FFPE slice

value: ileum


title: Onda-11 cells, CTRL, Replicate 3


title: Genomic DNA methylation from 9611518097_R06C02

value: Blood DNA

value: male


title: Genomic DNA methylation from 9611518097_R04C01


title: Onda-11 cells, ADD3 OE, Replicate 2


title: Onda-11 cells, CTRL, Replicate 2


title: Genomic DNA methylation from 9611518097_R03C01


title: Genomic DNA methylation from 9611518097_R02C01


title: Onda-11 cells, CTRL, Replicate 1


title: Genomic DNA methylation from 9611518097_R02C02


title: Genomic DNA methylation from 9611518097_R01C02


title: Onda-11 cells, ADD3 OE, Replicate 1


title: Genomic DNA methylation from 9611518063_R06C02


title: Genomic DNA methylation from 9611518097_R01C01


title: Genomic DNA methylation from 9611518063_R06C01


title: VB5, Mock, scRNAseq

city: Stanford

first: Jiaying

last: Toh

state: California

address: 1201 Welch Road

institute: Stanford University

description: 10x Chromium

data_processing:
Reads from 10x scRNA expression libraries were aligned to human genome assembly GRCh38 (hg19) and quantified using CellRanger count (10x Genomics).
Assembly: GRCh38 (hg19)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spontaneous lymphoblastoid cell line from EBV(+) B cell PTLD

growth_protocol: All cell lines were cultured in RPMI-1640 supplemented with 10% (v/v) heat-inactivated fetal bovine serum and 1% (v/v) Glutamax at 37°C with 5% CO2.

extract_protocol:
Freshly harvested cells from culture were washed in ice-cold culture medium. Cell viability was verified to be above 85% for all cell lines.
scRNAseq libraries were constructed using the Chromium Next GEM Single Cell 3' Reagent Kit (v3.1). 10,000 cells were loaded per lane. Sequencing was performed using an Illumina NovaSeq 6000.

value: B cell

value: Mock


title: JB7, Mock, scRNAseq

description: 10x Chromium

value: Spontaneous lymphoblastoid cell line from EBV(+) B cell PTLD


title: Genomic DNA methylation from 9611518097_R06C01

value: no


title: JB7, CD300A KO, scRNAseq

description: 10x Chromium

value: CD300A KO


title: Genomic DNA methylation from 9611518063_R05C01


title: Onda-11 cells, ADD3 OE, Replicate 3


title: Genomic DNA methylation from 9611518063_R04C02


title: AB5, Mock, scRNAseq

description: 10x Chromium

value: WT


title: Genomic DNA methylation from 9611518063_R04C01


title: AB5, CD300A KO, scRNAseq

description: 10x Chromium


title: Genomic DNA methylation from 9611518062_R05C01


title: Genomic DNA methylation from 9611518062_R06C01


title: VB5, CD300A KO, scRNAseq

description: 10x Chromium


title: Genomic DNA methylation from 9611518063_R03C02


title: Genomic DNA methylation from 9611518062_R04C01


title: Genomic DNA methylation from 9611518063_R01C02


title: MON(CuMn)-Q2

city: wuhan

first: zixuan

last: Ou

state: hubei

address: 1277 Liberation Avenue, Kong Hon

department: Tongji Medical College

country: China

institute: Huazhong University of Science and Technology

description: treatment 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to gossypium hirsutum using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes differential expression genes between Control and CuT_Que

source_name: bone marrow

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775L) was used with 0.4 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: bone marrow

value: hBMSCs

value: MON(CuMn)-Q


title: MON(CuMn)-Q3

description: treatment 3


title: Control3

description: control 3

value: control


title: MON(CuMn)-Q1

description: treatment 1


title: Control1

description: control 1


title: PBMC, Expanded CD56DimNK_ILC3, scCITE-Seq

city: Toronto

first: Sarah

last: Crome

state: ON

address: 101 College Street

country: Canada

institute: University Health Network

data_processing:
Expression matrices and alignment to the reference human genome (GRCh38/hg38) was done using CellRanger v6.1.2
Single cells were filtered to exclude cells that expressed >10% mitochondrial content, <1000 total transcripts and <200 unique genes.
Data was log-normalized and cell clustering and gene expression analysis was preformed using Seurat v4.3.0.1
Cell cycle genes were assigned using Seurat’s CellCycleScoring and regressed out during scaling
Assembly: GRCh38/hg38
Supplementary files format and content: tar files with barcodes, features and matrix
Supplementary files format and content: tar files with barcodes, features and matrix
Library strategy: CITE-seq

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from healthy whole blood, diluting 1:1 with FACS buffer (1x PBS + 2%FCS) and layered using Lymphoprep. Cells were washed in FACS, and platelets were removed by centrifugation for 10 min three times.  Red blood cells were lysed with ACK Lysing Buffer. Isolated PBMCs were resuspended in 1xPBS with 0.04% BSA (Millipore Sigma) and prepared according to 10X Genomics Single Cell 5’ v2 platform in accordance with manufacturers instructions. 12,000 cells were targeted for capture from each sample, sequenced to a depth of 40,000 reads.
other

value: Blood

value: PBMC


title: PBMC, Expanded CD56BrightNK_ILC2, scCITE-Seq


title: Genomic DNA methylation from 9611518062_R02C01

data_processing: Idat files were loaded with Minfi. CpGs with a detection rate lower than 99% (detection p-value > 0.05) or having a beadcount lower than 1% in at least 5% of samples were excluded. Additionally, CpGs at multi-hit or single-nucleotide polymorphism locations (MethylToSNP) were also excluded. Samples having a call-rate lower than 95% or sex mismatch were excluded. DNA methylation was expressed as beta values and we applied preprocessnoob and BMIQ normalizations

extract_protocol: DNA was extracted from whole peripheral blood collected in 10mL EDTA tubes during the first 24h after stroke onset.


title: Genomic DNA methylation from 9611518062_R01C02


title: Control2

description: control 2


title: Genomic DNA methylation from 9611518007_R06C01


title: Genomic DNA methylation from 9611518062_R02C02


title: Genomic DNA methylation from 9611518007_R04C01


title: Genomic DNA methylation from 9611518062_R03C02


title: Genomic DNA methylation from 9611518007_R03C02


title: Human liver, steatotic, AAV8, AAV5, AAV-LK03, AAV-NP59, SL #4 PHEP1

city: San Francisco

first: Simone

last: Kurial

state: CA

address: 35 Medical Center Way

department: Surgery

institute: UCSF

description: SeqWell

data_processing:
Demultiplexed paired-end FASTQ files were aligned to the hg38 (Homo sapiens GRCh38.p13) whole genome customized to include transgene and barcode sequences as pseudochromosomes using dropseq_workflow pipeline on Terra.
Read files split into two lanes were concatenated before alignment.
Assembly: Homo sapiens GRCh38.p13
Supplementary files format and content: Tab-delimited digital gene expression matrix (.txt) containing raw counts for every gene, transgene and barcode sequence, and unique cell-identifying barcodes.

source_name: Liver

extract_protocol:
Following NMP, livers were flushed with 10-15 L of ice-cold normal saline through the portal vein and hepatic artery until the efflux was clear, followed by 1 L UW solution. 50-70 g wedges of the right and left liver lobes were cut and immediately immersed in ice-cold UW solution. Sections were manually perfused with UW solution through open vessels before cell release. To release hepatocytes, sections were perfused with calcium- and magnesium-free HBSS containing 20 mM HEPES, penicillin-streptomycin and 1 mM EGTA for 15 minutes at 37°C followed by perfusion with 1 mg/mL collagenase IV in 20 mM HBSS containing HEPES, penicillin-streptomycin and 5 mM CaCl2.H20 for 22 minutes at 37°C. The crude cell preparation was suspended in DMEM containing penicillin-streptomycin and 5% FBS, filtered through sterile gauze, pelleted at 70g and washed twice with the same suspension media. Hepatocytes were further purified by centrifugation through 45% Percoll at 200g for 15 minutes. For isolation of NPCs, a liver section was perfused for 15 minutes with HBSS containing 1mM EGTA as described for hepatocytes, followed by perfusion with 300 mL of pronase (1 mg/mL in DMEM) and then by 1.5 mg/mL collagenase IV in HBSS containing 5 mM CaCl2 for 22 minutes. The crude cell preparation was filtered through sterile gauze, digested further in 200 mL pronase (0.5 mg/mL) for 30 minutes at 37°C with constant shaking, pelleted at 600g, washed twice and subjected to density gradient centrifugation with 9% Accudenz at 1400g for 17 minutes. Hepatic stellate cells were retrieved from the top of the 9% Accudenz gradient and other NPC populations were retrieved from the mid-portion of the gradient. For NL #2, NL #3, NL #4, and SL #3, some cells were isolated via chunk digestion: ~250 mg of liver tissue was minced and incubated in Gibco Liver Perfusion Media at 37°C for 15 minutes with 20 rpm rotation. After washing with PBS, the tissue sample was incubated with collagenase IV (minimum 600 U/mL) in HBSS supplemented with 1% HEPES for 30 minutes at 37°C with 100 rpm rotation. The tissue sample was then triturated using a 10 mL or 25 mL pipette 10-15 times and passed through a 70 µm filter to acquire single cells and red blood cells were lysed with ACK Lysis Buffer. For all samples, viability was assessed using trypan blue and cells were counted with a hemocytometer.
For each sample, libraries were prepared using the Nextera XT DNA Library Preparation kit: First, 800-1000 pg of DNA were dual-indexed with N700 and N500 oligonucleotides. SPRI beads were used to purify library products at sequential 0.6x and 1x ratios by volume. Library concentration was determined to be between 100-1000 bp using an Agilent HSD1000 TapeStation. 6 nM dilutions were prepared for each library.

treatment_protocol: AAV vectors reconstituted in injection buffer (20 mM Tris pH 8, 1 mM MgCl2, 200 mM NaCl and 0.001% Pluronic F-68 in water) to a final volume of 5-10 mL were injected into the portal vein using a syringe with a 27G needle over the course of 1 minute.

value: Liver

value: Hepatocytes and NPCs

tag: isolation method

value: Enzymatic perfusion

value: AAV8, AAV5, AAV-LK03, AAV-NP59


title: Human liver, steatotic, AAV8, AAV5, AAV-LK03, AAV-NP59, SL #4 HSC1

description: SeqWell


title: Human liver, steatotic, AAV8, AAV5, AAV-LK03, AAV-NP59, SL #4 HEP1

description: SeqWell


title: Human liver, steatotic, AAV8, AAV5, AAV-LK03, AAV-NP59, SL #4 HSC2

description: SeqWell


title: Human liver, steatotic, AAV8, AAV5, AAV-LK03, AAV-NP59, SL #4 HSC3

description: SeqWell


title: Human liver, steatotic, AAV8, AAV5, AAV-LK03, AAV-NP59, SL #4 HSC4

description: SeqWell


title: Human liver, steatotic, AAV8, AAV5, AAV-LK03, AAV-NP59, SL #4 PHEP2

description: SeqWell


title: Genomic DNA methylation from 9611518007_R02C02

value: Blood DNA

value: male


title: Human liver, normal, AAV8, AAV5, AAV-LK03, AAV6, NL #4 NPC2

description: SeqWell

value: Chunk digestion

value: AAV8, AAV5, AAV-LK03, AAV6


title: Genomic DNA methylation from 9611518062_R03C01

value: yes


title: Genomic DNA methylation from 9611518003_R06C01

value: no


title: Human liver, normal, AAV8, AAV5, AAV-LK03, AAV6, NL #4 Heps4

description: SeqWell


title: Genomic DNA methylation from 9611518007_R02C01


title: Human liver, normal, AAV8, AAV5, AAV-LK03, AAV6, NL #4 Heps3

description: SeqWell


title: Genomic DNA methylation from 9611518007_R03C01


title: Genomic DNA methylation from 9611518003_R05C01


title: Genomic DNA methylation from 9611518007_R05C01


title: Human liver, normal, AAV8, AAV5, AAV-LK03, AAV6, NL #4 Heps1

description: SeqWell


title: Genomic DNA methylation from 9611518003_R06C02

value: female


title: Human liver, normal, AAV8, AAV5, AAV-LK03, AAV6, NL #4 NPC1

description: SeqWell


title: Human liver, normal, AAV8, AAV5, AAV-LK03, AAV6, NL #4 HSC1

description: SeqWell


title: Genomic DNA methylation from 9611518003_R01C02


title: Human liver, steatotic, AAV8, AAV5, AAV-LK03, AAV-NP59, SL #4 HEP2

description: SeqWell


title: Genomic DNA methylation from 9611518003_R01C01


title: Human liver, normal, AAV8, AAV5, AAV-LK03, AAV6, NL #4 HSC2

description: SeqWell


title: Genomic DNA methylation from 9611518002_R06C02


title: Genomic DNA methylation from 9611518007_R01C02


title: Human liver, normal, AAV8, AAV5, AAV-LK03, NL #3 NPC2

description: SeqWell

value: AAV8, AAV5, AAV-LK03


title: Genomic DNA methylation from 9611518002_R05C01


title: Genomic DNA methylation from 9611518002_R04C02


title: Human liver, normal, AAV8, AAV5, AAV-LK03, NL #3 HSC1

description: SeqWell


title: Human liver, normal, AAV8, AAV5, AAV-LK03, NL #3 NPC1

description: SeqWell


title: Genomic DNA methylation from 9611518002_R04C01


title: Human liver, normal, AAV8, AAV5, AAV-LK03, AAV6, NL #4 Heps2

description: SeqWell


title: Human liver, normal, AAV8, AAV5, AAV-LK03, NL #3 Hep3

description: SeqWell


title: Genomic DNA methylation from 9611518002_R05C02


title: Genomic DNA methylation from 9611518002_R02C01


title: Genomic DNA methylation from 9611518003_R04C02


title: Genomic DNA methylation from 9611518002_R03C02


title: Human liver, normal, AAV8, AAV5, AAV-LK03, NL #3 Hep2

description: SeqWell


title: Human liver, normal, AAV8, AAV5, AAV-LK03, NL #3 HSC2

description: SeqWell


title: Human liver, normal, AAV8, AAV5, AAV-LK03, NL #3 Hep1

description: SeqWell


title: Human liver, normal, AAV8, AAV5, AAV-LK03, NL #3 Hep4

description: SeqWell


title: Genomic DNA methylation from 9611518002_R03C01


title: Genomic DNA methylation from 9611518002_R01C02


title: Human liver, normal, AAV8, NL #2 NPC2

description: SeqWell


title: Human liver, normal, AAV8, NL #2 NPC1

description: SeqWell


title: Genomic DNA methylation from 9611518002_R01C01


title: Human liver, normal, AAV8, NL #2 Heps3

description: SeqWell


title: Human liver, normal, AAV8, NL #2 Heps2

description: SeqWell


title: Genomic DNA methylation from 9610361002_R05C01


title: Human liver, normal, AAV8, NL #2 Heps1

description: SeqWell


title: Genomic DNA methylation from 9610361002_R04C02


title: Genomic DNA methylation from 9611518002_R06C01


title: Genomic DNA methylation from 9610361002_R04C01


title: Genomic DNA methylation from 9610361002_R03C01


title: Human liver, steatotic, AAV8, AAV5, SL #3 NPC

description: SeqWell

value: AAV8, AAV5


title: Genomic DNA methylation from 9610361002_R02C02


title: Genomic DNA methylation from 9610361002_R01C01


title: Genomic DNA methylation from 9610361002_R01C02


title: Genomic DNA methylation from 9534104045_R06C02


title: Human liver, steatotic, AAV8, AAV5, SL #3 Heps1

description: SeqWell


title: Genomic DNA methylation from 9534104045_R03C02


title: Human liver, steatotic, AAV8, AAV5, SL #3 Heps2

description: SeqWell


title: human neurons, differentiated, F12468, 2-week, H3K4me3, rep1  (PLAC-seq)

city: SAN FRANCISCO

first: Yin

last: Shen

state: CALIFORNIA

address: 513 Parnassus Ave

department: Department of Neurology

data_processing:
Samples were processed using Arima MAPS v2.0 pipeline using 2Mbp binning range, 5kbp bin size, X chromosome processing, pospoisson model, and 1kbp length cutoff
Anchor peaks were generated by calling peaks with default MACS2 settings “--broad --nolambda --broad-cutoff 0.3” from 20 million short BAM reads extracted from each replicate and merged.
Peaks were cross lifted to each genome and combined to generate a consensus peakset for each genome
Peaks were then used to rerun the maps pipline serving as the anchorset.
Samples were then merged and normalized by usable reads/FRiPs determined calculated from anchor peak bins multiplied by "LR Frips er Peak Bin" to call final interaction loops.
Assembly: hg38, pantro5
Supplementary files format and content: bedpe files

extract_protocol:
2% PFA crosslinked cells comprising 15 μg of genomic DNA were used per PLAC-seq reaction, which corresponds to 4~5 M human or chimpanzee neurons according to estimation. Then the crosslinked chromatin was digested using a restriction enzyme (RE) cocktail followed by the fill-in step of the 5’-overhangs with a biotinylated nucleotide. Next, the spatially proximal digested ends of DNA were ligated while capturing the genomic structure. The proximally-ligated chromatin is then fragmented by sonicator (Covaris S220), immunoprecipitated with anti-H3K4me3 antibody (Millipore 04-745) conjugated Dynabeads (M-280 sheep anti-rabbit IgG, invitrogen #11203D), and purified to yield fragmented proximally-ligated DNA.
PLAC-seq was performed according to the protocol from Arima-HiC+ Kit (Arima Genomics, #P/N A101020).

value: excitatory neurons

tag: chip antibody

value: H3K4me3 (Millipore, #04-745)


title: Human liver, steatotic, AAV8, AAV5, SL #3 HSC

description: SeqWell


title: Genomic DNA methylation from 9534104045_R02C01

first: Joan

address: Carrer del Doctor Aiguader, 88


title: human neurons, differentiated, F12468, 2-week, rep1 (ATAC-seq)

data_processing:
All libaries were processed using the ENCODE ATAC-seq pipeline (v1.10.0) using default settings and idr cutoff at 2%
Briefly, reads were mapped to bowtie2, duplicates removed by picard and peaks were called by MACS2
Assembly: hg38, pantro5
Supplementary files format and content: narrowPeak

growth_protocol: A well-characterized human iPSC line with a wildtype genetic background (WTC11) and a 2nd human iPSC F12468 iPSC line with the Ngn2 transgene were used for human cell culture. For chimpanzee cell culture, the iPS cell lines (C3649 and C3624), a gift from Yoav Gilad’s Lab, were used. iPSC lines were maintained on Matrigel-coated (Corning, 354277) plates with fresh mTeSR medium (StemCell Technologies, 5850) every two days. Both human and chimpanzee iPSCs were passaged using Accutase (STEMCELL Technologies, 07922) and mTeSR medium containing 10uM Rock inhibitor Y-27632 (STEMCELL Technologies, 72302). Human embryonic kidney (HEK) 293T cells were cultured in Dulbecco’s modified Eagle’s medium (Gibco, 11995065) supplemented with 10% fetal bovine serum (CPS Serum, FBS-500). HEK 293T cells were passaged with trypsin-EDTA (Gibco, 25200072). All cells were grown at 37°C with 5% CO2. Culture medium was routinely assessed for mycoplasma contamination with the MycoAlert Mycoplasma Detection Kit (LONZA, LT07-218).

extract_protocol:
Generally, live cells were washed once with ice-cold 1xPBS containing protease inhibitor then resuspended in ice-cold nuclei extraction buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA630, and 1× protease inhibitor) for 5 min. Next, counted 50,000 cells per reaction and exchanged into 50 μL 1× buffer TD, and added 2.5 μL TDE1 enzyme for 30 min at 37 °C with rotation for transposition. The fully transposed DNA was purified with Qiagen MinElute spin columns (Qiagen#28006), PCR amplified, and AMPure XP beads size-selected for fragments between 300 and 1,000 bp. Libraries were subjected to paired-end 150 bp sequencing on the Novaseq 6000.
ATAC-seq was performed by using the Nextera DNA Library Prep Kit (Illumina FC-121-1030).

value: WT

value: differentiation

tag: time

value: 2 week


title: human neurons differentiated, F12468, 2-week, rep2 (RNA-seq)

data_processing:
Raw paired-end fastq RNA-seq libraries were trimmed to 100 bp using fastp v0.20.1
FastP filtered reads were mapped to hg38 or panTro5 using STAR 2.7.9a with ENCODE recommended parameters
Transcript quantification was performed using RSEM 1.3.1 with gene annotations from GENCODE 44 for hg38 and Ensemble Pan_tro_3.0.110 for panTro5.
Assembly: hg38, pantro5
Supplementary files format and content: tab-delimited .genes.result files

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) following manufacturer's protocols.

treatment_protocol: Human and chimp excitatory neurons were generated by integration of the AAVS1 safe harbor locus of human iPSCs (i3N iPSCs). Based on the similarity (99%) of conserved sequence of AAVS1 between human and chimpanzee genome, the same iNgn2 cassette used in human iPSCs was knocked in chimpanzee AAVS1 safe harbor locus. The iPSCs were dissociated and seeded in Matrigel coated plate in N2 medium containing BDNF (PeproTech, #450-02), NT-3 (PeproTech, #450-03), mouse laminin (Lifetechnology, #23017-015), Doxycycline (Sigma, #D9891) and Rock Inhibitor (STEMCELL Technologies, 72302), and changed medium for the following two days without Rock Inhibitor. After three days in N2 medium, the pre-differentiated cells were dissociated and seeded in a Poly-L-Ornithine coated plate in Maturation medium containing those above factors except Rock Inhibitor. For the following differentiation procedures, half medium change was applied for the cells every 7 days.


title: Genomic DNA methylation from 9534104045_R01C02


title: human neurons, differentiated, F12468, 2-week, rep2 (ATAC-seq)


title: Genomic DNA methylation from 9534104045_R01C01


title: Genomic DNA methylation from 9534104044_R06C01


title: human neurons, differentiated, F12468, 2-week, rep4 (RNA-seq)


title: Genomic DNA methylation from 9534104044_R05C02


title: human neurons, differentiated, F12468, 2-week, rep3 (RNA-seq)


title: Genomic DNA methylation from 9534104044_R05C01


title: Human liver, normal, AAV8, NL #2 HSC

description: SeqWell

value: Liver

value: Hepatocytes and NPCs


title: human neurons, differentiated, WTC11, 2-week, rep4 (RNA-seq)


title: Genomic DNA methylation from 9534104044_R04C02


title: human neurons, differentiated F12468, 2-week (PIPseq)

data_processing:
Sequencing data were then aligned, and a gene expression matrix was generated for each cell using the software PIPseeker (Fluent BioSciences) with the hg38 or panTro5 reference genomes.
Assembly: hg38, pantro5
Supplementary files format and content: barcodes files (.tsv)
Supplementary files format and content: features files (.tsv)
Supplementary files format and content: counts files (.mtx)

extract_protocol:
The iPSC-derived excitatory neurons were dissociated using Accutase for 20 minutes. The reaction was neutralized with mTeSR medium, and the cells were then centrifuged at 1,000 rpm for 5 minutes. The non-viable cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101).
The pelleted cells were resuspended in Cell Suspension Buffer and processed according to the manufacturer’s recommendations (Fluent BioSciences). Briefly, cells were transferred into pre-templated instant partitions (PIPs) for mRNA capture. The integrity and quality of the PIPs/cell emulsions were visually inspected to ensure they met the manufacturer’s standards. The samples underwent the protocol of the PIPseq T2 3ʹ Single Cell Sequencing Kit, which includes mRNA isolation, synthesis of complementary DNA (cDNA), amplification of cDNA, library preparation, library pooling, and sequencing.
PIP-seq


title: Genomic DNA methylation from 9534104044_R04C01


title: human neurons, differentiated WTC11, 2-week (PIPseq)


title: human neurons, differentiated, F12468, 2-week, H3K4me3, rep2  (PLAC-seq)


title: Genomic DNA methylation from 9534104044_R03C01


title: Genomic DNA methylation from 9534104045_R03C01


title: Genomic DNA methylation from 9534104044_R02C02


title: Genomic DNA methylation from 9534104044_R01C01


title: Day 9, replicate 2B

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

description:
Features_count_matrix.csv.gz
Cell_annotation.csv.gz

data_processing:
Raw sequences where analysed using the default parameters of cellranger version 6.1.2 with the reference genome GRCh38 and annotations from Ensembl 98
From the cellranger output, clonal annotation was performed following the CellTagR pipeline (Biddy et al. Nature, 2018; https://github.com/morris-lab/CellTagR) using a minimum of 2 UMI counts per cell and a Jaccard similarity threshold of 0.6. Only cells with clonal annotation were kept and further filtered in Seurat (v4.2.1) based on feature counts (>2000) and mitochondrial content (<10%) prior to clustering and cell type annotation.
Assembly: GRCh38
Supplementary files format and content: The Features_count_matrix.csv.gz file contains the raw count
Supplementary files format and content: The Cell_annotation.csv.gz file contains cell type, time point, condition, and clone annotation

molecule: polyA RNA

source_name: Umbilical cord blood

growth_protocol: Cord blood cells were cultured in HSC expansion media consisting of StemSpan supplemented with human SCF (100ng/ml), FLT3 (100ng/ml), TPO (50ng/ml), and IL-6 (50ng/ml). Cells were treated with 35nM UM171 or DMSO vehicle control.

extract_protocol:
At day 4, half the cells were collected from the well for sequencing. The remaining cells were collected at d9. For each time point, the collected DMSO and UM171 cells were pooled into one reaction for the 10X Chromium. For replicate #2, the larger number of cells collected at d9 was pooled first and then aliquoted into two reactions.
Library construction was performed as per the manufacturer's instruction (Single cell 3' v3 protocol, 10X Genomics)

value: Umbilical cord blood


title: Genomic DNA methylation from 9534104044_R02C01

institute: Hospital del Mar Research Institute

value: Blood DNA


title: Day 4, replicate 2


title: Genomic DNA methylation from 9534104043_R06C01

value: male


title: PBMC, NoGVHD, B005, snRNAseq

data_processing:
Expression matrices and alignment to the reference human genome (GRCh38/hg38) was done using CellRanger v6.1.2
Cell clustering and gene expression analysis was preformed using Seurat v4.3.0.1
Doublets were excluded using DoubletFinder v2.0.3
Free mRNA contamination in each droplet was estimated and removed using SoupX v1.6.2
Assembly: GRCh38/hg38
Supplementary files format and content: tar files with barcodes, features and matrix

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from healthy whole blood, diluting 1:1 with FACS buffer (1x PBS + 2%FCS) and layered using Lymphoprep. Cells were washed in FACS, and platelets were removed by centrifugation for 10 min three times.  Red blood cells were lysed with ACK Lysing Buffer. Isolated patient PBMCs were resuspended in 1xPBS with 0.04% BSA (Millipore Sigma) and prepared according to 10X Genomics Single Cell 5’ v2 platform in accordance with manufacturers instructions. 12,000 cells were targeted for capture from each sample, sequenced to a depth of 40,000 reads.

value: Blood

value: PBMC

value: Male

tag: disease

value: No GVHD

tag: diagnosis

value: MF

tag: grade

tag: donorid


title: Genomic DNA methylation from 9534104043_R04C01

tag: tissue

value: yes


title: PBMC, NoGVHD, B004, snRNAseq

tag: cell type

value: Female

value: AML


title: Day 9, replicate 1


title: human neurons differentiated, F12468, 2-week, rep1 (RNA-seq)

value: excitatory neurons

tag: genotype


title: Genomic DNA methylation from 9534104043_R05C02

tag: Sex

value: female

value: no


title: Day 4, replicate 1


title: PBMC, NoGVHD, B003, snRNAseq


title: PBMC, NoGVHD, B002, snRNAseq


title: Genomic DNA methylation from 9534104043_R03C01


title: PBMC, NoGVHD, B001, snRNAseq

value: TCL


title: human neurons, differentiated, WTC11, 2-week, rep3 (RNA-seq)

value: WT

value: differentiation


title: Genomic DNA methylation from 9534104043_R02C02


title: Genomic DNA methylation from 9534104043_R02C01


title: PBMC, GVHD, G019, snRNAseq

value: GVHD


title: Genomic DNA methylation from 9534104004_R06C01

value: Blood DNA


title: Genomic DNA methylation from 9534104004_R06C02


title: PBMC, GVHD, G018, snRNAseq

value: CMML


title: PBMC, GVHD, G016, snRNAseq

value: Blood


title: Genomic DNA methylation from 9534104004_R05C02

value: male


title: Genomic DNA methylation from 9534104004_R04C01


title: PBMC, GVHD, G015, snRNAseq

value: PBMC


title: PBMC, GVHD, G011, snRNAseq

value: Male


title: Day 9, replicate 2A

value: Umbilical cord blood


title: Genomic DNA methylation from 9534104004_R01C02


title: Genomic DNA methylation from 9534104004_R03C01


title: PBMC, NoGVHD, G007, snRNAseq

value: No GVHD

value: T-ALL


title: PBMC, GVHD, G008, snRNAseq

value: AML


title: Genomic DNA methylation from 9534104003_R04C02


title: Genomic DNA methylation from 9534104004_R01C01


title: PBMC, GVHD, G002, snRNAseq

value: SDS


title: Genomic DNA methylation from 9534104003_R02C02


title: Genomic DNA methylation from 9534104001_R06C02

value: female


title: RR607466_R

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

data_processing:
Data were processed using a previoulsy published method[https://pubmed.ncbi.nlm.nih.gov/24972667/]. In brief, reads were quality controlled using FASTQC. Reads were mapped against hg38 genome using STAR aligner. HT-Seq was utilized to analyzed the aligned reads and generate gene-wise counts using Ensemble version 78 transcriptome. Extracted read data was processed using edgeR software. Timmed means of M-values method was utilized to normalized reads that were provided in the file named 20231208-For-GEO-Raw-Counts.tsv".
Assembly: hg38
Supplementary files format and content: 20231208-For-GEO-Raw-Counts.tsv; tab-delimited; Raw gene-count matrix

source_name: heart muscle

extract_protocol:
mRNA was extracted using Trizol and stored in RNAlater.
mRNA library was constructed using Illumina TruSeq Stranded kit following manufacturer's recommendations.
Paired end library strategy was utilized

value: heart muscle

value: HCM


title: Genomic DNA methylation from 9534104003_R01C02

city: Barcelona

value: yes


title: RRNM09


title: Genomic DNA methylation from 9534104001_R04C01

value: no


title: Genomic DNA methylation from 9534104001_R03C02


title: RNM02


title: Genomic DNA methylation from 9534104001_R03C01


title: RNM01


title: Genomic DNA methylation from 9534104001_R01C02


title: R8


title: R670152


title: Genomic DNA methylation from 9533774108_R06C02


title: R656518


title: Genomic DNA methylation from 9533774108_R05C02


title: R655639


title: Genomic DNA methylation from 9533774108_R05C01


title: Genomic DNA methylation from 9533774108_R04C01


title: Genomic DNA methylation from 9533774108_R03C02


title: R620009_R


title: R643724


title: R59


title: R58


title: RNM07


title: Genomic DNA methylation from 9533774108_R02C02


title: Genomic DNA methylation from 9534104001_R04C02


title: Genomic DNA methylation from 9533774108_R02C01


title: RNM04


title: R57


title: Genomic DNA methylation from 9533774108_R03C01


title: R53


title: Genomic DNA methylation from 9533774108_R01C02


title: R50


title: Genomic DNA methylation from 9533774099_R05C02


title: R40


title: R35


title: Genomic DNA methylation from 9533774099_R03C01


title: Genomic DNA methylation from 9533774099_R05C01


title: Genomic DNA methylation from 9533774099_R02C02


title: R342632


title: R34


title: R32


title: Genomic DNA methylation from 9533774099_R01C01


title: Genomic DNA methylation from 9533774098_R06C02


title: R26


title: R16_R


title: Genomic DNA methylation from 9533774098_R06C01


title: R1


title: Genomic DNA methylation from 9533774098_R05C02


title: NM08


title: Genomic DNA methylation from 9533774098_R04C02


title: Genomic DNA methylation from 9533774098_R04C01


title: NM05


title: NM06


title: Genomic DNA methylation from 9533774098_R01C01


title: Genomic DNA methylation from 9533774098_R03C02


title: Genomic DNA methylation from 9533774098_R01C02


title: NM03


title: Genomic DNA methylation from 9533774099_R01C02


title: Genomic DNA methylation from 9533774096_R06C01


title: 673368_R


title: 7_028

value: Control


title: Genomic DNA methylation from 9533774096_R05C01

value: Blood DNA


title: Genomic DNA methylation from 9533774096_R04C02


title: 673367_R


title: 670934_R


title: 671993_R


title: Genomic DNA methylation from 9533774096_R04C01


title: 639123_R


title: 634935_R


title: 632698_R


title: 6_086_R


title: Genomic DNA methylation from 9533774096_R01C02


title: Genomic DNA methylation from 9533774089_R06C01


title: Genomic DNA methylation from 9533774089_R03C01


title: 7_012


title: 6_038


title: Genomic DNA methylation from 9533774096_R01C01


title: 6_008


title: 5_14


title: Genomic DNA methylation from 9533774089_R02C02


title: Genomic DNA methylation from 9533774096_R05C02


title: Genomic DNA methylation from 9533774087_R06C02


title: 5_133


title: Genomic DNA methylation from 9533774089_R01C02


title: 5_128


title: Genomic DNA methylation from 9533774087_R05C01


title: Genomic DNA methylation from 9533774087_R06C01


title: 5_092


title: 5_126


title: Genomic DNA methylation from 9533774087_R03C02


title: Genomic DNA methylation from 9533774087_R04C02


title: Genomic DNA methylation from 9533774087_R04C01


title: Genomic DNA methylation from 9533774096_R03C01


title: 4_102


title: 5_059


title: Genomic DNA methylation from 9533774089_R05C01


title: 6_052


title: Genomic DNA methylation from 9533774087_R02C02


title: Genomic DNA methylation from 9533774087_R02C01


title: 30_03_05


title: 3_145


title: Genomic DNA methylation from 9533774086_R05C01


title: Genomic DNA methylation from 9533774086_R06C01


title: 29_R


title: IMR90_D85_P16OSK_R2

city: San Diego

first: sanjeeb

middle: k

last: sahu

address: Lajolla

institute: AltosLabs

data_processing:
The RNA-seq reads were initially processed using fastp (version 0.19.5) to obtain clean RNA-seq reads.
These clean reads were then used to quantify gene expression levels using Salmon (version 1.10.0) (Patro et al., 2017). Transcript fasta files of each species were obtained from the Gencode.
Transcript fasta files of each species were obtained from the Gencode
The transcript fasta file was indexed using the "Salmon index" command with default parameters. The clean RNA-seq reads were aligned to the indexed transcript using specific parameters (--useVBOpt --seqBias --gcBias) for sequence-specific bias correction and fragment GC bias correction.
Assembly: hg38
Supplementary files format and content: Excel. Expression (TPM) for each gene.

extract_protocol:
Column Purification
Libraries were prepared using the Illumina Total RNA Prep with the Ribo-Zero Plus kit (Cat: 20040529) with an initial starting material of 200 ng.

value: Primary Lung Fibroblast

tag: sample group


title: Genomic DNA methylation from 9533774086_R04C01


title: 28_9_97


title: IMR90_D85_GFP_R2


title: IMR90_D85_P16OSK_R1


title: IMR90_D85_GFP_R1


title: 26_3_09__R


title: Genomic DNA methylation from 9533774086_R03C02


title: 5_084


title: IMR90_D50_P16OSK_R1


title: Genomic DNA methylation from 9533774086_R03C01


title: 25_R


title: IMR90_D50_P16OSK_R2


title: Genomic DNA methylation from 9533774086_R02C02


title: IMR90_D50_GFP_R2


title: 19_10_02


title: IMR90_D20_P16OSK_R2


title: IMR90_D50_GFP_R1


title: IMR90_D20_P16OSK_R1


title: IMR90_D20_GFP_R2


title: 17_5_03


title: Genomic DNA methylation from 9533774086_R01C02


title: IMR90_D20_GFP_R1


title: 17_11_02__R


title: IMR90_D125_P16OSK_R2


title: Genomic DNA methylation from 9533774086_R01C01


title: IMR90_D125_P16OSK_R1


title: IMR90_D125_GFP_R2


title: Genomic DNA methylation from 9533774085_R06C02


title: IMR90_D125_GFP_R1


title: 12_2_03__R


title: chimpanzee neurons, differentiated, C3624, 2-week, H3K4me3, rep2  (PLAC-seq)

organism: Pan troglodytes

value: excitatory neurons

value: H3K4me3 (Millipore, #04-745)


title: Genomic DNA methylation from 9533774085_R06C01

value: male


title: 25_1_01


title: chimpanzee neurons, differentiated, C3624, 2-week, rep2 (ATAC-seq)

value: WT

tag: treatment

value: differentiation

value: 2 week


title: 683304


title: chimpanzee neurons, differentiated, C3624, 2-week, rep2 (RNA-seq)


title: chimpanzee neurons, differentiated, C3624, 2-week, rep1 (ATAC-seq)


title: 680701


title: Genomic DNA methylation from 9533774086_R02C01


title: Genomic DNA methylation from 9533774085_R05C01


title: Genomic DNA methylation from 9533774085_R05C02


title: chimpanzee neurons, differentiated, C3624, 2-week, rep1 (RNA-seq)


title: 676236


title: chimpanzee neurons, differentiated, C3624, 2-week, rep4 (RNA-seq)


title: chimpanzee neurons, differentiated, C3624, 2-week, rep3 (RNA-seq)


title: chimpanzee neurons, differentiated, C3649, 2-week, rep4 (RNA-seq)


title: Genomic DNA methylation from 9533774085_R02C02


title: chimpanzee neurons, differentiated, C3649, 2-week, rep2 (RNA-seq)


title: 676073


title: chimpanzee neurons, differentiated, C3649, 2-week, rep3 (RNA-seq)


title: Genomic DNA methylation from 9533774085_R02C01


title: 7433514


title: chimpanzee neurons, differentiated, C3624, 2-week, H3K4me3, rep1  (PLAC-seq)


title: chimpanzee neurons, differentiated, C3624, 2-week (PIPseq)


title: chimpanzee neurons, differentiated, C3649, 2-week, rep1 (RNA-seq)


title: 673482


title: neuron CRISPRi-hypr-seq screen rep2, XC168

data_processing:
Filter reads with fastp
Extract cell barcodes with UMI-Tools
Map reads to custom index with Bowtie
Convert to bam files with SAMTools
Generate count tables with UMI-Tools
Assembly: hg38
Supplementary files format and content: count tables (cells by probes or cells by genes) for all cells that passed QC
Library strategy: HyPR-Seq

extract_protocol:
The papain-dissociated single neurons were fixed in 4% formaldehyde solution followed with permeabilization in 70% ice-cold ethanol. The probes were pooled to a concentration of 20nM/probe and incubated with the neurons at 37°C overnight. The neurons were then harvested for the hybridization with B1H1 hairpin (Molecular Instruments) followed by ligation with readout oligo at 37°C for one hour, respectively. After ligation, cells were filtered through a 20-μm pluriStrainer (cat. #43-0020-01). The single-cell suspension was checked and counted for the emulsion droplet generation.
We made a 20-μL reaction with 1x EvaGreen Supermix (Bio-Rad cat. #186-4033), 500 nM indexing primer, 20,000 barcoded beads (Chemgenes) and 2,000 cells. The emulsions were generated by using QX200 Digital Droplet Generator (Bio-Rad 1864002) based on the instruction. Following the generation of droplets, the emulsions were UV-treated (6.5 J/cm2 at 365 nm) for 5 mins, with a distance from the UV bulb for 5 cm. Then the droplet PCR amplification was performed with the following program: 94°C for 30 sec for denaturation; 94°C for 5 sec, 64°C for 30 sec, and 72°C for 30 sec for 25 cycles; 72°C for 5 mins final extension. All PCR cycling steps were carried out with 50% ramp rate (2°C/min). To release the library cDNAs, all PCR products were combined, and the emulsions were broken and cleaned with introduction of 1/2 volume of 97% 1H,1H,2H,2H-Perfluoro-1-octanol (Sigma-Aldrich 370533). Then by vortexing and centrifugation, the top aqueous phase was collected and cleaned with 1.8x SPRI beads. Next, the purified libraries were ready for the deep sequencing step with customer primers.


title: chimpanzee neurons, differentiated, C3649, 2-week (PIPseq)


title: Genomic DNA methylation from 9533774070_R05C02


title: 669841


title: neuron CRISPRi-hypr-seq screen rep2, XC166


title: neuron CRISPRi-hypr-seq screen rep2, XC165


title: Genomic DNA methylation from 9533774070_R06C01


title: 666295


title: Genomic DNA methylation from 9533774085_R03C01


title: neuron CRISPRi-hypr-seq screen rep1, XC124


title: Genomic DNA methylation from 9533774070_R05C01


title: Genomic DNA methylation from 9533774070_R04C02


title: chimpanzee neurons, differentiated, C3649, 2-week, H3K4me3, rep2 (PLAC-seq)

description:
Merged-Chimp_on-hg38.srtd.5k.2.sig3Dinteractions.bedpe
consensus-humanAnchors_from-merged-Chimp+Human-peaks.sorted.lifted-to-human.bed

data_processing:
Samples were processed using Arima MAPS v2.0 pipeline using 2Mbp binning range, 5kbp bin size, X chromosome processing, pospoisson model, and 1kbp length cutoff
Anchor peaks were generated by calling peaks with default MACS2 settings “--broad --nolambda --broad-cutoff 0.3” from 20 million short BAM reads extracted from each replicate and merged.
Peaks were cross lifted to each genome and combined to generate a consensus peakset for each genome
Peaks were then used to rerun the maps pipline serving as the anchorset.
Samples were then merged and normalized by usable reads/FRiPs determined calculated from anchor peak bins multiplied by "LR Frips er Peak Bin" to call final interaction loops.
Assembly: hg38
Supplementary files format and content: bedpe files
Library strategy: PLAC-Seq


title: chimpanzee neurons, differentiated, C3649, 2-week, H3K4me3, rep1 (PLAC-seq)


title: 661552


title: 663118


title: Genomic DNA methylation from 9533774070_R03C01


title: chimpanzee neurons, differentiated, C3649, 2-week, rep2 (ATAC-seq)

description: raw_pantro5_2percent-idr.conservative_peak.narrowPeak.gz

data_processing:
All libaries were processed using the ENCODE ATAC-seq pipeline (v1.10.0) using default settings and idr cutoff at 2%
Briefly, reads were mapped to bowtie2, duplicates removed by picard and peaks were called by MACS2
Assembly: hg38, pantro5
Supplementary files format and content: bigwig, idr conserivative at 2%


title: chimpanzee neurons, differentiated, C3649, 2-week, rep1 (ATAC-seq)


title: 656880


title: Genomic DNA methylation from 9533774070_R02C02


title: 671852


title: 655638


title: ESR1-D538G-Palbo and fulv_1

city: Dallas

first: Chang-Ching

last: Lin

state: TX

address: 4554 Glenwick Ln, Apt 2203

department: Harold C. Simmons Comprehensive Cancer Center

institute: UT Southwestern Medical Center

data_processing:
Aligning sequencing reads to the human reference genome GRCh38 using STAR
DESeq2 was used to assess the statistical significance of differentially expressed genes
Assembly: GRCh38
Supplementary files format and content: TSV file include raw counts for each sample (Expression_Matrix_CPM)
Supplementary files format and content: TSV file include differential gene expression (DEG_full_adjP1_fc1)

growth_protocol: MCF7 cells were maintained in DMEM containing 10% FBS and 1x antibiotic-antimycotic.

extract_protocol:
Total RNA was extracted using Promega Maxwell RSC simply RNA extraction kit.
mRNA libraries were prepared using TruSeq Stranded mRNA Library prep kit (Illumina)

treatment_protocol: Cells were treated with vehicle (DMSO) or 200 nM palbociclib alone or in combination with estrogen-deprived media or 1 nM fulvestrant.

value: Breast cancer

value: ESR1 D538G

value: Palbociclib + fulvestrant


title: ESR1-D538G-Palbo and fulv_2


title: ESR1-D538G-Palbo and fulv_3


title: ESR1-D538G-Palbo and E2_3

value: Palbociclib + E2 deprivation


title: Genomic DNA methylation from 9513149117_R02C01

value: female


title: Genomic DNA methylation from 9513149117_R01C02


title: neuron CRISPRi-hypr-seq screen rep1, XC152


title: 653513

value: heart muscle

value: HCM


title: ESR1-D538G-Palbo and E2_1


title: 653448


title: Genomic DNA methylation from 9422492042_R06C01

value: no


title: ESR1-D538G-Palbo_1

value: Palbociclib


title: ESR1-D538G-Veh_3

value: DMSO


title: ESR1-D538G-Palbo_2


title: ESR1-D538G-Palbo_3


title: ESR1-D538G-Veh_2


title: Genomic DNA methylation from 9422492042_R05C02

value: Blood DNA


title: ESR1-D538G-Veh_1


title: 653447


title: ESR1-Y537S-Palbo and fulv_3

value: ESR1 Y537S


title: Genomic DNA methylation from 9513149117_R01C01


title: 647527


title: ESR1-Y537S-Palbo and fulv_1


title: ESR1-Y537S-Palbo and E2_3


title: Genomic DNA methylation from 9422492042_R04C02


title: ESR1-D538G-Palbo and E2_2


title: Genomic DNA methylation from 9422492042_R04C01


title: ESR1-Y537S-Palbo and E2_2


title: 647526


title: ESR1-Y537S-Palbo and E2_1


title: 645586


title: Genomic DNA methylation from 9422492042_R03C01


title: 653809


title: ESR1-Y537S-Palbo_2


title: Genomic DNA methylation from 9422492042_R02C01