title: E562, H3K27me3

value: EP


title: 3004

status: Public on Jul 05 2024

type: SRA

city: Houston

first: Marco

last: Gallo

state: TX

address: 1102 Bates Avenue

department: Pediatrics

country: USA

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Fastqs were processed to hic files using Juicer v1.6.
Contact domains were annotated from hic files using Arrowhead from Juicer Tools v1.19.02
Loops were annotated from hic files using HiCCUPS from Juicer Tools v1.19.02
Compartments were annotated from hic files using the leading eigenvectors of the Pearson correlation matrix.
Boundary scores were annotated from 50-kb contact matrices using Robustad v1.0
Multi-resolution cooler (.mcool) files were generated from hic files using hic2cool v0.8.3.
Significant long-range interactions were identified using Mustache v1.0.1 (https://github.com/ay-lab/mustache, PMID:  32998764) from 10kb contact matrices with default parameters.
Insulation scores were computed at 10-kb resolution with a window size of 100 kb using the diamond-insulation module of cooltools v0.4.0.
TULIP calls were generated by identifying 50-kb bins separated by > 10 Mb that exhibited unusually high interaction frequency. HiC contact signal was thresholded, B-B compartment interactions were isolated, then the pixels of the resulting Hi-C contact matrix were smoothed using ImageMagick v7.0.10_28.  Only bins covered by >10 interactions were maintained in final TULIP calls.
Transcriptome assembly was accomplished using HISAT2 alignment (v2.1.0), StringTie assembly (v2.0), and GffCompare (v 0.11.7) merging of transcripts with GenCode v34 annotation.
Transcript quantification was performed using kallisto (v 0.45.1)
Differential expression calling was performed using sleuth (v0.30.0)
Genome_build: GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set
Supplementary_files_format_and_content: TSV: BoundaryScores_chrAll_50kb.tsv; RobusTAD output containing genomic bin, Left Score, Right Score, and Max Score for each bin in the genome.
Supplementary_files_format_and_content: TSV: TADBoundaryCalls_chrAll_50kb.tsv; RobusTAD output containing genomic bin, Left Score, Right Score, and Max Score for likely boundary regions only.
Supplementary_files_format_and_content: BED: TADBoundaryCalls.50kb.bed; Boundary regions called by RobusTAD in BED format.
Supplementary_files_format_and_content: BED: eigenvalue_allChr_50kb.bed; Compartment status based on eigenvector of Pearson correlation matrix.
Supplementary_files_format_and_content: WIG: eigenvalue_allChr_50kb.wig; Eigenvalues for each big of leading eigenvector of the Pearson correlation matrix. Positive values should associate with Type A compartments with open chromatin.
Supplementary_files_format_and_content: HIC: .hic; Juicebox-formatted Hi-C contact map
Supplementary_files_format_and_content: MCOOL: .mcool; multi-resolution cooler formatted Hi-C contact map
Supplementary_files_format_and_content: TSV: PFA-wrt-nonPFA_LRT_byGene_w_FC_noNA.wGenomePos.tsv; Differential expression output from Sleuth either by gene or by transcript
Supplementary_files_format_and_content: Rdata: union.abundance.gene.Rdata; Binary R format of Kallisto-quantified abundance for each sample, either by gene or by transcript
Supplementary_files_format_and_content: TSV: union.abundance.gene.tsv; Tab-separated format of Kallisto-quantified abundance for each sample, either by gene or by transcript
Supplementary_files_format_and_content: TSV: union_arrowhead_scores.tsv; Arrowhead scores for each sample for the union of all Arrowhead domains called. First column contains the position as an underscore-delimited BEDPE entry with the resolution of the original call trailing the @ symbol
Supplementary_files_format_and_content: RDS: mustache.ep_union.dds.rds; Union of Mustache-called loop scores for all Ependymoma (subgroup==EP) samples.
Supplementary_files_format_and_content: TSV: insulation_scores; Output of cooltools insulation score metrics.
Supplementary_files_format_and_content: TSV: merged_loops.bedpe; Output of HiCCUPS loop calls
Supplementary_files_format_and_content: TSV: ; Output of Mustache loop calls
Supplementary_files_format_and_content: BED: tulips.bed; BED-format genome positions of TULIP calls for each sample.

molecule: genomic DNA

organism: Homo sapiens

source_name: Pediatric brain

growth_protocol: The majority of samples were uncultured, primary tissue. Cultured samples (with biotype==culture) were grown as described previously (Michealraj et al. Cell. 2020; PMID: 32445698).

extract_protocol: Approximately 2.5M cells were used for In-situ Hi-C library approach (Rao et al. Cell. 2014; PMID: 25497547) with library preparation performed as described previously (Johnston et al. Genome Research. PMID: 31249064). Hi-C libraries were sequenced at 150 bp PE with a Hi-Seq X instrument (Illumina) at McGill Genome Centre (Montreal, QC).

tag: tumor type

tag: subgroup

value: PFA K27M

tag: biotype


title: HEK293T_WT_BG4_rep

status: Public on Jun 20 2024

city: Guangzhou

first: Lijun

last: Xiang

state: Guangdong

address: No.55, West of Zhongshan Avenue

department: Guangzhou Key Laboratory of Insect Development Regulation and Application Research

country: China

institute: South China Normal University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
CUT&Tag reads were trimmed from 3' end until the final base had a quality score > 20, using TrimGalore-0.6.7, discarding reads left with < 20 bp
CUT&Tag reads were aligned to the UCSC hg38 genome using Bowtie2 version 2.4.5.
The aligned reads were removed with Picard MarkDuplicates, and the deduplicated BAM files were normalized to the total aligned reads (reads per million, BPM) with the bamCoverage command from deepTools 3.3.0
Peaks were called uing MACS v2.2.7.1 with the significance cut-off q-value <=1E-5
Assembly: hg38
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
CUT&Tag was performed essentially as described by Kaiwei Liang et al. 2021, with minor modifications according the Hyperactive Universal CUT&Tag Assay Kit protocol (Vazyme, Nanjing, China).One hundred thousand cells were used for the CUT&Tag experiment, and cell counting was performed by using a Cellometer Mini (Nexcelom Bioscience, Boston, MA, USA). pA-Tn5 transposase was used to cut the genome and add a special adaptor sequence to build a library.
Libraries were prepared according to Hyperactive Universal CUT&Tag Assay Kit protocol (Vazyme, Nanjing, China)

tag: cell line

tag: cell type

value: Human embryonic kidney

tag: genotype

value: WT


title: E519, H3K27me3

data_processing:
Reads were aligned to hg38 (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set) using bwa mem
Alignments were filtered out if (1) the chromosome name contained “chrUn”, “random”, or “_alt” (2) the alignment MAPQ was lower than 30 or (3) the alignment overlapped the ENCODE Unified GRCh38 Exclusion List (https://www.encodeproject.org/files/ENCFF356LFX/).
Peak calling was performed using MACS2 (v 2.1.2) including input control BAMs. Additional parameters to the MACS2 callpeak function include: “-f BAMPE -g hs --broad --bdg --SPMR”.
Fold enrichment traces were generated using MACS2 bdgcmp with the parameter “-m FE”.
TDF files generated using "igvtools toTDF -z 10"
Assembly: hg38 (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set)
Supplementary files format and content: broadPeaks: Output of MACS2 peak calling.
Supplementary files format and content: FE.sorted.bdg: Bedgraph fold-enrichment trace generated by MACS2 bdgcmp.
Supplementary files format and content: FE.tdf: Compressed Bedgraph for IGV viewing.

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma), followed by reverse crosslinking with glycine. Fixed cell preparations were washed in PBS, pelleted and stored at −80 °C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a Diagenode BioRuptor for 15 cycles, 30s on 30s off. After sonication, the chromatin was diluted to reduce SDS level to 0.1% and before ChIP reaction 2% of sonicated Drosophila S2 cell chromatin was spiked-in the samples.
ChIP-seq was performed as previously described for primary cultures (PMID 30890717).
ChIP-seq was performed as previously described for tumor tissue (PMID 29258295)
Library construction used Kapa HTP Illumina library preparation reagents, following manufacturer’s instructions

tag: tissue

value: Pediatric brain

value: PFA

tag: chip antibody

value: H3K27me3, Diagenode, C15410069


title: DIPG13_C8_K27M

source_name: Pediatric brain tumor derived cell culture

value: HGG

value: culture


title: 24, 38 and 48 hpf tails

status: Public on Jun 14 2024

city: Boston

first: Kalki

last: Kukreja

state: MA

address: 200 Longwood Avenue

institute: Harvard University

library_source: transcriptomic

data_processing:
Reads were mapped onto the Zebrafish genome as described in Kukreja et al. 2024 manuscript. Multi-seq barcodes for each sample were identified using a custom pipeline available here: https://github.com/AllonKleinLab/klunctions/. Barcode abundance was used to manually remove multiplet populations as well as assign cells to their appropriate sample. Data from only 24 hpf tails were used for the manuscript. We provide 8 FASTQ files (2 lanes x 4 reads per lane). The read files from an inDrops run have the following content: *_R1_001.fastq.gz : contains the 3' UTR cDNA read *_R2_001.fastq.gz : contains the first half of the cell barcode *_R3_001.fastq.gz : contains the library index for demultiplexing libraries *_R4_001.fastq.gz : contains the second half of the barcode and the UMI.  All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis (github.com/indrops).
Single-cell transcriptomes were barcoded using inDrops (Klein et al, Cell 2015). Standard transcriptome RNA-seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1, 14 cycles for Read2, 8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline (github.com/indrops/indrops). Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly (Assembly Accession: GCF_000002035.5) using bowtie version 1.1.143.
To obtain the final counts matrix used for data analysis, total count filters were applied as described in Kukreja et. al. 2024, method section "Single cell RNA-seq Data preprocessing"
Assembly: GRCz10 genome assembly (Assembly Accession: GCF_000002035.5)
Supplementary files format and content: Raw counts for transcriptome (tsv.gz): cell barcode, gene names, and raw counts for all cells
Supplementary files format and content: Raw counts for multi-seq tags (csv.gz): cell barcode, tag sequence, and raw counts for all cells
Supplementary files format and content: Filtered barcodes (filtered.h5ad): cell barcode, and associated metadata for all cells
Library strategy: inDrops v3 scRNA-seq

molecule: polyA RNA

organism: Danio rerio

source_name: embryo tail

extract_protocol:
Forty zebrafish tail samples collected at 24, 38 and 48 hpf, were dissected between the yolk ball and extension and dissociated according to a modified version of the protocol described by Bresciani et al. (2018). Briefly, the tails were dissociated with a mixture of DNaseI (20µg/mL), Collagenase/Dispase (8 mg/mL), and 0.25% Trypsin-EDTA at 30.5°C for 15 minutes. The proteases were quenched with DMEM + 10% FBS. Samples were washed and resuspend in PBS. Cells from each timepoint were hashed with a unique lipid modified oligo using Multi-seq. The barcoded samples were subsequently pooled, washed with 1% BSA + PBS, and resuspended in 0.1% BSA + 18% Optiprep in PBS at a final concentration of ~300,000 cells/mL. Single-cell transcriptomes were captured using inDrops.
NGS libraries were prepared by the Single-cell Core at Harvard Medical School and sequenced using an Illumina NovaSeq kit.

value: embryo tail


title: Perturbation experiment 3, 24 hpf biological replicate 1 to 3, technical replicate 1

status: Public on Jun 13 2024

data_processing:
Multiple samples are pooled for each sequencing run. Raw FASTQ were prepared from Illumina bcl files in a format compatible with the inDrops.py pipeline. Each nextseq run results in 16 FASTQ files (4 lanes x 4 reads per lane). For some pooled libraries, sequencing was run twice to get more UMIs per cell and hence we have deposited 16x2 = 32 raw files for those sequencing samples. The illumina library indices of different samples in a run are provided in the meta data. These can be used to demultiplex the raw file into separate libraries. The read files from an inDrops run have the following content: *_R1_001.fastq.gz : contains the 3' UTR cDNA read *_R2_001.fastq.gz : contains the first half of the cell barcode *_R3_001.fastq.gz : contains the library index for demultiplexing libraries *_R4_001.fastq.gz : contains the second half of the barcode and the UMI.  All subsequent processing steps from FASTQ files to count matrixes were performed using the custom pipeline for inDrops data analysis (github.com/indrops).
Single-cell transcriptomes were barcoded using inDrops (Klein et al, Cell 2015). Standard transcriptome RNA-seq libraries were processed as reported in Zilionis et al. Nature Protocol 2016 using inDrops v3 protocol. The transcriptome libraries were sequenced on reads Illumina NextSeq 500. Libraries used standard Illumina sequencing primers and 61 cycles for Read1, 14 cycles for Read2, 8 cycles each for IndexRead1 and IndexRead2. Raw fastq files was processed using inDrops.py pipeline (github.com/indrops/indrops). Sequenced reads were mapped to a zebrafish reference transcriptome built from the zebrafish GRCz10 genome assembly (Assembly Accession: GCF_000002035.5) using bowtie version 1.1.143.
To obtain the final counts matrix used for data analysis, total count filters were applied as described in Kukreja et. al. 2024, method section "Single cell RNA-seq Data preprocessing"
Assembly: GRCz10 genome assembly (Assembly Accession: GCF_000002035.5)
Supplementary files format and content: Raw counts (tsv.gz): cell barcode, gene names, and raw counts for all cells
Supplementary files format and content: Metadata (metadata.csv): library identity, cell barcode, and associated metadata for all cells - time point, treatment, replicate, annotated cell state, total number of counts, etc
Library strategy: inDrops v3 scRNA-seq

source_name: whole embryo

growth_protocol: AB wild-type strains were used for all HUA perturbation experiments. Zebrafish mutant line hi2648, a mutant for the gene emi1, was kindly gifted by Dr. Jennifer Rhodes. Embryos were developed within the ambient temperature of Zebrafish development. Time of fertilization at 28.5 C was used to stage each clutch and this was confirmed using morphological features of the embryos. All zebrafish were housed in a facility overseen by the Harvard Medical Area Standing Committee on Animals (our IACUC) which performs regular inspections and under which we have an approved protocol for all animal procedures.

extract_protocol:
Zebrafish embryos were dechorionated using 1mg/mL Pronase (Sigma P5147-1G) for 5-7 minutes followed by washing in egg water. Embryos were dissociated as previously described in Wagner et. al. Science 2018. Briefly, embryos were dissociated in 0.5mL LoBind microcentrifuge tubes that had been precoated with 10% w/v BSA for about 15 minutes at room temperature. They were homogenized in 1XDPBS/1% w/v BSA for 6 to 10 hpf embryos (early time points) and in 500 µL FACSmax cell dissociation solution (Genlantis T200100) for 14 to 24 hpf embryos (late time points). Cells were then filtered through a 40µm cell strainer mesh (Fisher 352340) and centrifuged in a swinging bucket rotor at 200g for 1 minute (early time points) or 300g for 5 minutes (late time points). Cells were then washed in 1XDPBS/1%BSA using the same centrifuge settings. They were then resuspended in 1XDPBS/0.5%BSA/18% optiprep density medium (Sigma D1556-250ML). Cell concentration was manually quantified using hemocytometer and adjusted to a final concentration of ~100,000 cells/mL before encapsulation.
Library construction as detailed in Zilionis, R. et al. 2016 Nature Protocols. Single-cell barcoding and sequencing was done using droplet microfluidics also described in the same paper.

treatment_protocol: Zebrafish embryos were arrested for cell cycle using two complementary approaches. S phase cell cycle arrest was induced using a cocktail of drugs – hydroxyurea (Sigma Aldrich H8627-5G) at 20 mM and aphidicolin (Sigma Aldrich A0781-5MG) at 150 µM concentration in 1% dimethyl sulfoxide (DMSO) in egg water. G2/M phase arrest was induced by crossing heterozygous emi1 wt/mut zebrafish to generate homozygous emi1 mut/mut embryos, referred as hi2648 in the manuscript. Homozygous mutants with cell cycle arrest were screened at 24 hpf as they have very clear phenotype by this time – these embryos are smaller and have bent tails and the heterozygous mutants and wildtype are indistinguishable.

value: whole embryo

tag: treatment

value: control and emi1 homozygous mutants


title: PFA4, H3K27me3

value: Pediatric brain tumor derived cell culture


title: E823, H3K27me3


title: Perturbation experiment 2, 24 hpf biological replicate 3, technical replicate 1 to 4

value: 1percent DMSO control and cell cycle arrest at 6 hpf


title: Perturbation experiment 3, 24 hpf biological replicate 1 to 3, technical replicate 2, 3


title: Perturbation experiment 2, 24 hpf biological replicate 2, technical replicate 1 to 6


title: Reference experiment, 14-24 hpf biological replicate 2 and 3, technical replicate 1

value: 1percent DMSO control and cell cycle arrest at 14 hpf


title: OE8

status: Public on Jun 06 2024

city: jiangsu yangzhou

first: chen

middle: yi

last: fei

address: No.368 hanjiang middle Road

institute: Yangzhou university

data_processing:
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones
Assembly: Hisat2 (v2.0.1)
Supplementary files format and content: processed data file.xlsx: count and fpkm

molecule: total RNA

organism: Rattus norvegicus

source_name: brain

extract_protocol:
Total RNA was extracted by TRIzol(Takara)
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions

value: brain


title: Perturbation experiment 1, 6-24 hpf biological replicate 3, technical replicate 1


title: Reference experiment, 14-24 hpf biological replicate 1, technical replicate 2


title: 180618

value: CPP

value: Unspecified


title: OE2


title: OE4


title: Perturbation experiment 1, 6-24 hpf biological replicate 2, technical replicate 1


title: D14


title: Perturbation experiment 2, 24 hpf biological replicate 1, technical replicate 1 to 4


title: Reference experiment, 14-24 hpf biological replicate 2 and 3, technical replicate 2


title: D13


title: D12


title: mRNA and lncRNA AX8

status: Public on May 26 2024

city: Shanghai

first: Yongzhi

last: Wang

state: Shanghai

address: Huashan Road 1954

institute: Shanghai Jiao Tong University

data_processing:
Data quality control was performed on raw RNA-sequencing results. For the mRNA and lncRNA sequencing data, we utilized the FastQC software (version 0.11.9) for initial quality checks and Cutadapt (version 4.2) software for adapter trimming. Following quality control, the sequencing reads were mapped to the mouse reference genome (Mus musculus GRCm38) using the HISAT2 software (version 2.2.1). Quantitative analysis of the RNA-Seq data was conducted using the StringTie software (version 2.1.5). The original expression profile was compared to the mouse annotation file to distinguish mRNA from lncRNA for further analysis.
For the miRNA sequencing data, quality control was performed and sequencing adapters were removed using Cutadapt software (version 4.2). After rigorous sequence filtering, target sequences within the 18 to 35 nucleotide (nt) range were selected. The distribution of these target sequences primarily fell within the 20 to 24 nt range, aligning with the typical length of microRNAs. Subsequently, the target sequences were mapped to the mouse reference genome (mm38) using Bowtie2 software (version 2.5.1). The aligned sequences were extracted and further mapped to the mouse reference microRNAs in miRbase using the Bowtie2 software (version 2.5.1). The CIRI2 software was employed for quantification and differential expression analysis of circle RNA.

organism: Mus musculus

source_name: liver

growth_protocol: Male C57BL/6 mice (n=45, six weeks old) were randomly assigned to three groups: the CCl4-induced liver cancer group (liver cancer group), the PTH and CCl4-treated group (treatment group), and the control group (normal control group), with 15 mice per group. The mice in the normal control group received intragastric administration of double distilled water daily and intraperitoneal injections of olive oil twice a week. The liver cancer group was treated with intragastric administration of double distilled water daily and intraperitoneal injection of CCl4 twice a week. PTH was administrated intragastrically once a day for the treatment group, and CCl4 was injected intraperitoneally twice a week. In the 22nd week, we selected six mice from each group for RNA sequencing.

extract_protocol:
We extracted RNA from the mice liver tissues following the TRIzol reagent protocol provided by the manufacturer(Sigma).
After the removal of ribosomal RNA, two sequencing libraries were generated: NEBNext RNA Library Prep Kit (from NEB, USA) was used for lncRNA, circRNA, and mRNA sequencing, while the small RNA libraries were constructed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme #NR801) following the manufacturer's recommendations, respectively. Following the manufacturer's instructions, subsequent sequencing was performed on the Illumina HiSeq 4000 platform for paired-end 150 bp sequencing of lncRNAs, circRNAs and mRNAs, and on the Illumina NovaSeq platform for paired-end 50 bp sequencing of miRNAs.

treatment_protocol: We construct two groups liver cancer mice model using CCl4, one group treated with PZH and the other not.

value: liver

value: PTH week 22


title: mRNA and lncRNA AX6


title: mRNA and lncRNA AX2


title: mRNA and lncRNA AX3


title: mRNA and lncRNA AX1


title: mRNA and lncRNA AT5

value: CCL4 week 22


title: mRNA and lncRNA AT8


title: mRNA and lncRNA AT1


title: mRNA and lncRNA AT2


title: mRNA and lncRNA AT4


title: mRNA and lncRNA AC5

value: water week 22


title: mRNA and lncRNA AC3


title: Reference experiment, 14-24 hpf biological replicate 1, technical replicate 1


title: mRNA and lncRNA AC2


title: RPMI Tat rep 1

status: Public on May 24 2024

city: Moscow

first: Anna

last: Valyaeva

address: Leninskiye Gory, MSU, 1-73

department: Faculty of Bioengineering and Bioinformatics

country: Russia

institute: Lomonosov Moscow State University

data_processing:
Basecalling was performed using bcl2fastq v2.17.1.14.
Sequenced reads were trimmed for adaptor sequences using BBDuk.
Raw reads were aligned to GRCh38.p10 genome using HISAT2 v2.0.5 with parameters --no-softclip --dta-cufflinks; splice sites were obtained from gene annotation GENCODE v26.
Gene counts per gene were calculated using HTSeq v0.12.4 with gene annotation GENCODE v26 and parameters -m intersection-strict --stranded=no -t gene.
Normalized counts were obtained using DESeq2 v1.30.1.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files with raw counts for each sample
Supplementary files format and content: Matrix table with pre-filtered and normalized gene counts for every gene and every sample

source_name: RPMI 8866

growth_protocol: Cells were grown at 37°C in the RPMI 1640-Gluta-Max medium (#61870-010, Gibco) with the addition of 10% tet system approved FBS (#631107, Takara) sodium pyruvate (#F023 PanEco), and an antibiotic and antimycotic solution (#LS15240062, Gibco). The induction was performed with doxycyclin in concentration 1µg/ml.

extract_protocol:
Cells were collected and stored in RNALater (#76106, Quigen). Total RNA was extracted using Rneasy Mini RNA isolation kit (#74134, Qiagen) following Qiagen protocol, with the following modifications: (1) lysis time is increased up to 40 min; (2) on-column DNase I treatment is performed.
cDNA libraries were constructedusingthe NEBNext Ultra II RNA Library Prep Kit for Illumina (cat#E7770S/E7770L) by NEB followingthe manufacturer’s protocol.

value: RPMI 8866

value: Human lymphoblastoid B cells

tag: exogenous expression

value: Tat protein co-expressed with EGFP


title: RPMI Tat rep 2


title: mRNA and lncRNA AC4


title: RPMI Tat rep 3


title: control RPMI rep 2


title: mRNA and lncRNA AC1


title: mRNA and lncRNA AC8


title: control RPMI rep 1


title: RPMI Tat-ind Doxy+ rep 1

value: doxycycline induced Tat protein expression; EGFP


title: mRNA and lncRNA AT7


title: RPMI Tat-ind Doxy+ rep 3


title: control RPMI rep 3


title: RPMI Tat-ind Doxy- rep 2

value: no induction of Tat protein expression; EGFP


title: RS1-1

status: Public on May 01 2024

city: Heidelberg

first: Haikun

last: Liu

address: INF 581

country: Germany

institute: DKFZ

library_source: transcriptomic single cell

data_processing:
RTA 1.18.64 was used for base-calling
For all single-cell/bulk libraries from neural stem cells or brain tumours, we obtained the gene expression profiles via mapping the sequencing reads to mouse mm10 transcriptome by RSEM (v1.3.0) (Li and Dewey, 2011). For single cells from brain tumours, we kept cells with 200 to 3500 genes and less than 10% of reads on mitochondrial genes and projected the cells into low dimension space using Monocle (Qiu et al., 2017; Trapnell et al., 2014) in R (R Core Team, 2018). We calculated the spearman correlation coefficient for single cells in neural stem cell populations and brain tumour populations using log2 transformed TPM value.
We used the R package DESeq2 (Love et al., 2014) to estimate the differentially expressed genes between bulk Tlx-GFP+/dsRed+ and Tlx-GFP-/dsRed+ using the estimated counts from RSEM results. The statistcally signficant genes were selected with fdr <= 0.1. Heatmaps for selected genes were produced with ComplexHeatmap (Gu et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: csv

source_name: mice brain tumors

growth_protocol: Mice were housed according to international standard conditions and all animal experiments complied with local and international guidelines for the use of experimental animals.

extract_protocol:
RNA extraction using the Arcturus PicoPure RNA Isolation kit was performed according to the manufacturer’s protocol (Life technologies). Briefly, 100 ul of extraction buffer was added to the cells, followed by brief incubation at room temperatue. While the lysate was incubated, the purification column was wetted (Pre-condition) by adding 250 ul of condition buffer, followed by centrifugation at 16,000 × g for 1 min. 100 ul of 70% ethanol was then added to the lysate, mixed well and the whole mixture was transferred to the prepared purification columns. Purification columns were centrifuged for 2 min at 100 × g, followed by centrifuging at 16,000 × g for 30 sec to remove flow through. 100 ul of wash buffer 1 was added to the purification columns, which were then centrifuged for 1 min at 8,000 × g. DNase treatment may was performed directly within the purification column. 10 µl DNase I stock solution (Qiagen, catalog#79254) was mixed with 30 µL Buffer RDD. 40 µL DNase incubation mix was applied directly into the purification column membrane followed by Incubation at room temperature for 15 minutes. 40 ul of wash buffer 1 was added to the purification columns, which were then centrifuged for 15 seconds at 8,000 × g. After that, 100 ul of wash buffer 2 was added to the purification columns, which were then centrifuged for 1 min at 8,000 × g. Another 100 ul of wash buffer 2 was added to the purification columns. Purification columns were centrifuged at 16,000 × g for 2 min. Another spin at 16,000 × g for 1 min was performed to remove the wash residue in the columns. Purification columns were transferred to new Eppendorf tubes and 11 ul of elution buffer was carefully added onto the column membrane followed by 1 min incubation at room temperature. Purification Columns were centrifuged at 1,000 × g for 1 min, and subsequently at 16,000 × g for 1 min to elute RNA. 10 ul of RNA solution was obtained.
Libraries were constructed using the Nextera XT kit as recommended by the manufacturer (Illumina, San Diego, USA). 0.5 ng of cDNA was tagmented, utilizing 5 μl of Amplicon Tagment Mix with 10 μl Tagment DNA Buffer. Tagmentation reaction was performed by incubation for 20 min at 55°C. Next, index primers were added together with Nextera PCR Master Mix. Tagmented cDNA was amplified by limited-cycle PCR (10 cycles). Libraries were purified using AMPure beads (Beckman Coulter, High Wycombe, UK) and quality validated using Agilent 2100 BioAnalyzer. Libraries were normalized and 8 nM pooled libraries were then sequenced on Illumina HiSeq2000.

treatment_protocol: FACS Sorting.Brain tumor tissues were isolated in Phosphate buffered saline solution (PBS) and enzymatically dissociated with 0.05% Trypsin/EDTA (Gibco) in HBSS containing 2mM glucose at 37°C for 30 min. During incubation, the tissue was repeatedly triturated with a fire polished Pasteur pipette. Enzyme activity was stopped by addition of equal volume of 4% BSA in Earle’s Balanced Salt Solution (EBSS, Gibco). The cell suspension was filtered through a 70μm cell strainer and centrifuged at 1200 rpm for 5 min and the pellet was re-suspended in 0.9 M sucrose in 0.5 x HBSS (Gibco). After further centrifugation for 20 min at 2000 rpm the cell pellet was re-suspended in 2 ml of 4 % BSA in EBSS solution and placed on top of 12 ml of 4 % BSA in EBSS solution, centrifuged again for 9 min at 1500 rpm.  The resulting pellet was then suspended in PBS containing Recombinant RNase Inhibitor, 1 unit/μl reaction (Clontech). After incubation with PI (1:1000) for 2 minutes; either the single cells or 1000 cells per tube were sorted at a FACS Aria (BD). Two population of cells were sorted, RFP positive and RFP / Tlx-GFP positive cells.

tag: mouse number

value: mouse one

tag: strain background

value: Tlx-GFP;Ntv-a mice

tag: genotype/variation

value: RCAS-AKT, RCAS-PDGFB and RCAS-RFP retroviruses transfection

tag: cell types

value: brain tumor cells

tag: sequencing type

value: Single-cell RNAseq


title: RS1-5


title: RPMI Tat-ind Doxy- rep 1


title: RS1-6


title: RS1-4


title: RS1-9


title: RS1-7


title: RS1-11


title: RS1-10


title: RS1-13


title: RS1-12


title: RS1-14


title: RS1-15


title: RPMI Tat-ind Doxy+ rep 2


title: RS1-17


title: RPMI Tat-ind Doxy- rep 3


title: RS1-18


title: RS1-19


title: RS1-2


title: RS1-16


title: mRNA and lncRNA AX7


title: RS1-21


title: RS1-20


title: RS1-3


title: RS1-24


title: RS1-26


title: RS1-22


title: RS1-30


title: RS1-8


title: RS1-28


title: RS1-29


title: RS1-23


title: RS1-27


title: RS1-31


title: RS1-33


title: RS1-34


title: RS1-35


title: RS1-38


title: RS1-37


title: RS1-39


title: RS1-40


title: RS2-3

value: mouse two


title: RS2-1


title: RS2-7


title: RS2-4


title: RS2-8


title: RS2-5


title: RS2-11


title: RS2-9


title: RS2-13


title: RS2-14


title: RS2-15


title: RS2-16


title: RS2-12


title: RS2-17


title: RS2-18


title: RS1-36


title: RS2-20


title: RS2-21


title: RS2-22


title: RS2-26


title: RS2-25


title: Perturbation experiment 1, 6-14 hpf biological replicate 1, technical replicate 1

value: whole embryo

value: 1percent DMSO control and cell cycle arrest at 6 hpf


title: RS2-10


title: RS2-24


title: RS2-32


title: RS2-29


title: RS2-6


title: RS2-35


title: RS2-28


title: RS2-34


title: RS2-31


title: RS2-30


title: RS2-36


title: RS2-39


title: RS2-33


title: RS2-37


title: RS2-38


title: GS1-2

value: brain tumor stem cells


title: RS2-40


title: GS1-8


title: GS1-10


title: RS2-19


title: GS1-1


title: GS1-3


title: GS1-6


title: GS1-12


title: GS1-4


title: GS1-5


title: GS1-7


title: GS1-14


title: GS1-18


title: GS1-17


title: GS1-9


title: GS1-21


title: GS1-11


title: GS1-26


title: GS1-13


title: GS1-19


title: GS1-15


title: GS1-23


title: GS1-29


title: GS1-20


title: GS1-22


title: GS1-24


title: GS1-32


title: GS1-27


title: GS1-38


title: GS1-16


title: GS1-40


title: GS2-1


title: GS1-37


title: GS1-34


title: GS1-35


title: GS1-28


title: GS1-31


title: GS2-2


title: GS2-8


title: GS2-3


title: GS2-5


title: GS1-25


title: GS2-6


title: GS2-4


title: GS2-11


title: GS2-15


title: GS2-10


title: GS2-13


title: GS2-18


title: GS2-17


title: GS2-12


title: GS2-19


title: GS1-36


title: GS2-20


title: GS2-33


title: GS2-27


title: GS2-26


title: GS2-23


title: GS2-7


title: GS2-21


title: GS2-29


title: GS2-30


title: GS2-25


title: GS2-35


title: GS2-28


title: GS2-24


title: GS2-36


title: GS2-22


title: GS2-34


title: Recurrent HGSOC (R2)

status: Public on Apr 18 2024

city: Incheon

first: Hye-Yeon

last: Ju

address: 119 Academy-ro Yeonsu-gu, Incheon Republic of Korea

country: South Korea

institute: Incheon National University

description: Fresh frozen10x Genomics Visium Spatial transcriptome sequencing

data_processing:
All specimens from patients with cancer were obtained with appropriate consent and approval from the institutional review board of Seoul St. Mary’s Hospital, The Catholic University of Korea, College of Medicine (KC22SISI0687). We obtained ovarian cancer tissues from eight treatment-naïve patients who underwent cytoreductive surgery.
Visium Spatial Gene Expression Solution was used to measure total mRNA in the tissue sections and locations where gene activity occurred (10x Genomics).
Libraries were prepared according to the Visium Spatial Gene Expression Guide CG000239 (10x Genomics, Pleasanton, CA, USA). Libraries were sequenced on the NovaSeq platform (Illumina, San Diego, CA, USA).
10x Genomics Space Ranger v2.0.0 was used to perform gene counting of the Visium sequencing data. Fastq files were processed using the GRCh38 reference, and raw gene expression matrices were used for downstream analyses.
Assembly: GRCh38
Supplementary files format and content: filtered_feature_bc_matrix.h5: filtered gene expression count data in h5 Format
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: image.tif: image of tissue
Supplementary files format and content: scalefactors_json.json
Supplementary files format and content: tissue_positions_list.csv
Library strategy: Spatial Transcriptomics

source_name: high-grade serous ovarian cancer

extract_protocol:
Visium Spatial Gene Expression Solution was used to measure total mRNA in the fresh frozen tissue sections and locations where gene activity occurred (10x Genomics). The tissue sections were fixed, stained on Visium Spatial Tissue Optimization Slide, and permeabilized.
Libraries were prepared according to the Visium Spatial Gene Expression Guide CG000239 (10x Genomics, Pleasanton, CA, USA). The tissue sections placed on Visium Spatial Gene Expression Slide were fixed and stained, and cellular mRNA was captured using primers at gene expression spots.

value: high-grade serous ovarian cancer

tag: group

value: Recurrent

tag: Sex

value: Female

tag: stage (figo)

value: III

tag: age

value: treatment-naïve


title: Non-recurrent HGSOC (NR1)

value: Non-recurrent


title: Non-recurrent HGSOC (NR2)

value: IV


title: Recurrent HGSOC (R5)


title: Recurrent HGSOC (R1)


title: LSM1_Mutant_MNase

status: Public on Apr 12 2024

city: Durham

first: David

last: MacAlpine

state: NC

address: 308 Research Dr, Durham, NC 27710

department: Department of Pharmacology and Cancer Biology

institute: Duke University

data_processing:
FASTQ reads were aligned to sacCer3 (Saccharomyces cerevisiae) using bowtie v1.1.1 (Langmead 2010) using the paired-end option with the following bowtie flags: -m1 -n 2 -l 20 --best --strata -S - y --phred 33 --nProc 32. Aligned files were processed and converted into BAM format using samtools v1.2 (Heng Li et al. 2009).
Overall chromatin, nucleosome, and TF occupancy changes were quantified by calculating differences between fixed windows across every gene in the genome between control and mutant. Specific methods are described in the methods section of the paper.
Assembly: sacCer3, R64
Supplementary files format and content: RDS files containing Jensen-Shannon divergence, transcription factor, and nucleosome occupancy quantifications for each mutant. Specific details of the analyses are described in the Methods section of the manuscript

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast cells were grown in yeast extract peptone dextrose (YEPD) medium to an OD of 0.6-0.8

extract_protocol:
Cultures were cross-linked with 1% formaldehyde at room temperature (RT) for 30 min. and quenched with 0.125 M glycine at RT for 5 min. to neutralize the formaldehyde. Cells were centrifuged, washed withwater, and treated with Buffer Z (0.56M sorbitol, 50mM Tris) with 0.5 mL of 10mg/ml zymolyase at 25°C for 30 min. Extracts were centrifuged at 1500 rpm for 6 min. at 4°C and resuspended in NP buffer (1M sorbitol, 50mM NaCl, 10mM Tris pH 7.4, 5mM Mgcl2, 1mM CaCl2) containing 250mM spermidine, 0.007% b-ME, and 0.075% NP-40. In separate tubes, MNase was aliquoted as follows: 4 µL, 2 µL, 1 µL, 2 µL of 1:4 in water, and 1 µL in 1:4 water. 400 µL of extract were added to each MNase aliquot and incubated for 20 min. at RT. After digestion, 100 µL stop buffer (5mM SDS, 1mM EDTA) and 10 µL of 10mg/ml Proteinase K were added. Samples incubated O/N at 65°C. To recover DNA, samples were phenol:chloroform extracted and precipitated with 400 µL of isopropanol. DNA was treated with 0.1mg/ml RNaseA to remove RNA.
Illumina sequencing libraries of MNase-treated DNA were prepared using 500 ng of DNA as previously described (Henikoff et al 2011).

value: Yeast cells

tag: strain


title: Recurrent HGSOC (R3)


title: BDF1_Mutant_MNase


title: Non-recurrent HGSOC (NR3)


title: Recurrent HGSOC (R4)


title: GSM1_Mutant_MNase


title: MAC1_Mutant_MNase


title: GS2-31


title: RSC2_Mutant_MNase


title: VHR1_Mutant_MNase


title: TOG1_Mutant_MNase


title: CHD1_Mutant_MNase


title: GS2-32


title: FKH1_Mutant_MNase


title: NUT1_Mutant_MNase


title: SOH1_Mutant_MNase


title: SNT2_Mutant_MNase


title: SUT1_Mutant_MNase


title: XRN1_Mutant_MNase


title: CUP2_Mutant_MNase


title: ADA2_Mutant_MNase


title: MBP1_Mutant_MNase


title: FLO8_Mutant_MNase


title: SSN2_Mutant_MNase


title: STP1_Mutant_MNase


title: HAA1_Mutant_MNase


title: URC2_Mutant_MNase


title: PLM2_Mutant_MNase


title: MSN2_Mutant_MNase


title: REC8_Mutant_MNase


title: DAL81_Mutant_MNase


title: MBF1_Mutant_MNase


title: WAR1_Mutant_MNase


title: SWI4_Mutant_MNase


title: CST9_Mutant_MNase


title: VPS71_Mutant_MNase


title: RAD24_Mutant_MNase


title: SPT4_Mutant_MNase


title: CYC8_Mutant_MNase


title: KSS1_Mutant_MNase


title: DAL80_Mutant_MNase


title: TEC1_Mutant_MNase


title: IOC3_Mutant_MNase


title: RPN4_Mutant_MNase


title: FKH2_Mutant_MNase


title: GAT4_Mutant_MNase


title: ASG1_Mutant_MNase


title: NRG2_Mutant_MNase


title: XBP1_Mutant_MNase


title: EDS1_Mutant_MNase


title: CRZ1_Mutant_MNase


title: RTG3_Mutant_MNase


title: HHT1_Mutant_MNase


title: CSE2_Mutant_MNase


title: FAP1_Mutant_MNase


title: TOS8_Mutant_MNase


title: PHO2_Mutant_MNase


title: UGA3_Mutant_MNase


title: DHH1_Mutant_MNase


title: PAF1_Mutant_MNase


title: TBS1_Mutant_MNase


title: SRB8_Mutant_MNase


title: HTL1_Mutant_MNase


title: MAL33_Mutant_MNase


title: PAT1_Mutant_MNase


title: HCM1_Mutant_MNase


title: NRG1_Mutant_MNase


title: GAT2_Mutant_MNase


title: BYE1_Mutant_MNase


title: LYS14_Mutant_MNase


title: HIR3_Mutant_MNase


title: HOT1_Mutant_MNase


title: SOD1_Mutant_MNase


title: JHD2_Mutant_MNase


title: BAS1_Mutant_MNase


title: CBF1_Mutant_MNase


title: RSF2_Mutant_MNase


title: THO1_Mutant_MNase


title: SIP4_Mutant_MNase


title: ZAP1_Mutant_MNase


title: GZF3_Mutant_MNase


title: MED1_Mutant_MNase


title: SMK1_Mutant_MNase


title: ARG81_Mutant_MNase


title: HAL9_Mutant_MNase


title: YAP5_Mutant_MNase


title: MOT3_Mutant_MNase


title: STP2_Mutant_MNase


title: MAL13_Mutant_MNase


title: SIR1_Mutant_MNase


title: ZNF1_Mutant_MNase


title: SWP82_Mutant_MNase


title: NHP6A_Mutant_MNase


title: INO4_Mutant_MNase


title: GAT1_Mutant_MNase


title: SEC28_Mutant_MNase


title: YAP6_Mutant_MNase


title: YTA7_Mutant_MNase


title: ASP1_Mutant_MNase


title: SRB2_Mutant_MNase


title: MET32_Mutant_MNase


title: ROX1_Mutant_MNase


title: OAF3_Mutant_MNase


title: AFT1_Mutant_MNase


title: LIF1_Mutant_MNase


title: URE2_Mutant_MNase


title: MET28_Mutant_MNase


title: MIG1_Mutant_MNase


title: PGD1_Mutant_MNase


title: PDR1_Mutant_MNase


title: HAP3_Mutant_MNase


title: SEF1_Mutant_MNase


title: HAC1_Mutant_MNase


title: FUS3_Mutant_MNase


title: MGA1_Mutant_MNase


title: PDR3_Mutant_MNase


title: SUM1_Mutant_MNase


title: ARR1_Mutant_MNase


title: HIR1_Mutant_MNase


title: CTF4_Mutant_MNase


title: PHO4_Mutant_MNase


title: ECM23_Mutant_MNase


title: PHO85_Mutant_MNase


title: RDS1_Mutant_MNase


title: MET31_Mutant_MNase


title: CAM1_Mutant_MNase


title: RLM1_Mutant_MNase


title: UPC2_Mutant_MNase


title: MIG2_Mutant_MNase


title: RED1_Mutant_MNase


title: CRF1_Mutant_MNase


title: ADR1_Mutant_MNase


title: FZF1_Mutant_MNase


title: HAP2_Mutant_MNase


title: CDC73_Mutant_MNase


title: SKO1_Mutant_MNase


title: NUP170_Mutant_MNase


title: PDR8_Mutant_MNase


title: REF2_Mutant_MNase


title: NUP42_Mutant_MNase


title: WTM1_Mutant_MNase


title: WTM2_Mutant_MNase


title: YRR1_Mutant_MNase


title: AZF1_Mutant_MNase


title: ELG1_Mutant_MNase


title: SRB5_Mutant_MNase


title: RSC1_Mutant_MNase


title: SFL1_Mutant_MNase


title: PHD1_Mutant_MNase


title: PUT3_Mutant_MNase


title: MSN4_Mutant_MNase


title: RGT1_Mutant_MNase


title: TOS4_Mutant_MNase


title: STB3_Mutant_MNase


title: YRM1_Mutant_MNase


title: ACA1_Mutant_MNase


title: MIG3_Mutant_MNase


title: RFX1_Mutant_MNase


title: KAR4_Mutant_MNase


title: GCN4_Mutant_MNase


title: LEU3_Mutant_MNase


title: SWI6_Mutant_MNase


title: ACE2_Mutant_MNase


title: SPT3_Mutant_MNase


title: CAD1_Mutant_MNase


title: ERT1_Mutant_MNase


title: HPC2_Mutant_MNase


title: SMP1_Mutant_MNase


title: ARO80_Mutant_MNase


title: CUP9_Mutant_MNase


title: HHO1_Mutant_MNase


title: GAL4_Mutant_MNase


title: GLN3_Mutant_MNase


title: RDS2_Mutant_MNase


title: SPP1_Mutant_MNase


title: PIP2_Mutant_MNase


title: SKN7_Mutant_MNase


title: TYE7_Mutant_MNase


title: HAP5_Mutant_MNase


title: DAL82_Mutant_MNase


title: TEA1_Mutant_MNase


title: HMS1_Mutant_MNase


title: TAF14_Mutant_MNase


title: HIR2_Mutant_MNase


title: ECM5_Mutant_MNase


title: SIP3_Mutant_MNase


title: MSS11_Mutant_MNase


title: RDR1_Mutant_MNase


title: ARG80_Mutant_MNase


title: TDA9_Mutant_MNase


title: SUB1_Mutant_MNase


title: SPT8_Mutant_MNase


title: FUN30_Mutant_MNase


title: FUN19_Mutant_MNase


title: GAL80_Mutant_MNase


title: HOG1_Mutant_MNase


title: CHA4_Mutant_MNase


title: ARP6_Mutant_MNase


title: IOC2_Mutant_MNase


title: PPR1_Mutant_MNase


title: animal J, untreated - right uterine horn

status: Public on Apr 01 2024

city: Palo Alto

first: Elisa

middle: Tiannuo

last: Zhang

state: CA

address: 300 Pasteur Drive, Alway M311

institute: Stanford University School of Medicine

data_processing:
RNAseq reads were aligned to the GRCm38.p4 mouse genome using STAR version 2.6.1d with the following specifications: --sjdbGTFfile {GRCm38.p4 gtf} –readFilesCommand zcat –outSAMtype BAM SortedByCoordinate
Aligned reads were counted using featureCounts from the subread package (version 1.6.4) with the following specifications -a {GRCm48.p4 gtf} -s 0 -R CORE --primary
The count file was loaded into R and processed with DESeq2 (version 1.30.0) for differential expression analysis.
Assembly: mm10 (GRCm38.p4)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: full-thickness uterine horn

extract_protocol:
TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Animals were either subjected to surgery in the left uterine horn during diestrus or estrus, or to no surgery. After ~1 mo. recovery, animals were sacrified at the estrus phase. ~2 mm of the midsection of each uterine horn was excised, placed in TRIZol Reagent, homogenized, and stored at -80 until RNA isolation. RNA was isolated according to the manufacturer's instructions.

value: no surgery

tag: uterine horn

value: R


title: GAT3_Mutant_MNase

tag: cell type


title: CAT8_Mutant_MNase

tag: genotype


title: STB4_Mutant_MNase


title: OAF1_Mutant_MNase


title: animal J, untreated - left uterine horn

value: L


title: uterine right horn - animal F, estrus uninjured

value: surgery


title: STB5_Mutant_MNase


title: RGM1_Mutant_MNase


title: animal I, untreated - left uterine horn


title: uterine left horn - animal E, estrus injured


title: uterine left horn - animal H, untreated


title: uterine left horn - animal D, estrus injured


title: animal I, untreated - right uterine horn


title: uterine right horn - animal E, estrus uninjured


title: uterine left horn - animal G, untreated


title: uterine right horn - animal C, diestrus uninjured


title: uterine right horn - animal D, estrus uninjured


title: uterine left horn - animal C, diestrus injured


title: uterine right horn - animal B, diestrus uninjured


title: uterine left horn - animal A, diestrus injured


title: uterine left horn - animal B, diestrus injured


title: uterine left horn - animal F, estrus injured


title: uterine right horn - animal A, diestrus uninjured


title: CD45+ brain leukocytes ATAC 32967

status: Public on Mar 26 2024

city: Woodland

first: Sonny

middle: Ramirez

last: Elizaldi

address: County Road 98 and, Hutchison Dr

department: Immunology

institute: University of California Davis

description: 10x Genomics

data_processing:
gene expression and chromatin accessible regions were generated using cellranger-arc (v2.0.2)
Assembly: Mmul_10
Supplementary files format and content: hdf5 binary files, gzipped tab delimited text files

organism: Macaca mulatta

source_name: CD45+ enriched leukocytes

extract_protocol:
Nuclei were isolated from brain derived live CD45+ and CD45- cells using the Chromium Nuclei Isolation Kit (10X Genomics) using manufacture instructions. Following isolation, nuclei were stored on ice and used immediately for subsequent library preparation.
Barcoded 3’ single cell gene expression library and ATAC library were prepared from single nuclei suspensions using the Chromium Single Cell Multiome kit (10X Genomics) following the manufacturer’s instruction. The libraries were quantified by fluorometry on a Qubit instrument (LifeTechnologies) and by qPCR with a Kapa Library Quant kit (Kapa Biosystems-Roche) prior to sequencing. The libraries were sequenced on a NovaSeq 6000 sequencer (Illumina) with paired-end 150 bp reads with approximately 35,000 reads pairs per nuclei for gene expression and 25,000 read pairs per nuclei for ATAC libraries.
10X single nuclei multiome (snRNASeq and snATACSeq)

value: TFP/TFP

tag: age (years.months)

value: F

value: CD45+ enriched leukocytes

value: Chronic SIV CL757 infection + ART (FTC/TDF/DTG)


title: CD45+ brain leukocytes ATAC 35595

description: 10x Genomics


title: CD45+ brain leukocytes GEX 35595

description: 10x Genomics


title: CD45+ brain leukocytes GEX 33994

description: 10x Genomics

value: N/A - healthy


title: CD45+ brain leukocytes GEX 33980

description: 10x Genomics


title: CD45+ brain leukocytes GEX 32967

description: 10x Genomics


title: CD45+ brain leukocytes ATAC 33994

description: 10x Genomics


title: Pa_44228_PeriInv_G

status: Public on Mar 25 2024

city: Milan

first: Pierluigi

last: Di Chiaro

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

data_processing:
Reads were pre-processed (quality trimming and adapter clipping) using Trim Galore v0.6.5, then reads with a minimum of 20 bp were aligned to human genome build GRCh38/hg38 using Kallisto v0.46.0 with default parameters and in the correct orientation (--rf-stranded). Only uniquely mapped reads were retained.
Transcript-level expression were summarized to gene level using tximport v1.14.2 R-package and only protein coding genes were retained.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text file providing raw read count values for each sample

source_name: primary tumor

extract_protocol:
FFPE sections (4 μm) were mounted on polyethylene naphthalate membrane (PEN) slides, were deparaffinized in xylene and then partially rehydrated in an ethanol gradient up to 75% EtOH. After that sections were counterstained with freshly prepared Cresyl Violet for 30 seconds, they were washed twice in 75% EtOH and air dried completely before proceeding to the microdissection using a UV-based LMD7 laser microdissection system (Leica Microsystems) at 20x magnification. Microdissected areas were collected by gravity into strip-tube caps.
Microdissected areas were digested with 0.01 U of Proteinase K (ThermoFisher) for 1 hour at 60 C. 1 ul of 5 mM Proteinase K inhibitor (Calbiochem) was added to stop the reaction and samples were stored at -80 C until library preparation. They were then processed using the SMART-seq Stranded kit (Takara Bio USA, Inc.) according to the manufacturer’s protocol removing the initial fragmentation step.

tag: source

value: perineural invasion

tag: disease

value: human pancreatic ductal adenocarcinoma (PDAC)

tag: tissue

value: primary tumor

tag: tumor

value: inside

tag: distance from perineurium


title: Pa_44228_PeriInv_F


title: Pa_40867_PeriInv_D


title: Pa_40867_PeriInv_G

value: outside


title: Pa_47691_PeriInv_C


title: Pa_3791_PeriInv_A


title: Pa_47691_PeriInv_A


title: Pa_47624_PeriInv_A


title: Pa_36203_PeriInv_D


title: Pa_36203_PeriInv_B


title: Pa_34136_PeriInv_H


title: Pa_40867_PeriInv_A2


title: Pa_34136_PeriInv_A2


title: Pa_34136_PeriInv_D


title: Pa_333855_PeriInv_F


title: Pa_34136_PeriInv_A1


title: Pa_333855_PeriInv_A


title: Pa_34136_PeriInv_F


title: Pa_31330_PeriInv_B


title: Pa_31330_PeriInv_C


title: CD45+ brain leukocytes ATAC 33980

description: 10x Genomics

tag: treatment


title: Pa_28402_PeriInv_A3


title: Pa_28402_PeriInv_C


title: Pa_28402_PeriInv_E


title: Pa_28402_PeriInv_H


title: Pa_28402_PeriInv_D


title: Pa_28402_PeriInv_D3


title: Pa_28402_PeriInv_A2


title: Pa_40867_PeriInv_A1


title: Pa_18523_PeriInv_F


title: Pa_27285_PeriInv_B


title: Pa_18523_PeriInv_C


title: Pa_27285_PeriInv_D


title: Pa_28402_PeriInv_A1


title: Pa_15938_PeriInv_G


title: Pa_15938_PeriInv_D


title: Pa_15938_PeriInv_E


title: Pa_31330_PeriInv_A


title: Pa_15938_PeriInv_H


title: Pa_15938_PeriInv_B


title: Pa_10663_PeriInv_B


title: Pa_15938_PeriInv_A3


title: Pa_15938_PeriInv_A1


title: 70200576-1-16_024

status: Public on Mar 01 2024

type: RNA

city: Brussels

first: Frederic

last: Lemaigre

address: Avenue Hippocrate, 75

department: de Duve Institute

country: Belgium

institute: UCLouvain

hyb_protocol: Spatial profiling was performed on 5 micrometer-thick formalin-fixed paraffin-embedded (FFPE) tissue sections using GeoMx technology (NanoString Technologies, Seattle, WA, USA) which was implemented by NanoString. FFPE human gallbladder slides were baked for 1 h at 65°C, and subsequently processed on Leica automation platform with a protocol that includes three steps: slide baking, antigen retrieval for 20 min at 100°C, and 1.0 microgr/ml proteinase K treatment for 15 min. After taking the slides off the Leica automation platform, each slide was incubated overnight with the GeoMx Whole Transcriptome Atlas assay probe cocktail which contains 18,677 probes (lot HWTA12002). The following day, the slides were washed and immunostained for markers of epithelium (anti-panCytokeratin), leukocytes (CD45), alpha smooth muscle actin (aSMA)-expressing mesenchymal cells, and cell nuclei (HuR), using the following antibodies: anti-CD45 (CST, #13917); anti-aSMA (AbCam, #ab202368); anti-HuR (Santa Cruz, #SC5261); anti-panCytokeratin (Novus, NBP2-33200AF488).

scan_protocol: Samples were scanned using GeoMx machine

data_processing: Raw counts were normalised using the DESeq2 method (DESeq2 Bioconductor package v1.32.0).

label: No labeling of the barcodes

source_name: Gallbladder epithelium

label_protocol: see extract protocol

growth_protocol: not relevant

extract_protocol: Fluorescently-labeled slides from the two patients were loaded onto a GeoMx machine and were scanned for selection of regions of interest (ROIs). Barcodes were collected and dispensed into a 96 wemm microtiter plate. Subsequent barcoding reading was performed on Illumina NGS platform. GeoMx NGS Pipeline  was version 2.3.4. ROIs subjected to spatial transcriptomic profiling encompassed pan-cytokeratin-expressing epithelial areas of approximately 200 cells.

treatment_protocol: not relevant

tag: tumor stage

value: Adenocarcinoma

tag: age and disease

value: Fifty-three year old man affected with primary sclerosing cholangitis


title: 70200576-1-16_015

value: BilIN High Grade


title: 70200576-1-16_012


title: 70200576-1-16_016


title: 70200576-1-16_019


title: 70200576-1-16_013


title: 70200576-1-16_010


title: 70200576-1-16_023


title: 70200576-1-16_020


title: 70200576-1-16_018


title: 70200576-1-16_003

value: BilIN Low Grade


title: 70200576-1-16_009


title: 70200576-1-16_005


title: 70200576-1-16_021


title: 70200576-1-19_008

value: Normal Epithelium


title: 70200576-1-16_008


title: 70200576-1-16_014


title: 70200576-1-16_011


title: 70200576-1-16_017


title: 70200576-1-19_006


title: 70200576-1-16_006


title: 70200576-1-19_005


title: 70200576-1-16_001


title: 70200576-1-16_007


title: 70200576-1-16_002


title: 70200576-1-19_003


title: 70200576-1-16_004


title: 70200576-1-16_022


title: 70200576-1-19_007


title: 70200576-1-19_001


title: 70200576-1-19_002


title: 16H5566_024

value: Eighty-one year old woman with cholecystitis


title: 16H5566_018


title: 16H5566_021


title: 16H5566_022


title: 16H5566_012


title: 16H5566_019


title: 16H5566_015


title: 16H5566_023


title: 16H5566_017


title: 16H5566_016


title: 16H5566_014


title: 16H5566_009


title: 16H5566_006


title: 16H5566_007


title: LGAS7884 (floxed control)

city: St. Louis

first: Steven

last: Funk

address: 660 S. Euclud Ave

institute: Washington University

description: biolrep c3

data_processing:
Sequencing was performed on a NovaSeq6000 at the Washington University GTAC
Aligned reads were processed through CellRanger to generate count matrices
Unsupervised, heirarchical clustering was performed in R with the Seurat package after ambient clean-up using SoupX and DoubletFinder, and data integration using Harmony.
Supplementary files format and content: A count matrix of the cleaned and Seurat-processed files, merged together, log-transformed with principal component analysis and dimension reduction.

source_name: kidney

growth_protocol: Mice were aged in a pathogen-free environment for 2 years.

extract_protocol:
RNA isolation and barcoding was performed with 10X Genomics' 3' v3.1 kit and protocol
Libraries prepared with 10X Genomics' 3' v3.1, library set TT

treatment_protocol: Mice were treated with doxycyline-containing food at aged 5-8 wks for a total of 3 weeks to induce recombination

value: kidney

tag: gender

value: male

value: floxed control

value: 3mo old


title: 16H5566_010


title: 16H5566_004


title: 16H5566_005


title: 16H5566_013


title: LGAS7883 (Cpt1aCKO)

description: biolrep c2


title: 16H5566_011


title: 16H5566_008


title: 16H5566_002


title: 16H5566_003


title: 16H5566_020


title: LGAS7885 (Cpt1aCKO)

description: biolrep c1


title: LGAS7358 (Cpt1aCKO)

description: biolrep f2


title: LGAS7432 (floxed control)

description: biolrep f1


title: 16H5566_001


title: Genomic DNA from ependymoma 2001

status: Public on Jan 31 2024

type: genomic

city: Hamburg

first: Michael

last: Bockmayr

address: Martinistr. 52

department: Pediatric Hematology and Oncology

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip or the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the iScan System and the standard recommended Illumina scanner setting.

data_processing:
Statistical analysis was performed using the minfi package version 1.46.0 with the statistical programming language R version 4.3.0.
Average beta-values after combining arrays and normalization using the Noob method.

label: Cy5 and Cy3

source_name: ependymoma 2001

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). The DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA.

tag: Sex

value: F

tag: localization

value: spinal

tag: patho diagnosis

value: Ependymoma II

tag: classification result v12

tag: classification score


title: Genomic DNA from ependymoma 2021

source_name: ependymoma 2021

value: M

tag: age

tag: resection

value: STR


title: Genomic DNA from ependymoma 1996

source_name: ependymoma 1996


title: Genomic DNA from ependymoma 1994

source_name: ependymoma 1994


title: Genomic DNA from ependymoma 1565

source_name: ependymoma 1565

value: GTR

tag: OS status

tag: os [months]

tag: pfs status

tag: pfs [months]


title: Genomic DNA from ependymoma 1563

source_name: ependymoma 1563


title: Genomic DNA from ependymoma 640

source_name: ependymoma 640


title: SP-EPN 185

status: Public on Jan 26 2024

first: Karoline

last: Hack

address: Martinistraße 52

department: Children's Cancer Center Hamburg

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Methylation data were processed using minfi and noob normalization. CpG sites associated with SNPs and sex chromosomes were excluded.

label: Cy3 and Cy5

source_name: Spinal ependymoma

label_protocol: not provided

extract_protocol: DNA was extracted from FFPE tissue using the ReliaPrep™ FFPE gDNA Miniprep System (Promega). About 100-500 ng DNA were used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). The DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA.

tag: tissue

value: Spinal ependymoma (FFPE tissue)

tag: array type

value: EPIC

tag: material type

value: FFPE


title: SP-EPN 36


title: Genomic DNA from ependymoma 397

source_name: ependymoma 397

value: Ependymoma III


title: SP-EPN 81


title: SP-EPN 32


title: SP-EPN 3


title: Genomic DNA from ependymoma 1568

source_name: ependymoma 1568


title: SP-EPN 8


title: SP-EPN 5


title: iPSC822_5m_organoid, snRNAseq

status: Public on Jan 16 2024

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description:
Single-nucleus RNA-seq
10x Genomics

data_processing:
The Cell Ranger 6.0.1 pipeline (10x Genomics) was used to align reads from snRNA-seq collected from the transplants to the 10x hg19 human reference genome v1.2.0 and 10x mm10 mouse reference genome v1.2.0 and produce the associated cell-by-gene count matrix. Default parameters were used, except for –include-introns argument.
The Cell Ranger 6.0.1 pipeline (10x Genomics) was used to align reads from snRNA-seq collected from the in vitro organoids to the 10x hg19 human reference genome v1.2.0 and produce the associated cell-by-gene count matrix. Default parameters were used, except for –include-introns argument.
Unique molecular identifier (UMI) counts were analyzed using the Seurat R package v.4.0.1(Hao et al., 2021). Human nuclei (defined as nuclei with >95% genes mapped to hg19) were kept for subsequent analysis. Nuclei with <1% of mitochondrial contamination and between 500 and 6000 genes expressed were retained for further analysis.
The top 3000 variable genes for each line were then used to integrate sample datasets with the SCT method (SCTransform, SelectIntegrationFeatures, PrepSCTIntegration, FindIntegrationAnchors and IntegrateData functions). PCA was performed on the scaled integrated data for the variable genes and the top 30 principal components were used for the unsupervised clustering.
Cells were clustered in PCA space using the FindNeighbors function (top 30 principal components) and FindClusters function. UMAP plots were used to visualize variation in the data.
Assembly: hg19 and mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv matrix.mtx).
Supplementary_files_format_and_content: integratedorganoid_withAnnot.txt: Contains annotations for 5-month-old organoids, as well as 5-month-old, 6-month-old, and 8-month-old transplants.
Supplementary_files_format_and_content: 10wOrg_withAnnot.txt: Contains annotations for 10-week-old organoids.

source_name: cortical organoid

growth_protocol: Glia-enriched cortical organoids were generated using the reported protocol. Glia-enriched cortical organoids cultured in vitro were collected at 10 weeks and 5 months of differentiation for single nucleus RNA-seq. Glia-enriched cortical organoids were cultured in vitro for 8 to 10 weeks prior to implantation into the retrosplenial cortex of immunodeficient NSG mice. At 5, 6, and 8 months of differentiation, mice were sacrificed, and four organoid implants were dissected and pooled for single nucleus RNA-seq.

extract_protocol:
In vitro organoids or fresh dissected in vivo brain organoids were pooled and lysed using a Dounce homogenizer in 1ml of freshly prepared cold lysis buffer (TrisHCl pH 7.4 10mM, NaCl 10mM, MgCl2 3mM, NP-40 0.1% in nucleus free water). Nuclei were centrifuged at 500g for 8 min and supernatant was discarded. Nuclei were then resuspended in freshly prepared cold nuclei wash & resuspension buffer (PBS, 1% BSA, RNase inhibitor 0.2U/μl) and filtered through a 35μm strainer (corning). Nuclei were centrifuged at 500g for 5 min and resuspended again in nuclei wash & resuspension buffer for a total of two washes. After the second wash, nuclei were resuspended in ice-cold nuclei wash & resuspension buffer at a concentration of 800-1,200 cells/μl, and approximately 17,400 cells per channel (to give estimated recovery of 10,000 cells per channel) were loaded onto a Chromium Next GEM Chip G (10x Genomics) and processed through the Chromium controller to generate single-cell gel beads in emulsion (GEMs).
Single nucleus RNA-seq libraries were prepared with the Chromium NextGEM Single Cell 3′ GEM Library & Gel Bead Kit v.3.1 (10x Genomics) as per manufacturer’s instruction.

value: cortical organoid

value: 5 months

tag: cell line used to derive organoid

value: hESC

tag: condition

value: in vitro organoid


title: Hues6_8m_transplant_CTRL, scRNAseq

description: 10x Genomics

data_processing:
The Cell Ranger 6.0.1 pipeline (10x Genomics) was used to align reads from snRNA-seq collected from the transplants to the 10x hg19 human reference genome v1.2.0 and 10x mm10 mouse reference genome v1.2.0 and produce the associated cell-by-gene count matrix. Default parameters were used.
Unique molecular identifier (UMI) counts were analyzed using the Seurat R package v.4.0.1(Hao et al., 2021). Human cells (defined as nuclei with >95% genes mapped to hg19) were kept for subsequent analysis. Cells with <20% of mitochondrial contamination and between 500 and 6000 genes expressed were retained for further analysis.
The top 3000 variable genes for each line were then used to integrate sample datasets with the SCT method (SCTransform, SelectIntegrationFeatures, PrepSCTIntegration, FindIntegrationAnchors and IntegrateData functions). PCA was performed on the scaled integrated data for the variable genes and the top 30 principal components were used for the unsupervised clustering.
Cells were clustered in PCA space using the FindNeighbors function (top 30 principal components) and FindClusters function. UMAP plots were used to visualize variation in the data.
Assembly: hg19 and mm10
Supplementary files format and content: Tab-separated values files and matrix files.
Supplementary_files_format_and_content: integratedorganoid_withAnnot.txt: Contains annotations for 5-month-old organoids, as well as 5-month-old, 6-month-old, and 8-month-old transplants.
Supplementary_files_format_and_content: 10wOrg_withAnnot.txt: Contains annotations for 10-week-old organoids.

source_name: human with minor mouse contamination

growth_protocol: Glia-enriched cortical organoids were generated using the reported protocol. Glia-enriched cortical organoids were cultured in vitro for 8 to 10 weeks prior to implantation into the retrosplenial cortex of immunodeficient NSG mice. At 8 months of differentiation, mice were sacrificed, and four to six organoid implants were dissected and pooled for single cell RNA-seq.

extract_protocol:
In vitro organoids or fresh dissected in vivo brain organoids were pooled and lysed using a Dounce homogenizer in 1ml of freshly prepared cold lysis buffer (TrisHCl pH 7.4 10mM, NaCl 10mM, MgCl2 3mM, NP-40 0.1% in nucleus free water). Nuclei were centrifuged at 500g for 8 min and supernatant was discarded. Nuclei were then resuspended in freshly prepared cold nuclei wash & resuspension buffer (PBS, 1%BSA, Rnase inhibitor 0.2U/μl) and filtered through a 35μm strainer (corning). Nuclei were centrifuged at 500g for 5 min and resuspended again in nuclei wash & resuspension buffer for a total of two washes. After the second wash, nuclei were resuspended in ice-cold nuclei wash & resuspension buffer at a concentration of 800-1,200 cells/μl, and approximately 17,400 cells per channel (to give estimated recovery of 10,000 cells per channel) were loaded onto a Chromium Next GEM Chip G (10x Genomics) and processed through the Chromium controller to generate single-cell gel beads in emulsion (GEMs).
single cell RNA-seq libraries were prepared with the Chromium NextGEM Single Cell 3′ GEM Library & Gel Bead Kit v.3.1 (10x Genomics) as per manufacture’s instruction.

value: cortical organiod

value: 8 months

tag: cell type

value: transplant


title: 70200576-1-19_004

tag: tumor stage

value: Normal Epithelium

tag: age and disease

value: Fifty-three year old man affected with primary sclerosing cholangitis


title: Hues6_10w_organoid, snRNAseq

description:
Single-nucleus RNA-seq
10x Genomics

value: 10 weeks

value: iPSC


title: Hues6_8m_transplant_TNFa, scRNAseq

description: 10x Genomics


title: iPSC822_10w_organoid, snRNAseq

description:
Single-nucleus RNA-seq
10x Genomics


title: Hues6_5m_organoid, snRNAseq

description:
Single-nucleus RNA-seq
10x Genomics


title: SP-EPN 4


title: iPSC822_8m_transplant, snRNAseq

description:
Single-nucleus RNA-seq
10x Genomics
Human with minor mouse contamination


title: Hues6_8m_transplant, snRNAseq


title: Hues6_5m_transplant, snRNAseq


title: SP-EPN 14


title: Hues6_6m_transplant, snRNAseq

description: human with minor mouse contamination

data_processing:
The Cell Ranger 6.0.1 pipeline (10x Genomics) was used to align reads from RNA-seq to the 10x hg19 human reference genome v1.2.0 and 10x mm10 mouse reference genome v1.2.0 and produce the associated cell-by-gene count matrix. Default parameters were used, except for –include-introns argument.
Unique molecular identifier (UMI) counts were analyzed using the Seurat R package v.4.0.1(Hao et al., 2021). Human nuclei (defined as nuclei with >95% genes mapped to hg19) were kept for subsequent analysis. Nuclei with <1% of mitochondrial contamination and between 500 and 4000 genes expressed were retained for further analysis.
The top 2,000 variable genes were calculated by Seurat (selection method vst and 2000 features) and the ScaleData function was used center and scale the data. Principal component analysis (PCA) was performed on the scaled data for the variable genes and the top 30 principal components were used for the unsupervised clustering.
Cells were clustered in PCA space using the FindNeighbors function (top 30 principal components) and FindClusters function (resolution = 0.5). Variation in the cells was visualized by UMAP.
Next, doublets were discarded using DoubletFinder v.2.0.3(McGinnis et al., 2019) with an expected doublet rate of 0.1 for iPSC822 and 0.18 for Hues6 according to the Cell Ranger summary.
The top 2,000 variable genes for each line were then used to integrate sample datasets (FindIntegrationAnchors and IntegrateData functions). PCA was performed on the scaled integrated data for the variable genes and the top 30 principal components were used for the unsupervised clustering.
Cells were clustered in PCA space using the FindNeighbors function (top 20 principal components) and FindClusters function (resolution = 0.5). UMAP plots were used to visualize variation in the data.
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: zipped file containing cellranger filtered matrix files.
Supplementary_files_format_and_content: integratedorganoid_withAnnot.txt: Contains annotations for 5-month-old organoids, as well as 5-month-old, 6-month-old, and 8-month-old transplants.
Supplementary_files_format_and_content: 10wOrg_withAnnot.txt: Contains annotations for 10-week-old organoids.

source_name: brain organoid

growth_protocol: Glia-enriched brain organoids were generated using the reported protocol. Glia-enriched brain organoids were cultured in vitro for 8 to 10 weeks prior to implantation into the retrosplenial cortex of immunodeficient NOD-SCID mice. At 6 months of differentiation, mice were sacrificed, and four organoid implants were dissected and pooled for single nucleus RNA-seq.

extract_protocol:
Fresh dissected in vivo brain organoids were pooled and lysed using a Dounce homogenizer in 1ml of freshly prepared cold lysis buffer (TrisHCl pH 7.4 10mM, NaCl 10mM, MgCl2 3mM, NP-40 0.1% in nucleus free water). Nuclei were centrifuged at 500g for 8 min and supernatant was discarded. Nuclei were then resuspended in freshly prepared cold nuclei wash & resuspension buffer (PBS, 1%BSA, Rnase inhibitor 0.2U/μl) and filtered through a 35μm strainer (corning). Nuclei were centrifuged at 500g for 5 min and resuspended again in nuclei wash & resuspension buffer for a total of two washes. After the second wash, nuclei were resuspended in ice-cold nuclei wash & resuspension buffer at a concentration of 800-1,200 cells/μl, and approximately 17,400 cells per channel (to give estimated recovery of 10,000 cells per channel) were loaded onto a Chromium Next GEM Chip G (10x Genomics) and processed through the Chromium controller to generate single-cell gel beads in emulsion (GEMs).
single nucleus RNA-seq libraries were prepared with the Chromium NextGEM Single Cell 3′ GEM Library & Gel Bead Kit v.3.1 (10x Genomics) as per manufacture’s instruction.

value: 6 months

value: brain organoid

tag: molecule subtype

value: single-nucleus RNA


title: SP-EPN 7

value: Spinal ependymoma (FFPE tissue)

value: EPIC


title: iPSC822_6m_transplant, snRNAseq

description: human with minor mouse contamination


title: Col-0_SA_G6_E

status: Public on Jan 11 2024

city: Freising

first: Zhilin

state: Bavaria

address: Emil-Ramann-Str. 4

department: School of Life Sciences

institute: Technical University of Munich

data_processing:
Run MethylStar pipeline (Shahryary et al., 2020), using TAIR10 as a reference.
When applicable, different files corresponding to the same sample were merged at the BAM stage using “samtools merge -n” (Samtools version 1.11).
Cytosine-level methylation states were called as either methylated (“M”), unmethylated (“U”) or intermediate methylated (“I”) using a three-state Hidden Markov Model (Taudt et al. 2018).
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files for methylome generated using METHimpute

organism: Arabidopsis thaliana

source_name: leaf tissue

growth_protocol: Arabidopsis thaliana (ecotype Col-0) seeds were suspended in 0.1% agarose (0.1% w/v agarose in deionised H2O (dH2O)) and stored in the dark for 2 days at 4 °C  to break dormancy, after which they were sown onto soil consisting of Levington Advance Pot & Bedding M3 compost (ICL) and sand in a 4:1 ratio and cultivated under the following conditions: 16:8 hr day:night, 22 °C, 60% relative humidity (RH) and 150 μmol m−2 s−1. At 10-14 days, seedlings were thinned to one per pot. Lines were propagated through collection of seed from single plants.

extract_protocol:
Seedlings were cultivated under the same growth conditions. After 3 weeks of growth, 28-35 seedlings per replicate were extracted, pooled, flash frozen and ground to a powder. Genomic DNA was extracted by Leonardo Furci using the GenElute Plant Genomic DNA Miniprep Kit (Sigma-Aldrich).
Bisulfite treatment, library preparation and 150 bp paired-end sequencing was performed by BGI genomics.

treatment_protocol: At 21, 28 and 35 days post-sowing, plants were treated with a mock treatment, salicylic acid (SA) or a pathogen. 10 mM MgSO4 was used as the mock treatment, while salicylic acid was delivered as 5 mM sodium salicylate in 10 mM MgSO4. For the pathogen treatment, 100 mL LB culture of Pseudomonas syringae pv. tomato DC3000 (Pst) was grown at 25-28ºC with shaking at 200 rpm. The Pst was resuspended in 10 mM MgSO4 at OD 0.1 (595nm). 0.01% Silwet L-77 was added to each solution immediately before plant spraying. Plants were covered for two days after each treatment. Material for DNA methylome analysis was collected by Sam Wilkinson from seedlings in the generation immediately following the mock, SA or Pst treatments, as detailed under DNA Extraction Protocol.

value: leaf tissue

tag: generation

tag: lineage

value: E

tag: treatment

value: SA

tag: genotype


title: Col-0_SA_G6_A

value: A


title: Col-0_SA_G6_C

value: C


title: Col-0_SA_G6_D

value: D


title: Col-0_SA_G2_D


title: Col-0_SA_G2_C


title: Col-0_SA_G2_A


title: Col-0_SA_G11_E


title: Col-0_SA_G11_C


title: Col-0_SA_G11_A


title: Col-0_Pst_G6_E

value: Pst


title: Col-0_SA_G11_D


title: Col-0_Pst_G6_D


title: Col-0_Pst_G6_A


title: Col-0_Pst_G2_C


title: Col-0_Pst_G6_C


title: Col-0_Pst_G2_D


title: Col-0_Pst_G11_E


title: Col-0_Pst_G2_E


title: Col-0_Pst_G2_A


title: Col-0_Pst_G11_D


title: Col-0_Pst_G11_C


title: iPSC822_5m_transplant, snRNAseq

value: cortical organoid

tag: age

value: 5 months

value: hESC

value: transplant


title: Col-0_Mock_G6_E

value: Mock


title: Col-0_SA_G2_E


title: Col-0_Mock_G6_A


title: Col-0_Mock_G6_C


title: Col-0_Pst_G11_A


title: Col-0_Mock_G2_A


title: Col-0_Mock_G2_C


title: Col-0_Mock_G6_D


title: Col-0_Mock_G2_E


title: Col-0_Mock_G2_D


title: BL6_Ctrl_1

status: Public on Dec 29 2023

city: Bethesda

first: Mingming

last: Zhao

address: 9000 Rockville Pike

institute: national institutes of health

data_processing:
TheReal Time Analysis software (RTA 3.9.25) was used for processing raw data files, the Illumina bcl2fastq v2.17 was used to demultiplex and convert binary base calls and qualities to fastq format.
Samples were trimmed for adapters using Cutadapt (1.18) before the alignment.
The trimmed reads were aligned with mm10 reference using Bowtie2(2.2.6) alignment.
The peaks were called using Genrich (0.6.1) (genrich -t sample_sortedByRead.bam -o sample.narroPeak -j -y -r -v -d 150 -m 5 -e chrM,chrY -E blacklist_regions.bed-f sample.bdg -b sample.bed)
Assembly: mm10
Supplementary files format and content: bigwig files were generated using Genrich (0.6.1)

source_name: peritoneal cells

growth_protocol: Macrophage cells were isolated from the peritoneal cells by using EasySep™ Mouse F4/80 Positive Selection Kit (100-0659, Stemcell Technologies)

extract_protocol:
100,000 macrophage cells were subjected to lysis using 100 µl of Lysis buffer (containing 10 mM Tris-Cl at pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, and 0.1% Tween-20). Following a centrifugation at 500g for 10 minutes at 4°C, the resulting nuclei were reconstituted with 50 µl of a transposition mixture (FC-121-1030, Illumina; comprising 1X Tagment DNA buffer, Tn5 Transposase, and nuclease-free H2O), and this mixture was then incubated for 30 minutes at 37°C in a thermomixer. The transposed DNA was subsequently purified using MinElute columns (28004, QIAGEN) and then amplified using Nextera sequencing primers and the NEB high-fidelity 2X PCR master mix for 11 cycles (M0541, New England Biolabs). PCR-amplified DNA was purified using MinElute columns
ATAC-seq samples were pooled and sequenced on NextSeq 2000 P2 using PI lab prepared library and paired-end sequencing.

treatment_protocol: Two replicates were IL-4 treated for 4 days in BL/6 and BALB/c mice

value: macrophages

tag: strain

value: untreated


title: BL6_IL4_2

value: treated with A fusion protein of mouse IL-4 with the Fc portion of IgG1


title: M-MOI-36h-D4

status: Public on Dec 24 2023

city: Madrid

first: Angeles

last: Domínguez Soto

address: Ramiro de Maeztu

country: Spain

institute: CSIC

data_processing:
Low quality reads were filtered using filtering software SOAPnuke (developed by BGI, Version v1.5.2, with parameters -l 15 -q 0.2 -n 0.05) to remove the reads containing the adaptor(adaptor pollution), the reads whose N content is greater than 5%, and low-quality reads (defined as those with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" were saved in FASTQ format. Sequences were mapped to GRCh38 genome (version GCF_000001405.38_GRCh38.p12) using Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

source_name: RNA from monocyte-derived macrophages 36 hours after cultured with SARS-CoV-2

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 1000 U/ml M-CSF to generate M-CSF-polarized macrophages.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Monocyte-derived macrophages were cultured with SARS-CoV-2 (SARS-CoV-2 clinical isolate Gisaid EPI_ISL_1120962, corresponding to ancestral S D614G, at an MOI=1) or nothing. After 4, 12 and 36 hours, cells were lysed and RNA isolated for transcriptional analysis.

tag: cell

value: Monocyte-derived M-CSF macrophages

value: Cultured with SARS-CoV-2

tag: time


title: M-MOI-36h-D3


title: M-MOI-36h-D2


title: Col-0_Mock_G11_E

tag: tissue

value: leaf tissue


title: M-MOI-12h-D3

source_name: RNA from monocyte-derived macrophages 12 hours after cultured with SARS-CoV-2


title: M-MOI-12h-D2


title: M-MOI-12h-D1


title: M-MOI-4h-D1

source_name: RNA from monocyte-derived macrophages 4 hours after cultured with SARS-CoV-2


title: M-MOI-4h-D4


title: M-UNT-36h-D4

source_name: RNA from monocyte-derived macrophages 36 hours after cultured without virus


title: M-MOI-4h-D3


title: M-MOI-12h-D4


title: M-UNT-36h-D3


title: M-MOI-4h-D2


title: M-UNT-36h-D2


title: M-UNT-36h-D1


title: M-UNT-12h-D4

source_name: RNA from monocyte-derived macrophages 12 hours after cultured without virus


title: M-UNT-12h-D3


title: Col-0_Mock_G11_D


title: Col-0_Mock_G11_C


title: Col-0_Mock_G11_A


title: M-UNT-4h-D4

source_name: RNA from monocyte-derived macrophages 4 hours after cultured without virus


title: M-UNT-4h-D3


title: M-UNT-4h-D2


title: M-MOI-36h-D1


title: M1_donor3_rep2_Multiome H3K27ac

status: Public on Nov 28 2023

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: UCSD

data_processing:
Fastq files are demultiplexed using cellranger-arc v.2.0.0 (10x Genomics) with command `cellranger-arc mkfastq`. DNA and RNA data were preprocessed using cellranger-atac v.2.0.0 and cellranger v.6.1.2, respectively, and barcodes were manually paired with custom script using the matching relationship provided in cellranger-arc.
Assembly: hg38 GRCh38
Supplementary files format and content: "barcode.tsv.gz" contains cell barcode information. "features.tsv.gz" consists of rows containing features (genes and peaks) and columns containing cell-associated barcodes. "matrix.mtx.gz" contains sparse feature-barcode matrix.
Library strategy: mutiome-seq

source_name: Multiome H3K27ac Paired-Tag

extract_protocol:
nuclei preparation protocol: Cells from frozen tissue were extracted by douncing in douncing buffer (0.25 M sucrose (Sigma, S7903), 25 mM KCl (Sigma, P9333), 5 mM MgCl2, 10 mM Tris-HCl pH 7.4, 1 mM DTT (Sigma, D9779), 1× Protease Inhibitor, 0.5 U µl−1 RNase OUT, 0.5 U µl−1 SUPERase Inhibitor). The cell suspension was filtered through a 30-µm Cell-Tric (Sysmex) to remove debris and spun down for 10min at 300g, 4 °C. Cell pellets were washed once with douncing buffer, spun down again, and resuspended in cold nuclei permeabilization buffer for 10mins. Permeablized nuclei were pelleted by centrifuge for 10 min at 1,000g, 4 °C, and washed with sort buffer (1× PBS (Gibco, 10010023), 1×Protease Inhibitor (Roche, 05056489001), 0.5 U µl−1 RNase OUT (Invitrogen, 10777-019), 0.5 U µl−1 SUPERase Inhibitor (Invitrogen, AM2694), 1mM EDTA (Invitrogen, 15575020), 1% BSA (Sigma, A1595)). Nuclei were resuspended in sort buffer and stained with  μM 7-AAD (Invitrogen, A1310) for 10mins on ice, and proceed to Fluorescence-activated cell sorting (FACS) with an SH800 cell sorter (Sony) to isolate of single nucleus. Nuclei were collected in collection buffer (1× PBS (Gibco, 10010023), 5×Protease Inhibitor (Roche, 05056489001), 2.5 U µl−1 RNase OUT (Invitrogen, 10777-019), 2.5 U µl−1 SUPERase Inhibitor (Invitrogen, AM2694), 1mM EDTA (Invitrogen, 15575020), 5% BSA (Sigma, A1595)) at 5 °C. After centrifugation for 10min at 750g at 4 °C. Nuclei were washed twice with sort buffer and counted on an RWD C100-pro fluorescence cell counter with DAPI staining. For each histone modification, around 0.5 million sorted nuclei were aliquoted and proceeded to Paired-Tag experiments.
DNA and RNA libraries were generated according to the Chromium Single Cell ATAC Library kit manual with increased number of amplification cycles (12-13 cycles) for DNA library.
All sequencing was performed with an Illumina Nextseq2000 sequencer.

tag: donor id

tag: Sex

value: M

tag: antibody


title: Day12, scRNAseq

status: Public on Aug 29 2023

city: New Brunswick

first: Xiyuan

state: NJ

address: 195 Little Albany St.

department: Pediatric Hematology/Oncology

institute: Rutgers Cancer Institute

description: 10x Genomics

data_processing:
Base calling was performed using RTA 3.4.4, demultiplexing was performed using cellranger v6.1.2 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v6.1.2 (STAR 2.7.2a). Sequenced reads were aligned to the 10x Genomics provided human reference sequence (refdata-gex-GRCh38-2020-A). HTOs used for the analysis are human HTO01 and HTO02, TotalSeqC from BioLegend.
Supplementary files format and content: hg38
Supplementary files format and content: h5 files

source_name: E7-TCR T cells

extract_protocol:
E7-TCR T cells were challenged with CaSki tumor cells and collected at days 0, 12, and 26 after the challenge. In each sample, we labeled the IL15 cells with TotalSeq-C0251, cat. no. 394661, barcode seq. GTCAACTCTTTAGCG; - IL15/21 cells TotalSeq-C0252, cat. no. 394663, barcode seq. TGATGGCCTATTGGG
The cellular samples were loaded in the lanes according to the 10x Genomics 5’v2 Single Cell Chromium User Guide (Dual Index), with a single capture lane consisting of two samples. The target recovery was 8,000 cells per lane.

value: E7-TCR T cells

value: E7-TCR T cells were continuously exposed to tumor cells and harvested after 5 challenges


title: Day26, scRNAseq

description: 10x Genomics

value: E7-TCR T cells were continuously exposed to tumor cells and harvested after 14 challenges


title: M1_donor3_rep1_Multiome Gene Expression

data_processing:
Fastq files are demultiplexed using cellranger-arc v.2.0.0 (10x Genomics) with command `cellranger-arc mkfastq`. DNA and RNA data were preprocessed using cellranger-atac v.2.0.0 and cellranger v.6.1.2, respectively, and barcodes were manually paired with custom script using the matching relationship provided in cellranger-arc.
Assembly: hg38 GRCh38
Supplementary files format and content: "barcode.tsv.gz" contains cell barcode information. "features.tsv.gz" consists of rows containing features (genes and peaks) and columns containing cell-associated barcodes. "matrix.mtx.gz" contains sparse feature-barcode matrix.

source_name: Multiome Gene Expression


title: Day0, scRNAseq

description: 10x Genomics

value: E7-TCR T cells with no tumor challenge.


title: M1_donor3_rep1_Multiome H3K27ac


title: SSc_Tocilizumab_2709

status: Public on Jul 26 2023

city: South San Francisco

first: Jason

middle: Anthony

last: Vander Heiden

address: 1 DNA Way

department: Biological Research AI Development

institute: Genentech

data_processing:
Sequencing reads were filtered and aligned using HTSeqGenie against the human genome assembly GRCh38.
Assembly: GRCh38
Supplementary files format and content: TSV count matrices

source_name: skin

extract_protocol:
Skin samples in RNAlater (Qiagen, Austin, TX, USA) were transferred to TRIzol (ThermoFisher Scientific, Waltham, MA, USA) filled tubes and homogenized using a Miltenyi gentleMACS Dissociator. Total RNA was extracted using RNeasy Fibrous Tissue mini kit.
Libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit.

value: skin

value: tocilizumab

tag: disease state

value: systemic sclerosis

tag: timepoint

value: Day 1 Baseline

tag: subject id


title: SSc_Tocilizumab_2705


title: SSc_Tocilizumab_2704


title: SSc_Tocilizumab_2708


title: SSc_Tocilizumab_2699


title: SSc_Tocilizumab_2698


title: M-UNT-12h-D2


title: SSc_Tocilizumab_2694


title: SSc_Tocilizumab_2692


title: SSc_Tocilizumab_2700


title: SSc_Tocilizumab_2693


title: M-UNT-12h-D1


title: SSc_Tocilizumab_2690


title: SSc_Tocilizumab_2683


title: SSc_Tocilizumab_2676


title: SSc_Tocilizumab_2680


title: SSc_Tocilizumab_2675

value: Week 48


title: M1_donor3_rep2_Multiome Gene Expression


title: SSc_Tocilizumab_2691


title: M-UNT-4h-D1


title: SSc_Tocilizumab_2673


title: SSc_Tocilizumab_2667


title: SSc_Tocilizumab_2666


title: SSc_Tocilizumab_2672


title: SSc_Tocilizumab_2665


title: SSc_Tocilizumab_2659


title: SSc_Placebo_2702

value: placebo


title: SSc_Placebo_2710


title: SSc_Tocilizumab_2662


title: SSc_Tocilizumab_2661


title: SSc_Placebo_2703


title: SSc_Tocilizumab_2650


title: SSc_Tocilizumab_2647


title: SSc_Tocilizumab_2652


title: SSc_Tocilizumab_2646


title: SSc_Placebo_2701


title: SSc_Placebo_2696


title: SSc_Placebo_2686


title: SSc_Placebo_2689


title: SSc_Tocilizumab_2668


title: SSc_Placebo_2682


title: SSc_Placebo_2688


title: SSc_Placebo_2681


title: SSc_Placebo_2677


title: SSc_Placebo_2671


title: SSc_Placebo_2674


title: SSc_Placebo_2684


title: SSc_Placebo_2679


title: SSc_Placebo_2669


title: SSc_Placebo_2687


title: SSc_Placebo_2685


title: SSc_Placebo_2678


title: SSc_Placebo_2663


title: SSc_Placebo_2695


title: SSc_Placebo_2660


title: SSc_Placebo_2658


title: SSc_Placebo_2655


title: SSc_Placebo_2656


title: SSc_Placebo_2654


title: SSc_Placebo_2657


title: SSc_Placebo_2651


title: SSc_Placebo_2649


title: SSc_Placebo_2648


title: SSc_Placebo_2645


title: Normal_None_3079

value: normal


title: Normal_None_3076


title: SSc_Placebo_2644


title: SSc_Placebo_2670


title: Normal_None_3077


title: Normal_None_3073


title: Normal_None_3078


title: Normal_None_3074


title: Normal_None_3069


title: Normal_None_3075


title: Normal_None_3071


title: Normal_None_3068


title: Normal_None_3072


title: Normal_None_3067


title: Normal_None_3066


title: Normal_None_3065


title: HCI013-107343

status: Public on Jul 18 2023

city: Richmond

first: Wright Center for Clinical and Translational Research

last: Bioinformatics Core

state: VA

address: 203 E Cary St

institute: Virginia Commonwealth University

data_processing:
Basecalling: BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14)
QC: Fastq files containing the read were analyzed with FastQC v.0.11.8 to identify any quality concerns with the raw data.
Alignment: Fastq files were aligned independently to the merged human/mouse hg19mm10 genome provided by 10X using CellRanger v6 "count" algorithm with the expected number of cells set to 5000.
Mouse Cell Removal: An in-house R script and the 10X-generated GEM file were used to identify and remove all mouse and multiplet cell barcodes from each PDX sample by using the CellRanger script "subset_bam".  The remaining reads were converted back to fastq files using the CellRanger script "bamtofastq".  These new filtered fastq files were then re-aligned independently to the GRCh38 human genome using the CellRanger "count" algorithm, however, this time the Force Cells option was set to the exact number of remaining human cells for each sample.
Dead Cell Removal: An in-house R script using the Seurat v4 R package was used to identify and remove barcodes associated with dead or poor quality cells.  The 10X "subset_bam" and "bamtofastq" scripte were once again used to filter the bam files for each sample to generate fastq files containing only the reads from good quality human cells.
Alignment: Each sample was re-aligned to the human GRCh38 genome provided by 10X using the CellRanger "count" algorithm with the Force Cells option set to the exact number of good quality cells identified in the previous step.
Assembly: GRCh38
Supplementary files format and content: The process data files include the 10X formatted features.tsv.gz, barcodes.tsv.gz, and matrix.mtx.gz files that can be imported directly into R using the Seurat package.

source_name: ER+ breast cancer patient-derived xenograft

growth_protocol: PDX tumors were grown orthotopically in NSG mice for 8 weeks.

extract_protocol: 10x Genomics Chromium kit

treatment_protocol:
Carboplatin Resistant:  Mice with PDXs were grown and treated three times spaced out every 4 days with 40mg/kg of carboplatin. Once the tumors regrew they were passaged to new recipient mice and then treated with another set of carboplatin. This proceeded until the tumors no longer responded to carboplatin; at this point they were termed carboplatin-resistant.
Tamoxifen Resistant: Mice harboring PDX tumors were given tamoxifen citrate chow. These PDXs were passaged under tamoxifen citrate selection until no difference in growth rate between treated and untreated tumors was observed. These models were then termed "tamoxifen resistant."
Tamoxifen citrate: Chow was replaced with Tamoxifen citrate chow from Envigo (600mg/kg) for 2 weeks prior to tumor excision.
Estradiol Withdrawal (EWD): Ovariectomy was performed and no exogenous estrogen pellet was provided.
Estrogen pellet:Two milligram slow-release estrogen pellets were implanted subcutaneously as an exogenous source of estrogen.
Ovariectomy (OVX): Both ovaries were surgically removed from mice to withdraw the primary source of estrogen.

tag: biomaterial provider

value: Huntsman Cancer Institute

tag: cell type

value: PDX

value: OVX, EWD

value: PDX mammary tumor


title: HCI-011_107324


title: HCI-011_107409

value: Estrogen pellet


title: HCI-011_107322


title: BCM-5097_107348

value: Baylor College of Medicine


title: BCM-15034_107244


title: BCM-15034_107352


title: BCM-15034_107634

value: Tamoxifen Resistant

value: Tamoxifen citrate, Estrogen pellet


title: BCM-15057-107673

value: Untreated


title: WHIM2_105940

source_name: Basal-like triple-negative breast cancer patient-derived xenograft

value: Washington University in St. Louis


title: BCM-0132_107455


title: UCD52CR_107269

value: University of Colorado Anschutz Medical Campus

value: Carboplatin Resistant

value: Carboplatin


title: HCI013_106663


title: UCD52CR


title: HCI013_106662


title: HCI001CR_105984


title: BCM-3887_107156


title: HCI013_106666-106667


title: HCI013-107785

value: Tamoxifen cirate, Estrogen pellet


title: UCD52_107080-107081


title: BCM-2147_107007