title: RNA-seq-Z rep5

description: ZXY-Z

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

extract_protocol:
Total RNA was extracted using TRIzol reagents (Thermo Fisher Scientific). RNA concentrations were measured by Qubit fluorometer (Thermo Fisher Scientific) and RNA quality were evaluated by 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Only samples with RIN higher than 7.0 were chosen for library preparation.
RNA library preparation was performed using VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme) with 1 μg of DNase-treated total RNA as input, following the manufacturer’s instructions.


title: 20210923_DN005_RNA_VOA_Dox_Rep2

status: Public on Aug 04 2025

type: SRA

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 440 Brookline Ave

department: Pediatric Oncology

country: USA

institute: Dana Farber Cancer Institute

library_source: transcriptomic

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the hg19 genome with STAR v2.5.2b, which output gene count tables to the hg19 refFlat annotation. For ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively. For ChIP Data, reads were aligned, then duplicates removed and read quality filtered using using Bowtie2 v2.29, Sambamba v0.7.1, and SAMtools v0.1.19.
For ChIP and ATACseq data, tracks were generated using deepTools bamCoverage (--normalizeUsing CPM -bs 40), ATACseq data was first filtered insert sizes between 38 and 100 bp.
Assembly: hg19
Supplementary files format and content: ChIP and ATACseq bigWig files give the normalized coverage of DNA fragments across the genome in RPM, and gene count tables give raw RNA read counts mapped to exons of given genes.

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
For ChIP-Seq: Cells were fixed with 2mM disuccinimidyl glutarate 40min room temperature then 1.0% paraformaldehyde 10min room temperature, quenced with 375mM Tris HCL and then sonicated using Covaris E220 ultra-focused sonicator. 1-10ng of immunoprecipitated DNA was used for library prep.  For ATAC-Seq: 100K cells were incubated in hypotonic buffer and lysis buffer, then were resuspended in transposase reaction mixture for 30 min at 37°C with gentle shaking followed by DNA purification and 8 cycles of amplification  For RNA-Seq from FFPE:  RNA was extracted from FFPE tissue using RNAeasy FFPE kit (Qiagen). Samples obtained from laser capture microdissection were deparaffinized and lysed in a buffer containing proteinase K and on column DNAse treatment. 100ng of purified RNA was used with the KAPA mRNA Hyperprep kit for library generation For RNA-Seq from cell lines: All RNA was collected using an RNAeasy mini kit (Qiagen) using manufacturer’s protocol. 1µg of DNAse-treated RNA was used for NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra II Directional RNA Library Prep Kit for standard Illumina sequencing.
ChIP-seq libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols. ChIP-seq was sequenced on Illumina NextSeq 500 using 37 bp pair-end sequencing parameters.  ATAC-seq samples were sequenced on Illumina NextSeq 500 using 37 bp pair-end sequencing parameters.  RNA-seq libraries were prepared using the Nebnext Poly(A) mRNA Magnetic Isolation Module and the Nebnext Ultra II Directional RNA Library Prep Kit for Illumina using standard protocols. RNA was sequenced on  Illumina NextSeq 500 using 37 bp pair-end sequencing parameters or NovaSeq using 50 bp pair-end sequencing parameters.

tag: cell line

tag: treatment

value: +Dox (+ARID1A)


title: BTRC_128_10X _HT_snRNA-seq

city: Indianapolis

first: Yunlong

last: Liu

state: IN

address: 410 West 10th Street, HITS 5001

institute: Indiana University School of Medicine

description: 'BTRC_128 ' in Seurat object's 'sample' metadata field

library_source: transcriptomic single cell

data_processing:
For libraries containing 'multiome': Cell Ranger ARC Analysis Cell Ranger ARC (cellranger-arc-2.0.0, http://support.10xgenomics.com/) was utilized to process the raw sequence data derived from the single-cell multiome libraries. Both the ATAC and gene expression FASTQ files were processed with the cellranger-arc count algorithm. The reference refdata-cellranger-arc-GRCh38-2020-A-2.0.0 (10x Genomics) was used. Demultiplexing: Cells from each of the sequencing pools were demultiplexed back into their samples of origin using the tool Demuxlet with default parameters. A Signac object, containing both RNA and ATAC-seq data, was created for each pool from the multiome assay from the hdf5 file from the Cell Ranger output. Data from multiple sequencing runs of the same pool were merged. Sample-level metadata were then added to the Signac objects, which were saved as .rds files.
For libraries containing 'HT': Cell ranger Count Analysis: Cell Ranger Count (cellranger-count-7.0.1, http://support.10xgenomics.com/) was utilized to process the raw sequence data derived from the single-cell multiome libraries. The gene expression FASTQ files were processed with the cellranger count algorithm. The reference refdata-cellranger-GRCh38-2020-A (10x Genomics) was used. The filtered gene-cell barcode matrices were used for further analysis. Demultiplexing: Cells from each of the sequencing pools were demultiplexed back into their samples of origin using the tool Demuxlet with default parameters. The data from the technical replicates were then combined. A Seurat object was created from the data from each pool from the HT assay using the gene expression count matrix from the Cell Ranger output. Data from multiple sequencing runs of the same pool were merged. Sample-level metadata was then added to each Seurat object, which were then saved as .rds files.
Assembly: GRCh38
Supplementary files format and content: .RDS files are Seurat objects containing unnormalized count matrices and metadata for each barcode, including sample assignments and sample-level information, such as age, gender, and AUD classification. For HT RNA-seq objects, gene expression counts are included. For multiome objects, counts for gene expression and chromatin peaks are included.

source_name: caudate nucleus (postmortem brain)

extract_protocol:
For libraries containing 'multiome': 184 fresh-frozen post-mortem caudate brain samples were utilized in the assay. The 184 specimens were divided into 23 pools, with 8 in each pool. The donors in each pool were both condition (with or without AUD) and sex balanced. For each pool, around 20 mg tissue from each donor specimen was collected and combined into a sterilized 2 ml Dounce homogenizer. 2 ml chilled NP40 lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet P40 Substitute, 1mM DTT, 1 U/µl RNase inhibitor) was added to the Dounce homogenizer before the tissues were thawed. The tissues were homogenized 15x using pestle A, and 10x using pestle B, and were transferred into a centrifuge tube to incubate for 2 minutes on ice. After that, 2 ml wash buffer containing PBS, 1% BSA and 1 U/µl RNase inhibitor was added and mixed well. The lysed tissue was centrifuged at 500 rcf for 5 minutes at 4°C, then washed twice more with wash buffer and filtered through 70 µm and then 40 µm cell strainer separately. The pellet was resuspended in 2 ml wash buffer and mixed with 3.6 ml Sucrose Cushion Buffer I (nuclei PURE prep isolation kit, Sigma) containing 1 U/µl RNase inhibitor. 2 ml Sucrose Cushion Buffer I with 1 U/µl RNase inhibitor was added into one 15 ml Beckman Coulter centrifuge tube.  After that, the 5.6 ml nuclei suspensions were gently added to the top of Sucrose Cushion Buffer I without mixing, and followed by centrifuging at 13,000 x rpm (30,000 rcf) (Beckman Coulter ultracentrifuge) with rotor SW40Ti for 45 minutes at 4°C. The purified nuclei pellet was washed by centrifuging at 300 rcf for 5 min at 4°C with wash buffer, and the washed nuclei pellets was resuspended in wash buffer to target ~ 1000 nuclei/μl. For libraries containing HT: Nuclei Isolation for Single-nuclei RNA-seq: 163 fresh-frozen post-mortem caudate brain samples (same individuals as in Multiome assay) were grouped into 17 pools, with roughly 10 in each pool. The donors in each pool were both condition (with or without alcohol use disorder) and sex balanced. For each pool, around 20 mg tissue from each donor specimen was collected and combined into a sterilized 2 ml Dounce homogenizer. 2 ml chilled NP40 lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Nonidet P40 Substitute, 1mM DTT, 1 U/µl RNase inhibitor) was added to the Dounce homogenizer before the tissues were thawed. The tissues were homogenized 15x using pestle A, and 10x using pestle B, and were transferred into a centrifuge tube to incubate for 2 minutes on ice. After that, 2 ml wash buffer containing PBS, 1% BSA and 1 U/µl RNase inhibitor was added and mixed well. The lysed tissue was centrifuged at 500 rcf for 5 minutes at 4°C, then washed twice more with wash buffer and filtered through 70 µm and then 40 µm cell strainer separately. The pellet was resuspended in 2 ml wash buffer and mixed with 3.6 ml Sucrose Cushion Buffer I (nuclei PURE prep isolation kit, Sigma).  Zero point two (or One fifth) unit per microliter of RNase inhibitor was used in the buffers. This was followed by centrifuging at 13,000 x rpm (30,000 rcf) (Beckman Coulter ultracentrifuge) with rotor SW40Ti for 45 minutes at 4°C. The purified nuclei pellet was washed by centrifuging at 300 rcf for 5 min at 4°C with wash buffer, and the washed nuclei pellets was resuspended in wash buffer to target ~ 1000 nuclei/μl.
For libraries containing 'multiome': 10X Single-cell Multiome Library Preparation and Sequencing: Paired ATAC and gene expression libraries were generated following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide CG000338_RevB (10X Genomics, Inc). In brief, the isolated nuclei from a pool of samples were first incubated in a transposition mix. The single nuclei master mixture containing tagmented single nuclei suspension was loaded into two well of a Next GEM Chip J, along with the single cell multiome gel beads and partition oil. The chip was then loaded to the Chromium X Controller for GEM generation and barcoding. Barcoded transposed DNA and cDNA were amplified after GEMs being released. At each step, the quality of cDNA, ATAC library and cDNA library was examined by Bioanalyzer 2000. The final single indexed ATAC libraries and the dual indexed gene expression libraries were sequenced on an Illumina Novaseq 6000, with index reads of 10 bp + 24 bp, and 100 bp paired-end reads. The libraries were sequenced twice (2 technical replicates for each BioSample). For libraries containing 'HT': 10X HT Single-nuclei RNA-seq Library Preparation and Sequencing: The Chromium Next GEM single cell 3’ HT reagent kits v3.1 (user guide CG000416, 10X Genomics, Inc.) was used for the single-nuclei RNA-seq assay. The single nuclei suspension from a pool of 10 donor tissue samples were loaded into two wells of a Chromium Next GEM chip M to target 60,000 cell recovery per well. The chip was run on a Chromium X (10x Genomics). Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated. cDNA was synthesized and amplified following cell capture and cell lysis, The quality and quantity of cDNA and resulting libraries were examined by Bioanalyzer. The final libraries were sequenced on an Illumina NovaSeq 6000. 100-bp reads including cell barcode and UMI sequences and 100-bp RNA reads were generated. The libraries were sequenced two or three times for each BioSample.
For libraries containing 'multiome', 10X single nucleus multiome assay (RNA+ATAC-seq). For libraries contatining 'HT', single nucleus RNA-seq.

tag: tissue

value: caudate nucleus (postmortem brain)


title: F1 worm, 230

city: Eugene

first: Amy

middle: K

last: Webster

state: Oregon

address: Institute of Ecology and Evolution

institute: University of Oregon

data_processing:
FASTQ files were aligned to WBcel235 version of the C. elegans genome using subread-align with flag -t 0
Bam files were counted using featureCounts with flag -T 5
For downstream analysis 12 of the 192 samples were filtered out due to low read counts (<1 million) or poor mapping quality (< 70% reads mapping to genome and assigned to a feature). Remaining 180 samples have an average of 5.8 million reads and 85.8% mapping to genome and assigned to a genomic feature.
Count data was CPM-normalized in edgeR and filtered to protein-coding genes. Genes were filtered either to include CPM >10 in at least 1 library (8824 genes) or CPM > 1 across all libraries (7938 genes), depending on the analysis.
To identify genes associated with reproductive traits, the nlme package was used in R to build linear mixed models for gene expression and traits while accounting for biological replicates
Assembly: WBcel235
Supplementary files format and content: .txt files include count data for each sample
Supplementary files format and content: singleworm_192samples.csv includes the reproductive trait data for each worm sequenced in addition to environmental perturbations and replicate information

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: C. elegans nematodes were maintained on NGM plates with E. coli OP50 at 20C.

extract_protocol:
Cell lysate including total RNA was obtained through chemical lysis 24 hours after egg-laying onset. 6 uL of lysis buffer (including elution buffer and proteinase K) was used for each worm and the lysis protocol used was 65C for 10 min, 85C for 1 min, and 4C hold.
KAPA mRNA-seq preparation kit

treatment_protocol: Day 1 (YA=young adult) or day 3 (OA=older adult) P0 adults were allowed to lay progeny, and progeny were then left constantly at 20C or shifted to 25C as young larvae (25C_8hr). 24 hours after egg-laying onset, F1 worms were individually sequenced.

value: whole worm

tag: genotype

tag: parental age

value: OA

tag: progeny treatment (early life temperature)

tag: replicate date


title: 20210923_DN004_RNA_VOA_Dox_Rep1


title: RNA-seq-N rep5

city: hangzhou

first: tian

last: dong

address: No.1, xueshi Road

country: China

institute: Women's Hospital, School of Medicine, Zhejiang University

description: ZXY-N

molecule: total RNA

source_name: the placenta tissue

growth_protocol: The tissue of placental implantation and adjacent normal placental tissues was obtained from the placenta of 5 pregnant women with placenta previa during cesarean section.All collected samples were washed in normal saline and frozen immediately with liquid nitrogen, and preserved at − 80 °C refrigerator.

value: the placenta tissue


title: F1 worm, 229

value: YA


title: BTRC_137_10X _HT_snRNA-seq

description: 'BTRC_137 ' in Seurat object's 'sample' metadata field


title: BTRC_127_10X _HT_snRNA-seq

description: 'BTRC_127 ' in Seurat object's 'sample' metadata field


title: F1 worm, 234


title: RNA-seq-Z rep4

description: ZJP-Z


title: F1 worm, 228


title: 20210923_DN003_RNA_VOA_NoDox_Rep3

value: -Dox


title: RNA-seq-N rep4

description: ZJP-N


title: F1 worm, 232


title: F1 worm, 227


title: 20210923_DN002_RNA_VOA_NoDox_Rep2


title: 20210923_DN001_RNA_VOA_NoDox_Rep1


title: F1 worm, 226


title: BTRC_125_10X _HT_snRNA-seq

description: 'BTRC_125 ' in Seurat object's 'sample' metadata field


title: BTRC_124_10X _HT_snRNA-seq

description: 'BTRC_124 ' in Seurat object's 'sample' metadata field


title: BTRC_121_10X _HT_snRNA-seq

description: 'BTRC_121 ' in Seurat object's 'sample' metadata field


title: RNA-seq-N rep3

description: WBJ-N


title: RNA-seq-Z rep2

description: qjq-Z


title: F1 worm, 224


title: RNA-seq-Z rep3

description: WBJ-Z


title: RNA-seq-N rep2

description: qjq-M


title: 20210416_JSL018_RNA_VOA_DMSO_Rep3

value: DMSO


title: F1 worm, 225


title: 20210416_JSL017_RNA_VOA_DMSO_Rep2


title: BTRC_116_10X _HT_snRNA-seq

description: 'BTRC_116 ' in Seurat object's 'sample' metadata field


title: F1 worm, 220


title: BTRC_12_10X _HT_snRNA-seq

description: 'BTRC_12 ' in Seurat object's 'sample' metadata field


title: RNA-seq-N rep1

description: FYY-N


title: F1 worm, 221


title: 20210416_JSL015_RNA_VOA_C12_Rep3


title: F1 worm, 219


title: 20210416_JSL016_RNA_VOA_DMSO_Rep1


title: Enzalutamide_8hr_3

city: Cambridge

first: Robert

last: Hanson

address: Hills Rd

department: Oncology

country: United Kingdom

institute: Early Cancer Institute

description: Library name: SLX-18713.RNAA019.HFGHMBBXY.s_7

data_processing:
Pre-processing of raw read data, alignment and transcript counting was performed using STAR (Dobin et al., 2013) and featureCounts (Liao et al., 2013) tools, providing a read count matrix for downstream analysis using the DESeq2 package (Love et al., 2014).
Assembly: hg38
Supplementary files format and content: gene count matrix

source_name: prostate

growth_protocol: Cell lines were cultured at 37°C in a humidified atmosphere containing 5% CO2 in RPMI 1640 Medium (10% FBS)

extract_protocol:
RNA was purified using the Qiagen All-Prep kit following manufacturer’s instructions (Qiagen). Cell lysates were harvested by the direct addition of lysis buffer to cell culture plates and collected using a cell scraper whist on ice. RNA samples were stored at -80°C.
1μg total RNA from each replicate condition was used as input for library preparation using the TruSeq RNA Library Prep kit and following the manufacturer’s protocol (Illumina). Final libraries were pooled to obtain equimolar pools each at 10nM concentration. Sample pools were submitted for paired-end sequencing (2x150bp) on Illumina HiSeq-4000, targeting ~30 million reads per sample.

value: prostate

value: LNCaP

tag: cell type

value: prostate cancer


title: BTRC_112_10X _HT_snRNA-seq

description: 'BTRC_112 ' in Seurat object's 'sample' metadata field


title: F1 worm, 218


title: BTRC_123_10X _HT_snRNA-seq

description: 'BTRC_123 ' in Seurat object's 'sample' metadata field


title: 20210416_JSL013_RNA_VOA_C12_Rep1


title: 20210416_JSL014_RNA_VOA_C12_Rep2


title: BTRC_11_10X _HT_snRNA-seq

description: 'BTRC_11 ' in Seurat object's 'sample' metadata field


title: F1 worm, 217


title: BTRC_107_10X _HT_snRNA-seq

description: 'BTRC_107 ' in Seurat object's 'sample' metadata field


title: Olaparib _8hr_2

description: Library name: SLX-18713.RNAA018.HFGHMBBXY.s_7

value: Olaparib _8hr


title: 20210416_JSL012_RNA_VOA_dBRD9a_Rep3


title: DMSO_8hr_1

description: Library name: SLX-18713.RNAA016.HFGHMBBXY.s_7


title: 20210416_JSL011_RNA_VOA_dBRD9a_Rep2


title: Combination_8hr_2

description: Library name: SLX-18713.RNAA015.HFGHMBBXY.s_7


title: F1 worm, 216


title: BTRC_106_10X _HT_snRNA-seq

description: 'BTRC_106 ' in Seurat object's 'sample' metadata field


title: 20210416_JSL010_RNA_VOA_dBRD9a_Rep1


title: F1 worm, 215


title: BTRC_105_10X _HT_snRNA-seq

description: 'BTRC_105 ' in Seurat object's 'sample' metadata field


title: RNA-seq-Z rep1

description: FYY-Z


title: Enzalutamide_24hr_2

description: Library name: SLX-18713.RNAA014.HFGHMBBXY.s_7


title: BTRC_115_10X _HT_snRNA-seq

description: 'BTRC_115 ' in Seurat object's 'sample' metadata field


title: 20230918_GXChIP092_VOA_posDox_input

library_source: genomic

molecule: genomic DNA

tag: chip antibody


title: BTRC_103_10X _HT_snRNA-seq

description: 'BTRC_103 ' in Seurat object's 'sample' metadata field


title: Olaparib _24hr_2

description: Library name: SLX-18713.RNAA013.HFGHMBBXY.s_7

value: Olaparib _24hr


title: F1 worm, 213


title: 20230918_GXChIP091_VOA_parental_input


title: BTRC_102_10X _HT_snRNA-seq

description: 'BTRC_102 ' in Seurat object's 'sample' metadata field


title: Enzalutamide_72hr_3

description: Library name: SLX-18713.RNAA012.HFGHMBBXY.s_7


title: Combination_24hr_1

description: Library name: SLX-18713.RNAA007.HFGHMBBXY.s_7


title: combination (biol rep 3)

city: Kanazawa

first: Tomohisa

last: Baba

address: Kakuma-machi

country: Japan

institute: Kanazawa University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.33 (parameter- TruSeq3-PE.fa:2:30:10 LEADING:20 MINLEN:30)
Trimmed sequence reads were mapped to hg38 using STAR v2.7.11a
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: blood

growth_protocol: RPMI1640 supplemented with 10% FBS

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.
RNA-Seq libraries were prepared using NEBNext Ultra II Directional RNA Library prep kit for Illumina.

treatment_protocol: HL-60 cells were treated with 1 μM ATRA and/or 1 μM palbociclib for 48 hours.

value: blood

value: myeloid leuekemia


title: F1 worm, 211


title: 20230918_GXChIP089_VOA_parental_H3K27ac


title: F1 worm, 212


title: 20230918_GXChIP090_VOA_posDox_H3K27ac


title: combination (biol rep 2)


title: Combination_72hr_2

description: Library name: SLX-18713.RNAA006.HFGHMBBXY.s_7


title: F1 worm, 209


title: combination (biol rep 1)


title: palbociclib (biol rep 3)


title: DMSO_72hr_2

description: Library name: SLX-18713.RNAA004.HFGHMBBXY.s_7


title: 20230918_GXChIP083_VOA_parental_GLTSCR1

value: GLTSCR1 (CST, E6I3A, Lot 1)


title: 20230918_GXChIP084_VOA_posDox_GLTSCR1


title: F1 worm, 210


title: palbociclib (biol rep 2)


title: F1 worm, 207


title: 20230918_GXChIP082_VOA_posDox_PBRM1

value: PBRM1 (CST, D3F70, Lot 3)


title: Olaparib _72hr_1

description: Library name: SLX-18713.RNAA002.HFGHMBBXY.s_7

value: Olaparib _72hr


title: F1 worm, 208


title: Olaparib _8hr_1

description: Library name: SLX-18712.RNAA019.HFGHMBBXY.s_6


title: F1 worm, 214


title: 20230918_GXChIP081_VOA_parental_PBRM1


title: F1 worm, 206


title: 20230820_GXChIP080_VOA_posDox_input

value: +Dox (+ARID1A)


title: ATRA (biol rep 3)


title: DMSO_24hr_2

description: Library name: SLX-18713.RNAA005.HFGHMBBXY.s_7


title: F1 worm, 205

value: whole worm


title: Combination_8hr_3

description: Library name: SLX-18712.RNAA016.HFGHMBBXY.s_6


title: ATRA (biol rep 2)


title: F1 worm, 204


title: Enzalutamide_72hr_2

description: Library name: SLX-18712.RNAA015.HFGHMBBXY.s_6


title: 20230820_GXChIP078_VOA_posDox_SS18

value: SS18 (CST, D6I4Z, Lot 1)


title: 20230820_GXChIP079_VOA_parental_input


title: Enzalutamide_24hr_1

description: Library name: SLX-18712.RNAA018.HFGHMBBXY.s_6


title: untreated (biol rep 3)


title: 20230820_GXChIP077_VOA_parental_SS18


title: ATRA (biol rep 1)


title: Olaparib _72hr_3

description: Library name: SLX-18712.RNAA014.HFGHMBBXY.s_6


title: untreated (biol rep 2)


title: Olaparib _24hr_3

description: Library name: SLX-18712.RNAA013.HFGHMBBXY.s_6


title: palbociclib (biol rep 1)


title: F1 worm, 203

value: OA


title: 20230820_GXChIP072_VOA_posDox_ARID1A

value: ARID1A (CST, D2A8U, Lot 4)


title: F1 worm, 200

value: YA


title: F1 worm, 202


title: Combination_24hr_2

description: Library name: SLX-18712.RNAA012.HFGHMBBXY.s_6


title: F1 worm, 199


title: untreated (biol rep 1)


title: combination

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v0.33 (parameter- TruSeq3-PE.fa:2:40:15, LEADING:10 MINLEN:50).
Trimmed sequence reads were mapped to the NCBI GRCH38  using bowtie2 v2.5.2.
Peaks were called using HOMER v4.11.1 (parameter- size 200)
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
DNA sample preparation was conducted using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling).
ChIP-Seq libraries were prepared using NEBNext Ultra II DNA Library prep kit for Illumina.

value: myeloid leukemia


title: DMSO_72hr_1

description: Library name: SLX-18712.RNAA007.HFGHMBBXY.s_6

value: prostate


title: F1 worm, 198


title: 20230820_GXChIP070_VOA_posDox_BRD9

value: BRD9 (CST, E4Q3F, Lot 1)


title: 20230820_GXChIP071_VOA_parental_ARID1A


title: 20230820_GXChIP069_VOA_parental_BRD9


title: palbociclib


title: ATRA


title: DMSO_8hr_3

description: Library name: SLX-18712.RNAA006.HFGHMBBXY.s_6

value: LNCaP

value: prostate cancer


title: Combination_72hr_1

description: Library name: SLX-18712.RNAA005.HFGHMBBXY.s_6


title: 20230820_GXChIP067_VOA_parental_BRG1


title: F1 worm, 196


title: untreated


title: F1 worm, 195


title: Enzalutamide_8hr_2

description: Library name: SLX-18712.RNAA002.HFGHMBBXY.s_6


title: DMSO_24hr_3

description: Library name: SLX-18712.RNAA004.HFGHMBBXY.s_6


title: Combination_72hr_3

description: Library name: SLX-18711.RNAA019.HFGHMBBXY.s_5


title: F1 worm, 193


title: 20220414_JSLRPF22_RNA_JSL9719

description: Dedifferentiated Endometrial Cancer, Patient 9

source_name: Patient Tissue

value: Patient Tissue


title: 20210826_JSL17_VOA_dox_ARID1A_Rep1


title: F1 worm, 194


title: 20220414_JSLRPF18_RNA_JSL9719

description: Dedifferentiated Endometrial Cancer, Patient 8


title: Enzalutamide_24hr_3

description: Library name: SLX-18711.RNAA018.HFGHMBBXY.s_5


title: F1 worm, 192


title: 2021011_JSL024_ATAC_VOA_C12_Rep2


title: 20220414_JSLRPF21_RNA_JSL9719

description: Well-differentiated Endometrial Cancer, Patient 9


title: 20220414_JSLRPF17_RNA_JSL9719

description: Well-differentiated Endometrial Cancer, Patient 8


title: F1 worm, 191


title: DMSO_72hr_3

description: Library name: SLX-18711.RNAA016.HFGHMBBXY.s_5


title: DMSO_24hr_1

description: Library name: SLX-18711.RNAA015.HFGHMBBXY.s_5


title: 20210826_JSL16_VOA_nodox_Rep2

value: -Dox


title: 20220414_RPF6_RNA_JSL9719

description: Dedifferentiated Endometrial Cancer, Patient 7


title: F1 worm, 197


title: 20220414_RPF5_RNA_JSL9719

description: Well-differentiated Endometrial Cancer, Patient 7


title: F1 worm, 190


title: 20210826_JSL18_VOA_dox_ARID1A_Rep2


title: F1 worm, 189


title: 2021011_JSL022_ATAC_VOA_DMSO_Rep2

value: DMSO


title: 2021011_JSL023_ATAC_VOA_C12_Rep1


title: 20220414_RPF4_RNA_JSL9719

description: Dedifferentiated Endometrial Cancer, Patient 6


title: F1 worm, 188


title: Combination_24hr_3

description: Library name: SLX-18711.RNAA013.HFGHMBBXY.s_5


title: 20210826_JSL15_VOA_nodox_Rep1


title: 20220414_RPF3_RNA_JSL9719

description: Well-differentiated Endometrial Cancer, Patient 6


title: F1 worm, 187


title: 2021011_JSL020_ATAC_VOA_dBRD9_Rep2


title: Olaparib _8hr_3

description: Library name: SLX-18711.RNAA012.HFGHMBBXY.s_5

value: Olaparib _8hr


title: Enzalutamide_8hr_1

description: Library name: SLX-18711.RNAA007.HFGHMBBXY.s_5


title: 20230712_JSLA10_normal_pt5_samp41

description: Normal Tissue, Patient 5


title: F1 worm, 186


title: 2021011_JSL019_ATAC_VOA_dBRD9_Rep1


title: 20210620_JSL026_RNA_AN3CA_none_Rep2

source_name: AN3 CA

value: AN3 CA


title: F1 worm, 185


title: 20230712_JSLA08_normal_pt4_samp40

description: Normal Tissue, Patient 4


title: Enzalutamide_72hr_1

description: Library name: SLX-18711.RNAA005.HFGHMBBXY.s_5


title: F1 worm, 184


title: 20210620_JSL025_RNA_AN3CA_none_Rep1


title: DMSO_8hr_2

description: Library name: SLX-18711.RNAA004.HFGHMBBXY.s_5


title: Olaparib _24hr_1

description: Library name: SLX-18711.RNAA014.HFGHMBBXY.s_5

value: Olaparib _24hr


title: F1 worm, 183


title: Combination_8hr_1

description: Library name: SLX-18711.RNAA006.HFGHMBBXY.s_5


title: 20210620_JSL024_RNA_AN3CA_nodox_Rep3


title: Olaparib _72hr_2

description: Library name: SLX-18711.RNAA002.HFGHMBBXY.s_5

value: Olaparib _72hr


title: F1 worm, 182

value: whole worm


title: 20210620_JSL023_RNA_AN3CA_nodox_Rep2


title: 2021011_JSL021_ATAC_VOA_DMSO_Rep1


title: 20230712_JSLA05_cancer_pt3_samp09

description: Dedifferentiated Endometrial Cancer, Patient 3


title: Adult bone marrow-derived CD34+ biological replicate 3

first: Steven

last: Coyne

state: MA

address: 1 Blackfan Ave. Karp Building RB8005G Karp Building RB8005G

department: Dept. of Hematology/Oncology

institute: Boston Children's Hospital

description: Library name: BM_3

data_processing:
adapter trimming > pseudocount with salmon > process pseudocounts with DEseq2 for differential gene expression analysis
Assembly: GRCh37.67
Supplementary files format and content: .sf - salmon quant files
Supplementary files format and content: .csv - DESeq2 results file comparing IGF2BP1 overexpression and control vector conditions

source_name: bone marrow

extract_protocol:
qiagen Rneasy
Illumina Truseq

value: bone marrow

value: human primary cells

value: CD34+ HSPC in vitro erythroid differentiation

tag: batch


title: F1 worm, 181

value: OA


title: 20230820_GXChIP068_VOA_posDox_BRG1

value: +Dox (+ARID1A)


title: Adult bone marrow-derived CD34+ biological replicate 2

description: Library name: BM_2


title: 20230712_JSLA04_normal_pt2_samp38

description: Normal Tissue, Patient 2


title: F1 worm, 179

value: YA


title: 20230712_JSLA03_cancer_pt2_samp05

description: Dedifferentiated Endometrial Cancer, Patient 2


title: Adult bone marrow-derived CD34+ biological replicate 1

description: Library name: BM_1


title: 20210620_JSL021_RNA_AN3CA_doxARID1A_Rep3


title: 20230712_JSLA09_cancer_pt5_samp36

description: Dedifferentiated Endometrial Cancer, Patient 5


title: 20210620_JSL020_RNA_AN3CA_doxARID1A_Rep2


title: F1 worm, 177


title: Cord blood-derived CD34+ biological replicate 3

description: Library name: CB_3

source_name: cord blood

value: cord blood


title: 20230712_JSLA07_cancer_pt4_samp07

description: Dedifferentiated Endometrial Cancer, Patient 4


title: 20230712_JSLA06_normal_pt3_samp39

description: Normal Tissue, Patient 3


title: Cord blood-derived CD34+ biological replicate 2

description: Library name: CB_2


title: 20230712_JSLA02_normal_pt1_samp37

description: Normal Tissue, Patient 1


title: F1 worm, 176


title: 20230712_JSLA01_cancer_pt1_samp17

description: Dedifferentiated Endometrial Cancer, Patient 1


title: Glioma_19_PBMC_TIL_CITEseq

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

description: 10X Genomics 5' v1

library_source: other

data_processing:
Demultiplexing was performed using bcl2fastq v2.20.0.
Gene expression libraries were aligned to GRCh38 using CellRanger v6.1.2. CITEseq libraries were aligned to hash tag sequences using CITEseqCount v1.4.3.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited barcodes, features, and matrix files

molecule: protein

source_name: peripheral blood and tumor tissue

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were isolated from whole blood by Ficoll-Hyapque density gradient centrifugation. Freshly resected glioma tumors were mechanically disrupted and the resulting tissue fragments were digested with 50 mg/mL of Liberase DL  in 5 mL of serum-free RPMI for 15 minutes at 37°C. Live CD45+ (i.e. all live immune cells) were sorted from PBMC and glioma tissues. Single-cell RNAseq was performed using 10X Genomics and libraries were sequenced on Illuman NovaSeq6000 instruments.
The library generation strategy was as per the manufacturer's instructions for either 10X Genomics 3' or 5' based chemistries for a given sample. For some samples, cell hashing was performed to run the PBMC and tumor infiltrating leukocytes (TIL) in the same lane of the 10X Chip. For these samples, oligonucleotide-labeled antibodies were used to label PBMC and TIL and as specified for each sample. Cell hashing libraries were generated as per the 10X Genomics manufacturer's instructions.

value: peripheral blood and tumor tissue

value: Live CD45+ cells

tag: idh status

tag: grade

value: IV


title: Cord blood-derived CD34+ biological replicate 1

description: Library name: CB_1


title: F1 worm, 175


title: 20210416_JSL007_RNA_AN3CA_DMSO_Rep1


title: 20210416_JSL009_RNA_AN3CA_DMSO_Rep3


title: Fetal liver-derived CD34+ biological replicate 3

description: Library name: FL_3

source_name: fetal liver

value: fetal liver


title: Glioma_19_PBMC_TIL_GEX

description: 10X Genomics 5' v1


title: 20210620_JSL022_RNA_AN3CA_nodox_Rep1

value: -Dox


title: 20210416_JSL006_RNA_AN3CA_C12_Rep3


title: Glioma_18_PBMC_TIL_CITEseq

description: 10X Genomics 5' v1


title: F1 worm, 174


title: Fetal liver-derived CD34+ biological replicate 2

description: Library name: FL_2


title: F1 worm, 178


title: F1 worm, 173


title: Fetal liver-derived CD34+ biological replicate 1

description: Library name: FL_1


title: F1 worm, 172


title: 20210416_JSL004_RNA_AN3CA_C12_Rep1


title: Glioma_18_PBMC_TIL_GEX

description: 10X Genomics 5' v1


title: Glioma_17_PBMC_TIL_CITEseq

description: 10X Genomics 5' v1


title: HUDEP-2 IGF2BP1 overexpression biological replicate 3

description:
Library name: IGF_3
res_table_IGFvEV.csv

source_name: cell line

value: cell line

value: WT

value: lentiviral IGF2BP1 overexpression vector


title: F1 worm, 171


title: 20210416_JSL003_RNA_AN3CA_dBRD9a_Rep3

value: AN3 CA


title: HUDEP-2 IGF2BP1 overexpression biological replicate 2

description:
Library name: IGF_2
res_table_IGFvEV.csv


title: Glioma_17_PBMC_TIL_GEX

description: 10X Genomics 5' v1


title: 20210620_JSL019_RNA_AN3CA_doxARID1A_Rep1


title: F1 worm, 170

value: whole worm


title: HUDEP-2 IGF2BP1 overexpression biological replicate 1

description:
Library name: IGF_1
res_table_IGFvEV.csv


title: 20210416_JSL002_RNA_AN3CA_dBRD9a_Rep2


title: 20210416_JSL001_RNA_AN3CA_dBRD9a_Rep1


title: Glioma_16_PBMC_TIL_GEX

description: 10X Genomics 5' v1

value: II


title: F1 worm, 169


title: HUDEP-2 empty vector control biological replicate 3

description:
Library name: EV_3
res_table_IGFvEV.csv

value: lentiviral control vector


title: 20230801_GXChIP066_AN3CA_posDox_input


title: HUDEP-2 empty vector control biological replicate 2

description:
Library name: EV_2
res_table_IGFvEV.csv


title: 20210416_JSL005_RNA_AN3CA_C12_Rep2


title: 20230801_GXChIP065_AN3CA_negDox_input


title: F1 worm, 168


title: Glioma_16_PBMC_TIL_CITEseq

description: 10X Genomics 5' v1


title: Glioma_15_PBMC_TIL_GEX

description: 10X Genomics 5' v1


title: HUDEP-2 empty vector control biological replicate 1

description:
Library name: EV_1
res_table_IGFvEV.csv


title: F1 worm, 167


title: Glioma_15_PBMC_TIL_CITEseq

description: 10X Genomics 5' v1


title: HUDEP-2 wild-type biological replicate 3

description: Library name: H2_3

value: NT


title: F1 worm, 165


title: Glioma_14_PBMC_TIL_CITEseq

description: 10X Genomics 5' v1

value: III


title: 20230801_GXChIP063_AN3CA_negDox_H3K27ac


title: 20230801_GXChIP064_AN3CA_posDox_H3K27ac

value: +Dox (+ARID1A)


title: F1 worm, 166

value: YA


title: Glioma_14_PBMC_TIL_GEX

description: 10X Genomics 5' v1


title: HUDEP-2 wild-type biological replicate 2

description: Library name: H2_2


title: HUDEP-2 wild-type biological replicate 1

description: Library name: H2_1


title: F1 worm, 163

value: OA


title: 20230801_GXChIP058_AN3CA_posDox_GLTSCR

value: GLTSCR1 (CST, E6I3A, Lot 1)


title: Glioma_13_PBMC_TIL_CITEseq

description: 10X Genomics 5' v1

value: peripheral blood and tumor tissue

value: Live CD45+ cells


title: 20230801_GXChIP057_AN3CA_negDox_GLTSCR


title: HUDEP-1 wild-type biological replicate 3

description: Library name: H1_3


title: F1 worm, 162


title: 20230801_GXChIP056_AN3CA_posDox_PBRM1

value: PBRM1 (CST, D3F70, Lot 3)


title: HUDEP-1 wild-type biological replicate 2

description: Library name: H1_2


title: Glioma_12_PBMC_TIL_CITEseq

description: 10X Genomics 5' v1

value: IV


title: F1 worm, 117


title: 20230801_GXChIP055_AN3CA_negDox_PBRM1

value: -Dox


title: Glioma_12_PBMC_TIL_GEX

description: 10X Genomics 5' v1


title: F1 worm, 116


title: HUDEP-1 wild-type biological replicate 1

description: Library name: H1_1

value: cell line

value: WT


title: 20230613_GXChIP038_AN3CA_posDox_input

value: AN3 CA


title: F1 worm, 114

value: whole worm


title: Glioma_11_PBMC_TIL_GEX

description: 10X Genomics 5' v1


title: 20230613_GXChIP032_AN3CA_posDox_SS18

value: SS18 (CST, D6I4Z, Lot 1)


title: 20230613_GXChIP037_AN3CA_negDox_input


city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description:
Library name: MR5A-H3K27ac
M. restricta (MR) was cultured at pH 5 by HCl treatment - immunoprecipitated by H3K27ac antibody

data_processing:
Paired-end reads were aligned to the M. restricta genome (ASM329048v1) using an iterative alignment strategy in bowtie2 (version 2.4.4). Each read from the paired-end dataset was independently aligned rather than being aligned in the paired-end mode.
Mean reads per million (RPM) values were calculated for each gene, and heat maps, as well as anchor plots, were generated using EaSeq
Assembly: ASM329048v1 for M. restricta KCTC 27527
Supplementary files format and content: bigwig

organism: Malassezia restricta

growth_protocol: Malassezia species were initially cultured on LNA at 34 °C for 3–4 days. Then, the cells were transferred to a 250-mL baffled flask containing 50 mL of mDixon medium and incubated at 34 °C with shaking at 160 rpm for 24 h. Subsequently, the OD600 of the culture in mDixon medium was adjusted to 1.0 before co-cultivation or acid treatment.

extract_protocol:
Dyna-G beads (ThermoFisher, 10004D) were pre-incubated at 4°C with either anti-H3K9ac (Abcam, ab177177) or anti-H3K27ac (Abcam, ab4729) antibodies. Cultured cells were fixed with 3% paraformaldehyde at 18 °C for 30 min, and then secondarily fixed with dimethyl adipimidate dihydrochloride (DMA) solution in PBS for 45 min at room temperature. The fixed cells were lysed in a buffer containing HEPES-KOH, NaCl, EDTA, Triton X-100, and phenylmethylsulfonyl fluoride (PMSF), disrupted with glass beads, and sonicated for DNA shearing. The lysate was pre-cleared with lysis buffer-washed beads, and immunoprecipitation was conducted overnight at 4°C with antibody-conjugated beads. The beads were sequentially washed with lysis buffer, high-salt buffer, wash buffer, and TE buffer. Then, bound DNA was eluted, reverse-crosslinked overnight at 65°C, treated with proteinase K, and purified using the QIAquick PCR Purification Kit (Qiagen, 28104).
The purified DNA was used for library preparation using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7770), incorporating S. cerevisiae spike-in DNA at a 0.1 ratio relative to the quantity of input DNA.

treatment_protocol: For co-cultivation, Staphylococcus species were first grown on TSA at 37 °C for 1 day. Then, the bacteria were transferred to TSB medium in a 14-mL round-bottom tube and incubated at 37 °C with shaking for 24 h. Next, the cultured bacteria were inoculated into Malassezia culture flasks at an OD600-based ratio of 0.1 or 0.01. For acid treatment, the pH of the medium was adjusted to 5.0 using HCl, lactic acid, or AcOH. Following incubation under these conditions for 12 h, the samples were used for Hi-C analysis, western blotting, ChIP-seq analysis, or RNA isolation.

value: pH 5 by HCl treatment

tag: antibody


title: F1 worm, 164


description:
Library name: MR-H3K27ac
M. restricta (MR) was cultured alone - immunoprecipitated by H3K27ac antibody


title: Glioma_10_PBMC_TIL_CITEseq

description: 10X Genomics 5' v1

value: II


title: Glioma_13_PBMC_TIL_GEX

description: 10X Genomics 5' v1

value: III


title: 20230613_GXChIP031_AN3CA_negDox_SS18


description:
Library name: MR-H3K9ac
M. restricta (MR) was cultured alone - immunoprecipitated by H3K9ac antibody


title: F1 worm, 109


title: Glioma_10_PBMC_TIL_GEX

description: 10X Genomics 5' v1


title: 20230613_GXChIP030_AN3CA_posDox_ARID1A

value: ARID1A (CST, D2A8U, Lot 4)

value: +Dox (+ARID1A)


title: Glioma_9_PBMC_TIL_CITEseq

description: 10X Genomics 5' v1


description:
Library name: MR-pH65
M. restricta (MR) was cultured at pH 5.0 by AcOH treatment and subsequently adjusted to pH 6.5 with NaOH

data_processing:
In situ Hi-C data were processed as previously described using the rfy_hic2 package (https://github.com/rafysta/rfy_hic2)
Paired-end reads were aligned to the M. restricta genome (ASM329048v1) using an iterative alignment strategy in bowtie2 (version 2.4.4). Each read from the paired-end dataset was independently aligned rather than being aligned in the paired-end mode.
To compare Hi-C matrices, the hicBuildMatrix function in HiCExplorer v3.7.5 was used with a bin size of 10 Kb. The matrices were normalized to the sample with the lowest read count using the “--normalize smallest” option under the hicNormalize function.
Following normalization, the matrices were refined using the “diagnostic_plot” and “correct” options under the hicCorrectMatrix function to remove unmapped bins or bins that exhibited abnormally high signals.
After bin filtering, the final matrices from each sample were compared using the “--operation log2ratio” option under the hicCompareMatrices function.
Finally, the matrices were visualized as plots using the “clearMaskedBins” option under the hicPlotMatrix function. Additionally, contact scores were measured as a function of genomic distance using the hicPlotDistVsCounts function with the “--maxDepth parameter” set to 20 million.
Assembly: ASM329048v1 for M. restricta KCTC 27527, Msy_ATCC_42132_Feb2016 for M. sympodialis ATCC 42132
Supplementary files format and content: h5

extract_protocol:
Malassezia cells were fixed with paraformaldehyde for 10 min at 34 °C to a final concentration of 1%; this was followed by 15 min of quenching using glycine. Next, the fixed Malassezia cells were harvested; in the case of co-cultured samples, Malassezia and Staphylococcus species were separated using a filter before being collected. The collected cells were bead-beaten using glass beads, and then treated with SDS for nuclei permeabilization. DNA within the permeabilized nuclei was cleaved using MboI to generate 5′ overhangs, which were filled with biotinylated nucleotides and subsequently ligated in situ. Next, the DNA was sheared using a Bioruptor Pico sonicator (Diagenode, Belgium), and biotinylated ligation junctions were captured using streptavidin beads.
The captured DNA was processed for library construction using the Illumina NEBNext Ultra II DNA Library Prep Kit (NEB, E7770). Finally, the libraries were submitted to Macrogen Inc. (Seoul, Korea) for paired-end (100 bp x 2) sequencing on a Novaseq6000 device (Illumina, Inc., San Diego, CA, USA).


title: F1 worm, 107

value: OA


title: Glioma_9_PBMC_TIL_GEX

description: 10X Genomics 5' v1


description:
Library name: MR-pH55
M. restricta (MR) was cultured at pH 5.5 by AcOH treatment

value: cultured at pH 5.5 by AcOH treatment


title: Glioma_8_PBMC_TIL_CITEseq

description: 10X Genomics 5' v1

value: peripheral blood and tumor tissue


title: F1 worm, 106


title: F1 worm, 112

value: YA


title: F1 worm, 105


title: Glioma_11_PBMC_TIL_CITEseq

description: 10X Genomics 5' v1

value: Live CD45+ cells


title: 20230613_GXChIP028_AN3CA_posDox_BRD9

value: BRD9 (CST, E4Q3F, Lot 1)


description:
Library name: MR5A-H3K9ac
M. restricta (MR) was cultured at pH 5 by HCl treatment - immunoprecipitated by H3K9ac antibody


description:
Library name: MR-pH-control
M. restricta (MR) was cultured alone - control for pH 5.5 and 6.5 samples


title: 20230613_GXChIP026_AN3CA_posDox_BRG1


title: Glioma_7_TIL_GEX

description: 10X Genomics 5' v1

source_name: tumor tissue

value: tumor tissue

value: IV


title: F1 worm, 103


title: F1 worm, 110


title: 20230613_GXChIP027_AN3CA_negDox_BRD9

value: -Dox


description:
Library name: MR-lac50-control
M. restricta (MR) was cultured alone - control for MR-lac50

value: WT


description:
Library name: MR-lac50
M. restricta (MR) was cultured at pH 5 by lactic acid treatment


title: Glioma_6_PBMC_TIL_CITEseq

description: 10X Genomics 3' v2


title: 20240125_GXATAC106_AN3CA_ARID1A_ARID1B_c2_rep2

value: AN3 CA

value: +Dox (+ARID1A +ARID1B)


title: 20230613_GXChIP029_AN3CA_negDox_ARID1A


description:
Library name: MRSE-2
M. restricta (MR) was co-cultured with S. epidermidis (SE) at OD = 0.1 for 12 h - replicate 2


title: F1 worm, 102

value: whole worm


title: Glioma_6_PBMC_TIL_GEX

description: 10X Genomics 3' v2


title: Glioma_5_PBMC_TIL_CITEseq

description: 10X Genomics 3' v2


title: F1 worm, 101


title: 20240125_GXATAC105_AN3CA_ARID1A_ARID1B_c1_rep2


title: Glioma_8_PBMC_TIL_GEX

description: 10X Genomics 5' v1

value: II


title: 20240125_GXATAC104_AN3CA_ARID1B_rep2

value: +Dox (+ARID1B)


title: F1 worm, 99


title: M. restricta (MR) was cultured alone - replicate 2.

description:
Library name: MR-2
M. restricta (MR) was cultured alone - replicate 2


title: 20240125_GXATAC103_AN3CA_ARID1A_rep2


title: F1 worm, 104


title: Glioma_5_PBMC_TIL_GEX

description: 10X Genomics 3' v2

value: III


title: Glioma_4_TIL_GEX

description: 10X Genomics 3' v2


title: M. restricta (MR) was cultured at pH 5 by HCl treatment - replicate 1.

description:
Library name: MR-pH5-1
M. restricta (MR) was cultured at pH 5 by HCl treatment - replicate 1

value: cultured at pH 5 by HCl treatment


title: F1 worm, 98


title: 20240125_GXATAC102_AN3CA_parental_rep2


title: M. restricta (MR) was cultured at pH 5 by HCl treatment - replicate 2.

description:
Library name: MR-pH5-2
M. restricta (MR) was cultured at pH 5 by HCl treatment - replicate 2


title: 20230613_GXChIP025_AN3CA_negDox_BRG1


title: Glioma_4_PBMC_GEX

description: 10X Genomics 3' v2

source_name: peripheral blood

value: peripheral blood


description:
Library name: MRSA-1
M. restricta (MR) was co-cultured with S. aureus (SA) at OD = 0.1 for 12 h - replicate 1


title: Glioma_3_TIL_GEX

description: 10X Genomics 3' v2


title: M. restricta (MR) was cultured alone - replicate 1.

description:
Library name: MR-1
M. restricta (MR) was cultured alone - replicate 1


title: 20240125_GXATAC101_AN3CA_ARID1A_ARID1B_c2_rep1


title: F1 worm, 96


title: Glioma_3_PBMC_GEX

description: 10X Genomics 3' v2


description:
Library name: MRSA-2
M. restricta (MR) was co-cultured with S. aureus (SA) at OD = 0.1 for 12 h - replicate 2


title: F1 worm, 95


title: 20240125_GXATAC099_AN3CA_ARID1B_rep1


description:
Library name: MRSE-1-001
M. restricta (MR) was co-cultured with S. epidermidis (SE) at OD = 0.01 for 12 h


title: F1 worm, 94


description:
Library name: MS-ac50
M. sympodialis (MS) was cultured at pH 5 by AcOH treatment

organism: Malassezia sympodialis

value: cultured at pH 5 by AcOH treatment


title: 20240125_GXATAC100_AN3CA_ARID1A_ARID1B_c1_rep1


description:
Library name: MRSE-1-01
M. restricta (MR) was co-cultured with S. epidermidis (SE) at OD = 0.1 for 12 h - replicate 1


title: M. sympodialis (MS) was cultured alone.

description:
Library name: MS-ac50-control
M. sympodialis (MS) was cultured alone


title: F1 worm, 93

value: OA


description:
Library name: MR-control
M. restricta (MR) was cultured alone - control for MRSE-1 samples


title: F1 worm, 97


title: 20240125_GXATAC098_AN3CA_ARID1A_rep1

value: +Dox (+ARID1A)


title: F1 worm, 92


title: F1 worm, 91

value: YA


title: 20240125_GXATAC097_AN3CA_parental_rep1


title: null strain replicate

city: Chapel Hill

first: Adam

last: Rosenthal

state: North Carolina

address: 1521 East Franklin Street, Apartment C213

department: Microbiology and Immunology

institute: UNC

description:
Library name: Sample4
Single cell data

data_processing:
Libraries were sequenced using an Illumina nextSeq2000 100-cycle kit and fastQ-files were demultiplexed, mapped and normalized using the 10X cellRanger and Seurat software packages using the standard analysis pipelines and default parameters.
Supplementary files format and content: H5 filtered feature files from cellRanger output are provided

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Soil bacterium

growth_protocol: The bacteria were grown in S750 minimal media comprising 1X S750 salt solution diluted in Teknova reagent grade water (W0225), supplemented with 1% glucose, 0.1% glutamic acid, 0.01% Casamino acids, 50mM NaCl, 40µg ml-1 tryptophan and 1X trace metals. The 10X S750 salt solution is prepared by dissolving 50mM MOPS, 10mM (NH4)2SO4, and 5mM KH2PO4 in ddH20, buffered to pH 7.0 with 5M KOH,  filter sterilised and stored at 4℃. The 100X trace metal solution was procured from Teknova (2M2755) comprising 200mM MgCl2, 70mM CaCl2, 5mM MnCl2, 0.1mM ZnCl2, 100µg ml-1 thiamine HCl, 0.5mM FeCl3, & 2mM HCl. When uracil auxotroph pyrD mutants were grown, uracil was supplemented at 40 µg ml-1 concentration. Cultures of bacterial strains from a single colony were grown in S750 minimal media until cultures reached an OD600 read of 0.3-0.4. The cultures were diluted to an initial OD600 read of 0.05 in S750 minimal media and grown to a time point near maximum Phpf-luc expression (~t=300 minutes)

extract_protocol:
At the indicated timepoints wildtype and ppGpp0 cells were fixed in 1% formaldehyde at room temperature for 30 minutes. After fixation cells were pelleted by centrifugation at 6000 RPM for 3 min at room temperature and washed with 0.02% saline sodium citrate (SSC, Invitrogen). The cell were pelleted again and resuspended in 300 µl MAAM mix (4:1 V:V dilution of methanol to glacial acetic acid) and stored at 20 oC until processing. ProBac-seq sample processing was done as described previously (see McNulty et al Nat Micro 2023). Briefly, samples were pelleted and resuspended in PBS to remove MAAM. Following PBS wash to remove MAAM the cells were incubated with lysozyme (Readylyse, Epicenter biotechnology) for 30 minutes in room temperature for cell wall hydrolysis. After an additional pelleting step and PBS wash the samples were further permeabilized by a 5 minute incubation in PBS-Tween (PBS with 1% final concentration of Tween 20 detergent) and a subsequent wash in PBS to remove the detergent. Permeabilized cells were resuspended in 100 ul of probe binding buffer (5 × SSC, 30% formamide, 9 mM citric acid (pH 6.0), 0.1% Tween 20, 50 ug ml−1 heparin and 10% low molecular weight dextran sulfate purchased from Molecular Instruments inc. as Probe Binding Buffer – Cells in Suspension). A transcriptome-wide probe-set containing approximately 30,000 mRNA binding probes designed against the B. subtilis genome (see McNulty et al Nat Micro 2023) was added to each sample before placing the samples to incubate overnight at 50oC.  After overnight incubation unbound probes were removed by a series of 7 washes with probe wash buffer (5 × SSC, 30% formamide, 9 mM citric acid pH 6.0, 0.1% Tween 20 and 50 ug ml-1 heparin Molecular Instruments inc.) and 2 final washes in PBS.
Probed and washed cells were enumerated using a flow-cytometer and approximately 10,000 cells per condition were processed using the ProBac-Seq protocols as described previously (see McNulty et al Nat Micro 2023). In short, 51 ul cell suspensions in PBS were mixed with 19 ul ddPCR master mix (Biorad), 3 ul in-droplet PCR primer, 2 ul reducing agent (10X genomics) to provide a 75ul reaction mix. 70 ul of this reaction mixture was loaded onto 10X Genomics microfluidic chip-G devices alongside 10X barcoding beads and emulsion oil. The devices were run using a 10X chromium controller and emulsions were processed to produce barcoded libraries as described previously.

value: (P)PGPP null bacillus 168


title: 20210601_JSL012_ATAC_AN3CA_C12_Rep2


title: null strain

description:
Library name: Sample3
Single cell data


description:
Library name: MR5H-2
M. restricta (MR) was cultured at pH 5 by HCl treatment - replicate 2

data_processing:
The sequencing adapter removal and quality-based trimming for the raw data were performed using Trimmomatic v. 0.36.
Cleaned reads were mapped to the reference genome using bowtie2 with a default parameter.
For counting the reads mapped to each CDS (coding sequence), featureCounts was used.
Finally, the count from each CDS was normalized using DeSeq2 package.
Assembly: ASM329048v1 for M. restricta KCTC 27527
Supplementary files format and content: txt file for mapped read counts

extract_protocol:
Total RNA was extracted through cell wall disruption via bead-beating using glass beads, and subsequently purified using the RNeasy Mini Kit (Qiagen, 74104) following the instructions of the manufacture. Before further processing, residual DNase was removed from the purified RNA using a TURBO DNA-free kit (Invitrogen, AM1907). The concentration of the extracted RNA was determined using a Qubit fluorometer (ThermoFisher, Q33226).
In total, 1 μg of the isolated RNA with 0.1 μg of S. cerevisiae spike-in RNA was used per library for mRNA isolation using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, E7490) following the protocol of the manufacturer; then, library preparation was carried out using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770) according to the protocol of the manufacturer.


title: F1 worm, 90


title: F1 worm, 87


description:
Library name: MR5H-1
M. restricta (MR) was cultured at pH 5 by HCl treatment - replicate 1


title: 20210601_JSL011_ATAC_AN3CA_C12_Rep1


title: Wildtype strain

description:
Library name: Sample1
Single cell data

value: Bacillus wildtype 168


title: Wildtype strain replicate

description:
Library name: Sample2
Single cell data


description:
Library name: MR5A-2
M. restricta (MR) was cultured at pH 5 by acetic acid treatment - replicate 2


description:
Library name: MR5A-1
M. restricta (MR) was cultured at pH 5 by acetic acid treatment - replicate 1


title: M. restricta (MR) was cultured alone - replicate 2


title: RH1 hybrid rep2

city: CLEVELAND

first: Yuan

last: Gao

state: OH

address: 2109 Adelbert Rd., Wood Building Research Tower 300-7, Wood Building Research Tower 300-7

department: Pharmacology

institute: Case Western Reserve University

description: Library name: 18

data_processing:
Sequencing reads were mapped to reference genome hg38 using RNA STAR with default parameters. Read count tables were created using FeatureCounts with a custom GTF file containing protein coding genes only. Differentially expressed genes were analyzed using DESeq2 with two independent replicates using default parameters. TPM values was calculated using Kallisto (version: 0.44.0).
Assembly: hg38
Supplementary files format and content: txt containing gene raw counts and tsv containg gene tpm value

source_name: human sarcoma cancer cell

growth_protocol: TC-71 cells (DSMZ, ACC-516) were cultured in IMDM supplemented with 10% fetal bovine serum, 1% penicillin-streptomycin. A673 cells (ATCC, CRL-1598) were cultured in DMEM supplemented with 10% FBS, 1% penicillin-streptomycin. RH-1 cells (DSMZ, ACC-493) were maintained in RPMI supplemented with 10% FBS and 1% penicillin-streptomycin. Normal human lung fibroblasts (NHLF; Lonza, MD, USA) were cultured in FGM™-2 BulletKit™ Fibroblast Growth Medium, according to the manufacturer’s instructions, under standard conditions (37°C, 5% CO₂). All cells were incubated at 37°C in a humidified atmosphere with 5% CO₂. Subculturing was performed either when cells reached approximately 90% confluency or every three days.

extract_protocol:
Hybrid or monoculture spheroids were digested into single cells using trypsin. GFP positive Ewing sarcoma cells were sorted using BD Symphony S6 (CWRU Cytometry & Imaging Microscopy Core), and subject to total RNA extraction using TRIzol (Thermo Fisher, 15596026) according to the manufacturer’s instructions.
250ng of total RNA was used to construct RNA-seq library using the NEBNext UltraExpress RNA Library Prep Kit (NEB #E3330) following manufacturer’s instructions. Briefly, RNA was polyA enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and enzymatically fragmented. cDNA was synthesized followed by end repair and adapter ligation, and PCR enrichment with indexed primers. Library was pair end sequenced for 76bp using NovaSeq platform.

value: human sarcoma cancer cell

value: co-culture with normal human lung fibroblast


title: F1 worm, 85


title: 20210601_JSL008_ATAC_AN3CA_dBRD9_Rep2


title: RH1 hybrid rep1

description: Library name: 17

value: WT


title: F1 worm, 86


title: F1 worm, 84


title: 20210601_JSL009_ATAC_AN3CA_DMSO_Rep1

value: AN3 CA

value: DMSO


title: TC71 hybrid rep2

description: Library name: 14


title: 20210601_JSL007_ATAC_AN3CA_dBRD9_Rep1


title: F1 worm, 82

value: whole worm


title: Yen6_mutant_2

city: Christchurch

first: Amber

middle: Rose

last: Paulson

address: Lincoln Research Centre, Cnr Springs Road And Gerald Street, Private Bag 4749

department: Forage Science

country: New Zealand

institute: AgResearch Litmited

data_processing:
Flexbar (v2.4) - barcode and adapter trimming in 'ANY' mode
BBMap (v12.2015) screen to remove rRNA using custom host and bacterial rRNA reference
Rockhopper alignment (v2.03)
Filtered out non-expressed features, with less than five aligned reads in two or fewer libraries.
Upper quartile normalization and voom transformation with Limma (v3.38.3) R package
Assembly: GCA_001656035.1/ASM165603v1
Supplementary files format and content: raw read counts; tab deliminated
Supplementary files format and content: normalized/transformed expression values represented as log2 counts-per-million; tab deliminated

organism: Yersinia entomophaga

source_name: enriched from hemolymph

growth_protocol: Bacterial cells were injected into the model host Galleria mellonella and grown in vivo for 10 h at 37 °C. Bacterial cells were enriched from hemolymph as described in Paulson et al. 2021.https://doi.org/10.1093/g3journal/jkaa024.

extract_protocol:
RNA was extracted with RNeasy mini kit (Qiagen), including both on-column and off-column DNAse (Qiagen) digestion, followed by isopropanol precipitation.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina
Ribo-Zero Gold ribosomal RNA (rRNA) Removal Kit (Epidemiology)|Magnetic kit (Illumina)

treatment_protocol: RNA was stabilized with RNAprotect Bacterial Reagent (Qiagen) and stored at -80 °C.

tag: strain

value: 37 °C in Galleria mellonella

tag: time

tag: disease state

value: septicemia

value: enriched from hemolymph


title: TC71 hybrid rep1

description: Library name: 13


title: Yen6_mutant_1


title: 20210601_JSL010_ATAC_AN3CA_DMSO_Rep2


title: F1 worm, 81


title: 20210601_JSL006_ATAC_AN3CA_none_Rep2


title: 20210601_JSL005_ATAC_AN3CA_none_Rep1


title: Wild_type_MH96_2


title: A673 hybrid rep2

description: Library name: 10


title: F1 worm, 80


title: A673 hybrid rep1

description: Library name: 9


title: F1 worm, 79


title: Wild_type_MH96_1


title: M. restricta (MR) was cultured alone - replicate 1


title: 20210601_JSL003_ATAC_AN3CA_neg_DOX_Rep1

value: -Dox


title: 20210601_JSL004_ATAC_AN3CA_neg_DOX_Rep2


title: RH1 monoculture rep2

description: Library name: 6

value: monoculture


title: E4-poly A

city: Farmington

first: Joel

middle: s

last: Pachter

state: CT

address: 263 Farmington Ave

institute: University of Connecticut Health

description: Library name: JPUCONN01_04

data_processing:
Raw base call (BCL) files were converted to FASTQ format and demultiplexed using Illumina’s bcl2fastq v2.20 software
Reads from .fastq files were aligned to GRCm38 genome (release 84) using hisat2 (2.2.1)
Created sorted .bam files using samtools sort (1.9)
Assembled and quantified transcripts using stringtie (2.2.1)
Assembly: GRCm38 release 84
Supplementary files format and content: csv file includes FPKM values for each sample

organism: Mus musculus

source_name: Brain vascular

extract_protocol:
RNA was extracted by using the the Quick-RNA Miniprep Plus kit from Zymo Research (ZYMO Research)
cDNA libraries were generated using the NEBNext® UltraExpress™ RNA Library Prep Kit for Illumina® (New England Biolabs), designed to convert 25–250 ng total RNA into high-quality sequencing libraries with minimal hands-on time. The workflow included mRNA enrichment, fragmentation, random-primed cDNA synthesis, end-repair, adapter ligation, and PCR amplification with indexed primers.

treatment_protocol: no treatment

value: Brain vascular

value: LCM-dissected endothelial cells


title: F1 worm, 78

source_name: whole worm

value: OA


title: TC71 monoculture rep2

description: Library name: 4


title: 20210601_JSL001_ATAC_AN3CA_pos_ARID1A_Rep1

value: +Dox (+ARID1A)


title: RH1 monoculture rep1

description: Library name: 5


title: 20210601_JSL002_ATAC_AN3CA_pos_ARID1A_Rep2


title: F1 worm, 77


title: F1 worm, 76


title: E3-poly A

description: Library name: JPUCONN01_03


title: TC71 monoculture rep1

description: Library name: 3


title: E1-poly A

description: Library name: JPUCONN01_01


title: input from TBX5 KO atria_rep2

first: William

middle: T.

last: Pu

state: Ma

address: 300 Longwood Ave

department: Cardiology

description:
Library name: Input-Cre-2
ChIP-Cre-2_narrow_0.05_peaks.narrowPeak

data_processing:
Peak calling was performed using MACS2, by comparing each sample to their input sample, using q-value <0.05
Samples were further compared using DiffBind
Assembly: mm10
Supplementary files format and content: peak coordinates are given in narrowPeak format

source_name: Right/Left atria

growth_protocol: TBX5flox/flox Mouse sample

extract_protocol:
Atria were dissected and flash frozen
CHD4 ChIP-seq using the ThruPLEX DNA-seq kit

treatment_protocol: Mice were injected at P2 with either AAV9:Nppa-Cre (CHD4 KO) or AAV9:Nppa-EGFP (control

value: Right/Left atria

value: Mixed

value: control


title: F1 worm, 74

value: YA


title: A673 monoculture rep2

description: Library name: 2

value: human sarcoma cancer cell

value: WT


title: A673 monoculture rep1

description: Library name: 1


title: HEL cells, SIAH2 knockout, rep1

city: Mainz

first: Giuseppe

last: Petrosino

state: --- Select a state ---

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology

data_processing:
Reads were aligned on the Homo sapiens genome assembly hg38 (ENSEMBL release 98) using STAR (version 2.7.10a, parameters: --outMultimapperOrder Random --outSAMattributes NH HI AS nM MD –outSJfilterReads Unique --outSAMunmapped Within --outFilterMismatchNoverReadLmax 0.04 –outFilterMismatchNmax 999 –sjdbOverhang 79).
The featureCounts program (version 2.0.0, parameter: -s2) was used to count the number of reads overlapping genes.
Differentially expressed genes (DEGs) were determined using DESeq2 (release: 1.34.0) with an FDR cutoff of 1%.
Assembly: hg38
Supplementary files format and content: Tab-separated values (TSV) files include raw counts for each Sample.
Supplementary files format and content: XLSX file includes TPM values for each Sample.

source_name: Blood

growth_protocol: Cells were maintained under sterile standard cell culture conditions in RPMI-1640 medium supplemented with 10-20% fetal calf serum (FCS), 1% penicillin/streptomycin in humidified, 5% CO2 atmosphere at 37 °C.

extract_protocol:
Cells were harvested and total RNA was isolated using the NucleoSpin RNA kit (Machery-Nagel).
NGS library prep was performed with Illumina's Stranded mRNA Prep Ligation Kit following Stranded mRNA Prep Ligation ReferenceGuide (June 2020) (Document # 1000000124518 v00). Libraries were prepared with a starting amount of 1000 ng and amplified in 9 PCR cycles. After PCR purification, an additional round of purification was performed using 1x of AMPure XP beads. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All 9 samples (three replicates of untreated HEL cells and three replicates of MERCK60 treated and SIAH2 KO cells) were pooled in equimolar ratio and sequenced on 1 NextSeq500 high output FC, SR for 1x79 cycles plus 10 cycles for the index read and 2 dark cycle upfront R1.

treatment_protocol: Wild-type HEL cells (WT) were left untreated or treated with 5 µM MERCK60 for 24 h. These two conditions were compared to SIAH2 knockout HEL cells.

value: Blood

value: HEL

value: Leukemic cells

value: SIAH2 knockout

value: Untreated


title: F1 worm, 75

value: whole worm


title: input from TBX5 KO atria_rep1

description:
Library name: Input-Cre-1
ChIP-Cre-1_narrow_0.05_peaks.narrowPeak


title: HEL cells, SIAH2 knockout, rep2


title: HEL cells, MERCK60, rep3


title: F1 worm, 73


title: input from control atria_rep2

description:
Library name: Input-GFP-2
ChIP-GFP-2_narrow_0.05_peaks.narrowPeak

value: TBX5 KO


title: Frontocentral_R_P025

city: Bogotá D.C

first: Jorge

last: Diaz-Riaño

address: Cra 1 Nº 18A - 12

country: Colombia

institute: Universidad de Los Andes

description:
Library name: P025
10x Genomics

data_processing:
Mapping and feature counting were performed using STARsolo v2.7.11a (Kaminow et al., 2021) against the GRCh38-2020-A human reference genome.
Assembly: Homo sapiens GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Brain cortex

extract_protocol:
Brain tissue samples from epileptogenic regions were collected during resective epilepsy surgery, immediately snap-frozen on dry ice, and stored at -80°C until processing. Nuclei were isolated by mechanical and enzymatic dissociation of frozen tissue following 10X Genomics guidelines for single-nucleus RNA-seq. Isolated nuclei were filtered and counted prior to library preparation.
Single-nucleus RNA libraries were constructed using the 10X Genomics Chromium Single Cell 3’ v3.1 kit, following the manufacturer’s Nuc-Seq protocol. Approximately 7,500 nuclei per sample were encapsulated and barcoded using the Chromium controller. Libraries were prepared with a target depth of ~150,000 reads per nucleus, following 10X Genomics recommendations.

value: Brain cortex

value: Glial and neuronal cells


title: E2-poly A

description: Library name: JPUCONN01_02

value: Brain vascular

value: LCM-dissected endothelial cells


title: F1 worm, 72

value: OA


title: HEL cells, MERCK60, rep2


title: HEL cells, MERCK60, rep1


title: F1 worm, 71


title: NotReported_RE_P024

description:
Library name: P024
10x Genomics


title: input from control atria_rep1

description:
Library name: Input-GFP-1
ChIP-GFP-1_narrow_0.05_peaks.narrowPeak

value: Right/Left atria

value: Mixed


title: Frontotemporal_RE_P020

description:
Library name: P020
10x Genomics


title: HEL cells, SIAH2 knockout, rep3


title: CHD4 ChIP from TBX5 KO atria_rep2

description:
Library name: Cre2
ChIP-Cre-2_narrow_0.05_peaks.narrowPeak

value: control


title: CHD4 ChIP from TBX5 KO atria_rep1

description:
Library name: Cre1
ChIP-Cre-1_narrow_0.05_peaks.narrowPeak


title: F1 worm, 70


title: HEL cells, control (Untreated), rep3


title: Frontal_RE_P018

description:
Library name: P018
10x Genomics


title: HEL cells, control (Untreated), rep2


title: F1 worm, 69


title: CHD4 ChIP from control atria_rep2

description:
Library name: GFP2
ChIP-GFP-2_narrow_0.05_peaks.narrowPeak


title: Parietal_RE_P010

description:
Library name: P010_parietal
10x Genomics


title: F1 worm, 68


title: HEL cells, control (Untreated), rep1


title: CHD4 ChIP from control atria_rep1

description:
Library name: GFP1
ChIP-GFP-1_narrow_0.05_peaks.narrowPeak


title: Frontal_RE_P010

description:
Library name: P010_frontal
10x Genomics


title: Sample23 after first treatment

status: Public on Aug 03 2025

city: Brussels

first: Jacob

last: SOUOPGUI

address: Avenue Franklin Roosevelt 50

country: Belgium

institute: ULB

description: Library name: P23 after treatment1

data_processing:
Raw fastq files generated were trimmed to remove adapters using Porechop version 0.2.4 (https://github.com/rrwick/Porechop). NanoFilt tool  version 2.8.0 [42] was used to filter reads with quality score < 10.
The trimmed and filtered reads were mapped on P. falciparum 3D7 reference genome using Minimap2 software version 2.28-r1209, generating a SAM file. BAM statistics, filtration, sorting, and indexing was done using different Samtools version 1.21 functionalities (flagstat, view, sort, and index) to obtain sorted Bam and their indexes.
BAM quality control was performed using the Qualimap software version 2.2.2 and BAM files were visualized using IGV software version 2.16.0.
Variance calling was performed using Clair3 Clair3 version 1.0.10, haploid calling by including --include_all_ctgs , --haploid_sensitive  and –gvcf parameters. The SNPs in gVCFs were filtered by quality (>10) and depth (>20) using bcftools version 1.21 and annotation to extract SNPs information was performed using  snpEff version 4.10.
Assembly: PlasmoDB-68_Pfalciparum3D7_Genome
Supplementary files format and content: VCF files

organism: Plasmodium falciparum

extract_protocol:
Total genomic DNA  was extracted from patient's blood collected  using Maxwell® RSC Whole Blood DNA Kit (Promega – AS1520) following manufecturer's instructions. Multiplex PCR of Plasmodium falciparum crt, mdr1, dhfr, dhps and csp genes was performed using primer paris reported in the manuscript. Single PCR of Kelch13 and MSP2 genes were also performed using primer paris reported in the manuscript. All target were pooled per sample and purifed using Wizard® SV Gel and PCR Clean-Up System (Promega – A9281) prior to library preparation.
Amplicon sequencing library was prepared using Ligation sequencing amplicons - Native Barcoding Kit 24 V14 (SQK-NBD114.24) from Oxford Nanopore Technology (ONT, UK). Prepared libraries were run on   Flongle Flow Cells (R10.4.1) for 24hrs using MinKNOW software version 24.06.16 (ONT, UK).


title: Sample21 after second treatment

description: Library name: P21 after treatment2


title: Sample22 before treatment

description: Library name: P22 before treatment


title: Sample21 after first treatment

description: Library name: P21 after treatment1


title: Sample21 before treatment

description: Library name: P21 before treatment


title: Sample20 before treatment

description: Library name: P20 before treatment


title: Sample19 after first treatment

description: Library name: P19 after treatment1


title: Sample19 before treatment

description: Library name: P19 before treatment


title: Sample15 after first treatment

description: Library name: P15 after treatment1


title: Sample15 before treatment

description: Library name: P15 before treatment


title: Sample20 after first treatment

description: Library name: P20 after treatment1


title: Sample17 before treatment

description: Library name: P17 before treatment


title: Sample18 after first treatment

description: Library name: P18 after treatment1


title: Sample18 before treatment

description: Library name: P18 before treatment


title: Sample14 before treatment

description: Library name: P14 before treatment


title: Sample12 after first treatment

description: Library name: P12 after treatment1


title: Sample13 before treatment

description: Library name: P13 before treatment


title: Sample16 before treatment

description: Library name: P16 before treatment


title: Sample14 after first treatment

description: Library name: P14 after treatment1


title: Sample11 before treatment

description: Library name: P11 before treatment


title: Sample23 before treatment

description: Library name: P23 before treatment


title: Sample14 after second treatment

description: Library name: P14 after treatment2


title: Sample11 after first treatment

description: Library name: P11 after treatment1


title: Sample9 after first treatment

description: Library name: P9 after treatment1


title: Sample10 before treatment

description: Library name: P10 before treatment


title: Sample8 after first treatment

description: Library name: P8 after treatment1


title: Sample7 before treatment

description: Library name: P7 before treatment


title: Sample10 after first treatment

description: Library name: P10 after treatment1


title: Sample8 before treatment

description: Library name: P8 before treatment


title: Sample6 before treatment

description: Library name: P6 before treatment


title: Sample12 before treatment

description: Library name: P12 before treatment


title: Sample9 before treatment

description: Library name: P9 before treatment


title: Sample3 after second treatment

description: Library name: P3 after treatment2


title: Sample5 after first treatment

description: Library name: P5 after treatment1


title: Sample4 before treatment

description: Library name: P4 before treatment


title: Sample3 after first treatment

description: Library name: P3 after treatment1


title: Sample13 after first treatment

description: Library name: P13 after treatment1


title: Sample5 before treatment

description: Library name: P5 before treatment


title: Sample3 before treatment

description: Library name: P3 before treatment


title: Sample2 after second treatment

description: Library name: P2 after treatment2


title: Sample2 after first treatment

description: Library name: P2 after treatment1


title: Sample2 before treatment

description: Library name: P2 before treatment


title: Sample4 after first treatment

description: Library name: P4 after treatment1


title: Sample1 after first treatment

description: Library name: P1 after treatment1


title: Sample6 after first treatment

description: Library name: P6 after treatment1


title: liver-E30-TM-rep7

type: RNA

city: Mont de Marsan

first: Marianne

last: Houssier

address: 371 rue du ruisseau

department: GB

country: France

institute: INRA NUMEA/IUT UPPA

data_processing:
Real time quantitative PCR results were analyzed using the Fluidigm real-time PCR analysis software v.4.1.3.   The relative expression was normalized with four reference genes (ActB, Luciferase, STAB1 and USP9X for for the hour kinetic, and HPRT1, Luciferase, STAB1 and UPS9X for the daily kinetic), selected according to the function GeNorm from the package CtrlGene of R (v.3.6.2).
Tests have been adapted to compare the relative expression between groups for the two trials (n=6 minimum) for each timing (2 ways analysis was excluded due to the flattening of the TM effects)

label: EVAGREEN

organism: Anas platyrhynchos x Cairina moschata

source_name: liver at embryonic day 30/hatch

label_protocol: The sample amplifications were realized in two steps by using the Fluidigm method. A first pre-amplification with Preamp Master Mix (Fluidigm) was done following program: 95°C/10 min and 14 cycles of 95°C/15 sec and 60°C/4 min. Pre-amplified samples were treated by exonuclease (NEB) before a low EDTA buffer (10mM Tris-HCL, 0.1 mM EDTA) dilution and before moving samples to a 96x96 chip for Fluidigm Gene Expression Array. The reaction was made using 20× EvaGreen (Interchim) dye following the program:70°C/2400 sec, 60°C/30 sec, 30 cycles of 96°C/5 sec and 60°C/20 sec.

extract_protocol: In the first trial whole livers (8 per condition) were collected 30 minutes, 1h, 2h, 3h, 4h, 5h and 7h after the first day of temperature increase (E13). In the second trial, whole livers (8 per condition) were collected 1 hour after the daily temperature increase (5 p.m.), 3, 7 and 11 days after the temperature increase (E16, E20 and E24) and three days after the end of the temperature increase, at hatching (E30). Similar samples were taken at the same times for the control group, not exposed to the temperature increase. The livers were immediately immersed in liquid nitrogen before being stored at -80°C.

value: liver

tag: developmental stage

value: embryonic day 30

value: hatch

tag: group

value: TM group


title: liver-E30-TM-rep8


title: liver-E30-TM-rep5


title: liver-E30-TM-rep6


title: liver-E30-TM-rep3


title: liver-E30-TM-rep2


title: liver-E30-TM-rep4


title: liver-E30-Ctl-rep4

value: Ctl group


title: liver-E30-Ctl-rep6


title: liver-E30-Ctl-rep7


title: liver-E30-Ctl-rep8


title: liver-E30-Ctl-rep5


title: liver-E30-TM-rep1


title: Sample1 before treatment

description: Library name: P1 before treatment

value: Blood


title: liver-E30-Ctl-rep2


title: liver-E28-TM-rep7

source_name: liver at embryonic day 28, 1h after the increase of temperature

value: embryonic day 28

value: 1h after the increase of temperature


title: liver-E28-TM-rep3


title: liver-E28-TM-rep2


title: liver-E30-Ctl-rep1


title: liver-E28-TM-rep4


title: liver-E28-TM-rep8


title: liver-E28-Ctl-rep7


title: liver-E28-TM-rep6


title: liver-E28-TM-rep5


title: liver-E30-Ctl-rep3


title: liver-E28-Ctl-rep5


title: liver-E28-Ctl-rep1


title: liver-E24-TM-rep7

source_name: liver at embryonic day 24, 1h after the increase of temperature

value: embryonic day 24


title: liver-E28-Ctl-rep4


title: liver-E28-Ctl-rep8


title: liver-E24-TM-rep8


title: liver-E24-TM-rep3


title: liver-E28-TM-rep1


title: liver-E24-TM-rep6


title: liver-E28-Ctl-rep2


title: liver-E28-Ctl-rep6


title: liver-E24-TM-rep1


title: liver-E24-TM-rep5


title: liver-E24-Ctl-rep7


title: liver-E24-Ctl-rep8


title: liver-E24-TM-rep4


title: liver-E24-Ctl-rep1


title: liver-E24-Ctl-rep2


title: liver-E20-TM-rep8

source_name: liver at embryonic day 20, 1h after the increase of temperature

value: embryonic day 20


title: liver-E24-Ctl-rep4


title: liver-E24-Ctl-rep3


title: liver-E28-Ctl-rep3


title: liver-E20-TM-rep7


title: liver-E24-Ctl-rep6


title: liver-E20-TM-rep4


title: liver-E20-TM-rep3


title: liver-E24-TM-rep2


title: liver-E20-TM-rep5


title: liver-E20-Ctl-rep7


title: liver-E20-Ctl-rep8


title: liver-E20-TM-rep1


title: liver-E24-Ctl-rep5


title: liver-E20-Ctl-rep5


title: liver-E20-Ctl-rep6


title: liver-E20-Ctl-rep4


title: liver-E20-Ctl-rep3


title: liver-E20-Ctl-rep2


title: liver-E16-TM-rep8

source_name: liver at embryonic day 16, 1h after the increase of temperature

value: embryonic day 16


title: liver-E20-Ctl-rep1


title: liver-E16-TM-rep5


title: liver-E16-TM-rep7


title: liver-E20-TM-rep6


title: liver-E16-TM-rep6


title: liver-E16-TM-rep3


title: liver-E16-TM-rep2


title: liver-E16-Ctl-rep7


title: liver-E16-TM-rep1


title: liver-E16-Ctl-rep3


title: liver-E16-Ctl-rep4


title: liver-E16-Ctl-rep2


title: liver-E12-TM-rep8

source_name: liver at embryonic day 12, 1h after the increase of temperature

value: embryonic day 12


title: liver-E16-Ctl-rep1


title: liver-E12-TM-rep7


title: liver-E20-TM-rep2


title: liver-E12-TM-rep6


title: liver-E12-TM-rep4


title: liver-E12-TM-rep1


title: liver-E12-TM-rep2


title: liver-E12-TM-rep5


title: liver-E16-TM-rep4


title: liver-E12-TM-rep3


title: liver-E12-Ctl-rep5


title: liver-E12-Ctl-rep8


title: liver-E12-Ctl-rep4


title: liver-E12-Ctl-rep6


title: liver-E12-Ctl-rep7


title: liver-E12-Ctl-rep1


title: liver-E12-Ctl-rep2


title: liver-E12-Ctl-rep3


title: liver-E13-7h-TM-rep8

source_name: liver at embryonic day 13, 7h after the increase of temperature

value: embryonic day 13

value: 7h after the increase of temperature


title: liver-E13-7h-TM-rep7


title: liver-E13-7h-TM-rep6


title: liver-E13-7h-TM-rep3


title: liver-E13-7h-TM-rep5


title: liver-E13-7h-TM-rep4


title: liver-E13-7h-Ctl-rep2


title: liver-E13-7h-TM-rep1


title: liver-E13-5h-TM-rep8

source_name: liver at embryonic day 13, 5h after the increase of temperature

value: 5h after the increase of temperature


title: liver-E13-7h-Ctl-rep6


title: liver-E13-7h-Ctl-rep7


title: liver-E13-7h-Ctl-rep3


title: liver-E13-7h-Ctl-rep4


title: liver-E13-7h-TM-rep2


title: liver-E13-5h-TM-rep7


title: liver-E13-7h-Ctl-rep5


title: liver-E13-5h-TM-rep1


title: liver-E13-5h-TM-rep5


title: liver-E13-5h-TM-rep6


title: liver-E13-5h-TM-rep4


title: liver-E13-5h-Ctl-rep4


title: liver-E13-7h-Ctl-rep8


title: liver-E13-5h-Ctl-rep3


title: liver-E13-5h-Ctl-rep8


title: liver-E13-5h-TM-rep3


title: liver-E13-5h-Ctl-rep1


title: liver-E13-5h-Ctl-rep6


title: liver-E13-5h-Ctl-rep7


title: liver-E13-4h-TM-rep7

source_name: liver at embryonic day 13, 4h after the increase of temperature

value: 4h after the increase of temperature


title: liver-E13-5h-Ctl-rep5


title: liver-E13-4h-TM-rep5


title: liver-E13-4h-TM-rep6


title: liver-E13-4h-TM-rep8


title: liver-E13-5h-TM-rep2


title: liver-E13-4h-Ctl-rep3


title: liver-E13-4h-Ctl-rep5


title: liver-E13-4h-TM-rep4


title: liver-E13-4h-TM-rep3


title: liver-E13-4h-TM-rep1


title: liver-E13-3h-TM-rep8

source_name: liver at embryonic day 13, 3h after the increase of temperature

value: 3h after the increase of temperature


title: liver-E13-4h-Ctl-rep1

value: liver


title: liver-E13-4h-Ctl-rep4


title: liver-E13-4h-Ctl-rep6


title: liver-E13-4h-TM-rep2


title: liver-E13-5h-Ctl-rep2


title: liver-E13-3h-TM-rep6


title: liver-E13-4h-Ctl-rep2


title: liver-E13-3h-TM-rep7


title: liver-E13-3h-TM-rep1


title: liver-E13-3h-TM-rep2


title: liver-E13-3h-TM-rep3


title: liver-E13-3h-TM-rep4


title: liver-E13-4h-Ctl-rep7


title: liver-E13-3h-TM-rep5


title: liver-E13-4h-Ctl-rep8


title: liver-E13-3h-Ctl-rep7


title: liver-E13-3h-Ctl-rep5


title: liver-E13-3h-Ctl-rep2


title: liver-E13-3h-Ctl-rep1


title: liver-E13-3h-Ctl-rep3


title: liver-E13-2h-TM-rep8

source_name: liver at embryonic day 13, 2h after the increase of temperature

value: 2h after the increase of temperature


title: liver-E13-2h-TM-rep4


title: liver-E13-2h-TM-rep6


title: liver-E13-2h-TM-rep7


title: liver-E13-2h-TM-rep3


title: liver-E13-3h-Ctl-rep8


title: liver-E13-2h-Ctl-rep5


title: liver-E13-2h-Ctl-rep6


title: liver-E13-2h-Ctl-rep7


title: liver-E13-3h-Ctl-rep4


title: liver-E13-2h-Ctl-rep4


title: liver-E13-2h-Ctl-rep1


title: liver-E13-2h-Ctl-rep2


title: liver-E13-3h-Ctl-rep6


title: liver-E13-2h-Ctl-rep3


title: liver-E13-1h-TM-rep8

source_name: liver at embryonic day 13, 1h after the increase of temperature


title: liver-E13-1h-TM-rep6


title: liver-E13-2h-TM-rep2


title: liver-E13-1h-TM-rep4


title: liver-E13-1h-TM-rep5


title: liver-E13-1h-TM-rep3


title: liver-E13-2h-TM-rep5


title: liver-E13-1h-TM-rep2


title: LP, Replicate3

city: Beijing

first: Zexian (Davis)

last: Zeng

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

description: Library name: Sample9

data_processing:
We applied the RNA-Seq immune analysis pipeline (RIMA) to analyze bulk RNA-Seq data. In brief, sequencing reads were aligned to the human reference genome (hg38) using STAR v2.6.1d. Salmon v0.13.1 was utilized to map transcripts to genes and generate a gene count matrix.
Differentially expressed genes were identified using DESeq2 v1.34.0, with an adjusted P-value (FDR) threshold of <0.05 for determining significance. The replicates of RNA-Seq from each condition were considered as a covariate in DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

growth_protocol: CD14+ monocytes were isolated and primed with M-CSF in vitro for 24 hours. Subsequent treatments were applied to investigate the roles of lactate, PGE2, and GM-CSF in macrophage polarization

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Macrophages were polarized under three conditions: vehicle control, 2 ng/mL GM-CSF, and a combination of 25 mM lactate with 100 nM PGE2

tag: cell line

value: Primary macrophages

value: Monocyte-derived macrophages


title: liver-E13-1h-TM-rep1

tag: tissue

value: TM group


title: LP, Replicate2

description: Library name: Sample8

value: Blood


title: liver-E13-2h-TM-rep1


title: liver-E13-1h-Ctl-rep8

value: Ctl group


title: LP, Replicate1

description: Library name: Sample7


title: liver-E13-2h-Ctl-rep8


title: G, Replicate3

description: Library name: Sample6


title: liver-E13-1h-Ctl-rep7

value: 1h after the increase of temperature


title: liver-E13-1h-Ctl-rep6


title: liver-E13-1h-TM-rep7


title: G, Replicate2

description: Library name: Sample5


title: ctrl, Replicate3

description: Library name: Sample3


title: liver-E13-1h-Ctl-rep3


title: liver-E13-1h-Ctl-rep4


title: liver-E13-1h-Ctl-rep2


title: liver-E13-1h-Ctl-rep5


title: ctrl, Replicate1

description: Library name: Sample1


title: liver-E13-1h-Ctl-rep1


title: A1CF KO EndoC-BH3 3

city: Barcelona

first: Edgar

last: Bernardo

state: Barcelona

address: C/ del Dr. Aiguader, 88,

country: Spain

institute: CRG

data_processing:
RNA-seq reads were aligned to the mouse (GRCm38.p6 v.M24) or human (GRCh38 gencode v.42) transcriptomes using STAR (v2.7.10b) and Salmon (v1.9.0)
Salmon quant files we employed for differential gene expression using DESeq2 (v1.38.0)
For RNA-seq track visualization, STAR was used to generate BAM files that were subsequently converted into bigwig files with Deeptools (v3.5.1)
BAM files were used for differential alternative splicing analysis with rMATS (turbo v4.1.2)
Assembly: mm10
Assembly: hg38
Supplementary files format and content: tab-delimited Excel files including TPM counts (mouse islets) or Log2 TPM (EndoC-BH3 cells), differential gene expression analysis (DESeq2) and differential alternative splicing analysis (rMATS)

source_name: Human β-cell line

growth_protocol:
EndoC-βH3 cells were cultured in plates coated with extracellular matrix gel from murine sarcoma and 2μg/mL fibronectin using Advanced DMEM/F12 supplemented with 2% fatty acid-free Bovine Serum Albumin Fraction V, 6.7ng/mL sodium selenite, 50μM 2-mercaptoethanol, 5.5μg/mL human transferrin, 10mM nicotinamide, 1% GlutaMAX and 100 U/mL Penicillin-Streptomycin.
MIN6 cells were cultured in DMEM High Glucose supplemented with 15% FBS, 1% GlutaMAX, 1% Penicillin-Streptomycin and 2.5μl β-mercaptoethanol.
Mouse pancreatic Islets cultured after isolation for 1-2 days in RPMI with 10% FBS and Pen-Strep (1:100) at 37ºC and 5% CO2.

extract_protocol:
Total RNA isolated using NucleoSpin Plus RNA kit (Cultek). 1ug of RNA was used for library preparation
RNAseq libraries were prepared using Trueseq Stranded mRNA Sample Prep Kit (Illumina)

value: EndoC-BH3 cell line

value: Human beta-cell line

tag: genotype

value: A1CF KO


title: A1CF KO EndoC-BH3 1


title: A1CF KO EndoC-BH3 2


title: liver-E13-30min-TM-rep8

source_name: liver at embryonic day 13, 30min after the increase of temperature

value: 30min after the increase of temperature


title: HNF1A KO EndoC-BH3 3

value: HNF1A KO


title: liver-E13-30min-TM-rep6

value: embryonic day 13


title: liver-E13-30min-TM-rep5


title: liver-E13-30min-TM-rep7


title: HNF1A KO EndoC-BH3 1


title: HNF1A KO EndoC-BH3 2


title: G, Replicate1

description: Library name: Sample4


title: liver-E13-30min-TM-rep4


title: liver-E13-30min-TM-rep3


title: Control EndoC-BH3 3

value: WT


title: liver-E13-30min-TM-rep2


title: ctrl, Replicate2

description: Library name: Sample2


title: Control EndoC-BH3 2


title: liver-E13-30min-Ctl-rep8


title: liver-E13-30min-TM-rep1


title: Control EndoC-BH3 1


title: liver-E13-30min-Ctl-rep7


title: MS-SH3

city: Shanghai

first: Yunhan

last: Liu

state: Shanghai

address: 639 Zhizaoju Road,

department: Department of Plastic and Reconstructive Surgery

institute: Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine

data_processing:
The quality of the library was assessed with an Agilent 2100 Bioanalyzer (Agilent, China).
For mRNAs, data were aligned to the reference genome using the software Hisat2.
The transcript abundances in each sample were estimated with StringTie.
Using the R software Ballgown, FPKM value and expression difference at the gene and transcript levels were calculated.
Assembly: hg19
Supplementary files format and content: The text files include FPKM values for each Sample

growth_protocol: CCD-1064sk dermal fibroblats were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics atmosphere with 5% CO2 at 37℃

extract_protocol:
The extraction of total RNA was performed using TRIzol Reagent (Invitrogen, USA), and the RNA concentration was determined using NanoDrop (ND-1000).  Following the removal of rRNAs, 2 ug of total RNA was used for the preparation of cDNA library.
The library for RNA-seq were prepared with a KAPA-Stranded RNA-Seq Library Prep Kit (Illumina, USA) following manufacturer's protocols.

treatment_protocol: We subjected the HDFs adhered to the rubber membrane to constant static MS using a cell-stretching device; this resulted in the membrane deforming as loading columns applied upward pressure. The cells of the MS group underwent mechanical loading for 48 hours, while the cells of the control group were cultured under the same conditions but without additional stress.

value: Dermal fibroblast

value: IL11RA knockdown

tag: treatment

value: Continuous static mechanical stress


title: MS-NC


title: liver-E13-30min-Ctl-rep6

value: liver


title: Ctrl-NC

value: Control


title: Ctrl-SH2


title: Ctrl-SH3


title: MS-SH2


title: liver-E13-30min-Ctl-rep5


title: liver-E13-30min-Ctl-rep4


title: liver-E13-30min-Ctl-rep3


title: Day 18 Ly29 Replicate 2

city: Los Angeles

first: Nils

last: Lindström

state: CA

address: 1425 San Pablo Street Lab 409

department: Stem Cell Biology and Regenerative Medicine

institute: University of Southern California (USC) -

description: Bulk mRNA-sequencing

data_processing:
For processed data, STAR alignment of fastq files to the genome was performed following fastqc check. The feature counts table was generated from the resulting .bam files using featurecounts and is provided here as a .txt file.
Assembly: Homo sapiens, hg38, Ensembl 105 annotation
Supplementary files format and content: Tab-delimited .txt file includes raw feature counts for each sample

source_name: Kidney organoid

growth_protocol: Takasato et al., 2016 Nature Protocols

extract_protocol:
Single organoids were collected into Buffer RLT from the Rneasy mini kit (Qiagen)
Total RNA was isolated from samples following instructions from the Rneasy mini kit (Qiagen)

treatment_protocol: Ly29-treated samples were treated with 10 uM LY294002 between days 10 and 12 of kidney organoid differentiation

value: Kidney organoid

value: Ly29 (10 uM from days 10-12)


title: liver-E13-30min-Ctl-rep1


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 15

city: Stanford

first: Emily

last: Shuldiner

address: 279 Campus Drive

department: Genetics

institute: Stanford University

description:
Library name: Parse library 15
Parse Biosciences WT Mega v2

data_processing:
The processing pipeline provided by Parse Biosciences (split-pipe v1.1.1) was used with default settings to align sequencing reads to the GRCm38 mouse reference genome. Each of the 16 sublibraries was first processed individually using the command split-pipe –mode all, and the output of the 16 sublibraries was combined using split-pipe –mode combine.
Cell barcodes were filtered to include only cells meeting the following criteria: (1) expressing between 200 and 10,000 genes, (2) having between 500 and 100,000 read counts, and (3) having less than 10% of reads map to mitochondrial genes. Scrublet was used to simulate doublets and assign doublet scores to cells based on a k-nearest-neighbor classifier.  Cells with doublet scores >0.12 were removed from the dataset. Read counts were normalized per cell using the scanpy function ‘normalize_total’ with default parameters and scaled for variance stabilization using a shifted logarithm transformation (log X+1,  where X is the normalized counts). Cell types were annotated using SCINA as described in the manuscript.
Assembly: GRCm38
Supplementary files format and content: h5ad file containing raw and normalized count data from all 16 sublibraries, annotated by sublibrary, cell type, sample and sample characteristics including type (bulk or cancer cell fraction), age (young or old) and tumor genotype.

source_name: Tumor-bearing lung

extract_protocol:
Whole tumor-bearing lungs were finely minced immediately after harvesting and enzymatically dissociated using collagenase IV, dispase, and trypsin at 37°C for 30 minutes. Bulk cell suspensions were viably frozen in Bambanker cryopreservation media (Wako Chemicals, 302-14681) at -80°C before transfer to liquid nitrogen. Cells were thawed and stained with antibodies against CD45, CD31, F4/80, and Ter119 (all from BioLegend) to identify hematopoietic and endothelial cells. Each sample was sorted for viability (DAPI-negative) and divided into two compartments: (1) “cancer cell” samples containing Tomatopos, CD45neg, CD3 neg , F4/80 neg  and Ter119 neg  cells which are presumed to be cancer cells, and (2) “bulk” samples containing all other viable cells. FACSAria™ sorters (BD Biosciences) were used for all cell sorting. Samples were fixed immediately after sorting using Parse Biosciences Cell Fixation kits (v2, May 2023) and stored at -20°C. To maximize recovery for cancer cell samples where we had limited input material, we used a modified version of the Parse fixation protocol. Specifically, all volumes were scaled down to ¼ of the recommended amount so that the entirety of the final suspension of fixed cells could be loaded into the plate used for barcoding and library preparation.
Samples were processed for multiplexed single-cell RNA-sequencing using the Parse Biosciences WT Mega v2 kit according to the manufacturer’s instructions. This kit uses a combinatorial barcoding approach, allowed multiplexing of all samples into 16 sublibraries, each containing a mixture of cells from all samples. Samples for this experiment were loaded into the kit and processed alongside and sequenced with samples from another experiment.

value: Tumor-bearing lung

value: Multiple

value: Kras(L/+); Tom (T/T); Cas9 (C/C)


title: Day 18 Control Replicate 1

description: Bulk mRNA-sequencing


title: Day 18 Ly29 Replicate 1

description: Bulk mRNA-sequencing


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 13

description:
Library name: Parse library 13
Parse Biosciences WT Mega v2


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 16

description:
Library name: Parse library 16
Parse Biosciences WT Mega v2


title: Day 18 Control Replicate 2

description: Bulk mRNA-sequencing


title: Day 14 Ly29 Replicate 1

description: Bulk mRNA-sequencing


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 11

description:
Library name: Parse library 11
Parse Biosciences WT Mega v2


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 14

description:
Library name: Parse library 14
Parse Biosciences WT Mega v2


title: Day 14 Control Replicate 1

description: Bulk mRNA-sequencing


title: Day 12 Ly29 Replicate 3

description: Bulk mRNA-sequencing


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 9

description:
Library name: Parse library 9
Parse Biosciences WT Mega v2


title: Day 14 Ly29 Replicate 2

description: Bulk mRNA-sequencing


title: Day 12 Ly29 Replicate 2

description: Bulk mRNA-sequencing


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 12

description:
Library name: Parse library 12
Parse Biosciences WT Mega v2


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 10

description:
Library name: Parse library 10
Parse Biosciences WT Mega v2


title: liver-E13-30min-Ctl-rep2

value: Ctl group


title: Day 12 Control Replicate 3

description: Bulk mRNA-sequencing


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 6

description:
Library name: Parse library 6
Parse Biosciences WT Mega v2


title: Day 12 Control Replicate 2

description: Bulk mRNA-sequencing


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 7

description:
Library name: Parse library 7
Parse Biosciences WT Mega v2


title: Day 12 Ly29 Replicate 1

description: Bulk mRNA-sequencing


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 3

description:
Library name: Parse library 3
Parse Biosciences WT Mega v2


title: Day 10 Replicate 3

description: Bulk mRNA-sequencing

value: Untreated


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 4

description:
Library name: Parse library 4
Parse Biosciences WT Mega v2


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 5

description:
Library name: Parse library 5
Parse Biosciences WT Mega v2


title: Day 12 Control Replicate 1

description: Bulk mRNA-sequencing


title: Day 14 Control Replicate 2

description: Bulk mRNA-sequencing


title: Day 10 Replicate 1

description: Bulk mRNA-sequencing


title: Day 10 Replicate 2

description: Bulk mRNA-sequencing


title: Dissociated tumor-bearing lung, mixed age and genotype (all samples represented), sublibrary 2

description:
Library name: Parse library 2
Parse Biosciences WT Mega v2