title: MD901 AZA_rep1

description: Library name: Sample 19


title: BTRC_7_10X _HT_snRNA-seq

status: Public on Aug 04 2025

type: SRA

city: Indianapolis

first: Yunlong

last: Liu

state: IN

address: 410 West 10th Street, HITS 5001

country: USA

institute: Indiana University School of Medicine

description: 'BTRC_7 ' 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.

molecule: polyA RNA

organism: Homo sapiens

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: MD901 HDAC3i_rep2

city: Nice

first: Pilar

middle: M

last: Dominguez

state: Provence-Alpes-Côte d'Azur

address: 151 Route de Saint-Antoine

country: France

institute: Centre Méditerranéen de Médecine Moléculaire: C3M

description: Library name: Sample 17

library_source: genomic

data_processing:
Bcl2fastq (v2.17.1.14) was used to demultiplex sequencing files and resulting Fastq output was quality checked using FASTQC (v0.11.9).
Sequencing reads were trimmed (Fastp) and mapped to GRCH38.p14 human genome (NCBI) using Bowtie2 with local alignment mode enabled (v2.5.4).
SAM files were converted to BAM format and sorted by genomic coordinates using Samtools (v1.21). Prior to the peak calling step, duplicates were removed with Sambamba (v0.6.6), and multi-mapped or unaligned reads were filtered out using Samtools (v1.21), retaining only uniquely aligned reads. Additionally, genomic artifact regions listed in the ENCODE blacklist were excluded using Bedtools (v2.27.1).
Deeptools bamCoverage function was used for BAM to BigWig file conversion using the following settings (--normalizeUsing CPM --smooth length 150 -bs 50 -e 150).
BAM file peak Calling was performed using MACS2 (v2.2.7.1)  with the following settings (-f BAM --qvalue 0.05 -g hs -c INPUT)
The peak annotation has been performed using ChIPseeker (v4.4) and the statistical analysis was carried out with DiffBind (v3.6.10).
Assembly: hg38
Supplementary files format and content: bigWig generated with the peak Calling step, contains information such as postion, score, Signal Value, qValue

molecule: genomic DNA

source_name: lymphoma cells

growth_protocol: Cells were passaged every 3-4 days when they were observed to have attained roughly 90% confluency, determined by light microscopy. New frozen vials of cells were thawed every month for use.

extract_protocol:
At day 5 cells were fixed with 1% formaldehyde for 10min and sonicated using the S220 Focused-ultrasonicator (Covaris) for 15min. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated after immunoprecipitation with the H3K27ac antibody (Abcam Cat# ab4729) using Protein A and Protein G Dyna beads (Invitrogen). Samples were washed prior to overnight reverse crosslinking.Chromatin was isolated with the ChIP DNA Clean and concentrator (Zymo Research) .
Libraries were prepared using the DNA Library Prep NEB (New England Biolabs)

treatment_protocol: Cells were treated daily with 0nM or 200nM 5-AZA from day 0 to day 4; and on day 2 and day 4 they were treated with either 0μM or 10μM HDAC3i

tag: cell type

value: lymphoma cells

tag: treatment

tag: antibody

value: H3K27ac antibody


title: MD901 vehicle_rep3

description: Library name: Sample 15

value: vehicle


title: BTRC_69_10X _HT_snRNA-seq

description: 'BTRC_69 ' in Seurat object's 'sample' metadata field


title: Normal

city: New York

first: Raman

last: Gill

state: NY

address: 1428 Madison Ave

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

description: Library name: Normal

data_processing:
Samples were sequenced and demultiplexed by Novogene (Novogene, Sacramento, CA) to produce raw fastq files for each sample. Fastq files were mapped to the mm10 mouse genome using the Cellranger (v.8.0) pipeline from 10X Genomics. UMI counts for each gene were quantified per cell to generate feature-barcode counts matrices.
Assembly: mm10
Supplementary files format and content: processed files are filtered cellranger matrix, feature, and barcode output files. Default filtering parameters in cellranger were used

organism: Mus musculus

source_name: skin

extract_protocol:
ear+neck skin samples were pooled for n=3 mice per library and immediately digested using the Multi Tissue Dissociation Kit 1 (Miltenyi). To enhance the detection rate of fibroblasts, Collagenase Ia (1 mg/mL, Sigma) was used in place of Enzyme D. Digestion was carried out at 37°C for 1 hour with gentle agitation using the GentleMACS Dissociator Program H. The digested cell suspensions were passed sequentially through 100 μm and 35 μm cell strainers to remove undigested tissue fragments. To ensure a high cell viability, the suspension was further processed using the MojoSort™ Mouse Dead Cell Removal Kit (BioLegend) twice. After confirming a cell viability of ≥80%, the cells were resuspended in PBS and proceeded to library preparation according to the protocol provided by 10x Genomics (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index))
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index)

treatment_protocol: Neck skin was shaved for each mouse 1 day prior to treatment. For MC903, 1nmol calcipotriol (Tocris Bioscience) dissolved in ethanol, was used to induce AD-like skin in mice. 100uL was applied to the ear and neck skin of the mouse every day for 9 days. For Oxazolone, Oxazolone (Sigma) was used as a hapten. Mice were sensitized with 100 µl of 3% (wt/vol) oxazolone in acetone–mineral oil  4:1 (v/v) on their shaved back and ear skin. Seven days after sensitization, 100 µl of 1.0% (wt/vol) oxazolone was applied every other day. Treated neck/ear skin was harvested at day 10 and day16

value: skin

tag: site

value: neck + ear

value: Untreated

tag: age

value: 6-8 weeks

tag: Sex

value: female

tag: host strain


title: MD901 HDAC3i_rep3

description: Library name: Sample 18


title: BTRC_6_10X _HT_snRNA-seq

description: 'BTRC_6 ' in Seurat object's 'sample' metadata field


title: MD901 vehicle_rep2

description: Library name: Sample 14


title: MD901 vehicle_rep1

description: Library name: Sample 13


title: Normal_sample2

description: Library name: WT_untreat_4_2

library_source: transcriptomic

data_processing:
Samples were sequenced and demultiplexed by Novogene (Novogene, Sacramento, CA) to produce raw fastq files for each sample. Fastq files were mapped to the GRCm39 mouse genome using Salmon (v1.2.1). Mapped quant.sf transcript reads were imported to R with the tximport (v1.34.0) package and analyzed using DESeq2 (v1.44.0)
Assembly: GRCm39
Supplementary files format and content: processed data includes the counts sample-by-gene matrix produced from imported salmon quant.sf output files using the tximport R package.

extract_protocol:
Skin tissues were harvested and placed inside aluminum cylinders (5 mm inner diameter) that had been cleaned with RNase Away (Molecular Bio Products) and filled with 60 μL of RNase-free ultrapure water. The cylinders were submerged in liquid nitrogen for 1 minute to freeze the tissues. The frozen tissues were stored at -80°C and transferred to a cryostat for sectioning prior to RNA extraction. The frozen sample was removed from the cylinder while keeping it on ice and mounted on a cryostat chuck using OCT compound. Approximately 20 frozen sections (20 μm each) were carefully cut and transferred to pre-chilled 2 mL tubes using cold tweezers. This process was repeated until the entire sample was sectioned. After sectioning, 1 mL of QIAzol was added to the tubes, and the contents were vortexed for 60 seconds. The samples were kept on ice until RNA purification. RNA was isolated and purified using the Quick-RNA Micro Prep Kit (Zymo Research), and RNA concentration and purity were evaluated using a Bioanalyzer (Agilent 2100).
libraries were constructed by Novogene (Sacramento, CA) from extracted and purified RNA

treatment_protocol: In the Isotype vs MAR1 experiment, 20ug MAR1 (Biolegend Cat# 134302) or Isotype control (Biolegend Cat#400902) neutralizing antibody was injected i.p. in 100uL PBS every other day. After 3 injections, 100uL of 1nmol calcipotriol (MC903) (Tocris Bioscience) dissolved inethanol or vehicle control was applied to shaved neck skin every day for 6 days. During this time, MAR-1 and Isotype control injections continued to be administered every other day. In the Il4rafl/fl and Il4raΔPdgfra experiment, MC903 was applied to shaved neck skin of each mouse every day for 6 days as described above - no injections were administered.

value: neck

value: untreated

value: 6 weeks


title: ∆wblA biological replicate #15 + WblA_Flag 16 hour

city: Norwich

first: Matt

last: Hutchings

state: Norfolk

address: Norwich Research Park, Colney Lane

country: United Kingdom

institute: John Innes Centre

description: Library name: Wbla15_16h _15-16

data_processing:
Basecalling was performed using bcl2fatq by Novogene
Assembly: Streptomyces venezuelae NRRL B-65442 GCA_001886595.1
Supplementary files format and content: Raw sequencing data were received as FASTQ files from Novogene and reads were aligned to the relevant reference genome. A normalized local enrichment was calculated along the chromosome by comparing the density of mapped reads in 30 nucleotide windows moving in steps of 15 nucleotides to the density of mapped reads in the 3000-nucleotide region surrounding the window.

organism: Streptomyces venezuelae

source_name: Whole cell

growth_protocol: Spore stocks of S. venezuelae wild-type and S. venezuelae ∆wblA complemented with wblA-3xFLAG were inoculated (30 µL) into 50 mL of MYM + TE broth in 250 mL baffled flasks and incubated at 30 °C with shaking at 200 rpm for 12 or 16 hours.

extract_protocol:
Lysates were cleared by centrifugation at 17,005×g for 20 minutes at 7 °C. Anti-FLAG M2 beads (100 µL) were pre-washed with 1 mL IPP150 buffer (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.1% NP-40) and incubated briefly with rotation at 4 °C before pelleting at 226×g for 5 minutes. The cleared lysate was adjusted by adding per mL: 10 µL of 1 M Tris-HCl pH 8.0, 20 µL of 5 M NaCl, and 10 µL of 10% NP-40. After brief centrifugation (226×g, 5 min), the lysate was added to the prepared beads and rotated overnight at 4 °C. A 20 µL aliquot was retained for DNA fragmentation assessment. Beads were washed five times with 1 mL IPP150 buffer (inverting 1–2 minutes, then centrifugation at 226×g for 5 minutes at 7 °C), followed by two washes with 1× TE buffer (10 mM Tris-HCl pH 7.4, 1 mM EDTA). All supernatant was carefully removed after the final wash. Elution was performed by incubating beads with 150 µL of elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) at 65 °C for 15 minutes. After centrifugation (226  RCF, 5 min), a second elution was performed with 100 µL of 1× TE + 1% SDS at 65 °C for 5 minutes. Eluates were pooled. Cross-links were reversed by incubating pooled eluates at 65 °C overnight. DNA was purified using a QIAquick PCR purification kit with 2.5 volumes of PB buffer, followed by two washes with PE buffer. Columns were spun dry and DNA was eluted twice in 20 µL dH₂O. DNA concentrations were measured with Qubit and samples were stored at –80 °C.
DNA was quatified using a Qubit flourometer with a High Sensitivity dsDNA kit and shipped on dry ice to Novogene. Once samples arrived at Novogene they were treating using their standard protocols to repaired the DNA fragments , A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount required

treatment_protocol: Formaldehyde was then added to a final concentration of 1% (v/v), and cultures were incubated for 30 minutes at 30 °C with gentle shaking (90 rpm). Cross-linking was quenched by transferring cultures into 50 mL tubes and adding glycine to 125 mM final concentration. Samples were gently inverted for 10 minutes at room temperature.

value: Whole cell

tag: genotype

value: dwblA + wblA_3xFlag


title: BTRC_71_10X _HT_snRNA-seq

description: 'BTRC_71 ' in Seurat object's 'sample' metadata field


title: BTRC_57_10X _HT_snRNA-seq

description: 'BTRC_57 ' in Seurat object's 'sample' metadata field


title: ∆wblA biological replicate #10 + WblA_Flag 16 hour

description: Library name: Wbla10_16h_42644


title: BTRC_58_10X _HT_snRNA-seq

description: 'BTRC_58 ' in Seurat object's 'sample' metadata field


title: MD901 AZA_rep3

description: Library name: Sample 21

value: AZA


title: BTRC_54_10X _HT_snRNA-seq

description: 'BTRC_54 ' in Seurat object's 'sample' metadata field


title: ∆wblA biological replicate #10 + WblA_Flag 12 hour

description: Library name: Wbla10_12h_45636


title: ∆wblA biological replicate #15 + WblA_Flag 12 hour

description: Library name: Wbla15_12h_45641


title: MD901 HDAC3i_rep1

description: Library name: Sample 16


title: Normal_sample1

description: Library name: WT_untreat_4


title: BTRC_150_10X _multiome_snRNAseq

description: BTRC_150 ' in Seurat object's 'Donor' metadata field, count information in 'RNA' assay


title: MAR1_sample3

description: Library name: MAR1_5

value: MC903 d6 + MAR1 i.p.


title: ∆wblA biological replicate #6 + WblA_Flag 16 hour

description: Library name: Wbla6_16h_42522

value: WT


title: MAR1_sample2

description: Library name: MAR1_2


title: WT 16 hours

description: Library name: WT-16


title: ∆wblA biological replicate #6 + WblA_Flag 12 hour

description: Library name: Wbla6_12h_45632


title: BTRC_51_10X _HT_snRNA-seq

description: 'BTRC_51 ' in Seurat object's 'sample' metadata field

value: caudate nucleus (postmortem brain)


title: OXA_d10

description: Library name: OXA10

value: Oxazolone d10


title: WT 12 hours

description: Library name: WT-12


title: Isotype_sample3

description: Library name: Isotype_4

value: MC903 d6 + Isotype i.p.


title: BTRC_47_10X _HT_snRNA-seq

description: 'BTRC_47 ' in Seurat object's 'sample' metadata field


title: BTRC_5_10X _HT_snRNA-seq

description: 'BTRC_5 ' in Seurat object's 'sample' metadata field


title: Glioma_2_TIL_GEX

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 3' v2

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

source_name: 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: tumor tissue

value: Live CD45+ cells

tag: idh status

tag: grade

value: IV


title: Glioma_1_TIL_GEX

description: 10X Genomics 3' v2


title: Glioma_2_PBMC_GEX

description: 10X Genomics 3' v2

source_name: peripheral blood

value: peripheral blood


title: Isotype_sample2

description: Library name: Isotype_3

value: skin


title: Glioma_1_PBMC_GEX

description: 10X Genomics 3' v2


title: BTRC_45_10X _HT_snRNA-seq

description: 'BTRC_45 ' in Seurat object's 'sample' metadata field


title: IL4RA_ff_sample3

description: Library name: IL4RA_ff_6

value: 6-7 weeks

value: female

value: C57BL/6J Il4rafl/fl


title: IL4RA_ff_sample2

description: Library name: IL4RA_ff_2

value: neck


title: BTRC_44_10X _HT_snRNA-seq

description: 'BTRC_44 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-24_3, D7

city: Barcelona

first: Cèlia

last: Torres Vilanova

address: Roselló 132

department: Malaria Immunology

country: Spain

institute: ISGlobal

description: Library name: SAINT-24_3

data_processing:
FASTQ pre-processing (including quality control and quality trimming), RNA-Seq alignment and read quantification was performed. FastQC v.0.1.2.1 was used for raw read quality control. Low-quality read trimming was conducted using sickle v.1.33. RNA-Seq reads were aligned against human reference genome GRCh38 using RNA-Seq aligner STAR v.2.7.10b with settings ‘-outSAMunmapped Within’ and ‘-ouSAMtype BAM SortedByCoordinate’. GENCODE human genome annotation v.43 was used for raw read counting. The gene read quantification was performed using htseq-count v.2.0.3 with settings ‘-r pos’ and ‘-t gene’. For downstream analysis of the transcriptomics data, 20,722 genes that had a minimum of 10 read counts in at least 12 samples were included, excluding globin-related genes. The trimmed means of M values (TMM) method was used to produce normalization factors correcting raw counts for different library sizes.
Assembly: GRCh38
Supplementary files format and content: The processed data file Raw counts.xlsx includes all 62,757 genes. Rows represent genes identified by their ENSEMBL codes, and columns correspond to individual samples labeled by library name.
Supplementary files format and content: The processed data file Normalized counts TMM.xlsx contains 20,722 genes that had at least 10 read counts in a minimum of 12 samples, with globin-related genes excluded. The trimmed means of M values (TMM) method was then applied to normalize raw counts, adjusting for differences in library sizes. Rows represent genes identified by their ENSEMBL codes, and columns correspond to individual samples labeled by library name.

molecule: total RNA

source_name: Whole blood

extract_protocol:
RNA extraction from whole blood samples was performed using the Qiagen Blood miRNA Purification Kit, following the manufacturer’s protocol. Whole blood was centrifuged to pellet the samples, washed with water, digested with proteinase K and homogenized via the provided PAXgene Shredder spin columns. Isopropanol was added to optimize binding conditions, and RNA was bound to the silica membrane in PAXgene RNA spin columns. After DNase digestion to remove genomic DNA, the RNA was washed and eluted with the provided buffer.
Library preparation and sequencing were performed at Centre de Regulació Genòmica (CRG, Spain). Universal Plus mRNA-Seq with NuQuant, Human Globin AnyDeplete, UDI-C kit for Illumina was used to process the samples. RNA sequencing was performed with the Illumina NextSeq 2000 using single-end 50 bp reads and achieving an average sequencing depth of 40 million reads per sample.

treatment_protocol: Patients were randomly assigned (1:1) to receive a single oral dose of ivermectin (400 μg/kg) or placebo on treatment day (D1).

value: Whole blood

tag: day

value: male

tag: group

value: Placebo

tag: rna availability_(ng)


title: Whole blood, SAINT-23_1, D1

description: Library name: SAINT-23_1


title: BTRC_42_10X _HT_snRNA-seq

description: 'BTRC_42 ' in Seurat object's 'sample' metadata field


title: Isotype_sample1

description: Library name: Isotype_1

value: 6 weeks


title: Whole blood, SAINT-24_2, D4

description: Library name: SAINT-24_2


title: Whole blood, SAINT-23_2, D4

description: Library name: SAINT-23_2


title: Whole blood, SAINT-23_3, D7

description: Library name: SAINT-23_3


title: Whole blood, SAINT-24_1, D1

description: Library name: SAINT-24_1


title: IL4RA_ff_sample1

description: Library name: IL4RA_ff_1


title: BTRC_41_10X _HT_snRNA-seq

description: 'BTRC_41 ' in Seurat object's 'sample' metadata field


title: BTRC_40_10X _HT_snRNA-seq

description: 'BTRC_40 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-22_1, D1

description: Library name: SAINT-22_1


title: cKO_sample3

description: Library name: cKO_4

value: C57BL/6J Pdgfra-CRE/Il4rafl/fl


title: Whole blood, SAINT-22_2, D4

description: Library name: SAINT-22_2


title: MAR1_sample1

description: Library name: MAR1_1

value: MC903 d6 + MAR1 i.p.


title: Whole blood, SAINT-21_3, D7

description: Library name: SAINT-21_3

value: Ivermectin-treated


title: BTRC_39_10X _HT_snRNA-seq

description: 'BTRC_39 ' in Seurat object's 'sample' metadata field

value: caudate nucleus (postmortem brain)


title: Whole blood, SAINT-21_2, D4

description: Library name: SAINT-21_2


title: Whole blood, SAINT-21_1, D1

description: Library name: SAINT-21_1


title: cKO_sample2

description: Library name: cKO_3_2


title: BTRC_35_10X _HT_snRNA-seq

description: 'BTRC_35 ' in Seurat object's 'sample' metadata field


title: cKO_sample1

description: Library name: cKO_1


title: Whole blood, SAINT-20_3, D7

description: Library name: SAINT-20_3


title: Con2 Control scATAC-seq library

city: Boston

first: William

middle: T.

last: Pu

state: Ma

address: 300 Longwood Ave

department: Cardiology

institute: Boston Children's Hospital

description:
Library name: Con2 scATAC-seq
ATAC portion of multiome

library_source: genomic single cell

data_processing:
Raw fastq files were processed with cellranger ARC using the mm10 genome
Outs files are given as processed data files
Assembly: mm10
Supplementary files format and content: ATAC reads are listed in indexed .tsv files
Supplementary files format and content: gene expression counts are given in filtered feature bc matrix H5 files

source_name: Right and Left Atria

growth_protocol: Chd4flox/flox Mouse sample

extract_protocol:
Atria were dissected and flash frozen
10x genomics multiome library construction protocol

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

value: Right and Left Atria

value: Control

value: AAV9:Nppa-EGFP at P2


title: Whole blood, SAINT-20_1, D1

description: Library name: SAINT-20_1


title: BTRC_34_10X _HT_snRNA-seq

description: 'BTRC_34 ' in Seurat object's 'sample' metadata field


title: Con1 Control scATAC-seq library

description:
Library name: Con1 scATAC-seq
ATAC portion of multiome


title: Whole blood, SAINT-22_3, D7

description: Library name: SAINT-22_3


title: Whole blood, SAINT-19_1, D1

description: Library name: SAINT-19_1


title: Whole blood, SAINT-18_3, D7

description: Library name: SAINT-18_3


title: BTRC_33_10X _HT_snRNA-seq

description: 'BTRC_33 ' in Seurat object's 'sample' metadata field


title: BTRC_326_10X _HT_snRNA-seq

description: 'BTRC_326 ' in Seurat object's 'sample' metadata field


title: KO1 CHD4 AKO scATAC-seq library

description:
Library name: KO1 scATAC-seq
ATAC portion of multiome

value: CHD4 AKO

value: AAV9:Nppa-Cre at P2


title: Whole blood, SAINT-17_3, D7

description: Library name: SAINT-17_3


title: KO2 CHD4 AKO scATAC-seq library

description:
Library name: KO2 scATAC-seq
ATAC portion of multiome


title: BTRC_321_10X _HT_snRNA-seq

description: 'BTRC_321 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-18_2, D4

description: Library name: SAINT-18_2


title: S4 CHD4 AKO scATAC-seq library

description:
Library name: S4 scATAC-seq
ATAC portion of multiome


title: BTRC_313_10X _HT_snRNA-seq

description: 'BTRC_313 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-17_1, D1

description: Library name: SAINT-17_1


title: Whole blood, SAINT-17_2, D4

description: Library name: SAINT-17_2


title: Whole blood, SAINT-20_2, D4

description: Library name: SAINT-20_2


title: S2 CHD4 AKO scATAC-seqlibrary

description:
Library name: S2 scATAC-seq
ATAC portion of multiome


title: Whole blood, SAINT-16_2, D4

description: Library name: SAINT-16_2


title: Whole blood, SAINT-19_2, D4

description: Library name: SAINT-19_2


title: BTRC_311_10X _HT_snRNA-seq

description: 'BTRC_311 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-16_1, D1

description: Library name: SAINT-16_1


title: Con2 Control scRNA-seq library

description:
Library name: Con2 scRNA-seq
RNA portion of multiome

molecule: nuclear RNA


title: Whole blood, SAINT-15_3, D7

description: Library name: SAINT-15_3


title: Whole blood, SAINT-19_3, D7

description: Library name: SAINT-19_3


title: BTRC_309_10X _HT_snRNA-seq

description: 'BTRC_309 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-18_1, D1

description: Library name: SAINT-18_1


title: BTRC_318_10X _HT_snRNA-seq

description: 'BTRC_318 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-15_1, D1

description: Library name: SAINT-15_1


title: Whole blood, SAINT-14_3, D7

description: Library name: SAINT-14_3


title: BTRC_304_10X _HT_snRNA-seq

description: 'BTRC_304 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-14_2, D4

description: Library name: SAINT-14_2


title: KO2 CHD4 AKO scRNA-seq library

description:
Library name: KO2 scRNA-seq
RNA portion of multiome


title: BTRC_303_10X _HT_snRNA-seq

description: 'BTRC_303 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-15_2, D4

description: Library name: SAINT-15_2


title: Whole blood, SAINT-16_3, D7

description: Library name: SAINT-16_3


title: BTRC_302_10X _HT_snRNA-seq

description: 'BTRC_302 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-13_2, D4

description: Library name: SAINT-13_2


title: S4 CHD4 AKO scRNA-seq library

description:
Library name: S4 scRNA-seq
RNA portion of multiome


title: Whole blood, SAINT-13_3, D7

description: Library name: SAINT-13_3


title: KO1 CHD4 AKO scRNA-seq library

description:
Library name: KO1 scRNA-seq
RNA portion of multiome


title: BTRC_30_10X _HT_snRNA-seq

description: 'BTRC_30 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-12_3, D7

description: Library name: SAINT-12_3


title: S2 CHD4 AKO scRNA-seq library

description:
Library name: S2 scRNA-seq
RNA portion of multiome


title: Whole blood, SAINT-12_2, D4

description: Library name: SAINT-12_2


title: Whole blood, SAINT-14_1, D1

description: Library name: SAINT-14_1


title: BTRC_3_10X _HT_snRNA-seq

description: 'BTRC_3 ' in Seurat object's 'sample' metadata field


title: BTRC_299_10X _HT_snRNA-seq

description: 'BTRC_299 ' in Seurat object's 'sample' metadata field


title: Con1 Control scRNA-seq library

description:
Library name: Con1 scRNA-seq
RNA portion of multiome


title: Cell YNBG, 0 h, rep 3

city: Ciudad de México

first: Francisco

last: Padilla-Garfias

state: Ciudad de México

address: Cto. Exterior s/n, C.U., Coyoacán, 04510 Ciudad de México, CDMX

department: Genética Molecular

country: Mexico

institute: Instituito de Fisiologia Celular, UNAM

description: Library name: Sample 15

data_processing:
Raw reads were quality-checked with FastQC and MultiQC. Adapters were trimmed using Cutadapt.
Reads were aligned to the D. hansenii CBS767 genome (GCF_000006445.2) using STAR.
Gene-level counts were obtained with FeatureCounts.
Differential expression was analyzed using DESeq2.
Functional enrichment was performed with FungiFun, based on GO and KEGG terms (adj. p < 0.05).
Assembly: Debaryomyces hansenii CBS767 genome, NCBI RefSeq GCF_000006445.2
Supplementary files format and content: Processed data include normalized count tables and differential expression results in tab-delimited text format.
Supplementary files format and content: Gene identifiers correspond to CBS767 RefSeq annotation; expression values are reported as counts and log2 fold-changes.

organism: Debaryomyces hansenii CBS767

source_name: single cell yeast

growth_protocol: Cells were grown in YNBG medium at 28 °C, 250 rpm, for 24 h. Cultures were then transferred to fresh YNB or YNBG ± 100 ppm BaP and incubated for 3 days under the same conditions.

extract_protocol:
Total RNA was extracted using the Schmitt et al. (1990) hot phenol method in AE buffer (50 mM sodium acetate, 10 mM EDTA, pH 5.2). RNA quality was checked on denaturing agarose gels.
Poly(A)+ mRNA was isolated using oligo(dT) beads, fragmented, and reverse transcribed. Libraries were prepared by end repair, adapter ligation, size selection (~150 bp), and PCR, Novogene Co.

treatment_protocol: 100 ppm benzo[a]pyrene was added to cultures from a 10 mg/mL acetone stock; final acetone concentration <1% (v/v). Control samples received no BaP.

value: single cell yeast

tag: batch


title: Whole blood, SAINT-12_1, D1

description: Library name: SAINT-12_1


title: Cell YNBG, 0 h, rep 2

description: Library name: Sample 14


title: Whole blood, SAINT-11_2, D4

description: Library name: SAINT-11_2


title: Whole blood, SAINT-13_1, D1

description: Library name: SAINT-13_1

value: female


title: Whole blood, SAINT-11_1, D1

description: Library name: SAINT-11_1


title: Whole blood, SAINT-10_3, D7

description: Library name: SAINT-10_3


title: BTRC_295_10X _HT_snRNA-seq

description: 'BTRC_295 ' in Seurat object's 'sample' metadata field


title: Cell YNBG, 0 h, rep 1

description: Library name: Sample 13


title: BTRC_291_10X _HT_snRNA-seq

description: 'BTRC_291 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-09_3, D7

description: Library name: SAINT-09_3


title: Whole blood, SAINT-10_2, D4

description: Library name: SAINT-10_2


title: Whole blood, SAINT-10_1, D1

description: Library name: SAINT-10_1


title: BTRC_29_10X _HT_snRNA-seq

description: 'BTRC_29 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-09_2, D4

description: Library name: SAINT-09_2


title: Cell YNBG without treatment, 72 h, rep 2

description: Library name: Sample 11


title: BTRC_289_10X _HT_snRNA-seq

description: 'BTRC_289 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-08_2, D4

description: Library name: SAINT-08_2


title: Whole blood, SAINT-08_3, D7

description: Library name: SAINT-08_3


title: Whole blood, SAINT-09_1, D1

description: Library name: SAINT-09_1


title: Whole blood, SAINT-11_3, D7

description: Library name: SAINT-11_3


title: Whole blood, SAINT-08_1, D1

description: Library name: SAINT-08_1


title: Cell YNBG plus treatment, 72 h, rep 3

description: Library name: Sample 9


title: BTRC_282_10X _HT_snRNA-seq

description: 'BTRC_282 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-07_2, D4

description: Library name: SAINT-07_2


title: Whole blood, SAINT-06_3, D7

description: Library name: SAINT-06_3


title: Whole blood, SAINT-06_2, D4

description: Library name: SAINT-06_2


title: BTRC_281_10X _HT_snRNA-seq

description: 'BTRC_281 ' in Seurat object's 'sample' metadata field


title: Cell YNBG plus treatment, 72 h, rep 2

description: Library name: Sample 8


title: Whole blood, SAINT-07_1, D1

description: Library name: SAINT-07_1


title: Whole blood, SAINT-07_3, D7

description: Library name: SAINT-07_3


title: Cell YNBG plus treatment, 72 h, rep 1

description: Library name: Sample 7


title: Cell YNBG without treatment, 72 h, rep 3

description: Library name: Sample 12


title: BTRC_280_10X _HT_snRNA-seq

description: 'BTRC_280 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-06_1, D1

description: Library name: SAINT-06_1


title: Cell YNB plus treatment, 72 h, rep 3

description: Library name: Sample 6


title: BTRC_28_10X _HT_snRNA-seq

description: 'BTRC_28 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-05_3, D7

description: Library name: SAINT-05_3


title: Cell YNBG without treatment, 72 h, rep 1

description: Library name: Sample 10


title: Whole blood, SAINT-05_1, D1

description: Library name: SAINT-05_1


title: Whole blood, SAINT-05_2, D4

description: Library name: SAINT-05_2


title: Whole blood, SAINT-04_3, D7

description: Library name: SAINT-04_3


title: Cell YNB plus treatment, 72 h, rep 1

description: Library name: Sample 4


title: BTRC_276_10X _HT_snRNA-seq

description: 'BTRC_276 ' in Seurat object's 'sample' metadata field


title: BTRC_274_10X _HT_snRNA-seq

description: 'BTRC_274 ' in Seurat object's 'sample' metadata field


title: BTRC_284_10X _HT_snRNA-seq

description: 'BTRC_284 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-04_1, D1

description: Library name: SAINT-04_1


title: Cell YNBG, 72 h, rep 3

description: Library name: Sample 3


title: BTRC_273_10X _HT_snRNA-seq

description: 'BTRC_273 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-03_3, D7

description: Library name: SAINT-03_3


title: Whole blood, SAINT-03_2, D4

description: Library name: SAINT-03_2


title: Whole blood, SAINT-02_1, D1

description: Library name: SAINT-02_1


title: BTRC_272_10X _HT_snRNA-seq

description: 'BTRC_272 ' in Seurat object's 'sample' metadata field


title: Cell YNBG, 72 h, rep 1

description: Library name: Sample 1


title: Cell YNBG, 72 h, rep 2

description: Library name: Sample 2


title: Whole blood, SAINT-02_3, D7

description: Library name: SAINT-02_3


title: Whole blood, SAINT-01_3, D7

description: Library name: SAINT-01_3


title: Whole blood, SAINT-02_2, D4

description: Library name: SAINT-02_2


title: BTRC_269_10X _HT_snRNA-seq

description: 'BTRC_269 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-01_2, D4

description: Library name: SAINT-01_2


title: Whole blood, SAINT-04_2, D4

description: Library name: SAINT-04_2


title: Whole blood, SAINT-01_1, D1

description: Library name: SAINT-01_1


title: Cell YNB plus treatment, 72 h, rep 2

description: Library name: Sample 5


title: H3K27ac ChIP-seq of Adult Ground Squirrel Hypothalamus sample2

city: Salt Lake City

first: Chris

last: Gregg

state: UT

address: 20 South 2030 East

department: Neurobiology and Anatomy

institute: University of Utah

description:
Library name: Sq_ChIPseq_H3K27ac_IT2
Squirrel Hypothalamus H3K27ac ChIP-seq

data_processing:
Aligned with bowtie2 with the following parameters: -p 2 -q --local
Sorted and indexed with samtools.
Peaks called with MACS2 with the following parameters: --format BAMPE -g 1.47e9 -B -t -q 0.10
BigWig created with deeptools bamCoverage with the parameter ‘-of bigwig’.
Assembly: speTri3
Supplementary files format and content: BigWig
Supplementary files format and content: Union Peaks, qvalue < 0.10

organism: Ictidomys tridecemlineatus

source_name: hypothalamus

extract_protocol:
AMPure XB beads.
Arima Hi-C Library Prep with single index.

value: hypothalamus

tag: chip antibody

value: Active Motif AbFlex rAb H3K27ac Cat# 91193


title: BTRC_266_10X _HT_snRNA-seq

description: 'BTRC_266 ' in Seurat object's 'sample' metadata field


title: H3K27ac ChIP-seq of Adult Ground Squirrel Hypothalamus input2

description:
Library name: Sq_ChIPseq_H3K27ac_IT2input
Squirrel Hypothalamus H3K27ac ChIP-seq


title: H3K27ac ChIP-seq of Adult Ground Squirrel Hypothalamus input1

description:
Library name: Sq_ChIPseq_H3K27ac_IT1input
Squirrel Hypothalamus H3K27ac ChIP-seq


title: BTRC_264_10X _HT_snRNA-seq

description: 'BTRC_264 ' in Seurat object's 'sample' metadata field


title: Whole blood, SAINT-03_1, D1

description: Library name: SAINT-03_1

value: Whole blood


title: BTRC_262_10X _HT_snRNA-seq

description: 'BTRC_262 ' in Seurat object's 'sample' metadata field


title: EV_519

city: Fort Collins

first: Cali

middle: Madison

last: McEntee

state: CO

address: 910 Moby Dr

department: Health and Exercise Science

institute: Colorado State University

description: Library name: EV_519

data_processing:
Reads were mapped to the canine genome (canFam6) with STAR. Transposable elements (TEs) were identified using the canine RepeatMasker and TEtranscripts. Differentially expressed genes and TEs were analyzed with DESeq2.
Assembly: canFam6
Supplementary files format and content: Cortex_EV_NormCounts.xlsx

organism: Canis lupus familiaris

source_name: plasma extracellular vesicle

extract_protocol:
Prefrontal cortex RNA was isolated using the Zymo Direct-zol RNA miniprep kit (Zymo). EV RNA was isolated using the Exosomal RNA Isolation Kit (Norgen Biotek Corp.)
Polyadenylated RNA libraries were generated for prefrontal cortex RNA (Tecan), whereas total RNA libraries were generated for EV RNA (Zymo-Seq RiboFree), both according the manufacturers' protocols. All libraries were sequenced on an Illumina NovaSeq 6000 platform to generate >40M 150 bp paired-end reads per sample.

value: plasma extracellular vesicle

tag: condition

value: old


title: BTRC_27_10X _HT_snRNA-seq

description: 'BTRC_27 ' in Seurat object's 'sample' metadata field

tag: tissue


title: EV_523

description: Library name: EV_523

value: CCD


title: F1 worm, 402

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: parental age

value: OA

tag: progeny treatment (early life temperature)

tag: replicate date


title: F1 worm, 401


title: F1 worm, 400


title: F1 worm, 398


title: F1 worm, 399


title: BTRC_261_10X _HT_snRNA-seq

description: 'BTRC_261 ' in Seurat object's 'sample' metadata field


title: EV_377

description: Library name: EV_377

value: young


title: F1 worm, 373

value: YA


title: BTRC_267_10X _HT_snRNA-seq

description: 'BTRC_267 ' in Seurat object's 'sample' metadata field

value: caudate nucleus (postmortem brain)


title: EV_358

description: Library name: EV_358


title: EV_354

description: Library name: EV_354


title: F1 worm, 372


title: EV_353

description: Library name: EV_353


title: BTRC_26_10X _HT_snRNA-seq

description: 'BTRC_26 ' in Seurat object's 'sample' metadata field


title: H3K27ac ChIP-seq of Adult Ground Squirrel Hypothalamus sample1

description:
Library name: Sq_ChIPseq_H3K27ac_IT1
Squirrel Hypothalamus H3K27ac ChIP-seq


title: F1 worm, 371


title: EV_270

description: Library name: EV_270


title: EV_264

description: Library name: EV_264


title: BTRC_259_10X _HT_snRNA-seq

description: 'BTRC_259 ' in Seurat object's 'sample' metadata field


title: EV_253

description: Library name: EV_253


title: F1 worm, 370


title: BTRC_258_10X _HT_snRNA-seq

description: 'BTRC_258 ' in Seurat object's 'sample' metadata field


title: EV_250

description: Library name: EV_250


title: EV_502

description: Library name: EV_502


title: F1 worm, 369


title: EV_163

description: Library name: EV_163


title: cortex_377

description: Library name: cortex_377

source_name: prefrontal cortex

value: prefrontal cortex


title: BTRC_251_10X _HT_snRNA-seq

description: 'BTRC_251 ' in Seurat object's 'sample' metadata field


title: F1 worm, 368


title: cortex_354

description: Library name: cortex_354


title: F1 worm, 367


title: BTRC_245_10X _HT_snRNA-seq

description: 'BTRC_245 ' in Seurat object's 'sample' metadata field


title: F1 worm, 366


title: BTRC_256_10X _HT_snRNA-seq

description: 'BTRC_256 ' in Seurat object's 'sample' metadata field


title: cortex_253

description: Library name: cortex_253


title: BTRC_242_10X _HT_snRNA-seq

description: 'BTRC_242 ' in Seurat object's 'sample' metadata field


title: cortex_264

description: Library name: cortex_264


title: cortex_270

description: Library name: cortex_270


title: F1 worm, 365


title: BTRC_241_10X _HT_snRNA-seq

description: 'BTRC_241 ' in Seurat object's 'sample' metadata field


title: cortex_163

description: Library name: cortex_163


title: F1 worm, 359


title: F1 worm, 364


title: BTRC_24_10X _HT_snRNA-seq

description: 'BTRC_24 ' in Seurat object's 'sample' metadata field


title: BTRC_235_10X _HT_snRNA-seq

description: 'BTRC_235 ' in Seurat object's 'sample' metadata field


title: Female Pancreatic Islet, Rnf20 KO 2

city: Birmingham

first: Chad

middle: S

last: Hunter

state: AL

address: 1825 University Blvd

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
FastQ files underwent quality control with FastQC v0.11.9
FastQ files were trimmed for low-quality reads, short reads, and adaptor sequences with Trim Galore v0.6.7 , followed by an additional QC with FastQC.
With STAR v2.7.3a , the trimmed reads were aligned to the GRCm39 genome for exons and were converted to Bam files.
Read counts were generated with FeatureCounts through Rsubread v2.12.3, using the Ensembl GTF annotations (GRCm39.109.gtf)
Assembly: mm39
Supplementary files format and content: Excel sheets with all expressed genes, genes with fold change >=+-2, and genes with fold change >=+-2 with a p05 or q05

source_name: Pancreatic Islet

extract_protocol:
Islets were isolated using standard collagenase-P digestion and hand-picked. RNA extraction was performed using TRIzol  mediated lysis and the RNeasy Mini Plus Kit
RNA libraries were prepared by the UAB Genomics core

treatment_protocol: At 4 weeks of age, mice were given 5 tamoxifen gavages 150 ug/g of body weight.

value: Pancreatic Islet

value: Female

value: Rnf20 F/F; Pdx1 Cre ER (KO)

tag: treatment

value: 5 tamoxifen gavages at 4 weeks of age


title: Female Pancreatic Islet, Ctl 3

value: Rnf20 Flox Control


title: F1 worm, 356


title: cortex_358

description: Library name: cortex_358


title: BTRC_234_10X _HT_snRNA-seq

description: 'BTRC_234 ' in Seurat object's 'sample' metadata field


title: Female Pancreatic Islet, Ctl 1


title: Female Pancreatic Islet, Ctl 2


title: cortex_250

description: Library name: cortex_250


title: F1 worm, 355


title: BTRC_231_10X _HT_snRNA-seq

description: 'BTRC_231 ' in Seurat object's 'sample' metadata field


title: Male Pancreatic Islet, Rnf20 KO 3

value: Male


title: Male Pancreatic Islet, Ctl 1


title: Male Pancreatic Islet, Ctl 2


title: F1 worm, 328


title: BTRC_232_10X _HT_snRNA-seq

description: 'BTRC_232 ' in Seurat object's 'sample' metadata field


title: BTRC_228_10X _HT_snRNA-seq

description: 'BTRC_228 ' in Seurat object's 'sample' metadata field


title: cortex_353

description: Library name: cortex_353


title: F1 worm, 352


title: Male Pancreatic Islet, Ctl 3


title: BTRC_227_10X _HT_snRNA-seq

description: 'BTRC_227 ' in Seurat object's 'sample' metadata field


title: 03SF Batch 6 Neuron, Astrocyte, Microglia triculture, 75 mM

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description: Library name: B675

data_processing:
Fastq files were aligned with genome using HISAT2 v2.0.5
Gene expression was quantified using featureCounts v1.5.0-p3
Differential expression was determined using edgeR (v3.22.5) with a glm model
Assembly: GRCh38
Supplementary files format and content: Matrix of samples x Enseml gene id, values are FPKM

growth_protocol: iPSC-derived neurons, astrocytes, and microglia were maintained on Matrigel-coated plates in Neurobasal (Gibco), GlutaMAX-I (Gibco), B27 (Gibco), P/S, supplemented with BDNF (10 ng/ml, PeproTech), NT-3 (10 ng/mL, PeproTech), GDNF (10 ng/mL, PeproTech), L-Ascorbic Acid (L-AA, 200 µM, Sigma), ß-Mercaptoethanol (55 µM, Gibco), Interleukin-34 (IL-34, 100 ng/ml, Peprotech), and granulocyte-macrophage colony-stimulating factor (GM-CSF, 10 ng/ml, Peprotech).

extract_protocol:
Total cellular RNA was prepared using the Qiagen RNeasy Plus Mini Kit
Libraries were constructed using Illumina standard procedures by Novogene, Inc.

treatment_protocol: Ethanol was replenished daily for 7 days to account for evaporation.

tag: cell line

tag: cell type

value: Neuron, Astrocyte, Microglia triculture

value: 75 mM Ethanol


title: 03SF Batch 6 Neuron, Astrocyte, Microglia triculture, 40 mM

description: Library name: B640

value: 40 mM Ethanol


title: BTRC_230_10X _HT_snRNA-seq

description: 'BTRC_230 ' in Seurat object's 'sample' metadata field


title: F1 worm, 308


title: 03SF Batch 6 Neuron, Astrocyte, Microglia triculture, 20 mM

description: Library name: B620

value: 20 mM Ethanol


title: Male Pancreatic Islet, Rnf20 KO 2

tag: Sex


title: 03SF Batch 6 Neuron, Astrocyte, Microglia triculture, 0 mM

description: Library name: B600

value: 0 mM Ethanol


title: Male Pancreatic Islet, Rnf20 KO 1

tag: genotype


title: F1 worm, 306

value: whole worm


title: 03SF Batch 5 Neuron, Astrocyte, Microglia triculture, 40 mM

description: Library name: B540


title: 03SF Batch 5 Neuron, Astrocyte, Microglia triculture, 20 mM

description: Library name: B520


title: F1 worm, 348


title: F1 worm, 307

value: OA


title: 03SF Batch 5 Neuron, Astrocyte, Microglia triculture, 75 mM

description: Library name: B575


title: BTRC_225_10X _HT_snRNA-seq

description: 'BTRC_225 ' in Seurat object's 'sample' metadata field


title: BTRC_223_10X _HT_snRNA-seq

description: 'BTRC_223 ' in Seurat object's 'sample' metadata field


title: 03SF Batch 4 Neuron, Astrocyte, Microglia triculture, 0 mM

description: Library name: B400


title: 03SF Batch 4 Neuron, Astrocyte, Microglia triculture, 40 mM

description: Library name: B440


title: BTRC_220_10X _HT_snRNA-seq

description: 'BTRC_220 ' in Seurat object's 'sample' metadata field


title: BTRC_221_10X _HT_snRNA-seq

description: 'BTRC_221 ' in Seurat object's 'sample' metadata field


title: 03SF Batch 5 Neuron, Astrocyte, Microglia triculture, 0 mM

description: Library name: B500


title: F1 worm, 305


title: F1 worm, 294


title: 03SF Batch 4 Neuron, Astrocyte, Microglia triculture, 75 mM

description: Library name: B475


title: 03SF Batch 4 Neuron, Astrocyte, Microglia triculture, 20 mM

description: Library name: B420


title: F1 worm, 292


title: BTRC_219_10X _HT_snRNA-seq

description: 'BTRC_219 ' in Seurat object's 'sample' metadata field


title: BTRC_218_10X _HT_snRNA-seq

description: 'BTRC_218 ' in Seurat object's 'sample' metadata field


title: E0771 Doramapimod Treated RNA Replicate 3

city: Seattle

first: Mehlam

last: Saifudeen

state: WA

address: 1100 Fairview Ave North

department: Human Biology

institute: Fred Hutchinson Cancer Center

description:
Library name: E0771 Doramapimod 3
Column Name in Table S4.xlsx: E0771-Dora3

data_processing:
Raw RNA-seq reads were aligned to the hg38 reference genome using STAR v2.7.7a with two-pass mode and gene-level quantification enabled (--quantMode GeneCounts). BAM files were sorted and indexed using SAMtools. Gene expression counts were obtained using featureCounts (Subread package) with GENCODE v40 GTF, allowing multimapping reads (-M) and paired-end assignment (-p). The resulting raw gene count matrix was used for downstream analysis. From here egdeR in R was used on the raw counts in order to generate processed CPM values and compare control vs experimental raw counts using DGEList function and using thresholds of logCPM > 1 across all samples, FDR < 0.1 and |logFC| > 0.5.
Assembly: mm10_149 and hg38_149
Supplementary files format and content: comma separated file includes DGE results for each sample along with raw counts for the samples for which DGE was run

source_name: Breast tumor

extract_protocol:
Total RNA from CAFs was isolated using the GenCatch Total RNA mini prep kit (Epoch Life Science, Inc. Missouri City, TX, USA). Total RNA from control and doramapimod-treated tumors was isolated using Trizol (Invitrogen) according to the manufacturer’s instructions. Library preparation, sequencing, and alignment were conducted by the Novogene. Pair-end sequencing was performed on an Illumina HiSeq 2500 machine using the poly-A capturing protocol with a read length of 43 base pairs. Libraries were prepared with the TruSeq Stranded Sample Preparation Kit (Illumina, RS-122-2201) starting from 1000 ng of total RNA. cDNA libraries were amplified and sequenced on the HiSeq2500. RNA-Seq data were filtered and normalized using the edgeR Bioconductor package in R. Differentially expressed genes (DEGs) were identified between the two cell-line groups using edgeR with parameters: log fold change > 1 (absolute fold change > 2) and P < 0.05.
RNA libraries for RNA sequencing were prepared using Novogene and following the Illumina manufacturer’s protocol.

value: Breast tumor

value: Tissue

value: WT

value: Doramapimod treatment


title: E0771 Doramapimod Treated RNA Replicate 1

description:
Library name: E0771 Doramapimod 1
Column Name in Table S4.xlsx: E0771-Dora1


title: E0771 Doramapimod Treated RNA Replicate 2

description:
Library name: E0771 Doramapimod 2
Column Name in Table S4.xlsx: E0771-Dora2


title: KPC1 Doramapimod Treated RNA Replicate 2

description:
Library name: KPC1 Doramapimod 2
Column Name in Table S4.xlsx: KPC-Dora2

source_name: Pancreatic tumor

value: Pancreatic tumor


title: E0771 Vehicle Control RNA Replicate 1

description:
Library name: E0771 Control 1
Column Name in Table S4.xlsx: Control 1

value: 50% PEG400 and 50% of 20% sodium sulphobutylether-beta-cyclodextrin in normal saline.


title: E0771 Vehicle Control RNA Replicate 2

description:
Library name: E0771 Control 2
Column Name in Table S4.xlsx: Control 2


title: KPC1 Doramapimod Treated RNA Replicate 1

description:
Library name: KPC1 Doramapimod 1
Column Name in Table S4.xlsx: KPC-Dora1


title: KPC1 Vehicle Control RNA Replicate 2

description:
Library name: KPC1 Control 2
Column Name in Table S4.xlsx: Control 2


title: F1 worm, 291

value: YA


title: F1 worm, 288


title: F1 worm, 290


title: BTRC_216_10X _HT_snRNA-seq

description: 'BTRC_216 ' in Seurat object's 'sample' metadata field

value: caudate nucleus (postmortem brain)


title: KPC1 Vehicle Control RNA Replicate 1

description:
Library name: KPC1 Control 1
Column Name in Table S4.xlsx: Control 1


title: BTRC_214_10X _HT_snRNA-seq

description: 'BTRC_214 ' in Seurat object's 'sample' metadata field


title: F1 worm, 293


title: CHD4 WT atria 2

description: Library name: 15390-4 WT2

data_processing:
Genomic alignment using STAR via the bcbio-nextgen RNA-seq pipeline
DEseq2
Assembly: mm10
Supplementary files format and content: combined counts are given the the Atria_Chd4_annotated_combined.counts.txt file

source_name: Right/Left atria

extract_protocol:
Atria were dissected and flash frozen
Oligo-dT selection

value: Right/Left atria

value: Mixed

value: CHD4 control


title: BTRC_212_10X _HT_snRNA-seq

description: 'BTRC_212 ' in Seurat object's 'sample' metadata field

source_name: caudate nucleus (postmortem brain)


title: CHD4 WT atria 1

description: Library name: 15390-2 WT1


title: F1 worm, 287


title: CHD4 WT atria 3

description: Library name: 16301-1 WT3


title: BTRC_211_10X _HT_snRNA-seq

description: 'BTRC_211 ' in Seurat object's 'sample' metadata field


title: CHD4 WT atria 4

description: Library name: 16301-2 WT4


title: F1 worm, 286


title: BTRC_215_10X _HT_snRNA-seq

description: 'BTRC_215 ' in Seurat object's 'sample' metadata field


title: CHD4 KO atria 4

description: Library name: 15394-3 KO4

value: CHD4 KO


title: F1 worm, 283


title: BTRC_21_10X _HT_snRNA-seq

description: 'BTRC_21 ' in Seurat object's 'sample' metadata field


title: Nip-1

city: Beijing

first: Xiaofeng

last: Gu

address: Zhongguancun south street

country: China

institute: Chinese Academy of Agricultrual Sciences

data_processing:
Raw sequencing reads were processed using the 10x Genomics Cell Ranger pipeline for quality control, alignment to the reference genome, and generation of gene expression matrices. The data was further analyzed for cell type identification and differential gene expression using Seurat and custom scripts. Quality control steps included filtering out low-quality cells and doublets. Normalization and scaling were performed to ensure accurate representation of gene expression levels.
The raw sequencing data for scRNA  was processed using CellRanger. Rice MSU 7.0 was used as the reference genome.Raw count matrix data were imported into R (V.4.2.2) using the Seurat (V.5.1.0) package. Low-quality cells were removed by filtering out cells that had fewer than 500 genes or 1,000 unique molecular identifiers (UMIs). Doublets and multiplets were filtered out using DoubletFinder. ScaleData and NormalizeData functions with the parameters selection.method = vst, and nfeatures = 2000 were used to scaled and normalized the data.We subsequently performed linear dimensional reduction using the RunPCA function with the parameter npcs = 50. To integrate all different samples, the Harmony method was utilized to remove the batch effect. K-nearest neighbor clustering was used the FindClusters function with the parameter resolution = 0.2 and the UMAP non-linear dimensionality reduction for visualization with the parameter dims = 1:20.
Assembly: MSU7
Supplementary files format and content: LTP_NIP_label_240622.rds

organism: Oryza sativa

source_name: Root

extract_protocol:
Take 5 mm radicle root tips from Nip or mutant seeds three days after germination, cut into pieces with a blade, and then perform nuclei extraction using extraction solution.
Single-cell RNA sequencing was performed using the 10x Genomics Chromium system. Single cells were encapsulated in microfluidic droplets along with barcoded beads and reverse transcription reagents. Cells were lysed within the droplets, and RNA was reverse transcribed into complementary DNA (cDNA). The cDNA was then amplified and prepared for sequencing by adding unique barcodes and fragmenting the cDNA. The resulting library was sequenced to obtain transcriptomic data.

value: Root

value: Nip


title: F1 worm, 285


title: CHD4 KO atria 2

description: Library name: 15394-1 KO2


title: Nip-2


title: F1 worm, 282


title: osltpl120-1

value: osltpl120 mutant


title: BTRC_210_10X _HT_snRNA-seq

description: 'BTRC_210 ' in Seurat object's 'sample' metadata field

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.

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.


title: osltpl120-2


title: CHD4 KO atria 1

description: Library name: 15386-1 KO1


title: F1 worm, 281

value: whole worm


title: F1 worm, 279

value: OA


title: LPO_3

city: Nanjing

first: Yehogn

last: Li

address: Jiangning

institute: China Pharmaceutical University

description: bone marrow macrophages, LDLR-/-P2Y6R-/-

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow macrophages

growth_protocol: Bone marrow macrophageswere maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 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: Foam cell formation was induced by treatment of 7-day post confluent cells with 50ug/ml ox-LDL (Yiyuan Biotechnologies)

value: bone marrow macrophages

value: Foam cell formation


title: 6tdGO_rep3

city: Duarte

first: Haiqing

state: CA

address: 1500 E Durate Rd

department: Shared Resources Department

institute: City of Hope National Medical Center

description: Library name: Sample 12

data_processing:
RNAseq reads were aligned to the human reference genome (hg38) using the STAR (v2.7.9) software.
RNAseq expression was quantified as read count using featureCounts from Subread (ver 2.0.3) with Genecode v38.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read count  values for each Sample

source_name: cell line

growth_protocol: Cells were cultured in RPMI1640 medium/10% FBS for <6 months and tested bimonthly as mycoplasma-free.

extract_protocol:
RNA was extracted using the Maxwell RSC simplyRNA tissue kit (Promega).
RNA libraries for RNA-seq were prepared illumina RNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were pre-treated for 1 h with 50μg/ml dextran sulfate (#42867), 1 mM amiloride (#A7410), 50μg/ml chondroitin sulfate (#4384/Sigma-Aldrich) or kept at +4°C, before adding ODNs and analysis.

value: cell line


title: BTRC_201_10X _HT_snRNA-seq

city: Indianapolis

first: Yunlong

address: 410 West 10th Street, HITS 5001

institute: Indiana University School of Medicine

description: 'BTRC_201 ' in Seurat object's 'sample' metadata field


title: BTRC_204_10X _HT_snRNA-seq

description: 'BTRC_204 ' in Seurat object's 'sample' metadata field


title: LPO_2


title: 6tdGO_rep1

description: Library name: Sample 10


title: 6tdGO_rep2

description: Library name: Sample 11


title: F1 worm, 278


title: F1 worm, 277


title: CHD4 KO atria 3

description: Library name: 15394-2 KO3


title: LPO_1


title: CpG_rep3

description: Library name: Sample 9

value: CpG-ODN


title: BTRC_207_10X _HT_snRNA-seq

description: 'BTRC_207 ' in Seurat object's 'sample' metadata field


title: BTRC_20_10X _HT_snRNA-seq

description: 'BTRC_20 ' in Seurat object's 'sample' metadata field


title: BTRC_205_10X _HT_snRNA-seq

description: 'BTRC_205 ' in Seurat object's 'sample' metadata field


title: F1 worm, 275


title: BTRC_2_10X _HT_snRNA-seq

description: 'BTRC_2 ' in Seurat object's 'sample' metadata field


title: BTRC_198_10X _HT_snRNA-seq

description: 'BTRC_198 ' in Seurat object's 'sample' metadata field


title: LO_2

description: bone marrow macrophages, LDLR-/-

value: LDLR-/-


title: LO_1

description: bone marrow macrophages, LDLR-/-


title: LO_3

description: bone marrow macrophages, LDLR-/-


title: CpG_rep1

description: Library name: Sample 7


title: F1 worm, 274


title: BTRC_196_10X _HT_snRNA-seq

description: 'BTRC_196 ' in Seurat object's 'sample' metadata field


title: CpG_rep2

description: Library name: Sample 8


title: BTRC_197_10X _HT_snRNA-seq

description: 'BTRC_197 ' in Seurat object's 'sample' metadata field


title: 6tdG_rep2

description: Library name: Sample 5


title: F1 worm, 272


title: MD901_HDAC3i_AZA_rep3

city: Nice

first: Pilar

address: 151 Route de Saint-Antoine

institute: Centre Méditerranéen de Médecine Moléculaire: C3M

description:
Library name: Sample 12
MD901-AZA-200-HDAC3i-10-rep3

data_processing:
Sequencing files were demultiplexed (Bcl2fastq, v2.17.1.14) and QC was performed on FASTQ files using FASTQC (v0.11.6).
Sequencing reads were trimmed (cutadapt v2.1) and aligned to the hg38 human reference genome using HISAT2 (v2.1.0).
Read counting across genomic features was performed using FeatureCounts (Subread, v2.0.0)
Differential gene expression analysis was performed using Voom-Limma in R (v3.46.0)
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: lymphoma cells

extract_protocol:
Lymphoma cells were pelleted, RNA was isolated using Trizol reagent and the Direct-zol RNA MicroPrep kit (Zymo Research) according to the manufacturers instructions
mRNA libraries were generated using QuantSeq 3’-mRNA Seq Library Prep Kit for Ilumina

value: lymphoma cells


title: BTRC_195_10X _HT_snRNA-seq

description: 'BTRC_195 ' in Seurat object's 'sample' metadata field


title: 6tdG_rep1

description: Library name: Sample 4


title: MD901_HDAC3i_AZA_rep2

description:
Library name: Sample 11
MD901-AZA-200-HDAC3i-10-rep2


title: BTRC_193_10X _HT_snRNA-seq

description: 'BTRC_193 ' in Seurat object's 'sample' metadata field


title: F1 worm, 271

value: YA


title: PBS_rep3

description: Library name: Sample 3

value: PBS


title: F1 worm, 276


title: mixed samples, MACseq-1

description: Library name: Sample 42

data_processing:
The paired-end 75bp reads were demultiplexed using bcl2fastq (v2.17.1.14) and Cutadapt (v2.1) was used for R2 read trimming.
The R2 trimmed reads were demultiplexed according to well barcodes and filtered for PCR duplicates using unique molecular identifiers (UMIs) both present in R1 reads, using the scruff R package (v4.0.2).
The R2 reads were subsequently mapped to the mouse reference genome (mm10) and ERCC sequences and counted across exon genomic intervals using the scruff R package (v4.0.2).
Count processing was perfromed using RUVseq (v1.24.1) and Seurat (v3.2.1) R packages.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Lysates were generated by incubating cell pellets in MAC-seq lysis buffer and incubation at room termperatue with agitation for 15 minutes.
Cell lysate was transferred into each well of a new 96-well plate previously prepared with 1µl of 10 nM well-specific RT MAC-seq primer and 7.5µl RT mix; the RT mix contains a TSO primer and external ERCC RNAs for normalization. The mixture was incubated for 2hr at 42C to create well-barcoded full-length cDNA, and then all the wells of a plate were combined into a single tube. Concentration and clean-up were done with DNA Clean & ConcentratorTM-100 (Zymo Research), and RNAClean XP (Beckman Coulter) and each plate were eluted in 22µl nuclease-free water. The purified cDNA was pre-amplified with KAPA HiFi HotStart ReadyMix (Roche), and MAC-seq PreAmp PCR primer and the quality checked on a D5000 Screentape (TapeStation, Agilent). One barcoded library was prepared per plate using TD buffer and TDE1 enzyme (Illumina) for tagmentation and KAPA HiFi HotStart Ready Mix (Roche) and custom primers (MAC-seq P5 PCR and MAC-seq Indexing Mix) for amplification. Libraries were purified with DNA AMPure XP (Beckman Coulter), quality checked on a DNA1000 tape (TapeStation, Agilent) and quantity verified by qPCR. Two indexed libraries were sequenced on a NextSeq 500 instrument (Illumina) using a custom sequencing primer (MAC-seq Read primer) and a High Output Kit v2.5 75 Cycles (Illumina) with paired-end configuration (25 base pairs for read 1 and 50 base pairs for read 2).

treatment_protocol: Cells were treated daily with 0nM or 200nM 5-AZA from day 0 to day 4; and on day 2 and day 4 they were treated with either 1) 0μM, 5μM or 10μM HDAC3i, 2) 0nM, 1nM or 2nM Panobinostat, 3) 0nM, 50nM or 100nM Vorinostat

value: vehicle, 5-Aza, HDAC3i, panobinostat, vorinostat, A485, A421


title: F1 worm, 270


title: MD901_HDAC3i_AZA_rep1

description:
Library name: Sample 10
MD901-AZA-200-HDAC3i-10-rep1


title: BTRC_191_10X _HT_snRNA-seq

description: 'BTRC_191 ' in Seurat object's 'sample' metadata field

value: caudate nucleus (postmortem brain)


title: F1 worm, 269


title: MD901_AZA_rep3

description:
Library name: Sample 9
MD901-AZA-200-HDAC3i-0-rep3

value: AZA


title: BTRC_190_10X _HT_snRNA-seq

description: 'BTRC_190 ' in Seurat object's 'sample' metadata field


title: PBS_rep2

description: Library name: Sample 2


title: 6tdG_rep3

description: Library name: Sample 6


title: PBS_rep1

description: Library name: Sample 1


title: F1 worm, 268


title: F1 worm, 273


title: MD901_AZA_rep2

description:
Library name: Sample 8
MD901-AZA-200-HDAC3i-0-rep2


title: BTRC_182_10X _HT_snRNA-seq

description: 'BTRC_182 ' in Seurat object's 'sample' metadata field


title: F1 worm, 267


title: MD901_HDAC3i_rep3

description:
Library name: Sample 6
MD901-AZA-0-HDAC3i-10-rep3


title: U87MG cells,shCREPT, rep3

city: Chongqing

first: Guanhu

address: No. 313, Jinyue Road,High‑Tech Zone

institute: Jinfeng Laboratory

description: Library name: U87_sh3

data_processing:
The raw data was aligned to the GRCh38 genome using HISAT2, and gene expression counts were generated using HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: csv files include normalized values for each Sample

extract_protocol:
RNA was hanvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used forthe construction of sequencing libraries.
RNA library preparation was conducted by using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs)

value: glioblastoma

value: CREPT Knockdown

tag: shRNA

value: shCREPT


title: U87MG cells,shCREPT, rep2

description: Library name: U87_sh2


title: BTRC_180_10X _HT_snRNA-seq

description: 'BTRC_180 ' in Seurat object's 'sample' metadata field


title: MD901_HDAC3i_rep2

description:
Library name: Sample 5
MD901-AZA-0-HDAC3i-10-rep2


title: BTRC_18_10X _HT_snRNA-seq

description: 'BTRC_18 ' in Seurat object's 'sample' metadata field


title: F1 worm, 265


title: F1 worm, 264


title: MD901_HDAC3i_rep1

description:
Library name: Sample 4
MD901-AZA-0-HDAC3i-10-rep1


title: BTRC_179_10X _HT_snRNA-seq

description: 'BTRC_179 ' in Seurat object's 'sample' metadata field


title: BTRC_176_10X _HT_snRNA-seq

description: 'BTRC_176 ' in Seurat object's 'sample' metadata field


title: F1 worm, 263


title: U87MG cells,shControl, rep1

description: Library name: U87_sh_NC1

value: NC

value: shControl


title: Female Pancreatic Islet, Rnf20 KO 3

value: Pancreatic Islet

value: Female

value: Rnf20 F/F; Pdx1 Cre ER (KO)

value: 5 tamoxifen gavages at 4 weeks of age


title: MD901_AZA_rep1

description:
Library name: Sample 7
MD901-AZA-200-HDAC3i-0-rep1


title: F1 worm, 262

value: whole worm


title: MD901_vehicle_rep3

description:
Library name: Sample 3
MD901-AZA-0-HDAC3i-0-rep3

value: vehicle


title: BTRC_174_10X _HT_snRNA-seq

description: 'BTRC_174 ' in Seurat object's 'sample' metadata field


title: MD901_vehicle_rep2

description:
Library name: Sample 2
MD901-AZA-0-HDAC3i-0-rep2

value: lymphoma cells


title: F1 worm, 261

value: OA


title: U87MG cells,shControl, rep2

description: Library name: U87_sh_NC2

value: cell line


title: U87MG cells,shCREPT, rep1

description: Library name: U87_sh1


title: Pancreas CAFs Gant61 Treated RNA Replicate 2

description:
Library name: Pancreatic CAFs Gant61 Treatment 2
Column Name in Table S8.xlsx: Gant61_2

source_name: fibroblast

value: fibroblast

value: Cell line

value: WT

value: Gant61 Treatment


title: Pancreas CAFs Gant61 Treated RNA Replicate 1

description:
Library name: Pancreatic CAFs Gant61 Treatment 1
Column Name in Table S8.xlsx: Gant61_1


title: U87MG cells,shControl, rep3

description: Library name: U87_sh_NC3

value: glioblastoma


title: MD901_vehicle_rep1

description:
Library name: Sample 1
MD901-AZA-0-HDAC3i-0-rep1


title: BTRC_173_10X _HT_snRNA-seq

description: 'BTRC_173 ' in Seurat object's 'sample' metadata field

value: caudate nucleus (postmortem brain)


title: F1 worm, 266


title: 20231115_GXRNA118_AN3CA_ARID1A_ARID1B_c2_rep2

first: Cigall

last: Kadoch

state: Massachusetts

address: 440 Brookline Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

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.

source_name: AN3 CA

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.

value: AN3 CA

value: +Dox (+ARID1A +ARID1B)


title: F1 worm, 260


title: F1 worm, 259


title: Pancreas CAFs DMSO Replicate 2

description:
Library name: Pancreatic CAFs Control 2
Column Name in Table S8.xlsx: Control2

value: DMSO


title: BTRC_171_10X _HT_snRNA-seq

last: Liu

description: 'BTRC_171 ' in Seurat object's 'sample' metadata field


title: BTRC_183_10X _HT_snRNA-seq

description: 'BTRC_183 ' in Seurat object's 'sample' metadata field


title: 20231115_GXRNA117_AN3CA_ARID1A_ARID1B_c2_rep1


title: 20231115_GXRNA116_AN3CA_ARID1A_ARID1B_c1_rep2


title: BTRC_170_10X _HT_snRNA-seq

description: 'BTRC_170 ' in Seurat object's 'sample' metadata field


title: Breast CAFs Gant61 Treated RNA Replicate 2

description:
Library name: Breast CAFs Gant61 Treatment 2
Column Name in Table S8.xlsx: Gant61_2


title: Pancreas CAFs DMSO Replicate 1

description:
Library name: Pancreatic CAFs Control 1
Column Name in Table S8.xlsx: Control1


title: F1 worm, 258


title: F1 worm, 257

value: YA


title: 20231115_GXRNA115_AN3CA_ARID1A_ARID1B_c1_rep1


title: Female Pancreatic Islet, Rnf20 KO 1

value: Pancreatic Islet

value: Female

value: Rnf20 F/F; Pdx1 Cre ER (KO)


title: F1 worm, 256

value: whole worm


title: Breast CAFs DMSO Replicate 2

description:
Library name: Breast CAFs DMSO Control2
Column Name in Table S8.xlsx: Control2


title: BTRC_172_10X _HT_snRNA-seq

description: 'BTRC_172 ' in Seurat object's 'sample' metadata field


title: 20231115_GXRNA114_AN3CA_ARID1B_rep2

value: +Dox (+ARID1B)


title: BTRC_169_10X _HT_snRNA-seq

description: 'BTRC_169 ' in Seurat object's 'sample' metadata field


title: BTRC_17_10X _HT_snRNA-seq

description: 'BTRC_17 ' in Seurat object's 'sample' metadata field


title: Breast CAFs Gant61 Treated RNA Replicate 1

description:
Library name: Breast CAFs Gant61 Treatment 1
Column Name in Table S8.xlsx: Gant61_1


title: 20231115_GXRNA113_AN3CA_ARID1B_rep1


title: Breast CAFs DMSO Replicate 1

description:
Library name: Breast CAFs DMSO Control1
Column Name in Table S8.xlsx: Control1


title: F1 worm, 255


title: Breast CAFs MAPK12 Knockdown RNA Replicate 2

description:
Library name: Breast CAFs MAPK12 Knockdown 2
Column Name in Table S7.xlsx: MAPK12KD2

value: MAPK12 Knockdown

value: MAPK12 siRNA Knockdown


title: F1 worm, 254


title: F1 worm, 253


title: 20231115_GXRNA112_AN3CA_ARID1A_rep2

value: +Dox (+ARID1A)


title: 20231115_GXRNA111_AN3CA_ARID1A_rep1


title: BTRC_167_10X _HT_snRNA-seq

description: 'BTRC_167 ' in Seurat object's 'sample' metadata field


title: BTRC_164_10X _HT_snRNA-seq

description: 'BTRC_164 ' in Seurat object's 'sample' metadata field


title: BTRC_168_10X _HT_snRNA-seq

description: 'BTRC_168 ' in Seurat object's 'sample' metadata field


title: Breast CAFs MAPK12 Knockdown RNA Replicate 1

description:
Library name: Breast CAFs MAPK12 Knockdown 1
Column Name in Table S7.xlsx: MAPK12KD1

value: fibroblast

value: Cell line


title: Breast CAFs DDR2 Knockdown RNA Replicate 1

description:
Library name: Breast CAFs DDR2 Knockdown 1
Column Name in Table S7.xlsx: DDR2KD1

value: DDR2 Knockdown

value: DDR2 siRNA Knockdown


title: BTRC_162_10X _HT_snRNA-seq

description: 'BTRC_162 ' in Seurat object's 'sample' metadata field

value: caudate nucleus (postmortem brain)


title: F1 worm, 249


title: 20231115_GXRNA110_AN3CA_parental_rep2

value: AN3 CA


title: F1 worm, 252


title: 20231115_GXRNA109_AN3CA_parental_rep1


title: BTRC_161_10X _HT_snRNA-seq

description: 'BTRC_161 ' in Seurat object's 'sample' metadata field


title: 20220312_JSL045_RNA_Xenograft_dBRD9_Sample_26

source_name: Patient Derived Xenograft

value: Patient Derived Xenograft


title: F1 worm, 248


title: Breast CAFs DDR1 Knockdown RNA Replicate 2

description:
Library name: Breast CAFs DDR1 Knockdown 2
Column Name in Table S7.xlsx: DDR1KD2

value: DDR1 Knockdown

value: DDR1 siRNA Knockdown


title: 20220312_JSL044_RNA_Xenograft_dBRD9_Sample_25


title: BTRC_16_10X _HT_snRNA-seq

description: 'BTRC_16 ' in Seurat object's 'sample' metadata field


title: Breast CAFs DDR1 Knockdown RNA Replicate 1

description:
Library name: Breast CAFs DDR1 Knockdown 1
Column Name in Table S7.xlsx: DDR1KD1


title: F1 worm, 247

value: YA


title: BTRC_159_10X _HT_snRNA-seq

description: 'BTRC_159 ' in Seurat object's 'sample' metadata field


title: 20220312_JSL043_RNA_Xenograft_dBRD9_Sample_24


title: Breast CAFs DDR1/2, MAPK12 Non-targeting Control RNA Replicate 2

description:
Library name: Breast CAFS, Control-siRNA knockdown 2
Column Name in Table S7.xlsx: Control2

value: WT

value: Non-targeting Control


title: F1 worm, 246

value: whole worm


title: BTRC_163_10X _HT_snRNA-seq

description: 'BTRC_163 ' in Seurat object's 'sample' metadata field


title: Breast CAFs DDR2 Knockdown RNA Replicate 2

description:
Library name: Breast CAFs DDR2 Knockdown 2
Column Name in Table S7.xlsx: DDR2KD2


title: BTRC_158_10X _HT_snRNA-seq

description: 'BTRC_158 ' in Seurat object's 'sample' metadata field


title: 20220312_JSL041_RNA_Xenograft_dBRD9_Sample_21


title: Breast CAFs DDR1/2, MAPK12 Non-targeting Control RNA Replicate 1

description:
Library name: Breast CAFS, Control-siRNA knockdown 1
Column Name in Table S7.xlsx: Control1


title: Breast CAFs Doramapimod High RNA Replicate 2

description:
Library name: Doramapimod Breast CAFs High 2
Column Name in Table S5.xlsx: Dora_high2

value: Doramapimod drug treatment


title: 20220312_JSL042_RNA_Xenograft_dBRD9_Sample_23


title: F1 worm, 250


title: F1 worm, 245

value: OA


title: F1 worm, 244


title: 20220312_JSL040_RNA_Xenograft_dBRD9_Sample_20


title: BTRC_15_10X _HT_snRNA-seq

description: 'BTRC_15 ' in Seurat object's 'sample' metadata field


title: Breast CAFs Doramapimod High RNA Replicate 1

description:
Library name: Doramapimod Breast CAFs High 1
Column Name in Table S5.xlsx: Dora_high1


title: BTRC_149_10X _HT_snRNA-seq

description: 'BTRC_149 ' in Seurat object's 'sample' metadata field


title: Breast CAFs DMSO RNA Replicate 2

description:
Library name: Breast CAFs Dora Control 2
Column Name in Table S5.xlsx: Breast_CAF2

value: DMSO


title: F1 worm, 242


title: 20220312_JSL037_RNA_Xenograft_C14_Sample_17


title: BTRC_148_10X _HT_snRNA-seq

description: 'BTRC_148 ' in Seurat object's 'sample' metadata field


title: Breast CAFs DMSO RNA Replicate 1

description:
Library name: Breast CAFs Dora Control 1
Column Name in Table S5.xlsx: Breast_CAF1


title: BTRC_147_10X _HT_snRNA-seq

description: 'BTRC_147 ' in Seurat object's 'sample' metadata field


title: 20220312_JSL036_RNA_Xenograft_C14_Sample_16


title: F1 worm, 241


title: BTRC_150_10X _HT_snRNA-seq

description: 'BTRC_150 ' in Seurat object's 'sample' metadata field


title: F1 worm, 240


title: miRNA-seq,Z,rep5

city: hangzhou

first: tian

last: dong

address: No.1, xueshi Road

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

description: ZXY-Z

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Samples were analyzed by the Illumina HiSeq 2500 High-throughput sequencing platform of Genesky Biotechnologies Inc. (Shanghai, China) according to the manufacturer’s instruction
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Mapping to Rattus norvegicus genomes using miRDeep2's mapper.pl
The differentially expressed miRNA was regarded when∣log2 (fold change)∣＞1 and p value＜0.05 by DEseq2.
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

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.

extract_protocol:
Total RNA was extracted using TRIzol reagents (Thermo Fisher Scientific). RNA concentrations were measured by Qubit fluorometer (Thermo Fisher Scientific) .
Samples were analyzed by the Illumina HiSeq 2500 High-throughput sequencing platform of Genesky Biotechnologies Inc. (Shanghai, China) according to the manufacturer’s instruction.

value: the placenta tissue


title: miRNA-seq,N,rep5

description: ZXY-N


title: BTRC_146_10X _HT_snRNA-seq

description: 'BTRC_146 ' in Seurat object's 'sample' metadata field


title: BTRC_145_10X _HT_snRNA-seq

description: 'BTRC_145 ' in Seurat object's 'sample' metadata field


title: F1 worm, 238


title: F1 worm, 243


title: BTRC_143_10X _HT_snRNA-seq

description: 'BTRC_143 ' in Seurat object's 'sample' metadata field


title: 20220312_JSL039_RNA_Xenograft_C14_Sample_18


title: 20220312_JSL035_RNA_Xenograft_C14_Sample_15


title: miRNA-seq,Z,rep3

description: WBJ-Z


title: 20220312_JSL034_RNA_Xenograft_C14_Sample_12


title: F1 worm, 239


title: 20220312_JSL033_RNA_Xenograft_C14_Sample_10


title: F1 worm, 236


title: miRNA-seq,N,rep4

description: ZJP-N


title: 20220312_JSL031_RNA_Xenograft_Control_Sample_7


title: BTRC_139_10X _HT_snRNA-seq

description: 'BTRC_139 ' in Seurat object's 'sample' metadata field


title: miRNA-seq,N,rep3

description: WBJ-N


title: F1 worm, 235


title: miRNA-seq,Z,rep2

description: qjq-Z


title: 20220312_JSL030_RNA_Xenograft_Control_Sample_5


title: 20220312_JSL029_RNA_Xenograft_Control_Sample_3


title: miRNA-seq,Z,rep4

description: ZJP-Z


title: miRNA-seq,N,rep2

description: qjq-N


title: 20220312_JSL028_RNA_Xenograft_Control_Sample_2


title: 20220312_JSL032_RNA_Xenograft_Control_Sample_8


title: F1 worm, 237


title: BTRC_142_10X _HT_snRNA-seq

description: 'BTRC_142 ' in Seurat object's 'sample' metadata field


title: F1 worm, 233


title: BTRC_136_10X _HT_snRNA-seq

description: 'BTRC_136 ' in Seurat object's 'sample' metadata field


title: BTRC_134_10X _HT_snRNA-seq

description: 'BTRC_134 ' in Seurat object's 'sample' metadata field


title: 20220312_JSL027_RNA_Xenograft_Control_Sample_1


title: BTRC_132_10X _HT_snRNA-seq

description: 'BTRC_132 ' in Seurat object's 'sample' metadata field


title: miRNA-seq,Z,rep1

description: FYY-Z


title: 20210923_DN006_RNA_VOA_Dox_Rep3

value: +Dox (+ARID1A)


title: F1 worm, 231


title: miRNA-seq,N,rep1

description: FYY-N


title: BTRC_131_10X _HT_snRNA-seq

description: 'BTRC_131 ' in Seurat object's 'sample' metadata field