title: s8

city: Beijing

first: Ruoqi

last: Cheng

address: NO.5, Yiheyuan Road, Haidian District

department: School of Life Sciences

institute: Peking University

description:
Library name: Sample 8
10x Genomics

library_source: transcriptomic single cell

data_processing:
The clean single-cell RNA-seq reads were mapped to mouse reference genome mm10 using Cell Ranger v5.0.1.
Assembly: mm10
Supplementary files format and content: gz archives contain Cell Ranger output (barcodes.tsv, features.tsv, matrix.mtx).

source_name: synthetic-embryo

extract_protocol:
S1-S8 embryoids were digested by 0.05% trypsin/TripLE into single cells, then washed and resuspended in 1X PBS (calcium and magnesium free) containing 2% FBS. Cell suspensions were filtered through a 40 μm cell strainer.Cell viability was determined by Count Star, and the density of living cells were adjusted to 300-600 living cells per microliter. Cell suspension was loaded onto the Chromium single cell controller (10x Genomics). Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics) and Chromium Single Cell B Chip Kit (10x Genomics) were used to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol. In short, single cells were suspended in PBS containing 0.04% BSA. About 6,000 cells were added to each channel, and the target cells were recovered (about 3,000 cells). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°Cfor 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200.
Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 according to the manufacture’s introduction. The libraries were finally sequenced using an IlluminaNovaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy.

value: synthetic-embryo

value: WT

value: S7 E7.5-like embryoids were treated by post-implantation medium 2 for 2 days on roller culture system.


title: TNBC_0626

status: Public on Sep 18 2025

type: SRA

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

country: USA

institute: LSUHSC

library_source: transcriptomic

data_processing:
FASTQ files were uploaded to Partek Flow
Contaminants removed with Bowtie v2.2.5
Aligned to STAR v2.6.1d
Quantification with RefSeq 96 (release 2020-11-02) and normalized using loess normalization method implemented using Bioconductor R-package LIMMA
Assembly: Reference genome hg38
Supplementary files format and content: txt file containing raw counts

molecule: total RNA

organism: Homo sapiens

source_name: Breast

extract_protocol:
TNBC tissues from African American AA and EA women with or without obesity from Louisiana were used as source of RNA. Covaris kits (truXTRAC FFPE total NA (column)) were used for RNA extraction following the manufacturer's instructions. The RNA was treated with DNaseI, quantified by Qubit (Invitrogen), and qualified high sensitivity RNA Agilent chips
Genomic libraries were constructed using the Illumina TruSeq RNA Exome protocol. Briefly, 300 ng of total RNA (DV200≥30) were fragmented and used as template for the generation of double-stranded cDNA to which adapters were ligated. DNA fragments were enriched by PCR and the size of the fragments checked on Agilent Bioanalyzer 2100 DNA chips. Exome regions are captured, cleaned, pooled and enriched by PCR. Finally, the library quality and concentration are checked and diluted to the suggested final concentration for sequencing in an Illumina NextSeq500 at 2 x 75 bp

tag: tissue id

tag: tissue

value: Breast

tag: race

value: Black

tag: age

tag: chemotherapy

tag: bmi

tag: summary stage

value: Local

tag: grade


title: TNBC_0638


title: s4-2

state: Beijing

country: China

description:
Library name: Sample 7
10x Genomics

organism: Mus musculus

tag: cell line

tag: genotype

tag: treatment

value: S3 cell aggregates were treated by blastiod medium for 3 days on Aggrewell.


title: TNBC_0619


title: TNBC_0614

value: Regional


title: TNBC_0613


title: DSS_GIVKO_MDP_1_S38

city: La Jolla, CA 92093

first: Pradipta

last: Ghosh

state: CA

address: 9500 Gilman Drive (MC 0651)

department: Departments of Medicine and Cellular and Molecular Medicine

institute: University of California San Diego

description: Library name: DSS_GIVKO_MDP_1_S38_L003

data_processing:
Low quality sequences were trimmed or removed with Trimmomatic; STAR (version 2.6.0a) was used to align reads on reference genome (human genome hsGRCh38_94 ); The resulting transcriptome-aligned sequences were used for expression quantification by using RSEM (version 1.3.3) with “–forward-prob 0 ” option
Assembly: GRCm38 Ensembl 94
Supplementary files format and content: Normalized count

source_name: Colon

growth_protocol: In this study, to investigate the role of macrophage GIV in the colon, Katkar et al. employed a myeloid-specific GIV-KO (Ccdc88afl/fl/LysMCre) mouse model to analyze colon transcriptomic data from wild-type (WT) and macrophage-specific GIV-KO mice treated with dextran sulfate sodium (DSS) colitis, with or without muramyl dipeptide (MDP) treatment.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Life Technologies) and Quick-RNA MiniPrep Kit (Zymo Research, USA).
cDNA

treatment_protocol: To induce colitis, mice were fed with drinking water containing 2.5% dextran sulfate sodium (DSS, w/v) (MP Biomedicals, MW 36–50 kDa) for five days and then replaced normal drinking water as described. For treatment study, MDP (100 mg/mouse/day) was administered via intraperitoneal route in 100 ml total volume sterile saline every alternate day starting from day 0 of experiment. Mice were sacrificed on the 14th day, and colon length was assessed. Colon samples were collected for assessing gene expression the levels of mRNA (by qPCR). To induce colitis, 8–10-week-old mice were administered 2.5% (w/v) dextran sulfate sodium (DSS; MW 36,000–50,000) in drinking water for 5 consecutive days, followed by regular water for an additional 2 days. Control mice received regular drinking water throughout the experiment. Colonic tissues were harvested on day 7 for RNA extraction. Total RNA was isolated using TRIzol reagent (Life Technologies) and Quick-RNA MiniPrep Kit (Zymo Research, USA), and RNA integrity was assessed using a RNA ScreenTape (Agilent Technologies).

value: Colon

value: GIV-KO

value: DSS +MDP


title: TNBC_0611


title: TNBC_0687


title: DSS_GIVKO_MDP_4_S48

description: Library name: DSS_GIVKO_MDP_4_S48_L003


title: 2dpi, s78

city: Wageningen

first: Jose

last: Lozano-Torres

state: Gelderland

address: Radix, Building no. 107, Droevendaalsesteeg 1

department: Plant Sciences

country: Netherlands

institute: Wageningen University & Research

description:
Library name: Athaliana_Hschachtii_2dpi_sample78
Fresh frozen spatial transcriptomics sequencing

data_processing:
Raw sequencing data were processed with NextSeq 2000 DRAGEN pipeline to generate FASTQ files
Raw sequencing data were mapped to the TAIR11(A.thaliana) and  Bonn (H.schachtii) reference genome using SingleCellMultiOmics pipeline
Assembly: TAIR11 (A.thaliana), Bonn (H.schachtii)
Supplementary files format and content: 8bp_96_barcodes_list.txt: List of 96 barcodes.
Supplementary files format and content: 69_Atha_processed__deduplicated.csv: Raw count-tables by mapping reads to the TAIR 11 genome (1 dpi sample)
Supplementary files format and content: 69_Hsch_processed__deduplicated.csv: Raw count-tables by mapping reads to the Bonn genome (1 dpi sample)
Supplementary files format and content: 78_Atha_processed__deduplicated.csv: Raw count-tables by mapping reads to the TAIR 11 genome (2 dpi sample)
Supplementary files format and content: 78_Hsch_processed__deduplicated.csv: Raw count-tables by mapping reads to the Bonn genome (2 dpi sample)
Library strategy: Spatial Transcriptomics

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Sterile Arabidopsis thaliana seeds were sown in RoPoD microscopic chambers filled with 3 mL of modified KNOP medium and incubated at 21°C with 16h light, 8h dark cycles.

extract_protocol:
One and two days post inoculation, Arabidopsis roots were selected for a single nematode infection using microscopy. Infected seedlings were placed in a mold filled with tissue freezing medium and blue beads were placed near the nematode head to indicate the starting point for slicing before freezing the sample on dry ice. Frozen roots were cryo-sliced into 96 sections of 20-micrometer.
The slices were collected using tweezers in a pre-cooled hard-shell 96-wells plate filled with 40 µL mineral oil (M8410, Sigma-Aldrich) and 7.5 ng/µL primer containing a T7 promoter, Illumina 5’adapter, 6 bp unique molecular identifier (UMI), an 8 bp section-specific barcode and a poly-T-sequence (Schild et al. 2021). The T7 promoter in the Cel-Seq2-based primers (Hashimshony et al. 2016) facilitates in vitro transcription but is not involved in the sequencing reaction. The UMI distinguishes molecules from each other, while the barcodes contribute to the spatial aspect to the Illumina sequencing library. Primers were synthesized by Integrated DNA Technologies (Leuven, Belgium). RNA amplification, cDNA synthesis and Illumina library preparation To each tissue section, 0.1 µL of 10 mM dNTPs (Promega) and 0.2 µL (1:500.000x diluted) ERCC spike-ins were added using the Nanodrop II robot (GC Biotech). The plate was heated to 65°C for 5 minutes to release the RNA and spun down in a pre-chilled centrifuge at 20.000g for 10 seconds. Next, a mix containing 0.05 µL nuclease free water, 0.4 µL First Strand Buffer (5x), 0.2 µL DTT (0.1 M), 0.1 µL RNase OUT (40 U/ µL), and 0.1 µL SuperScript II (200 U/ µL) was prepared and 0.75 µL of this mix was added to each well using the Nanodrop II for reverse transcription before incubation for 1 h at 42°C, 5 min at 4°C and 10 min at 70°C. To generate a second strand cDNA, a mix consisting of 7 µL nuclease free water 2.5 µL Second Strand Buffer (5x), 0.25 µL dNTPs (10 mM), 0.35 µL E. coli DNA ligase, 0.09 µL E. coli DNA polymerase, and 0.09 µL E. coli RNAse H was prepared and 10 µL of the mix was added to each well, followed by a 2 h incubation step at 16°C. NucleoMag NGS Clean-up and Size Select beads (LOT 102228, Machery-Nagel) were used to purify the cDNA (slightly modified from (Schild et al. 2021)). Next, the amplified cDNA was transcribed into RNA using the MEGAScript T7 transcription kit (CAT#AM1334, Ambion), and the RNA was fragmented by incubating the sample with aRNA-fragmentation buffer at 94°C for 1.5 minutes. The RNA was then cleaned up using RNA MagClean beads (C-100, Aline Biosciences) before preparing the DNA library, following the protocol of (Schild et al. 2021). The libraries were sequenced twice on the Illumina NextSeq 2000 platform using P3 reagents (100 cycles, 240Gb) at Leiden University (The Netherlands) to achieve sufficient sequencing depth. FASTQ files from both runs, containing paired-end 100 base pair sequencing reads, were merged. Read 1 was used for transcript counting based on the unique molecular identifier (UMI) and section-specific barcode, while Read 2 contained the gene-specific data.

treatment_protocol: Four-day-old Arabidopsis seedlings were inoculated with ~20 Heterodrea schachtii J2s per 3 seedlings.

value: root

tag: cell type

value: H.schachtii 2 dpi

tag: batch

value: first


title: TNBC_0610

value: White


title: 1dpi, s69

description:
Library name: Athaliana_Hschachtii_1dpi_sample69
Fresh frozen spatial transcriptomics sequencing

value: H.schachtii 1 dpi


title: TNBC_0606


title: DSS_GIVKO_MDP_3

description: Library name: DSS_GIVKO_MDP_3_S53_L003


title: DSS_GIVKO_4_S47

description: Library name: DSS_GIVKO_4_S47_L003

value: DSS +Veh


title: GBA1_B2_D30

city: Belval

first: Matthieu

last: Gobin

address: 6, avenue du Swing

country: Luxembourg

institute: LCSB

data_processing:
RNA sequencing data were pre-processed on the Galaxy server version 23.2.rc1 following Galaxy training tutorial (REF: see below1-3). Reads were mapped to the human reference genome hg38 using the HISAT2 tool. Mapped reads were counted using the featureCounts function on the BAM output files of HISAT2.
Assembly: hg38
Supplementary files format and content: matrix xls file raw counts

molecule: polyA RNA

source_name: midbrain oragnoid

extract_protocol: For RNA extraction from each organoid generation batch, 20 organoids were pooled at day 30 and 15 organoids at day 60 of midbrain organoid culture. RNA isolation was done using RNeasy Mini Kit (Qiagen, cat.no. 74106) following the manufacturer’s protocol. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.Library preparations were sequenced on an Illumina platform by Novogene sequencing service.

value: midbrain oragnoid

value: UOX

value: NESC derived midbrain organoids


title: TNBC_0583

value: Breast


title: tumor, Vehicle, rep1

city: Nanjing

first: chenming

last: xu

address: 163 Xianlin Road, Qixia District

institute: Nanjing university

description: Library name: NC1

data_processing:
Raw reads were quality filtered with fastp (v0.22.0) to remove adapters and low quality or ambiguous bases, discarding reads <75 bp after trimming; the remaining high quality clean reads were used for downstream bioinformatic analyses.
Assembly: Clean reads were aligned to the reference genome GRCh38 using HISAT2 (v2.2.1).
Supplementary files format and content: FPKM values for each sample

source_name: tumor

growth_protocol: The 4- to 5-week-old male C57BL/6 mice were housed in filter-topped cages with autoclaved food and water on a 12-hour light/dark cycle.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, 74136).
RNA was quantified on NanoDrop and RNA quality was assessed on an Agilent 2100 Bioanalyzer. First, poly(A)+ mRNA was enriched from total RNA using oligo(dT)-coated magnetic beads and fragmented. Reverse transcriptase was then used to synthesize the first and second strands of cDNA. The cDNA fragments underwent end repair and A-tailing at the 3' ends, followed by ligation of sequencing adapters. After purification to remove incompletely ligated adapters and adapter dimers, libraries were PCR-amplified using primers complementary to the adapter sequences. Finally, the sequencing libraries were purified using magnetic beads. RNA-seq (paired end 150 bp) was performed by illumina NovaSeq 6000.

treatment_protocol: LLC cells (5 × 10^6) were injected subcutaneously into the right flank of mice. Five days later, mice were randomized into three groups and treated intraperitoneally with vehicle (PBS) or digoxin (0.1 or 1 mg/kg).

value: tumor

value: Vehicle


title: AML-548327_H3K36me3_Plate_1

city: Saint Louis

first: Michael

middle: P

last: Meers

state: Missouri

address: 660 Euclid Ave

institute: Washington University School of Medicine

description:
Library name: LIB008339_22FCGGLT3_S59_L005
BJ323

library_source: genomic

data_processing:
Raw fastq files were aligned to the UCSC hg38 genome build using Bowtie2, version 2.4.2, with parameters –end-to-end–very-sensitive–no-mixed–no-discordant -q–phred33 -I 10 -X 700.
Mapped reads were filtered using Samtools view -b -F 12 and converted to paired-end BED files containing coordinates for the termini of each read pair.
Paired-end bed files were converted to bedGraph files using BEDTools genomecov with parameter –bg.
Bedgraphs were converted to BigWig files using the UCSC bedgraphToBigwig function for visualization in the Integrative Genomics Viewer Genome Browser.
Assembly: hg38
Supplementary files format and content: bed, bigwig
Library strategy: CUT&Tag

molecule: genomic DNA

growth_protocol: K562 and RS4-11 cells were cultured in liquid suspension; the former in IMDM (ATCC) with 10% FBS added (Seradigm), and the latter in RPMI (ATCC) with 10% FBS added.

extract_protocol:
Lightly cross-linked nuclei were prepared from cells as described in steps 2–14 of the Bench Top CUT&Tag protocol on protocols.io (https://doi.org/10.17504/protocols.io.bcuhiwt6). In brief, cells were pelleted for 3 minutes at 600g, resuspended in hypotonic NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM spermidine, 10% Triton X-100 and 20% glycerol) and incubated on ice for 10 minutes. The mixture was pelleted for 4 minutes at 1,300g, resuspended in 1× PBS and fixed with 0.1% formaldehyde for 2 minutes before quenching with 60 mM glycine. Nuclei were counted using the ViCell Automated Cell Counter (Beckman Coulter) and frozen at −80 °C in 10% DMSO at a concentration of 1M nuclei/mL for future use. Blood and bone marrow samples were collected at presentation from adult patients with de novo AML on an Institutional Review Board–approved banking protocol (#201011766). Nuclei were extracted from samples according to the nuclei preparation protocol listed above with the following modifications: NE1 hypotonic lysis buffer incubation time was optimized for each individual patient sample based on percentage of trypan blue-positive nuclei yield from input cells, with all samples incubated for between 45 seconds-2 minutes. All patient samples were preserved as native nuclei without formaldehyde crosslinking at a maximum concentration of 1M nuclei/mL. Specific samples for which fewer than 1M nuclei were recovered were preserved at a concentration lower than 1M nuclei/mL.
CUT&Tag-Direct: CUT&Tag-Direct was carried out as previously described (https://doi.org/10.17504/protocols.io.bcuhiwt6). In brief, nuclei were thawed and bound to washed paramagnetic concanavalin A (ConA) beads (Bangs Laboratories) at a concentration of 5 µL washed beads per 50K nuclei, and then incubated with primary antibody at 4 °C overnight in Wash Buffer (10 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and Roche Complete Protease Inhibitor Cocktail) with 2 mM EDTA. Bound nuclei were washed and incubated with 1:100 secondary antibody for 1 hour at room temperature and then washed 2x and incubated in Wash-300 Buffer (Wash Buffer with 300 mM NaCl) with 1:50 5 µM loaded pA–Tn5 for 1 hour at room temperature. Nuclei were washed 2x and tagmented in Wash-300 Buffer with 10 mM MgCl2 for 1 hour at 37 °C and then resuspended sequentially in 50 µl of 10 mM TAPS and 5 µl of 10 mM TAPS with 0.1% SDS and incubated for 1 hour at 58 °C. The resulting suspension was mixed well with 16 µl of 0.9375% Triton X-100, and then 2 µL each of F and R primers and 25 µL 2× NEBNext Master Mix (New England Biolabs) were added for direct amplification with the following conditions: (1) 58 °C for 5 minutes, (2) 72 °C for 5 minutes, (3) 98 °C for 30 seconds, (4) 98 °C 15 seconds, (5) 60 °C for 15 seconds, (6) repeat steps 4–5 13 times, (7) 72 °C for 1 minute and (8) hold at 8 °C. DNA from amplified product was purified using 1.1× ratio of HighPrep PCR Cleanup System (MagBio) and resuspended in 25 µl of 10 mM Tris-HCl with 1 mM EDTA, and concentration was quantified using the Qubit (Thermo Fisher Scientific) and TapeStation (Agilent) systems. Plate-CUT&Tag: CUT&Tag-Direct experiments were carried out in individual wells of twin.tec lo-bind 96-well PCR microplates (Eppendorf) using multi-channel pipettes and reservoirs, with the following modifications: After tagmentation and washing with 10 mM TAPS, beads were resuspended individually well-by-well in 16 µL 10 mM TAPS with 0.1% SDS using a single-channel pipette with vigorous pipette mixing. The plate was sealed and vortexed briefly for 10 seconds at 1000 RPM on a Thermomixer (Eppendorf). The sealed plate was spun briefly in a swinging bucket rotor, then denatured on a 96 well deep block thermal cycler (BioRad) for 1 hour at 58˚C. After denaturation, samples were neutralized with 5 µL 10% Triton X-100, and the plate was re-sealed and vortexed briefly for 10 seconds at 1000 RPM on the Thermomixer. Primers and NEBNext 2x Master Mix were then added, mixed, and the plate amplified according to the CUT&Tag-Direct thermal cycler program on a 96 well block. Libraries were purified and eluted as described above.

value: AML

tag: patient id

tag: method

value: Plate

tag: replicate


title: TNBC_0599

value: Black

value: Local


title: DSS_GIVKO_2_S28

description: Library name: DSS_GIVKO_2_S28_L003

value: Colon

value: GIV-KO


title: GBA1_B1_D60


title: TNBC_0592


title: GBA1_B1_D30


title: TNBC_0647

value: Regional


title: GBA1_B3_D60


title: TNBC_0580


title: AML-548327_H3K36me3_Plate_2

description:
Library name: LIB008340_22FCGGLT3_S82_L005
BJ324


title: TNBC_0572


title: TNBC_0561


title: AML-548327_H3K27ac_Plate_2

description:
Library name: LIB008338_22FCGGLT3_S72_L005
BJ322


title: TNBC_0557


title: DSS_GIVKO_1_S34

description: Library name: DSS_GIVKO_1_S34_L003


title: TNBC_0547


title: AML-548327_H3K27ac_Plate_1

description:
Library name: LIB008337_22FCGGLT3_S48_L005
BJ321


title: DSS_WT_MDP_3_S31

description: Library name: DSS_WT_MDP_3_S31_L003

value: WT

value: DSS +MDP


title: TNBC_0536

value: White


title: TNBC_0534


title: DSS_WT_MDP_1_S60

description: Library name: DSS_WT_MDP_1_S60_L003


title: AML-548327_H3K4me_Plate_2

description:
Library name: LIB008336_22FCGGLT3_S51_L005
BJ320


title: DSS_WT_MDP_2_S49

description: Library name: DSS_WT_MDP_2_S49_L003


title: AML-548327_H3K4me_Plate_1

description:
Library name: LIB008335_22FCGGLT3_S18_L005
BJ319


title: AML-548327_H3K4me3_Plate_2

description:
Library name: LIB008334_22FCGGLT3_S25_L005
BJ332


title: TNBC_0510


title: TNBC_0516


title: TNBC_0502


title: DSS_WT_1_S17

description: Library name: DSS_WT_1_S17_L003

value: DSS +Veh


title: DSS_WT_3_S55

description: Library name: DSS_WT_3_S55_L003


title: TNBC_0508


title: AML-548327_H3K4me3_Plate_1

description:
Library name: LIB008333_22FCGGLT3_S49_L005
BJ331


title: TNBC_0499


title: TNBC_0501


title: AML-548327_H3K9me3_Plate_2

description:
Library name: LIB008332_22FCGGLT3_S89_L005
BJ316


title: AML-548327_H3K9me3_Plate_1

description:
Library name: LIB008331_22FCGGLT3_S105_L005
BJ315


title: TNBC_0496


title: DSS_WT_2_S26

description: Library name: DSS_WT_2_S26_L003


title: TNBC_0497


title: TNBC_0482


title: TNBC_0485


title: TNBC_0541


title: TNBC_0480


title: CEBPb Chip-seq in WT BMDM, untreated control, replicate1

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology

description: Library name: WT_UT_R1

data_processing:
ChIP-seq workflow is available at https://github.com/fgualdr/mmchipseq
FASTQ files were filtered and trimmed using FASTP (v0.23.2)
Reads were aligned to the mouse genome (mm39; GCA_000001635.9) using STAR (v2.7.9a) with parameters: --runMode alignReads, --alignIntronMax 1, --alignMatesGapMax 100000, --alignEndsType EndToEnd, --outSAMtype BAM Unsorted, and --outSAMattributes All.
Duplicate reads were identified and marked using PICARD (v2.27.4).
Multi-mapped reads were assigned using a custom Bayesian EM algorithm (https://github.com/fgualdr/mmatac).
Peaks were called using MACS2 (v2.2.7.1) with parameters: --nomodel --keep-dup all and the narrowPeak setting enabled.
Reference peak set were created by selecting peaks with q-value ≤ 10⁻³ and ≥ 40% overlap between replicates.
Bigwig files were generated using deeptools (v3.5.1).
Normalization was performed using invariant peaks with GeneralNormalizer (https://github.com/fgualdr/GeneralNormalizer).
Unsupervised clustering was done using PCA (FactoMineR, v2.11), UMAP (uwot, v0.1.16), k-nearest neighbor (FNN, v1.1.4.1), and Louvain clustering (igraph, v1.4.2).
Heatmaps were generated using ComplexHeatmap (v2.14.0).
Assembly: mm39
Supplementary files format and content: bigWig

source_name: BMDM

growth_protocol: Bone marrow-derived macrophages (BMDMs) were harvested from Csf1r-Cre wild-type (WT) and SMARCA5 knockout Smarca5lox/lox Csf1r-Cre (KO) mice and cultured under standard conditions. Cells were differentiated into BMDMs over 7 days with daily treatment of 4-hydroxytamoxifen (4-OHT).

extract_protocol:
For ChIP-seq, nuclear extracts were prepared as described in Gualdrini et al., 2022. Chromatin was sheared by sonication (Branson Ultrasonics Sonifier). Immunoprecipitations were performed with target-specific antibodies prebound to Dynabeads™ Protein G. Beads were washed with RIPA buffer and TE buffer, and DNA was eluted, de-crosslinked, and purified using Qiagen kits (QIAquick PCR purification or MinElute PCR purification).
DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB) or following Gualdrini et al., 2022, protocols. Libraries were assessed for size and quality using the Agilent TapeStation High Sensitivity D5000 assay. Libraries were diluted to 4 nM and sequenced as paired-end reads (61-bp) on an Illumina NextSeq6000 platform.

treatment_protocol: Individual Chip-seq were performed on mouse primary BMDMs derived from wild-type or SMARCA5-deleted cells under untreated or LPS-stimulated 2 hours. For specific details, refer to individual sample metadata. Cells were either processed directly for ChIP-seq or treated with 1% formaldehyde for 10 minutes at room temperature for chromatin crosslinking, followed by quenching with 0.125 mM Tris-HCl (pH 7.6).

value: BMDM

value: wild type

tag: antibody

value: C/EBPβ:Bethyl, Cat# A302-739A


title: CEBPb Chip-seq in WT BMDM, untreated control, replicate2

description: Library name: WT_UT_R2


title: AML-548327_H3K27me3_Plate_2

description:
Library name: LIB008330_22FCGGLT3_S91_L005
BJ314


title: TNBC_0460

tag: tissue id

value: Breast

value: Distant


title: TNBC_0529

tag: tissue


title: AML-548327_H3K27me3_Plate_1

description:
Library name: LIB008329_22FCGGLT3_S6_L005
BJ330


title: AML-225373_H3K36me3_Plate_2

description:
Library name: LIB008328_22FCGGLT3_S116_L005
BJ312


title: TNBC_0474

tag: race


title: TNBC_0459

tag: age


title: CEBPb Chip-seq in WT BMDM, 2h LPS 10ng/ml, replicate2

description: Library name: WT_LPS_R2

value: 2h LPS 10 ng/ml


title: CEBPb Chip-seq in WT BMDM, 2h LPS 10ng/ml, replicate1

description: Library name: WT_LPS_R1


title: TNBC_0458

tag: chemotherapy


title: TNBC_0441

tag: bmi


title: CEBPb Chip-seq in SMARCA5 KOBMDM, untreated control, replicate2

description: Library name: KO_UT_R2


title: AML-225373_H3K36me3_Plate_1

description:
Library name: LIB008327_22FCGGLT3_S73_L005
BJ311

value: AML


title: TNBC_0438

tag: summary stage


title: TNBC_0437

tag: grade


title: AML-225373_H3K27ac_Plate_2

description:
Library name: LIB008326_22FCGGLT3_S104_L005
BJ310

tag: cell line

value: Plate


title: TNBC_0435

value: Black


title: TNBC_0430


title: TNBC_0427

value: Local


title: CEBPb Chip-seq in SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate2

description: Library name: KO_LPS_R2

tag: genotype


title: AML-225373_H3K4me_Plate_2

description:
Library name: LIB008324_22FCGGLT3_S119_L005
BJ308

tag: treatment


title: TNBC_0426


title: CEBPb Chip-seq in SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate1

description: Library name: KO_LPS_R1

tag: cell type


title: AML-225373_H3K4me_Plate_1

description:
Library name: LIB008323_22FCGGLT3_S26_L005
BJ307


title: AML-225373_H3K4me3_Plate_2

description:
Library name: LIB008322_22FCGGLT3_S4_L005
BJ306


title: TNBC_0420


title: TNBC_0419


title: SMG, IR + iEVs day 30, rep3

city: College Station

first: Fei

last: Liu

address: 206 Olsen Blvd

institute: Texas A&M University Health Science Center

description: Library name: IR-EV-30d-3

data_processing:
Sequences were aligned to GRCm39 using TopHat alignment software. The number of reads aligning to genes was counted with Htseq. Normalized counts between samples were computed by DESeq2.
Assembly: GRCm39
Supplementary files format and content: csv, normalized counts
Supplementary files format and content: Fei-deseq2_cn_10_counts IR4d-30d.csv

source_name: Submandibular glands (SMG)

extract_protocol:
TRIzol
PerkinElmer NEXTFLEX Rapid Directional RNA-Seq Kit 2.0

value: Submandibular glands (SMG)

value: Tissue

value: Male

value: Wildtype


title: TNBC_0415


title: SMG, IR + iEVs day 30, rep2

description: Library name: IR-EV-30d-2


title: TNBC_0413


title: TNBC_0412


title: SMG, IR + iEVs day 30, rep1

description: Library name: IR-EV-30d-1


title: AML-225373_H3K4me3_Plate_1

description:
Library name: LIB008321_22FCGGLT3_S118_L005
BJ305


title: AML-225373_H3K9me3_Plate_2

description:
Library name: LIB008320_22FCGGLT3_S11_L005
BJ304


title: TNBC_0408


title: TNBC_0394

value: Regional


title: TNBC_0403


title: CEBPb Chip-seq in SMARCA5 KOBMDM, untreated control, replicate1

description: Library name: KO_UT_R1


title: AML-225373_H3K27ac_Plate_1

description:
Library name: LIB008325_22FCGGLT3_S5_L005
BJ309


title: SMG, IR day 30, rep3

description: Library name: IR-30d-3


title: TNBC_0436

value: White


title: TNBC_0414


title: TNBC_0404


title: SMG, IR day 30, rep2

description: Library name: IR-30d-2


title: AML-225373_H3K27me3_Plate_2

description:
Library name: LIB008318_22FCGGLT3_S13_L005
BJ302


title: TNBC_0369


title: SMG, IR + iEVs day 4, rep3

description: Library name: IR-EV-4d-3


title: AML-387919_H3K36me3_Plate_2

description:
Library name: LIB008316_22FCGGLT3_S68_L005
BJ300


title: Quad muscle, critical VML injured, ADT

city: Atlanta

first: Lauren

last: Hymel

state: GA

address: 315 Ferst Dr NW

institute: Georgia Institute of Technology

description:
Library name: ADT_critical
R1 file contains cell barcode and UMI; R2 file contains Antibody Derived Tag and Hashtag Oligonucleotide reads

library_source: other

data_processing:
BCL files were demultiplexed to FASTQ files using Illumina’s “bcl2fastq” function.
FASTQ files were aligned to the GRCm39/mm39 mouse reference genome and converted to count matrices using Cell Ranger’s “count” function.
Assembly: GRCm39/mm39
Supplementary files format and content: CellRanger output files: Uninjured_barcodes.tsv.gz, Uninjured_features.tsv.gz, Uninjured_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: Subcritical_barcodes.tsv.gz, Subcritical_features.tsv.gz, Subcritical_matrix.mtx.gz
Supplementary files format and content: CellRanger output files: Critical_barcodes.tsv.gz, Critical_features.tsv.gz, Critical_matrix.mtx.gz
Library strategy: CITE-seq

molecule: protein

source_name: Quadriceps muscle

extract_protocol:
Entire injured (or uninjured for controls), left quadriceps were harvested and digested with 5,500U/ml collagenase II and 2.5U/ml Dispase II for 1.5 h in a shaking 37 °C water bath. The digested muscles were filtered through a cell strainer to obtain a single cell suspension. Red blood cells were lysed for 15 minutes at room temperature, samples were centrifuged, and pelleted cells were washed with cell staining buffer after supernatant was aspirated. Cells were counted so that 125,000 cells per sample were transferred to new tubes, centrifuged, and resuspended with Fc blocking antibody in cell staining buffer for 10 minutes. Cells from each sample were subsequently stained with TotalSeq-C cell hashtag reagents (BioLegend) to barcode cells from individual animals. Samples from animals in the same experimental group (n=4) were washed and then pooled to total 500,000 cells per condition (3 conditions: uninjured, subcritical, critical VML). Each pooled treatment group was stained with 25uL of reconstituted TotalSeq-C Mouse Universal Cocktail (BioLegend) in a total staining volume of 50uL for 30 minutes at 4°C. Cells were washed and resuspended to a final concentration of 1,000 cells/μL.
The 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index) protocol was followed to complete single cell preparation for sequencing (CG000331). ~10,000 cells (per 500,000 pooled condition group) were loaded onto Chromium Next GEM Chip K for Gel Beads-in-emulsion (GEM) generation. After GEM generation, Gel Beads were dissolved, and co-partitioned single cells were lysed using a thermal cycler to produce 10x Barcoded, full-length cDNA from mRNA. GEMs were broken and pooled following cDNA synthesis, and 10x Barcoded cDNA was purified and subsequently amplified according to protocol. Quality control and quantification of cDNA was analyzed on an Agilent Bioanalyzer High Sensitivity chip and Qubit fluorometer. 5’ gene expression libraries were constructed from amplified cDNA, and sample indices were added to allow for simultaneous sequencing of multiple samples in accordance with 10x Genomics protocol. Post library construction quality control was validated with Agilent Bioanalyzer High Sensitivity chip and Qubit fluorometer. Samples were sequenced on an Illumina sequencer using the NextSeq Mid Output (150 cycles) kit.

value: Quadriceps muscle

tag: strain

value: WT

tag: Sex

value: 2-3 months old

tag: injury

value: Critical VML injury (3mm)

tag: timepoint

value: Day 7


title: SMG, IR + iEVs day 4, rep2

description: Library name: IR-EV-4d-2


title: TNBC_0390

value: Breast


title: TNBC_0376


title: TNBC_0366


title: AML-225373_H3K27me3_Plate_1

description:
Library name: LIB008317_22FCGGLT3_S108_L005
BJ301

tag: patient id

tag: method

tag: replicate


title: SMG, IR + iEVs day 4, rep1

description: Library name: IR-EV-4d-1

tag: tissue


title: TNBC_0364

tag: tissue id

tag: race

tag: age


title: AML-387919_H3K36me3_Plate_1

description:
Library name: LIB008315_22FCGGLT3_S44_L005
BJ299


title: SMG, IR day 30, rep1

description: Library name: IR-30d-1


title: SMG, IR day 4, rep2

description: Library name: IR-4d-2


title: SMG, IR day 4, rep1

description: Library name: IR-4d-1


title: AML-387919_H3K27ac_Plate_1

description:
Library name: LIB008313_22FCGGLT3_S10_L005
BJ297


title: TNBC_0353

tag: chemotherapy

tag: bmi

tag: summary stage


title: AML-387919_H3K27ac_Plate_2

description:
Library name: LIB008314_22FCGGLT3_S58_L005
BJ298

tag: cell line


title: Quad muscle, uninjured, ADT

description:
Library name: ADT_uninjured
R1 file contains cell barcode and UMI; R2 file contains Antibody Derived Tag and Hashtag Oligonucleotide reads

tag: genotype


title: TNBC_0356

tag: grade


title: AML-387919_H3K4me_Plate_2

description:
Library name: LIB008312_22FCGGLT3_S20_L005
BJ296

tag: cell type

tag: treatment


title: SMG, nontreated, rep3

description: Library name: NT-3


title: SMG, IR day 4, rep3

description: Library name: IR-4d-3


title: Quad muscle, critical VML injured, GEX

description:
Library name: GE_critical
R1 file contains cell barcode and UMI; R2 file contains transcript

tag: strain

tag: Sex

tag: injury


title: Quad muscle, uninjured, GEX

description:
Library name: GE_uninjured
R1 file contains cell barcode and UMI; R2 file contains transcript

tag: timepoint


title: AML-387919_H3K4me_Plate_1

description:
Library name: LIB008311_22FCGGLT3_S76_L005
BJ295

tag: patient id

tag: method

tag: replicate


title: SMG, nontreated, rep2

description: Library name: NT-2

tag: tissue


title: TNBC_0348

tag: tissue id

tag: race

tag: age


title: AML-387919_H3K4me3_Plate_2

description:
Library name: LIB008310_22FCGGLT3_S112_L005
BJ294


title: wt BMDM UT; wt BMDM 2hLPS; Smarca5KO BMDM UT; Smarca5KO BMDM 2hLPS; CMOs

description:
Library name: S54703_Smarca5SC
CMO (Cell Multiplexing Oligos) FASTQ: contains reads from the CellPlex barcodes, used to assign each cell to its original sample based on multiplexed labeling.

data_processing:
Raw FASTQ files were trimmed using cutadapt v4.1 to truncate read 2 (R2) files to 80 nucleotides, following 10x Genomics CellPlex guidelines.
Trimmed FASTQs were then processed using Cell Ranger v7.1.0 with the cellranger multi function and a custom config.csv (provided) sample sheet.
A custom reference genome for Mus musculus (mm39) was generated for use with Cell Ranger v7.1.0. The UCSC mm39 genome assembly (FASTA) and the corresponding Ensembl GTF annotation (release 109) were first modified to ensure compatibility with Cell Ranger requirements. Output included gene expression matrices and Cell Multiplexing Oligo (CMO) assignments for sample demultiplexing.
Following Cell Ranger processing, sample-specific expression matrices were extracted from the CellPlex output using Seurat v4.3 (accessed via the satijalab/seurat Singularity container). For each individual sample, the filtered h5 expression matrices were imported using Read10X_h5(), and gene expression counts were converted to standard dense format and exported as tab-delimited text files for downstream analysis.
Gene expression matrices exported from Cell Ranger were normalized using the GeneralNormalizer R package (https://github.com/fgualdr/GeneralNormalizer), which identifies invariant features across samples and conditions for robust scaling.
Assembly: mm39
Supplementary files format and content: tab-separated matrix

molecule: other

extract_protocol:
Single-cell RNA sequencing was performed using the 10x Genomics Chromium Next GEM Single Cell 3’ Kit v3.1, following the protocol (CG00391 Rev B) provided by the manufacturer. Cultured cells were first diluted in PBS, washed, and labeled using Cell Multiplexing Oligos (10x Genomics, 3’ CellPlex Kit Set A 1000261), in accordance with the manufacturer’s guidelines. After labeling, cells were washed again, counted to ensure a viability above 80% and minimal aggregation, and then prepared for loading. Labeled cells were pooled, recounted, and loaded onto a Chromium Next GEM Chip G using the Chromium Controller (10x Genomics).
Reverse transcription, cDNA amplification, and library preparation, were carried out as per the manufacturer’s protocol (CG000388). Library quality was assessed using the Agilent TapeStation HSD5000 ScreenTape system, and quantification was performed with both the Quantifluor Fluorometer (Promega). Sequencing was conducted on an Illumina NovaSeq6000, with paired-end reads (28 bp Read 1 and 90 bp Read 2).

treatment_protocol: Mouse primary BMDMs derived from wild-type or SMARCA5-deficient cells followed by either no stimulation or LPS stimulation for 2 hours. For detailed conditions, refer to the individual sample metadata.

value: BMDM

value: mixed sample (WT and SMARCA-/-)

value: mixed sample (untreated and 2h LPS 10 ng/ml)


title: AML-387919_H3K9me3_Plate_2

description:
Library name: LIB008308_22FCGGLT3_S65_L005
BJ292

value: AML

value: Plate


title: Old Cartilage 4

city: Liverpool

first: Ufuk

last: Ersoy

address: William Henry Duncan Building

country: United Kingdom

institute: University of Liverpool

description:
Library name: Sample 20
YC_vs_OC_results.csv

data_processing:
Polyadenylation sites were identified and their usage compared as a result of age or tissue type. QuantSeq Reverse reads were analysed using a modified build of PolyAMiner software.
Assembly: Equus caballus EquCab3.0 primary assembly (Ensembl release 114)
Supplementary files format and content: csv files containing RNA half-life and synthesis rate

organism: Equus caballus

source_name: Cartilage

growth_protocol: articular cartilage or synovium was dissected from the metacarpophalangeal joint, snap frozen in liquid nitrogen, and stored at -80°C.

extract_protocol:
Frozen tissue samples from young and old horses were homogenised using a Braun Mikrodismembrator and extracted in TRIzol (Thermo Fisher Scientific, Waltham, MA, USA, #15596018). Following the addition of chloroform and phase separation, the aqueous layer was removed and processed through RNeasy mini kits (Qiagen, Manchester, UK, #74104), including on-column DNase digestion.
QuantSeq-Reverse library preparation and NextSeq 75 cycle[M1] [TS2] High Output sequencing with V2chemistry was performed by Lexogen (Vienna, Austria)

treatment_protocol: Cells were treated with 4sU for 4 hours

value: Cartilage

value: Old

tag: batch


title: AML-225373_H3K9me3_Plate_1

description:
Library name: LIB008319_22FCGGLT3_S1_L005
BJ303

tag: cell line


title: Quad muscle, subcritically injured, GEX

description:
Library name: GE_subcritical
R1 file contains cell barcode and UMI; R2 file contains transcript

tag: genotype

value: Male

value: Subcritical injury (2mm)


title: AML-387919_H3K9me3_Plate_1

description:
Library name: LIB008307_22FCGGLT3_S79_L005
BJ291


title: TNBC_0347

value: Black

tag: chemotherapy

tag: bmi

tag: summary stage

value: Local

tag: grade


title: Quad muscle, subcritically injured, ADT

description:
Library name: ADT_subcritical
R1 file contains cell barcode and UMI; R2 file contains Antibody Derived Tag and Hashtag Oligonucleotide reads

value: Quadriceps muscle

tag: strain

tag: Sex


title: Old Cartilage 6

description:
Library name: Sample 22
YC_vs_OC_results.csv

value: WT


title: TNBC_0342

value: White


title: Old Cartilage 3

description:
Library name: Sample 19
YC_vs_OC_results.csv


title: Old Cartilage 1

description:
Library name: Sample 17
YC_vs_OC_results.csv


title: Old Cartilage 5

description:
Library name: Sample 21
YC_vs_OC_results.csv


title: TNBC_0329


title: WT BMDM, untreated, replicate1

description: Library name: WT_UT_R1

data_processing:
All samples were analysed following the Nextflow pipeline that can be freely downloaded from https://github.com/fgualdr/mmrnaseq. Briefly:
FASTQ files were filtered and trimmed using FASTP (v0.23.2).
Reads were aligned to the mouse genome (mm39; GCA_000001635.9) using STAR (v2.7.9a) with parameters: --alignEndsType EndToEnd, --quantMode TranscriptomeSAM, --twopassMode Basic, --outSAMtype BAM Unsorted, and --outSAMattributes All.
Duplicate reads were identified and marked using PICARD (v2.27.4).
Multi-mapped reads were assigned to unique positions using a custom Bayesian Expectation-Maximization (EM) algorithm (https://github.com/fgualdr/mmrnaseq).
Per-gene read counts were obtained using the R/Bioconductor library GenomicAlignments (v1.26.0) with the summarizeOverlaps function and the RefSeq annotation UCSC_Mus_musculus.GRCm39.109.
Normalization was performed using invariant genes with the R library GeneralNormalizer (https://github.com/fgualdr/GeneralNormalizer).
Differentially expressed genes were identified using DESeq2 (R/Bioconductor version 1.38.0) with the default normalization turned off.
Assembly: mm39
Supplementary files format and content: bigWig

extract_protocol:
Total RNA was extracted using  TRIzol™ Reagent (Invitrogen, Cat# 15596026) with glycogen added as a carrier to improve RNA recovery. For TRIzol extracted samples, DNA contamination was removed using the RNase-Free DNase Set (Qiagen, Cat# 79254), and RNA was precipitated with sodium acetate. RNA quality was assessed using the High Sensitivity RNA ScreenTape Assay (Agilent, Cat# 5067-5579) on the Agilent TapeStation system, and only samples with RIN > 9 were used for library preparation.
Stranded RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, Cat# 20020598) with 300 ng of high-quality RNA per sample. Library size distribution was confirmed using the Agilent TapeStation D5000 ScreenTape Assay (Agilent, Cat# 5067-5592), with an average fragment size of ~300 bp. Libraries were quantified with the QuantiFluor dsDNA System (Promega, Cat# E2670), normalized to 4 nM, pooled, and sequenced as 51-bp paired-end reads on an Illumina NovaSeq 6000 platform.

treatment_protocol: RNA-seq was performed on mouse primary BMDMs derived from wild-type or SMARCA5-deficient cells, pre-treated for 1 hour with either DMSO or the TBK1 inhibitor MRT67307 (5 µM), followed by either no stimulation or LPS stimulation for 2 hours. For detailed conditions, refer to the individual sample metadata.

tag: cell type

value: wild type

tag: treatment


title: wt BMDM UT; wt BMDM 2hLPS; Smarca5KO BMDM UT; Smarca5KO BMDM 2hLPS; GEX

description:
Library name: S54702_Smarca5SC
GEX (Gene Expression) FASTQ: contains reads derived from cellular mRNA, used to quantify gene expression per cell.


title: AML-387919_H3K4me3_Plate_1

description:
Library name: LIB008309_22FCGGLT3_S8_L005
BJ329

tag: patient id

tag: method


title: Old Cartilage 2

description:
Library name: Sample 18
YC_vs_OC_results.csv

tag: tissue


title: TNBC_0346

tag: tissue id

value: Distant


title: TNBC_0331

value: Breast

tag: race

value: Regional


title: Young Cartilage 6

description:
Library name: Sample 16
YC_vs_OC_results.csv

tag: age

value: Young


title: WT BMDM, untreated, replicate2

description: Library name: WT_UT_R2

value: BMDM


title: WT BMDM, 2h LPS 10ng/ml, replicate2

description: Library name: WT_LPS_R2

value: 2h LPS 10 ng/ml


title: Young Cartilage 5

description:
Library name: Sample 15
YC_vs_OC_results.csv

tag: batch


title: AML-740266_H3K36me3_Plate_1

description:
Library name: LIB008303_22FCGGLT3_S19_L005
BJ287

tag: cell line

value: AML

value: Plate

tag: replicate


title: TNBC_0343

tag: chemotherapy


title: TNBC_0328

tag: bmi


title: TNBC_0326

tag: summary stage


title: WT BMDM, 2h LPS 10ng/ml, replicate1

description: Library name: WT_LPS_R1

tag: genotype


title: Young Cartilage 4

description:
Library name: Sample 14
YC_vs_OC_results.csv

value: Cartilage


title: AML-387919_H3K27me3_Plate_2

description:
Library name: LIB008306_22FCGGLT3_S56_L005
BJ290


title: AML-740266_H3K27ac_Plate_2

description:
Library name: LIB008302_22FCGGLT3_S92_L005
BJ286


title: TNBC_0325

tag: grade


title: WT BMDM, 1h MRT67307 (5 µM), replicate2

description: Library name: WT_UTTBKi_R2


title: AML-740266_H3K27ac_Plate_1

description:
Library name: LIB008301_22FCGGLT3_S28_L005
BJ285


title: TNBC_0320


title: AML-387919_H3K27me3_Plate_1

description:
Library name: LIB008305_22FCGGLT3_S78_L005
BJ289


title: Young Cartilage 3

description:
Library name: Sample 13
YC_vs_OC_results.csv


title: Young Cartilage 2

description:
Library name: Sample 12
YC_vs_OC_results.csv


title: AML-740266_H3K4me_Plate_2

description:
Library name: LIB008300_22FCGGLT3_S97_L005
BJ284


title: TNBC_0319


title: AML-740266_H3K36me3_Plate_2

description:
Library name: LIB008304_22FCGGLT3_S37_L005
BJ288


title: Young Cartilage 1

description:
Library name: Sample 11
YC_vs_OC_results.csv


title: WT BMDM, 1h MRT67307 (5 µM), 2h LPS 10ng/ml, replicate2

description: Library name: WT_LPSTBKi_R2

value: 1h MRT67307 (5 µM), 2h LPS 10 ng/ml


title: TNBC_0317


title: Old Synovium 5

description:
Library name: Sample 10
YS_vs_OS_results.csv

source_name: Synovium

value: Synovium

value: Old


title: AML-740266_H3K4me_Plate_1

description:
Library name: LIB008299_22FCGGLT3_S29_L005
BJ283


title: SMARCA5 KOBMDM, untreated, replicate2

description: Library name: KO_UT_R2


title: WT BMDM, 1h MRT67307 (5 µM), 2h LPS 10ng/ml, replicate1

description: Library name: WT_LPSTBKi_R1


title: AML-740266_H3K4me3_Plate_2

description:
Library name: LIB008298_22FCGGLT3_S27_L005
BJ282


title: TNBC_0316

value: Local


title: Old Synovium 4

description:
Library name: Sample 9
YS_vs_OS_results.csv


title: AML-740266_H3K4me3_Plate_1

description:
Library name: LIB008297_22FCGGLT3_S34_L005
BJ281


title: TNBC_0303

value: Black


title: Old Synovium 3

description:
Library name: Sample 8
YS_vs_OS_results.csv

value: WT


title: AML-740266_H3K9me3_Plate_2

description:
Library name: LIB008296_22FCGGLT3_S110_L005
BJ280


title: TNBC_0301


title: Old Synovium 1

description:
Library name: Sample 6
YS_vs_OS_results.csv


title: TNBC_0265

value: White


title: WT BMDM, 1h MRT67307 (5 µM), replicate1

description: Library name: WT_UTTBKi_R1

value: wild type


title: AML-740266_H3K9me3_Plate_1

description:
Library name: LIB008295_22FCGGLT3_S109_L005
BJ279


title: SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate1

description: Library name: KO_LPS_R1


title: Old Synovium 2

description:
Library name: Sample 7
YS_vs_OS_results.csv


title: TNBC_0264


title: AML-740266_H3K27me3_Plate_2

description:
Library name: LIB008294_22FCGGLT3_S107_L005
BJ278


title: TNBC_0259


title: SMARCA5 KOBMDM, 1h MRT67307 (5 µM), replicate2

description: Library name: KO_UTTBKi_R2


title: AML-740266_H3K27me3_Plate_1

description:
Library name: LIB008293_22FCGGLT3_S9_L005
BJ277


title: AML-868442_H3K36me3_Plate_2

description:
Library name: LIB008292_22FCGGLT3_S38_L005
BJ276


title: SMARCA5 KOBMDM, 1h MRT67307 (5 µM), replicate1

description: Library name: KO_UTTBKi_R1


title: Young Synovium 4

description:
Library name: Sample 4
YS_vs_OS_results.csv


title: TNBC_0258


title: SMARCA5 KOBMDM, untreated, replicate1

description: Library name: KO_UT_R1


title: TNBC_0256


title: AML-868442_H3K36me3_Plate_1

description:
Library name: LIB008291_22FCGGLT3_S3_L005
BJ275


title: Young Synovium 3

description:
Library name: Sample 3
YS_vs_OS_results.csv


title: SMARCA5 KOBMDM, 1h MRT67307 (5 µM), 2h LPS 10ng/ml, replicate1

description: Library name: KO_LPSTBKi_R1


title: Young Synovium 2

description:
Library name: Sample 2
YS_vs_OS_results.csv


title: Young Synovium 1

description:
Library name: Sample 1
YS_vs_OS_results.csv


title: TNBC_0255


title: AML-868442_H3K4me_Plate_2

description:
Library name: LIB008288_22FCGGLT3_S43_L005
BJ272


title: Young Synovium 5

description:
Library name: Sample 5
YS_vs_OS_results.csv


title: COLO320DM_WGS

city: Seattle

first: Chia-Lin

last: Wei

state: WA

address: 3720 15th Ave NE

department: The Northwest Genomics Center (NWGC)

institute: University of Washington

data_processing:
Raw reads in fastq format were trimmed with Trim Galore version: 0.6.6 (command: trim_galore --trim-n --stringency 3 -q 30 -e .20 --length 15)
Reads alignment to human genome hg38 was done with bwa mem (version  0.7.17-r1188)
Aligned reads with MAPQ above 30 were filtered from hg38 blacklist for copy number calling with ReadDepth (https://github.com/chrisamiller/readDepth)
Assembly: hg38
Supplementary files format and content: Comma separated text for copy number per chromosomal region
Library strategy: WGS

source_name: COLO320 DM

growth_protocol: Cells were cultivated in a humidified incubator set to 37°C and 5% CO2. PC3 DM cells were cultivated in F-12K (Kaighn's modification of Ham's F-12 medium) (30-2004, ATCC) supplemented with 10% FBS. COLO320 DM cells were grown in RPMI-1640 medium (30-2001, ATCC) supplemented with 10% FBS. GBM171 DM neurospheres were cultivated in ultra-low attachment dishes (Corning) using DMEM/F-12 with GlutaMAX (10565018, Thermofisher Scientific) supplemented with B27 supplement without vitaminA (12587010, ThermoFisher Scientific), 20 ng/ml FGF-Basic (154 a. a.) recombinant Human protein (100-18B, PeproTech), 20 ng/ml EGF recombinant Human protein (AF-100-15, Pepro Tech), 2.5 µg/ml heparin sodium salt (H3149-50KU, Sigma) and penicillin-streptomycin (15140122, ThermoFisher Scientific).

extract_protocol:
Genomic DNA were extracted using AllPrep DNA/RNA Mini Kit (Qiagen).
Genomic DNA were fragmented to 400 bp and subjected to end-repair, A-tailing and adaptor ligation (IDT for Illumina TruSeq DNA UD Indices) using KAPA Hyper Prep Kit (KK8505, KAPA Biosystems)

value: COLO320 DM

value: Colorectal adenocarcinoma


title: GLP_ALC2

city: New Haven

first: Frhaan

last: Zahrawi

state: CT

address: 300 cedar st

department: Internal Medicine

institute: Yale University

description: Library name: Sample 8

data_processing:
HISAT software was used to compare the reads against the mouse reference genome.
we obtained mapped reads using HTSeq
we used DESeq2 package for normalization
Assembly: mm39
Supplementary files format and content: csv files includes, gene count matrix, normalized count by Deseq2 for each sample

source_name: liver

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1.5μg of total RNA was used for the construction of sequencing libraries. RNA integrity was checked using Agilent Technologies 2100 Bioanalyzer. (poly (A) tail containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. Following purification, poly (A) RNA was fragmented using divalent cation buffer in elevated temperature.
Poly(a) RNA sequncing library was prepared using Illumina's Truseq-stranded mRNA sample preparation protocol. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 bioanalyzer high sensitivity DNA chip. Paired-ended sequencing was performed on Illumina's Novaseq 6000 sequencing system.

value: liver

tag: Sex

value: male

tag: strain

tag: diet

value: alcohol

value: glp


title: GLP_ALC1

description: Library name: Sample 7

tag: treatment


title: AML-868442_H3K27ac_Plate_1

description:
Library name: LIB008289_22FCGGLT3_S80_L005
BJ273

tag: cell type

value: AML

tag: patient id

tag: method


title: TNBC_0253

tag: tissue id

tag: tissue

value: Breast

tag: race


title: GLP2

description: Library name: Sample 6

value: control


title: TNBC_0252

tag: age


title: AML-868442_H3K27ac_Plate_2

description:
Library name: LIB008290_22FCGGLT3_S117_L005
BJ274

tag: cell line

value: Plate

tag: replicate


title: GLP1

description: Library name: Sample 5


title: TNBC_0240

tag: chemotherapy

tag: bmi

value: Regional


title: AML-868442_H3K4me_Plate_1

description:
Library name: LIB008287_22FCGGLT3_S114_L005
BJ271


title: AML-868442_H3K4me3_Plate_2

description:
Library name: LIB008286_22FCGGLT3_S50_L005
BJ270


title: SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate2

description: Library name: KO_LPS_R2

value: BMDM

tag: genotype

value: 2h LPS 10 ng/ml


title: Reeler Mutant P23

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

description:
Library name: ReelerM
Reeler_seurat.RDS

data_processing:
The raw data (fastq files) were processed with cellranger v6.1.1
Assembly: mm10
Supplementary files format and content: Seurat object in RDS format

source_name: neocortex

extract_protocol:
Somatosensory cortices were collected from E17 embryos and P1, P7, and P14 CD1 mice. For the Reeler model, at P23, three brains were collected from three independent litters of Relnrl+/+mutants and corresponding Relnrl+/−control littermate. VB− somatosensory cortices were collected from three Slc6a4-Cre;LSL-DTA mutant mice and from three LSL-DTA+/−control mice at P14 from the same litter. For E17 time point, somatosensory cortices from five embryos were microdissected in 1X×ice-cold HBSS (Gibco, catalog no. 14025092). For postnatal time points, 300- to 400-μm-thick coronal slices were prepared, and primary somatosensory cortices were microdissected. The tissue was preserved at- −80°C until use for the single-nuclei suspension, which was obtained through douncer homogenization (Sigma- Aldrich, D8938) using an adaptation of the protocol for the Nuclei EZ buffer kit (Sigma-Aldrich, NUC101). For dissociations, after being thawed on ice, the tissue was resuspended in 2ml of ice-cold extraction buffer (Nuclei EZ prep buffer) and dounce-homogenized on ice until disintegration (15 to 25 pestle A and B). After incubation for 5min in 4 ml of EZ buffer total, the extracted nuclei were collected by centrifugation (500g at 4°C, 5min). The extraction procedure was repeated once, before performing a washing step, in which nuclei were resuspended in washing buffer composed of 1% bovine serum albumin (BSA) in phosphate-buffered saline (PBS), with SuperASE-In (50 U/ml; Thermo Fisher Scientific, catalog no. AM2696) and RNasin (50 U/ml; Promega, catalog no. N2611), after centrifugation. Last, the nuclei were resuspended in 1ml of washing buffer and filtered through a 30-μm strainer into a new low-binding 1.5-ml tube and processed for fluorescence-activated nuclei sorting (FANS) on Beckman Coulter MoFlo Astrios, after incubation with Hoechst (1:500; Invitrogen, H3570) for 5 to 10min on ice. A total of 20,000<<Q18- Query:OK to change “20k” to “20,000”?Ans:sabine.fievre@unige.ch: OK>>nuclei were sorted, and 42 μl of nuclei suspension was used to load the Chromium Next GEM Single Cell 3’ Kit v2 (10x Genomics), according to the manufacturer’s instructions. Each library contained nuclei from only one time point. snRNA-seq from primary cultures Single-nuclei suspensions were obtained as indicated in the manual of the Nuclei EZ prep (catalog no. NUC-101), and nuclei isolation was performed through FANS as indicated for in vivo preparations. snRNA-seq preparations were performed as indicated in manufacturers’ instructions. snRNA-seq from organotypic cultures Nuclei were harvested from cortical organotypic slices by douncer homogenization (pestle A seven times and pestle B six times) by Nuclei EZ buffer extraction, similarly to tissue preparations. Nuclei were isolated through FANS, and snRNA-seq preparations were performed according to manufacturers’ instructions.
10x 3' Gene expression single cell sequencing

value: neocortex


title: TNBC_0239

tag: summary stage

value: Local

tag: grade


title: SMARCA5 KOBMDM, 1h MRT67307 (5 µM), 2h LPS 10ng/ml, replicate2

description: Library name: KO_LPSTBKi_R2

value: 1h MRT67307 (5 µM), 2h LPS 10 ng/ml


title: CT2

description: Library name: Sample 4

tag: Sex

tag: strain


title: TNBC_0238

value: White


title: CT1

description: Library name: Sample 3

tag: diet

tag: treatment


title: VB- Control P14

description:
Library name: VBC
VB-_seurat.RDS


title: AML-868442_H3K4me3_Plate_1

description:
Library name: LIB008285_22FCGGLT3_S75_L005
BJ269

tag: cell type

tag: patient id


title: VB_ Mutant P14

description:
Library name: VBM
VB-_seurat.RDS


title: TNBC_0363

tag: tissue id

value: Black


title: TNBC_0230

tag: tissue


title: AML-868442_H3K9me3_Plate_2

description:
Library name: LIB008284_22FCGGLT3_S12_L005
BJ268

tag: method


title: ALC2

description: Library name: Sample 2


title: TNBC_0229

tag: race

tag: age


title: DIV17-2 in vitro Organotypic

description:
Library name: DIV17-2_organo
Invivo_invitro_organo_seurat.RDS


title: AML-868442_H3K9me3_Plate_1

description:
Library name: LIB008283_22FCGGLT3_S83_L005
BJ267

tag: cell line

tag: replicate


title: ALC1

description: Library name: Sample 1


title: DIV17-1 in vitro Organotypic

description:
Library name: DIV17-1_organo
Invivo_invitro_organo_seurat.RDS


title: Reeler Control P23

description:
Library name: ReelerC
Reeler_seurat.RDS


title: TNBC_0221

tag: chemotherapy

tag: bmi


title: AML-868442_H3K27me3_Plate_2

description:
Library name: LIB008282_22FCGGLT3_S84_L005
BJ266


title: DIV10-1 in vitro Organotypic

description:
Library name: DIV10-1_organo
Invivo_invitro_organo_seurat.RDS


title: AML-868442_H3K27me3_Plate_1

description:
Library name: LIB008281_22FCGGLT3_S32_L005
BJ265


title: 416L- P28 ME RLT Vav Txp LSK (E10.5 ME)

city: St Louis

first: Jeffery

last: Magee

address: 660 South Euclid Ave

institute: Washington University In St Louis

description: Library name: 24

data_processing:
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 101 top-level assembly with STAR version 2.7.9a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3.
Assembly: Mouse Ensembl GRCm38.101
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: Bone marrow

extract_protocol:
Quiagen Rneasy Plus RNA Etraction Kit
Clontech SMRTr

value: Bone marrow

value: LSK


title: 379nt- P28 ME RLT Vav Txp LSK (E10.5 ME)

description: Library name: 23


title: TNBC_0216

tag: summary stage


title: DIV17 High Potassium

description:
Library name: DIV17HiK
DIV17_High_K.RDS


title: TNBC_0218

tag: grade


title: 378RR- P28 ME RLT Vav Txp LSK (E10.5 ME)

description: Library name: 22


title: AML-245450_H3K36me3_Plate_2

description:
Library name: LIB008280_22FCGGLT3_S30_L005
BJ264


title: 378R- P28 ME RLT Vav Txp LSK (E10.5 ME)

description: Library name: 21


title: AML-245450_H3K27ac_Plate_2

description:
Library name: LIB008278_22FCGGLT3_S22_L005
BJ262


title: DIV17-3 in vitro 2D

description:
Library name: DIV17-3
Invivo_invitro_organo_seurat.RDS


title: P28 MLL-ENL LSK (P0 ME)_4

description: Library name: 20


title: DIV17-2 in vitro 2D

description:
Library name: DIV17-2
Invivo_invitro_organo_seurat.RDS


title: AML-245450_H3K36me3_Plate_1

description:
Library name: LIB008279_22FCGGLT3_S103_L005
BJ263


title: TNBC_0207


title: AML-245450_H3K27ac_Plate_1

description:
Library name: LIB008277_22FCGGLT3_S96_L005
BJ261


title: DIV17 in vitro 2D

description:
Library name: DIV17-1
Invivo_invitro_organo_seurat.RDS


title: P28 MLL-ENL LSK (P0 ME)_3

description: Library name: 19


title: TNBC_0205


title: DIV10-2 in vitro 2D

description:
Library name: DIV10-2
Invivo_invitro_organo_seurat.RDS


title: DIV10-1 in vitro 2D

description:
Library name: DIV10-1
Invivo_invitro_organo_seurat.RDS


title: AML-245450_H3K4me_Plate_2

description:
Library name: LIB008276_22FCGGLT3_S100_L005
BJ260


title: TNBC_0189


title: P28 MLL-ENL LSK (P0 ME)_2

description: Library name: 18


title: DIV4 in vitro 2D

description:
Library name: DIV4
Invivo_invitro_organo_seurat.RDS


title: AML-245450_H3K4me_Plate_1

description:
Library name: LIB008275_22FCGGLT3_S94_L005
BJ259


title: TNBC_0188

value: Distant


title: P28 MLL-ENL LSK (E10.5 ME)_4

description: Library name: 16


title: P28 MLL-ENL LSK (P0 ME)_1

description: Library name: 17


title: AML-245450_H3K4me3_Plate_2

description:
Library name: LIB008274_22FCGGLT3_S62_L005
BJ258


title: DIV1 in vitro 2D

description:
Library name: DIV1
Invivo_invitro_organo_seurat.RDS


title: P28 MLL-ENL LSK (E10.5 ME)_3

description: Library name: 15


title: TNBC_0209


title: TNBC_0187


title: TNBC_0208


title: AML-245450_H3K4me3_Plate_1

description:
Library name: LIB008273_22FCGGLT3_S64_L005
BJ257


title: P14 in vivo

description:
Library name: P14
Invivo_invitro_organo_seurat.RDS


title: TNBC_0186


title: P28 MLL-ENL LSK (E10.5 ME)_2

description: Library name: 14


title: P7 in vivo

description:
Library name: P7
Invivo_invitro_organo_seurat.RDS


title: TNBC_0184


title: AML-245450_H3K9me3_Plate_1

description:
Library name: LIB008271_22FCGGLT3_S74_L005
BJ255


title: P28 MLL-ENL LSK (E10.5 ME)_1

description: Library name: 13


title: P1 in vivo

description:
Library name: P1
Invivo_invitro_organo_seurat.RDS


title: AML-245450_H3K27me3_Plate_2

description:
Library name: LIB008270_22FCGGLT3_S71_L005
BJ254


title: TNBC_0182


title: P28 WT LSK_4

description: Library name: 12


title: E17 in vivo

description:
Library name: E17
Invivo_invitro_organo_seurat.RDS


title: AML-245450_H3K27me3_Plate_1

description:
Library name: LIB008269_22FCGGLT3_S14_L005
BJ253


title: DIV17 neurons electroporated with ChR2 at E14

description: Library name: DIV17_E14 ChR2

data_processing:
The sequenced reads were aligned to the mouse genome (GRCm38) using STAR aligner. The number of reads per transcript was calculated with the open-source HTSeq Python library.
Assembly: mm10
Supplementary files format and content: Seurat object in RDS format

extract_protocol:
cDNA synthesis and preamplification were performed using the SMART-Seq v4 3′ DE Kit following the manufacturer’s instructions (Takara).
Single-cell RNA-sequencing libraries of the cDNA were prepared using the Nextera XT DNA library prep kit (Illumina).

value: electroporated at E14 with a mix of pCAG-tdTomato plasmid and pAAV CAG 439 ChR2 E123T T159C 2A tDimer plasmid


title: AML-817156_H3K36me3_Plate_2

description:
Library name: LIB008268_22FCGGLT3_S115_L005
BJ328


title: TNBC_0180

data_processing:
FASTQ files were uploaded to Partek Flow
Contaminants removed with Bowtie v2.2.5
Aligned to STAR v2.6.1d
Quantification with RefSeq 96 (release 2020-11-02) and normalized using loess normalization method implemented using Bioconductor R-package LIMMA
Assembly: Reference genome hg38
Supplementary files format and content: txt file containing raw counts

extract_protocol:
TNBC tissues from African American AA and EA women with or without obesity from Louisiana were used as source of RNA. Covaris kits (truXTRAC FFPE total NA (column)) were used for RNA extraction following the manufacturer's instructions. The RNA was treated with DNaseI, quantified by Qubit (Invitrogen), and qualified high sensitivity RNA Agilent chips
Genomic libraries were constructed using the Illumina TruSeq RNA Exome protocol. Briefly, 300 ng of total RNA (DV200≥30) were fragmented and used as template for the generation of double-stranded cDNA to which adapters were ligated. DNA fragments were enriched by PCR and the size of the fragments checked on Agilent Bioanalyzer 2100 DNA chips. Exome regions are captured, cleaned, pooled and enriched by PCR. Finally, the library quality and concentration are checked and diluted to the suggested final concentration for sequencing in an Illumina NextSeq500 at 2 x 75 bp


title: TNBC_0181


title: P28 WT LSK_2

description: Library name: 10


title: AML-817156_H3K36me3_Plate_1

description:
Library name: LIB008267_22FCGGLT3_S113_L005
BJ251


title: TNBC_0177


title: AML-245450_H3K9me3_Plate_2

description:
Library name: LIB008272_22FCGGLT3_S7_L005
BJ256


title: TNBC_0175


title: AML-817156_H3K27ac_Plate_2

description:
Library name: LIB008266_22FCGGLT3_S16_L005
BJ250


title: P0 MLL-ENL LSK (E10.5 ME)_4

description: Library name: 8

source_name: Liver

value: Liver


title: 48hpl-2

city: Erlangen

first: Daniel

last: Wehner

address: Staudtsraße 2

department: Division Biological Optomechanics

country: Germany

institute: Max Planck Institut for the Science of Light

data_processing:
indexed with v4.3.2 zebrafish transcript annotations using CellRanger v7.1 software
Assembly: GRCz11
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

organism: Danio rerio

source_name: 5 dpf zebrafish trunk

growth_protocol: zebrafish larvae were kept in E3 medium at 28.5°C

extract_protocol:
dissociation of larval trunk tissue, spanning four somites in lenght, with 0.25% Trypsin-EDTA, FACS sort for Calcein blue viable dye
library construction followed the instruction from the Chromium Single Cell 3' kit manual

treatment_protocol: spinal cord was transsected 6-24 hours before harvesting trunk tissue from age-matched samples (age of animals: 4 days [dpf]) or 48 hours before harvesting (age of animals: 5 days [dpf])

value: 5 dpf zebrafish trunk

tag: genotype


title: AML-817156_H3K27ac_Plate_1

description:
Library name: LIB008265_22FCGGLT3_S42_L005
BJ249

value: AML


title: P28 WT LSK_1

description: Library name: 9


title: 48hpl-1


title: TNBC_0173

value: Breast


title: P0 MLL-ENL LSK (E10.5 ME)_3

description: Library name: 7


title: 24hpl-2

source_name: 4 dpf zebrafish trunk

value: 4 dpf zebrafish trunk


title: AML-817156_H3K4me_Plate_2

description:
Library name: LIB008264_22FCGGLT3_S106_L005
BJ248

value: Plate


title: 24hpl-1


title: P0 MLL-ENL LSK (E10.5 ME)_2

description: Library name: 6


title: TNBC_0164

source_name: Breast


title: P28 WT LSK_3

description: Library name: 11


title: P0 MLL-ENL LSK (E10.5 ME)_1

description: Library name: 5


title: 12hpl-2


title: AML-817156_H3K4me3_Plate_2

description:
Library name: LIB008262_22FCGGLT3_S55_L005
BJ327


title: TNBC_0163


title: 12hpl-1


title: P0 WT LSK_4

description: Library name: 4


title: TNBC_0161

value: Regional


title: DIV17 neurons electroporated with TdTomato at E14

description: Library name: DIV17_E14 tom

value: electroporated at E14 with pCAG-tdTomato plasmid alone


title: AML-817156_H3K4me3_Plate_1

description:
Library name: LIB008261_22FCGGLT3_S2_L005
BJ245


title: AML-817156_H3K9me3_Plate_2

description:
Library name: LIB008260_22FCGGLT3_S53_L005
BJ244


title: P0 WT LSK_3

description: Library name: 3


title: P0 WT LSK_2

description: Library name: 2


title: 6hpl-1


title: P0 WT LSK_1

description: Library name: 1


title: AML-817156_H3K9me3_Plate_1

description:
Library name: LIB008259_22FCGGLT3_S24_L005
BJ243


title: TNBC_0160


title: TNBC_0171


title: TNBC_0150


title: TNBC_0151


title: unlesioned-2


title: unlesioned-1


title: AML-817156_H3K4me_Plate_1

description:
Library name: LIB008263_22FCGGLT3_S63_L005
BJ247


title: SMARCA5 KOBMDM, 1h IFN 100U/ml, replicate1 (RNA-seq)

description: Library name: RNA_KO_1hIFN_REP1

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA Miniprep Kit (Zymo Research, Cat# ZYR1055) following the manufacturer’s instructions. RNA quality was assessed using the High Sensitivity RNA ScreenTape Assay (Agilent, Cat# 5067-5579) on the Agilent TapeStation system, and only samples with RIN > 9 were used for library preparation.
Stranded RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, Cat# 20020598) with 300 ng of high-quality RNA per sample. Library size distribution was confirmed using the Agilent TapeStation D5000 ScreenTape Assay (Agilent, Cat# 5067-5592), with an average fragment size of ~300 bp. Libraries were quantified with the QuantiFluor dsDNA System (Promega, Cat# E2670), normalized to 4 nM, pooled, and sequenced as 51-bp paired-end reads on an Illumina NovaSeq 6000 platform.

treatment_protocol: RNA-seq was performed on mouse primary BMDMs derived from wild-type or SMARCA5-deleted cells under untreated, LPS-stimulated, or IFNβ-stimulated conditions for 1 and 2 hours. For specific details, refer to individual sample metadata.

value: BMDM

value: 1h IFNb 100 U/ml


title: AML-817156_H3K27me3_Plate_1

description:
Library name: LIB008257_22FCGGLT3_S52_L005
BJ241


title: SMARCA5 KOBMDM, 1h IFN 100U/ml, replicate2 (RNA-seq)

description: Library name: RNA_KO_1hIFN_REP2


title: TNBC_0147

value: Local


title: trunk tissue, ablated 2, 24hpl

extract_protocol:
dissociation of larval trunk tissue (4 dpf), spanning four somites in lenght, with 0.25% Trypsin-EDTA, FACS sort for Calcein blue viable dye
library construction followed the instruction from the Chromium Single Cell 3' kit manual

treatment_protocol: from 2 dpf E3 medium was supplemented with 0.25% MTZ-DMSO (final concentration 2nM MTZ) or 0.25% DMSO control

value: MTZ


title: AML-335640_H3K36me3_Plate_2

description:
Library name: LIB008256_22FCGGLT3_S120_L005
BJ240


title: TNBC_0134

value: White


title: SMARCA5 KOBMDM, 1h IFN 100U/ml, replicate3 (RNA-seq)

description: Library name: RNA_KO_1hIFN_REP3


title: 6hpl-2


title: trunk tissue, ablated 1, 24 hpl


title: SMARCA5 KOBMDM, 1h IFN 100U/ml, replicate4 (RNA-seq)

description: Library name: RNA_KO_1hIFN_REP4


title: AML-335640_H3K36me3_Plate_1

description:
Library name: LIB008255_22FCGGLT3_S111_L005
BJ239


title: trunk tissue, control 2, 24 hpl

value: DMSO


title: TNBC_0126


title: SMARCA5 KOBMDM, 1h LPS 10ng/ml, replicate1 (RNA-seq)

description: Library name: RNA_KO_1hLPS_REP1

value: 1h LPS 10 ng/ml


title: trunk tissue, control 1, 24 hpl


title: AML-335640_H3K27ac_Plate_2

description:
Library name: LIB008254_22FCGGLT3_S88_L005
BJ333


title: TNBC_0098

value: Black


title: AML-817156_H3K27me3_Plate_2

description:
Library name: LIB008258_22FCGGLT3_S69_L005
BJ242


title: Sol_12M_DMD21b

city: EVRY-COURCOURONNES

first: Tao

last: WANG

state: France

address: 1 bis, rue de l’Internationale

department: R & D

country: France

institute: genethon

description:
Library name: Sol_12M_DMD21b
Sol21b

data_processing:
paired-end reads were aligned to the reference transcriptome using STAR version  2.7.11b using default settings and Gene expression was measured by featureCounts version 2.0.6
Read count extraction was performed using R 4.4.1 and the tximport package (v1.28.0)
genes with more than 50 reads per samples were kept
Differential gene expression was performed using R and the package DESeq2 (v1.48.1) and using arguments lfcThreshold = 0, pAdjustMethod = "fdr", independentFiltering = T
Assembly: Rattus_norvegicus. mRatBN7.2
Supplementary files format and content: Tab-delimited text file (.tsv) containing counts per gene (rows) and samples (columns), generated by featureCounts (v2.0.6).

organism: Rattus norvegicus

source_name: Sol

growth_protocol: Cells/muscles were maintained and processed under standard laboratory conditions (details can be added if necessary).

extract_protocol:
Total RNA extraction was performed from muscle lysates using the RNeasy Plus kit (Qiagen). Total RNA concentration was quantified using a Nanodrop spectrophotometer (ND8000 Labtech, Wilmington Delaware). The RNA quality was evaluated using an Agilent RNA 6000 Pico Kit on a 2100 Bioanalyzer instrument (Agilent Technologies) and Illumina RNA seq was performed on three replicates of each selected clone.
The sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced according to the Illumina NovaSeq™ 6000 protocol.

treatment_protocol: untreated

value: Sol

value: DMD

value: untreated


title: SMARCA5 KOBMDM, 1h LPS 10ng/ml, replicate2 (RNA-seq)

description: Library name: RNA_KO_1hLPS_REP2


title: SMG, nontreated, rep1

description: Library name: NT-1

value: Submandibular glands (SMG)

value: Tissue

value: Male

value: Wildtype


title: AML-335640_H3K4me_Plate_2

description:
Library name: LIB008252_22FCGGLT3_S99_L005
BJ236

extract_protocol:
Lightly cross-linked nuclei were prepared from cells as described in steps 2–14 of the Bench Top CUT&Tag protocol on protocols.io (https://doi.org/10.17504/protocols.io.bcuhiwt6). In brief, cells were pelleted for 3 minutes at 600g, resuspended in hypotonic NE1 buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 0.5 mM spermidine, 10% Triton X-100 and 20% glycerol) and incubated on ice for 10 minutes. The mixture was pelleted for 4 minutes at 1,300g, resuspended in 1× PBS and fixed with 0.1% formaldehyde for 2 minutes before quenching with 60 mM glycine. Nuclei were counted using the ViCell Automated Cell Counter (Beckman Coulter) and frozen at −80 °C in 10% DMSO at a concentration of 1M nuclei/mL for future use. Blood and bone marrow samples were collected at presentation from adult patients with de novo AML on an Institutional Review Board–approved banking protocol (#201011766). Nuclei were extracted from samples according to the nuclei preparation protocol listed above with the following modifications: NE1 hypotonic lysis buffer incubation time was optimized for each individual patient sample based on percentage of trypan blue-positive nuclei yield from input cells, with all samples incubated for between 45 seconds-2 minutes. All patient samples were preserved as native nuclei without formaldehyde crosslinking at a maximum concentration of 1M nuclei/mL. Specific samples for which fewer than 1M nuclei were recovered were preserved at a concentration lower than 1M nuclei/mL.
CUT&Tag-Direct: CUT&Tag-Direct was carried out as previously described (https://doi.org/10.17504/protocols.io.bcuhiwt6). In brief, nuclei were thawed and bound to washed paramagnetic concanavalin A (ConA) beads (Bangs Laboratories) at a concentration of 5 µL washed beads per 50K nuclei, and then incubated with primary antibody at 4 °C overnight in Wash Buffer (10 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and Roche Complete Protease Inhibitor Cocktail) with 2 mM EDTA. Bound nuclei were washed and incubated with 1:100 secondary antibody for 1 hour at room temperature and then washed 2x and incubated in Wash-300 Buffer (Wash Buffer with 300 mM NaCl) with 1:50 5 µM loaded pA–Tn5 for 1 hour at room temperature. Nuclei were washed 2x and tagmented in Wash-300 Buffer with 10 mM MgCl2 for 1 hour at 37 °C and then resuspended sequentially in 50 µl of 10 mM TAPS and 5 µl of 10 mM TAPS with 0.1% SDS and incubated for 1 hour at 58 °C. The resulting suspension was mixed well with 16 µl of 0.9375% Triton X-100, and then 2 µL each of F and R primers and 25 µL 2× NEBNext Master Mix (New England Biolabs) were added for direct amplification with the following conditions: (1) 58 °C for 5 minutes, (2) 72 °C for 5 minutes, (3) 98 °C for 30 seconds, (4) 98 °C 15 seconds, (5) 60 °C for 15 seconds, (6) repeat steps 4–5 13 times, (7) 72 °C for 1 minute and (8) hold at 8 °C. DNA from amplified product was purified using 1.1× ratio of HighPrep PCR Cleanup System (MagBio) and resuspended in 25 µl of 10 mM Tris-HCl with 1 mM EDTA, and concentration was quantified using the Qubit (Thermo Fisher Scientific) and TapeStation (Agilent) systems. Plate-CUT&Tag: CUT&Tag-Direct experiments were carried out in individual wells of twin.tec lo-bind 96-well PCR microplates (Eppendorf) using multi-channel pipettes and reservoirs, with the following modifications: After tagmentation and washing with 10 mM TAPS, beads were resuspended individually well-by-well in 16 µL 10 mM TAPS with 0.1% SDS using a single-channel pipette with vigorous pipette mixing. The plate was sealed and vortexed briefly for 10 seconds at 1000 RPM on a Thermomixer (Eppendorf). The sealed plate was spun briefly in a swinging bucket rotor, then denatured on a 96 well deep block thermal cycler (BioRad) for 1 hour at 58˚C. After denaturation, samples were neutralized with 5 µL 10% Triton X-100, and the plate was re-sealed and vortexed briefly for 10 seconds at 1000 RPM on the Thermomixer. Primers and NEBNext 2x Master Mix were then added, mixed, and the plate amplified according to the CUT&Tag-Direct thermal cycler program on a 96 well block. Libraries were purified and eluted as described above.

value: AML

value: Plate


title: AML-335640_H3K27ac_Plate_1

description:
Library name: LIB008253_22FCGGLT3_S70_L005
BJ237


title: TNBC_0097

value: Breast


title: SMARCA5 KOBMDM, 1h LPS 10ng/ml, replicate3 (RNA-seq)

description: Library name: RNA_KO_1hLPS_REP3

value: BMDM


title: AML-335640_H3K4me_Plate_1

description:
Library name: LIB008251_22FCGGLT3_S35_L005
BJ235


title: Sol_12M_WT25

description:
Library name: Sol_12M_WT25
Sol25

value: WT


title: TNBC_0096

value: Local


title: Pso_12M_DMD21b

description:
Library name: Pso_12M_DMD21b
Pso21b

source_name: Pso

value: Pso


title: SMARCA5 KOBMDM, 1h LPS 10ng/ml, replicate4 (RNA-seq)

description: Library name: RNA_KO_1hLPS_REP4


title: AML-335640_H3K4me3_Plate_2

description:
Library name: LIB008250_22FCGGLT3_S45_L005
BJ234


title: TNBC_0094

value: White

value: Distant


title: SMARCA5 KOBMDM, 2h IFN 100U/ml, replicate1 (RNA-seq)

description: Library name: RNA_KO_2hIFN_REP1

value: 2h IFNb 100 U/ml


title: Pso_12M_WT25

description:
Library name: Pso_12M_WT25
Pso25


title: TNBC_0133

value: Black


title: AML-335640_H3K4me3_Plate_1

description:
Library name: LIB008249_22FCGGLT3_S102_L005
BJ233


title: SMARCA5 KOBMDM, 2h IFN 100U/ml, replicate2 (RNA-seq)

description: Library name: RNA_KO_2hIFN_REP2


title: AML-335640_H3K9me3_Plate_2

description:
Library name: LIB008248_22FCGGLT3_S61_L005
BJ232


title: Heart_12M_DMD21b

description:
Library name: Heart_12M_DMD21b
Cr21b

source_name: Heart

value: Heart

value: DMD


title: Heart_12M_WT25

description:
Library name: Heart_12M_WT25
Cr25

value: untreated


title: TNBC_0093


title: Dia_12M_DMD21b

description:
Library name: Dia_12M_DMD21b
Dia21b

source_name: diaphragm

value: diaphragm


title: SMARCA5 KOBMDM, 2h IFN 100U/ml, replicate3 (RNA-seq)

description: Library name: RNA_KO_2hIFN_REP3

source_name: BMDM


title: TNBC_0082


title: SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate1 (RNA-seq)

description: Library name: RNA_KO_2hLPS_REP1

value: 2h LPS 10 ng/ml


title: TNBC_0083

value: Regional


title: AML-335640_H3K9me3_Plate_1

description:
Library name: LIB008247_22FCGGLT3_S77_L005
BJ231

value: AML


title: AML-335640_H3K27me3_Plate_2

description:
Library name: LIB008246_22FCGGLT3_S40_L005
BJ230

value: Plate


title: TNBC_0072

value: Breast


title: Dia_12M_WT25

description:
Library name: Dia_12M_WT25
Dia25


title: TNBC_0074


title: AML-126620_H3K36me3_Plate_2

description:
Library name: LIB008244_22FCGGLT3_S15_L005
BJ202


title: AML-335640_H3K27me3_Plate_1

description:
Library name: LIB008245_22FCGGLT3_S66_L005
BJ229


title: SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate2 (RNA-seq)

description: Library name: RNA_KO_2hLPS_REP2

value: BMDM


title: TNBC_0062


title: SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate3 (RNA-seq)

description: Library name: RNA_KO_2hLPS_REP3


title: TNBC_0060


title: Sol_6M_WT8

description:
Library name: Sol_6M_WT8
Sol8

value: Sol

value: WT


title: AML-126620_H3K27ac_Plate_2

description:
Library name: LIB008243_22FCGGLT3_S41_L005
BJ201


title: SMARCA5 KOBMDM, 2h LPS 10ng/ml, replicate4 (RNA-seq)

description: Library name: RNA_KO_2hLPS_REP4


title: AML-126620_H3K4me_Plate_2

description:
Library name: LIB008242_22FCGGLT3_S23_L005
BJ200


title: Pso_6M_DMD3

description:
Library name: Pso_6M_DMD3
Pso3

value: Pso


title: TNBC_0059

value: White

value: Local


title: Pso_6M_WT8

description:
Library name: Pso_6M_WT8
Pso8


title: SMARCA5 KOBMDM, untreated, replicate1 (RNA-seq)

description: Library name: RNA_KO_UT_REP1


title: AML-126620_H3K4me3_Plate_2

description:
Library name: LIB008241_22FCGGLT3_S90_L005
BJ199


title: SMARCA5 KOBMDM, 2h IFN 100U/ml, replicate4 (RNA-seq)

description: Library name: RNA_KO_2hIFN_REP4

value: 2h IFNb 100 U/ml


title: Heart_6M_DMD3

description:
Library name: Heart_6M_DMD3
Cr3


title: TNBC_0010


title: SMARCA5 KOBMDM, untreated, replicate2 (RNA-seq)

description: Library name: RNA_KO_UT_REP2


title: AML-126620_H3K9me3_Plate_2

description:
Library name: LIB008240_22FCGGLT3_S81_L005
BJ198


title: Heart_6M_WT8

description:
Library name: Heart_6M_WT8
Cr8


title: SMARCA5 KOBMDM, untreated, replicate3 (RNA-seq)

description: Library name: RNA_KO_UT_REP3


title: Sol_6M_DMD3

description:
Library name: Sol_6M_DMD3
Sol3


title: AML-126620_H3K27me3_Plate_2

description:
Library name: LIB008239_22FCGGLT3_S39_L005
BJ197


title: SMARCA5 KOBMDM, untreated, replicate4 (RNA-seq)

description: Library name: RNA_KO_UT_REP4


title: Dia_6M_DMD3

description:
Library name: Dia_6M_DMD3
Dia3


title: AML-126620_H3K36me3_Plate_1

description:
Library name: LIB008238_22FCGGLT3_S87_L005
BJ196


title: Org_18

city: Los Angeles

first: Ana

middle: C

last: Maretti-Mira

address: 1450 Biggy Street, NRT 3514

department: Medicine

institute: USC

description: 10X Genomics

data_processing:
Raw data processing: Cell by gene count matrices were generated by processing FASTQ files using the Cell Ranger count (version 5.0.1, 10X Genomics) pipeline with the GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics) human genome reference for each sample.
Gene expression data were processed using the R package Seurat (version 4) [PMID: 29608179].
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver spheroids Insphero

growth_protocol: 7 days in low glucose media (media obtained from InSphero)

extract_protocol:
not extracted, spheroids cells were dissociated for 15min using Trypsin, at 37˚C. Dead cells were removed using Dead Cell Removal Kit (Miltenyi Biotec). Viable cells were particioned using 10x Chromium Controller and kit 3' v3.1.
Library was performed according to the manufacter’s instructions

treatment_protocol: PFHpA replenished every 2-3 days with media change

value: liver spheroids Insphero

value: PFHpA


title: WT BMDM, 1h IFN 100U/ml, replicate2 (RNA-seq)

description: Library name: RNA_WT_1hIFN_REP2

value: wild type

value: 1h IFNb 100 U/ml


title: Org_16

description: 10X Genomics

value: DMSO


title: WT BMDM, 1h IFN 100U/ml, replicate3 (RNA-seq)

description: Library name: RNA_WT_1hIFN_REP3


title: AML-126620_H3K4me_Plate_1

description:
Library name: LIB008236_22FCGGLT3_S33_L005
BJ194


title: WT BMDM, 1h IFN 100U/ml, replicate4 (RNA-seq)

description: Library name: RNA_WT_1hIFN_REP4


title: Dia_6M_WT8

description:
Library name: Dia_6M_WT8
Dia8

value: diaphragm

value: untreated


title: Sol_12M_WT24

description:
Library name: Sol_12M_WT24
Sol24


title: AML-126620_H3K4me3_Plate_1

description:
Library name: LIB008235_22FCGGLT3_S93_L005
BJ193

value: AML


title: Lhx1KO, day 6, rep 1

city: Westmead

first: Riley

last: McMahon

address: 214 Hawkesbury Road

country: Australia

institute: Children's Medical Research Institute

description: Library name: Sample 22

data_processing:
Nucleotide sequences were mapped to the Mus Musculus (mm10) reference genome using the splice-aware aligner, STAR v020201
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Day 6 EB

growth_protocol: Naïve ESCs were grown on gelatin coated plates for two passages before being passaged and counted for embryoid body differentiation. AggreWell™ 400 24-wells (Stem Cell Technologies) were filled with 1 mL of EB media (DMEM, 15% FBS, 1x NEAA, 1x pen/strep, 0.1 mM  b-mercaptoethanol) and spun at 3000 g for 30 seconds to remove air bubbles. 2 x 106 ESCs per Aggrewell in 1mL of EB media were then added and the plate was spun at 500 g for 3 minutes. The plates were incubated at 37°C, 5% CO2 for 24 hours before the EBs were gently dislodged from the wells using a 1 mL pipette and transferred to a non-adherence 10 cm plate in 10mL of EB media. EBs were then incubated on a rocking plate and media was replaced every two days.

extract_protocol:
Total RNA was extracted using RNA Mini kit (Qiagen). 3ug of RNA was used for sequencing libraries
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®).

value: Day 6 EB

value: R1 ESC

value: mouse embryonic stem cell


title: Lhx1KO, day 6, rep 2

description: Library name: Sample 23


title: Lhx1KO, day 6, rep 3

description: Library name: Sample 24


title: WT BMDM, 1h LPS 10ng/ml, replicate1 (RNA-seq)

description: Library name: RNA_WT_1hLPS_REP1

value: BMDM

value: 1h LPS 10 ng/ml


title: TNBC_0055

city: New Orleans

first: Jovanny

last: Zabaleta

address: 1700 Tulane Ave

institute: LSUHSC

value: Breast


title: WT BMDM, 1h LPS 10ng/ml, replicate2 (RNA-seq)

description: Library name: RNA_WT_1hLPS_REP2


title: Pso_12M_WT24

description:
Library name: Pso_12M_WT24
Pso24

value: Pso

value: WT


title: Lhx1KO, day 4, rep 3

description: Library name: Sample 21

source_name: Day 4 EB

value: Day 4 EB


title: AML-126620_H3K27me3_Plate_1

description:
Library name: LIB008233_22FCGGLT3_S21_L005
BJ191

data_processing:
Raw fastq files were aligned to the UCSC hg38 genome build using Bowtie2, version 2.4.2, with parameters –end-to-end–very-sensitive–no-mixed–no-discordant -q–phred33 -I 10 -X 700.
Mapped reads were filtered using Samtools view -b -F 12 and converted to paired-end BED files containing coordinates for the termini of each read pair.
Paired-end bed files were converted to bedGraph files using BEDTools genomecov with parameter –bg.
Bedgraphs were converted to BigWig files using the UCSC bedgraphToBigwig function for visualization in the Integrative Genomics Viewer Genome Browser.
Assembly: hg38
Supplementary files format and content: bed, bigwig
Library strategy: CUT&Tag

value: Plate


title: Lhx1KO, day 4, rep 2

description: Library name: Sample 20


title: Heart_12M_DMD20

description:
Library name: Heart_12M_DMD20
Cr20

value: Heart

value: DMD


title: AML-875663_H3K36me3_Plate_2

description:
Library name: LIB008232_22FCGGLT3_S17_L005
BJ190


title: Heart_12M_WT24

description:
Library name: Heart_12M_WT24
Cr24


title: Sol_12M_DMD20

description:
Library name: Sol_12M_DMD20
Sol20

value: Sol


title: WT BMDM, 1h LPS 10ng/ml, replicate4 (RNA-seq)

description: Library name: RNA_WT_1hLPS_REP4

value: wild type


title: AML-875663_H3K27ac_Plate_2

description:
Library name: LIB008231_22FCGGLT3_S46_L005
BJ189


title: Lhx1KO, day 4, rep 1

description: Library name: Sample 19


title: WT BMDM, 2h IFN 100U/ml, replicate1 (RNA-seq)

description: Library name: RNA_WT_2hIFN_REP1

value: 2h IFNb 100 U/ml


title: Lhx1KO, day 2, rep 3

description: Library name: Sample 18

source_name: Day 2 EB

value: Day 2 EB


title: AML-875663_H3K4me_Plate_2

description:
Library name: LIB008230_22FCGGLT3_S101_L005
BJ188

value: AML


title: Dia_12M_DMD20

description:
Library name: Dia_12M_DMD20
Dia20

value: diaphragm

value: untreated


title: Dia_12M_WT24

description:
Library name: Dia_12M_WT24
Dia24


title: AML-875663_H3K4me3_Plate_2

description:
Library name: LIB008229_22FCGGLT3_S47_L005
BJ187


title: Pso_12M_DMD20

description:
Library name: Pso_12M_DMD20
Pso20


title: Sol_6M_DMD2

description:
Library name: Sol_6M_DMD2
Sol2


title: Lhx1KO, day 2, rep 1

description: Library name: Sample 16

value: R1 ESC

value: mouse embryonic stem cell


title: WT BMDM, 2h IFN 100U/ml, replicate3 (RNA-seq)

description: Library name: RNA_WT_2hIFN_REP3

value: BMDM


title: AML-126620_H3K9me3_Plate_1

description:
Library name: LIB008234_22FCGGLT3_S36_L005
BJ192


title: WT BMDM, 2h IFN 100U/ml, replicate4 (RNA-seq)

description: Library name: RNA_WT_2hIFN_REP4


title: Lhx1KO, day 0, rep 3

description: Library name: Sample 15

source_name: Day 0 EB

value: Day 0 EB


title: WT BMDM, 1h LPS 10ng/ml, replicate3 (RNA-seq)

description: Library name: RNA_WT_1hLPS_REP3

value: 1h LPS 10 ng/ml


title: Lhx1KO, day 0, rep 2

description: Library name: Sample 14


title: Sol_6M_WT7

description:
Library name: Sol_6M_WT7
Sol7

value: WT


title: AML-875663_H3K27me3_Plate_2

description:
Library name: LIB008227_22FCGGLT3_S31_L005
BJ185


title: WT BMDM, 2h LPS 10ng/ml, replicate1 (RNA-seq)

description: Library name: RNA_WT_2hLPS_REP1

value: 2h LPS 10 ng/ml


title: AML-875663_H3K36me3_Plate_1

description:
Library name: LIB008226_22FCGGLT3_S86_L005
BJ184

value: Plate


title: Lhx1KO, day 0, rep 1

description: Library name: Sample 13


title: Pso_6M_DMD2

description:
Library name: Pso_6M_DMD2
Pso2

value: Pso


title: Pso_6M_WT7

description:
Library name: Pso_6M_WT7
Pso7


title: AML-875663_H3K27ac_Plate_1

description:
Library name: LIB008225_22FCGGLT3_S85_L005
BJ183


title: WT BMDM, 2h LPS 10ng/ml, replicate2 (RNA-seq)

description: Library name: RNA_WT_2hLPS_REP2


title: Lhx1KO, day 2, rep 2

description: Library name: Sample 17


title: WT BMDM, 2h IFN 100U/ml, replicate2 (RNA-seq)

description: Library name: RNA_WT_2hIFN_REP2


title: Wildtype, day 6, rep 3

description: Library name: Sample 12

value: Day 6 EB


title: Heart_6M_DMD2

description:
Library name: Heart_6M_DMD2
Cr2

value: Heart

value: DMD


title: WT BMDM, 2h LPS 10ng/ml, replicate3 (RNA-seq)

description: Library name: RNA_WT_2hLPS_REP3

value: wild type


title: AML-875663_H3K9me3_Plate_2

description:
Library name: LIB008228_22FCGGLT3_S98_L005
BJ186


title: Wildtype, day 6, rep 2

description: Library name: Sample 11


title: Heart_6M_WT7

description:
Library name: Heart_6M_WT7
Cr7


title: Dia_6M_DMD2

description:
Library name: Dia_6M_DMD2
Dia2


title: Wildtype, day 4, rep 3

description: Library name: Sample 9

value: Day 4 EB


title: AML-875663_H3K4me3_Plate_1

description:
Library name: LIB008223_22FCGGLT3_S54_L005
BJ181

value: AML


title: WT BMDM, untreated, replicate1 (RNA-seq)

description: Library name: RNA_WT_UT_REP1


title: AML-126620_H3K27ac_Plate_1

description:
Library name: LIB008237_22FCGGLT3_S67_L005
BJ195


title: Dia_6M_WT7

description:
Library name: Dia_6M_WT7
Dia7

value: diaphragm


title: AML-875663_H3K9me3_Plate_1

description:
Library name: LIB008222_22FCGGLT3_S60_L005
BJ180


title: Wildtype, day 6, rep 1

description: Library name: Sample 10


title: WT BMDM, untreated, replicate2 (RNA-seq)

description: Library name: RNA_WT_UT_REP2


title: AML-875663_H3K27me3_Plate_1

description:
Library name: LIB008221_22FCGGLT3_S57_L005
BJ179


title: AML-875663_H3K27me3_Direct_1

description:
Library name: HFVWCDSX7_CGCAGCTAGA-ACCTAAGAGC_L004
BJ045

value: Direct


title: Wildtype, day 4, rep 2

description: Library name: Sample 8

value: R1 ESC


title: Sol_12M_DMD19

description:
Library name: Sol_12M_DMD19
Sol19

value: Sol

value: untreated


title: Wildtype, day 4, rep 1

description: Library name: Sample 7

value: mouse embryonic stem cell


title: Wildtype, day 2, rep 3

description: Library name: Sample 6

value: Day 2 EB


title: AML-875663_H3K4me1_Direct_1

description:
Library name: HFVWCDSX7_TGACCTGCTG-ACCTAAGAGC_L004
BJ044


title: Sol_12M_WT23

description:
Library name: Sol_12M_WT23
Sol23

value: WT


title: AML-875663_H3K4me_Plate_1

description:
Library name: LIB008224_22FCGGLT3_S95_L005
BJ182


title: PU1 Chip-seq in WT BMDM, untreated, replicate2

description: Library name: WT_PU1_R2

data_processing:
ChIP-seq workflow, which was also used for MNase-seq and MNase ChIP-seq, is available at https://github.com/fgualdr/mmchipseq
FASTQ files were filtered and trimmed using FASTP (v0.23.2)
Reads were aligned to the mouse genome (mm39; GCA_000001635.9) using STAR (v2.7.9a) with parameters: --runMode alignReads, --alignIntronMax 1, --alignMatesGapMax 100000, --alignEndsType EndToEnd, --outSAMtype BAM Unsorted, and --outSAMattributes All.
Duplicate reads were identified and marked using PICARD (v2.27.4).
Multi-mapped reads were assigned using a custom Bayesian EM algorithm (https://github.com/fgualdr/mmatac).
Peaks were called using MACS2 (v2.2.7.1) with parameters: --nomodel --keep-dup all and the narrowPeak setting enabled.
Reference peak set were created by selecting peaks with q-value ≤ 10⁻³ and ≥ 40% overlap between replicates.
Bigwig files were generated using deeptools (v3.5.1).
Normalization was performed using invariant peaks with GeneralNormalizer (https://github.com/fgualdr/GeneralNormalizer).
Unsupervised clustering was done using PCA (FactoMineR, v2.11), UMAP (uwot, v0.1.16), k-nearest neighbor (FNN, v1.1.4.1), and Louvain clustering (igraph, v1.4.2).
Heatmaps were generated using ComplexHeatmap (v2.14.0).
Assembly: mm39
Supplementary files format and content: bigWig

extract_protocol:
For ChIP-seq, nuclear extracts were prepared as described in Gualdrini et al., 2022. Chromatin was sheared by sonication (Branson Ultrasonics Sonifier or Diagenode Bioruptor Pico). For SMARCA5 MNase ChIP-seq, nuclei were digested with MNase (9 U; Roche) in digestion buffer (20 mM Tris-HCl, pH 7.6; 5 mM CaCl₂) at 37°C for 2 hours, followed by EDTA quenching (50 mM). Digested chromatin was sonicated in lysis buffer (10 mM Tris-HCl, pH 8.0; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% sodium deoxycholate; 0.5% sodium lauroyl sarcosinate) to promote nuclear lysis. Immunoprecipitations were performed with target-specific antibodies prebound to Dynabeads™ Protein G. Beads were washed with RIPA buffer and TE buffer, and DNA was eluted, de-crosslinked, and purified using Qiagen kits (QIAquick PCR purification or MinElute PCR purification).
DNA libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB) or following Gualdrini et al., 2022, protocols. Libraries were assessed for size and quality using the Agilent TapeStation High Sensitivity D5000 assay. Libraries were diluted to 4 nM and sequenced as paired-end reads (51-bp or 61-bp) on an Illumina NextSeq6000 platform.

treatment_protocol: Individual Chip-seq were performed on mouse primary BMDMs derived from wild-type or SMARCA5-deleted cells under untreated, LPS-stimulated, or IFNβ-stimulated conditions for 1 and 2 hours. For specific details, refer to individual sample metadata. Cells were either processed directly for ChIP-seq or treated with 1% formaldehyde for 10 minutes at room temperature for chromatin crosslinking, followed by quenching with 0.125 mM Tris-HCl (pH 7.6).

value: BMDM

tag: chip antibody

value: PU.1:Cell Signaling, Cat# 2258


title: PU1 Chip-seq in WT BMDM, untreated, replicate1

description: Library name: WT_PU1_R1


title: Wildtype, day 2, rep 2

description: Library name: Sample 5


title: WT BMDM, 2h LPS 10ng/ml, replicate4 (RNA-seq)

description: Library name: RNA_WT_2hLPS_REP4

value: 2h LPS 10 ng/ml


title: Pso_12M_DMD19

description:
Library name: Pso_12M_DMD19
Pso19

value: Pso


title: WT BMDM, untreated, replicate4 (RNA-seq)

description: Library name: RNA_WT_UT_REP4


title: Pso_12M_WT23

description:
Library name: Pso_12M_WT23
Pso23


title: AML-875663_H3K36me3_Direct_1

description:
Library name: HFVWCDSX7_ATTAAGGTCG-ACCTAAGAGC_L004
BJ042


title: AML-875663_H3K4me3_Direct_1

description:
Library name: HFVWCDSX7_GTGGCAACAT-ACCTAAGAGC_L004
BJ043


title: Wildtype, day 2, rep 1

description: Library name: Sample 4


title: CEBPb Chip-seq in WT BMDM, untreated, replicate2

description: Library name: WT_CEBPb_R2

value: C/EBPβ:Bethyl, Cat# A302-739A


title: AML-875663_H3K9me3_Direct_1

description:
Library name: HFVWCDSX7_CTCCGCTTAT-ACCTAAGAGC_L004
BJ041


title: Heart_12M_DMD19

description:
Library name: Heart_12M_DMD19
Cr19

value: Heart

value: DMD


title: WT BMDM, untreated, replicate3 (RNA-seq)

description: Library name: RNA_WT_UT_REP3

value: wild type


title: AML-875663_H3K27ac_Direct_1

description:
Library name: HFVWCDSX7_GACCAAGTTA-ACCTAAGAGC_L004
BJ040

value: AML


title: Dia_12M_DMD19

description:
Library name: Dia_12M_DMD19
Dia19

value: diaphragm


title: Wildtype, day 0, rep 2

description: Library name: Sample 2

value: Day 0 EB


title: K562_IgG_Direct_1

description:
Library name: HLYJJDSX5_CTCCGCTTAT+GTCGTGAATC_L003
BJ012

value: CML

value: IgG

value: Direct


title: SMARCA5 Mnase Chip-seq in WT BMDM, untreated, replicate2

description: Library name: SMARCA5_WT_UT_R2

value: SMARCA5:Abcam, Cat# ab3749


title: Wildtype, day 0, rep 1

description: Library name: Sample 1

value: R1 ESC

value: mouse embryonic stem cell


title: SMARCA5 Mnase Chip-seq in WT BMDM, untreated, replicate1

description: Library name: SMARCA5_WT_UT_R1

value: BMDM


title: Dia_12M_WT23

description:
Library name: Dia_12M_WT23
Dia23

value: WT

value: untreated


title: mmNrf2KO5

city: Baltimore

first: Zhenhua

last: Xu

state: MD

address: 400 North Broadway Smith BLDG 3001 Smith BLDG 3001

institute: Johns Hopkins University

description: Library name: mmNrf2KO5

data_processing:
Raw paired-end RNA-seq reads (200 bp) were quality-checked and aligned to the mouse reference genome using STAR with default parameters.
Only uniquely mapped reads were retained for downstream analysis. Gene-level read counts were generated, and differential expression analysis was performed using edgeR in R.
Assembly: Raw reads of RNA-seq were uniquely mapped to the GRCm38/mm10 genome assembly using STAR
Supplementary files format and content: csv file including FKPM values for all samples

source_name: retina

extract_protocol:
RNA was extracted using RNeasy Micro kit (Qiagen).
NEBNext Poly (A) Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina were used to generate libraries.

value: retina

value: Muller cells

value: Muller-specific Nrf2 cKO

value: OIR

tag: time