title: S_h2al2WT_rep2

city: Grenoble

first: Florent

last: Chuffart

state: La Tronche

address: Site Santé - Allée des Alpes

country: France

institute: IAB - INSERM (U1209) - CNRS (UMR5309)

description: Library name: S_h2al2WT_rep2

data_processing:
The fastq files were aligned on the UCSC mm10 genome using STAR (2.7.11b) [PMID:23104886] to produce bam files.
Bam files were counted using HTSeq framework (2.0.5) [PMID:25260700], with options: -t exon -f bam -r pos –stranded=reverse -m intersection-strict –nonunique none
Normalization and differential analysis were performed using the R software [R Core Team. R: A language and environment for statistical computing. Vienna, Austria : R Foundation for Statistical Computing, 2017], DESeq2 (1.22.2) [PMID:20979621, PMID:25516281] and SARTools [PMID:27280887] packages.
Assembly: Mus musculus, mm10
Supplementary files format and content: raw counts

source_name: testis

extract_protocol:
Spermatogenic cell fraction purification was performed as previously described (Shiota et al. 2018).
For each sample, one µg of RNA (RIN = 10) was used for library preparation with TruSeq Stranded Total RNA (RiboZero Human/Mouse/Rat) Library Prep (Illumina, Cat#RS-122-2201) according to the manufacturer’s instructions. Each library was quantified on Qubit with the Qubit® dsDNA HS Assay Kit (Life Technologies) and the size distribution was examined on the Fragment Analyzer with High Sensitivity NGS Fragment Analysis kit (Agilent). The libraries were then sequenced on the Illumina NextSeq 500 (paired-end 75) at the TGML Platform of Aix-Marseille University (France).

value: testis

value: Spermatozoa

value: H2al2 WT


title: FA171_female_56day_PFOA_0.5

status: Public on Jan 05 2026

type: SRA

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
Library name: FA171_Female_PFOA_D2_Sept2024
Templated oligo sequencing (TempO-seq)

library_source: transcriptomic

data_processing:
BCL files were converted to FASTQ format and demultiplexed using bcl2fastq (v2.20). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the Omics Data Analysis Frameworks for Regulatory application (R-ODAF) Health Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed April 2025). The pipeline uses snakemake (v8.0) (Mölder et al., 2021) and scripts in R (v.4.3.2) to manage workflows. Fasta and GTF-formatted reference files were produced using the manifest provided by Biospyder. First, fastp (v0.23.2) was used for trimming, followed by STAR (v2.7.8a) (Dobin et al., 2013) to align raw reads to the reference sequence. Feature counts were extracted from the aligned reads (BAM files) using the qCount function of the QuasR R package (v1.30.0) (Gaidatzis et al., 2015) according to the features specified in a GTF file. A samples-by-probes count matrix was generated. Across experimental samples, the median number of mapped reads was 1,148,263.
Assembly: mm39
Supplementary files format and content: Tab-delimited table of absolute probe counts per sample.

molecule: total RNA

organism: Mus musculus

source_name: liver

growth_protocol: All animal work has been approved by the Health Canada Animal Care Committee (HC-ACC) protocol: 2023-010. 6 to 9-week-old male and female C57BL/6-Elite (SOPF) mice (Charles River, cat#475C57BL/6-E) were acclimatized for two weeks and tail tattooed with the Somark Labstamp (green ultraviolet ink; Somark, cat#01-99032). Throughout the study, mice were housed individually (male) or in pairs (female) in the Tecniplast IVC cage system under negative pressure with a 12:12 light cycle. Mice were fed irradiated Teklad global 14% protein chow (Inotiv, cat#2914) ad libitum and provided autoclaved reverse osmosis water in Tecniplast bottles.

extract_protocol:
Snap-frozen livers were cut on dry ice using a cooled scalpel. 12-25 mg of livers were homogenized in PowerBead tubes (Qiagen, cat#13114-50) containing 2.8mm ceramic beads and 600 μL of RLT buffer (from the RNeasy Mini Kit; Qiagen, cat#74104) supplemented with β-mercaptoethanol (10 μL/mL of RLT; Sigma-Aldrich, cat#M3148-25ML). Homogenization was carried out in a Qiagen PowerLyzer 24 Homogenizer (two 45-second cycles at 3500 rpm with a 30-second pause in between). Following homogenization, the lysate was transferred to a new tube and centrifuged at 13,000xg for 2 minutes. The supernatant (lysate) was transferred to a new tube, and ribonucleic acid (RNA) was extracted with Qiagen RNeasy Mini Kit (Qiagen, cat#74104) according to the manufacturer’s instructions.
TempO-Seq mouse S1500+ surrogate gene panel (version 1.2; BioSpyder Technologies Inc.) was used to generate sequencing libraries to measure gene expression in total RNA purified from mouse liver tissues. Each RNA sample was first diluted to 100 ng/mL in water, then mixed with an equal volume of 2× TempO-Seq Lysis buffer, resulting in a final RNA concentration of 50 ng/µL. Two microliters of this diluted mixture (approximately 100 ng of RNA) were used as input for TempO-Seq library building. As per the manufacturer’s protocol, RNA was first hybridized with the detection oligos (DOs). Unbound DOs were digested with a nuclease, and the remaining bound DOs were ligated. These ligated oligos were then amplified by PCR using primers with sequencing tags to create the sequencing libraries. The resulting libraries were pooled together and quantified using qPCR with the KAPA SYBR FAST Universal kit, compatible with Illumina platforms (Roche, Wilmington, MA). The pooled libraries were sequenced using a 75-cycle flow cell on an Illumina NextSeq 500.

treatment_protocol: At 8 to 11 weeks of age, mice were exposed to 1.5 mg/kg/day of perfluorooctanoic acid (PFOA) or perfluorooctanesulfonic acid (PFOS) for 28 days or 0.166, 0.5, 1.0, or 1.5 mg/kg/day of PFOA or PFOS for 56 days by daily oral gavage (gavage volume: 7.5 mL/Kg). Gavage solutions were prepared as follows. In brief, Tween 20 (Sigma-Aldrich, cat#P1379) was diluted in optima water (Fisher, cat#W64) to obtain a 0.5% (v/v) Tween 20 solution. PFOA (Sigma-Aldrich, cat#171468) or PFOS (Sigma-Aldrich, cat#77283) was added to 0.5% Tween 20 to achieve a 1.5 mg/kg/day gavage solution. The 1.0, 0.5, and 0.166 mg/kg/day gavage solutions were obtained through serial dilution. The vehicle groups were gavaged with 0.5% Tween 20 in optima water (Fisher, cat#W64) while the naïve groups were not gavaged. Body weight was collected daily, and water consumption was measured weekly. Water consumption was calculated by multiplying the weight difference between the water bottle after one week of use and the full water bottle before use by the water density (1.3019 g/mL1). 24 hours following the last oral gavage, mice treated for 28 or 56 days were euthanized by exsanguination (cardiac puncture) under isoflurane.  The livers were collected and weighed followed, by flash freezing.

tag: tissue

value: liver

tag: Sex

value: female

tag: strain

tag: treatment

value: Pefluorooctanoic acid

tag: treatment time_dose


title: FA165_female_56day_PFOA_0.166

description:
Library name: FA165_Female_PFOA_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: FA162_female_56day_PFOA_0.166

description:
Library name: FA162_Female_PFOA_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: FA161_female_56day_PFOA_0.166

description:
Library name: FA161_Female_PFOA_D1_Sept2024
Templated oligo sequencing (TempO-seq)


title: FA170_female_56day_PFOA_0.5

description:
Library name: FA170_Female_PFOA_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: H3K4me1, SAßGal-low, donor 2

city: Piscataway

first: Ricardo

middle: Iván

last: Martínez Zamudio

state: New Jersey

address: 675 Hoes Lane West

department: Pharmacology

country: USA

institute: Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School

description: Library name: H3K4me1_SAßGal-low_donor-2

library_source: genomic

data_processing:
In-house pipeline
Adaptors were trimmed using cutadapt version 5.1.
Trimmed reads were mapped to GRCh38.d1.v1 using bowtie2 with the following parameters: -no-mixed --no-discordant --maxins 2000
Alignments de-deduplicated using Picard and Samtools and subsequently blacklisted regions were removed using Bedtools.
Cleaned alignments were then used as input for peak calling using MACS2 with a relaxed threshold of q-value = 0.01 and a master peakset was constructed using bedops with individual sample peak sets as input. Differential chromatin states were identified using chromstaR as described in Martínez-Zamudio et al, Cell Genomics, 2023 except that the fold enrichment cut-off of >=1 was used.
Assembly: GRCh38.d1.v1
Supplementary files format and content: BW; 1X normalized signal tracks per sample are provided. These were generated using deeptools normalized against the effective GRCh38 genome size.

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood

growth_protocol: Cells were isolated from peripheral blood and immediately stained for SA-ßGal and isolated via FACS.

extract_protocol:
Nuclei were isolated and transposed as in Buenrostro et al, Nature Methods, 2013, from ~50,000 CD8+ T cells
Libraries were constructed as indicated in the Epycypher CuTANA Cut&Tag Kit.

treatment_protocol: No treatment.

value: Peripheral blood

tag: cell type

value: CD8+ T cell


title: H3K4me1, SAßGal-low, donor 3

description: Library name: H3K4me1_SAßGal-low_donor-3


title: H3K4me1, SAßGal-high, donor 2

description: Library name: H3K4me1_SAßGal-high_donor-2


title: S_h2al2WT_rep1

description: Library name: S_h2al2WT_rep1

tag: genotype


title: H3K4me1, SAßGal-low, donor 1

description: Library name: H3K4me1_SAßGal-low_donor-1


title: R_h2al2WT_rep3

description: Library name: R_h2al2WT_rep3

value: Round spermatids


title: R_h2al2WT_rep2

description: Library name: R_h2al2WT_rep2


title: FA169_female_56day_PFOA_0.5

description:
Library name: FA169_Female_PFOA_D2_Sept2024
Templated oligo sequencing (TempO-seq)


title: IgG, SAßGal-high, donor 2

description: Library name: IgG_SAßGal-high_donor-2


title: IgG, SAßGal-low, donor 2

description: Library name: IgG_SAßGal-low_donor-2


title: R_h2al2KO_rep3

description: Library name: R_h2al2KO_rep3

value: H2al2 KO


title: R_h2al2WT_rep1

description: Library name: R_h2al2WT_rep1


title: S_h2al2KO_rep1

description: Library name: S_h2al2KO_rep1


title: IgG, SAßGal-low, donor 3

description: Library name: IgG_SAßGal-low_donor-3


title: IgG, SAßGal-high, donor 1

description: Library name: IgG_SAßGal-high_donor-1


title: P_h2al2WT_rep1

description: Library name: P_h2al2WT_rep1

value: Pachytene spermatocytes


title: DMOG_HIF1A_R1

city: Umea

first: Silvia

last: Remeseiro

state: Vasterbottens lan

address: Johan Bures vag 12, MBC-huset

department: Umea Centre for Molecular Medicine

country: Sweden

institute: Umea University

description: Library name: DMOG_HIF1A_R1

data_processing:
Data processing followed previously published pipelines (Meers et al, 2019). Raw sequencing files (FASTQ) were quality-checked using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Adapter trimming was performed with Trimmomatic (v0.39), and reads were aligned to both the human genome (GRCh38.p14/hg38) and the D. melanogaster genome (FlyBase r6.62) using Bowtie2 (v2.4.5) with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700. Duplicate reads were identified and removed using collate, fixmate, and markdup functions in samtools. Genome-wide signal coverage was normalized to Reads Per Genomic Content (RPGC) per bin (bin size: 50 bp) and scaled using a spike-in-derived factor based on the ratio of D. melanogaster reads per sample to total D. melanogaster reads aligned in IgG controls with deepTools (3.5.5). Fraction of reads in peaks (FRiP) was calculated using the featureCounts subtool from SubRead (v2.1.1). Peak calling was performed using SEACR (1.3) with a stringent FDR cutoff of 0.01. Pairwise comparisons of HIF1α binding were conducted between AA vs. NA and DMOG-treated vs. control U87 cells using ChIPpeakAnno and ChIPseeker in R. Annotated peaks (sample-specific and common) were assigned to genes using EnsDb.Hsapiens.v86 and TxDb. Hsapiens. UCSC. hg38. knownGene. To quantify binding near key gene sets, genomic bins within 5, 10, and 100 kb of selected gene promoters were analyzed. Gene sets related to chondroitin sulfate synthesis, proteoglycans, and glycosaminoglycan metabolism were retrieved from EnsDb.Hsapiens.v86 and compared to genes associated with sample-specific and shared HIF1α binding sites. Genome coverage files and peak sets for NA vs. AA and DMOG vs. control were uploaded to Galaxy (usegalaxy.org, 25.0.rc1) and visualized using the UCSC Genome Browser (hg38)
Assembly: GRCh38.p14, hg38
Supplementary files format and content: bigWig, bed
Library strategy: CUT&Run

source_name: tumour

growth_protocol: NA cells (U87MG cultured at pH 7.4) AA cells (U87MG cultured at pH 6.4) Ctrl cells (U87MG cultured in serum-free media at pH 7.4) DMOG-treated cells (U87MG treated with 0.5 mM dimethyloxalylglycine at pH 7.4) All cells were routinely cultured in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Genome-wide binding sites of HIF1α were determined in U87 derived NA, AA, Ctrl an DMOG treated cells using the CUT&RUN Assay kit (Active motif, #53180, version 47) following the manufacturer’s instructions. A total of 5x10^5 cells per line and per CUT&RUN reaction were collected and mildly fixed with 0.1% formaldehyde for 2 minutes at room temperature on a shaker. Crosslinking was quenched with 125 mM glycine for 5 minutes, and samples were washed in cold 1xPBS and flash frozen. Upon thawing, 5,000 Drosophila melanogaster nuclei (Active Motif, #53183) were added as spike-in before sample nuclei isolation.  Nuclei isolated per CUT&RUN reaction was first incubated with the concavalin beads, followed by overnight incubation with 1ug of HIF1⍺ antibody (GeneTex, GTX127309) at 4°C. Thereafter, chromatin-bound beads were mixed with pAG-MNase in cell permeabilization buffer, and the enzyme was activated by adding 1ul of 0.1M cold calcium chloride and incubated at 4°C for 2 hours while rotating at a speed of 25 RPM. Decrosslinking was performed by incubation with Stop Solution containing RNase and Glycogen at 37°C for 10min.  Enriched DNA was purified using the DNA purification Columns SF,  provided in the kit
Library preparation was done using the NEBNext Ultra II DNA library Prep Kit, For Illumina and Multiplex Oligos (New England Biolabs, #E7645S, E7500S, E7335S) following Active Motif’s CUT&RUN library preparation protocol. Library size distribution was assessed via TapeStation High Sensitivity DNA Analysis assay (Agilent High Sensitivity DNA screentape analysis # 5067-5592) and libraries were sequenced as PE150 on a NovaSeqX Sequencing System (Illumina).

value: tumour

tag: cell line

value: mesenchymal/ proneural subtype


title: P_h2al2WT_rep2

description: Library name: P_h2al2WT_rep2


title: DMOG_HIF1A_R2

description: Library name: DMOG_HIF1A_R2


title: IgG, SAßGal-low, donor 1

description: Library name: IgG_SAßGal-low_donor-1


title: R_h2al2KO_rep2

description: Library name: R_h2al2KO_rep2


title: R_h2al2KO_rep1

description: Library name: R_h2al2KO_rep1


title: P_h2al2WT_rep3

description: Library name: P_h2al2WT_rep3


title: P_h2al2KO_rep2

description: Library name: P_h2al2KO_rep2


title: C_h2al2WT_rep3

description: Library name: C_h2al2WT_rep3

value: Condensing spermatids


title: Ctrl_HIF1A_R2

description: Library name: Ctrl_HIF1A_R2


title: C_h2al2KO_rep3

description: Library name: C_h2al2KO_rep3


title: P_h2al2KO_rep3

description: Library name: P_h2al2KO_rep3


title: P_h2al2KO_rep1

description: Library name: P_h2al2KO_rep1


title: C_h2al2KO_rep2

description: Library name: C_h2al2KO_rep2


title: Ctrl_HIF1A_R1

description: Library name: Ctrl_HIF1A_R1


title: C_h2al2WT_rep2

description: Library name: C_h2al2WT_rep2


title: NA_IgG

description: Library name: NA_IgG


title: Ctrl_IgG

description: Library name: Ctrl_IgG


title: NA_HIF1A_R2

description: Library name: NA_HIF1A_R2


title: C_h2al2KO_rep1

description: Library name: C_h2al2KO_rep1


title: AA_HIF1A_R2

description: Library name: AA_HIF1A_R2


title: IgG, SAßGal-high, donor 3

description: Library name: IgG_SAßGal-high_donor-3


title: NA_HIF1A_R1

description: Library name: NA_HIF1A_R1


title: C_h2al2WT_rep1

description: Library name: C_h2al2WT_rep1


title: AA_HIF1A_R1

description: Library name: AA_HIF1A_R1


title: PFF Duodenal Immune Cells 1

city: GAINESVILLE

first: Phillip

middle: Michael

last: Mackie

state: FL

address: 1149 Newell Drive BLDG 59 L4-151

department: Neuroscience

institute: University of Florida

description:
Library name: PFF
10x Genomics

library_source: transcriptomic single cell

data_processing:
The de-multiplexing, alignement, mapping, gene counting and aggregation were all done with 10x's Cell Ranger software.
Assembly: mouse mm10
Supplementary files format and content: tab separated values and matrices

source_name: Duodenum

extract_protocol:
Harvested duodenum was mechanically cut into fine pieces and then digested in Accumax for 5 minutes at 37 degrees C with vigorous shaking. The digested solution was then filtered, counted, and split in half for 2 parallel simultaneous separation protocols. One half was subject to CD45-FITC antibody and DAPI labelling followed by FACS-based enrichmen. The other half was subject to CD11b magnetic bead based enrichment followed by DAPI labelling with FACS-based exclusion of dead cells. The enriched fractions from each protocol were then combined before loading onto the 10x Chromium.
Library construction was performed according to the 10x single-cell 3' v3 protocol. Briefly, the master mix was combined with the partitioning oil and sample then loaded onto the chip for creation of gel-bead emulsions (GEM). Each individual GEM reaction produced poly-A RNA that was converted to cDNA tagged with an Illumina R1 transcript, Unique Molecular Identifier (UMI) and 10x barcode. The cDNA library was cleaned with DynaBeads, amplified by PCR, and separated for size-appropriate fragments using SPRI-select. Quality-checking of the library was performed with Agilent Bioanalyzer. Library construction was completed by adding the paired-end fragments and indexing samples as approrpaite.

treatment_protocol: Intramuscular injection of mouse recombinant preformed fibrils (PFFs) of alpha synuclein into the duodenum

value: Duodenum

value: Immune Cells

value: PFF

tag: batch


title: Saline Control Duodenal Immune Cells 2

description:
Library name: Saline
10x Genomics

value: saline


title: Saline Control Duodenal Immune Cells 1

description:
Library name: Control (Saline)
10x Genomics


title: SLC229_SP Surface Protein Library (HTO/ADT)

city: Berkeley

first: Shaina

middle: Laufer

last: Carroll

state: CA

address: 405 Weill Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
Library name: SLC229_SP
ADT/HTO library: Read1 contains 10X cell barcode and UMI, Read 2 contains feature barcode (ADT/HTO)

library_source: other

data_processing:
CITE-seq and Multiome were processed with CellRanger v9.0.0 using 10X Genomics Cloud Analysis
Assembly: Mouse GRCm39 2024-A
Supplementary files format and content: CellRanger Output File: sample_filtered_feature_bc_matrix.tar.gz
Library strategy: CITE-seq

molecule: protein

source_name: lymph node

extract_protocol:
Dendritic cells sorted from  gut-draining lymph nodes. Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X controller with a GEM-X Universal 3' Gene Expression v4 kit along with the Chromium GEM-X Single Cell 3 Feature Barcode Kit v4
The 10X Protocol for Chromium Next GEM Single Cell 3' Reagents Kits v4 (Dual Index) with Feature Barcode technology was used for preparation of 3' gene expression library and HTO/ADT library

treatment_protocol: 4 animals received 1 mg isotype control antibodies and 5 animals received 1 mg anti-IL10R blocking antibodies

value: lymph node

value: dendritic cells

value: mixed samples (isotype control, anti-IL-10R)

tag: library type

value: ADT/HTO

tag: adt

value: TotalSeq-B0014 anti-mouse/human CD11b Antibody, TotalSeq-B0568 anti-mouse/rat XCR1 Antibody, TotalSeq-B0911 anti-phycoerythrin (PE) Antibody

tag: hto

value: TotalSeq-B0301 anti-mouse Hashtag 1 Antibody (ASF), TotalSeq-B0302 anti-mouse Hashtag 2 Antibody (isotype), TotalSeq-B0303 anti-mouse Hashtag 3 Antibody (aIL10R), TotalSeq-B0304 anti-mouse Hashtag 4 Antibody (isotype), TotalSeq-B0305 anti-mouse Hashtag 5 Antibody (aIL10R), TotalSeq-B0306 anti-mouse Hashtag 6 Antibody (isotype), TotalSeq-B0307 anti-mouse Hashtag 7 Antibody (aIL10R), TotalSeq-B0308 anti-mouse Hashtag 8 Antibody (isotype), TotalSeq-B0309 anti-mouse Hashtag 9 Antibody (aIL10R), TotalSeq-B0310 anti-mouse Hashtag 10 Antibody (aIL10R)


title: FA163_female_56day_PFOA_0.166

description:
Library name: FA163_Female_PFOA_D1_Sept2024
Templated oligo sequencing (TempO-seq)

value: liver

value: female

value: Pefluorooctanoic acid


title: AA263yne-3

city: La Jolla

first: Gabriel

last: Kline

address: 10550 N Torrey Pines Rd

institute: Scripps Research Institute

description:
Library name: Sample 9
AA263yne

data_processing:
Alignment of reads was performed using DNAstar Lasergene SeqMan NGen 17 to the human genome GRCh38-dbSNP150 assembly.
Aligned reads were imported into ArrayStar 17 as linear counts data.
Differential expression analysis and statistical significance comparisons were assessed using DESeq2 (v. 1.40.1) in R compared to DMSO-treated cells.
Assembly: human genome GRCh37-dbSNP150 assembly
Supplementary files format and content: Raw counts of sequencing reads for each gene following alignment. Format is .csv.
Supplementary files format and content: Normalized abundance measurements for each gene following DESeq2. Format is .csv.

growth_protocol: HEK293 cells were plated at 200,000 cells/well in a 6-well plate in DMEM with 10% FBS and 1% PennStrep

extract_protocol:
Cells were collected with 0.25% trypsin, neutralized with cell culture media, and pelleted at 200 x g for 5 min. Total RNA was extracted using the Quick-RNA MiniPrepKit (Zymo Research), following the protocol suggested by the manufacturer.
Libraries were constructed by BGI using their standard methodology. mRNA was enriched from total RNA samples via their polyA tails using oligo dT beads. mRNA was then fragmented and converted to cDNA using random primers to synthesize the first cDNA strand. The second cDNA strand was synthesized using dUTP instead of dTTP. The cDNA was subjected to end-repair and 3’ adenylated. Adaptors were ligated to the ends of these cDNA fragments. The U-labeled second-strand template was digested with uracil-DNA-glycosylase. The remaining cDNA fragments were then amplified by PCR. The library was quality controlled, then circularized and amplified to make a DNA nanoball (DNB). Finally, the library was sequenced using the DNBSEQ platform.

treatment_protocol: After 24 hours, the cells were treated with the indicated concentration of compound for 6 h.

value: WT

value: 6h AA263yne (10 μM)


title: AA263-5-1

description:
Library name: Sample 10
AA263_5


title: AA263-5-2

description:
Library name: Sample 11
AA263_5


title: AA263-5-3

description:
Library name: Sample 12
AA263_5


title: SLC_229_GELib Gene Expression Library

description:
Library name: SLC_229_GELib
GEX (3' mRNA) library: Read1 contains 10x cell barcode and UMI, Read2 contains transcript

data_processing:
CITE-seq and Multiome were processed with CellRanger v9.0.0 using 10X Genomics Cloud Analysis
Assembly: Mouse GRCm39 2024-A
Supplementary files format and content: CellRanger Output File: sample_filtered_feature_bc_matrix.tar.gz

molecule: polyA RNA

value: mRNA


title: AA263yne-2

description:
Library name: Sample 8
AA263yne


title: Surface Protein Library (HTO/ADT)

description:
Library name: SLC184_SP
ADT/HTO library: Read1 contains 10X cell barcode and UMI, Read 2 contains feature barcode (ADT/HTO)

data_processing:
CITE-seq and Multiome were processed with CellRanger v9.0.0 using 10X Genomics Cloud Analysis
Assembly: Mouse GRCm39 2024-A
Supplementary files format and content: CellRanger Output File: filtered_feature_bc_matrix.tar.gz
Library strategy: CITE-seq

extract_protocol:
Dendritic cells sorted from steady state gut-draining lymph nodes . Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X controller with a Chromium Next GEM Single Cell 3' Kit v3.1 along with the 3’ Feature Barcode Kit
The 10X Protocol for Chromium Next GEM Single Cell 3' Reagents Kits v3.1 (Dual Index) with Feature Barcode technology was used for preparation of 3' gene expression library and HTO/ADT library

value: TotalSeq-B0301 anti-mouse Hashtag 1 Antibody, TotalSeq-B0302 anti-mouse Hashtag 2 Antibody, TotalSeq-B0303 anti-mouse Hashtag 3 Antibody, TotalSeq-B0304 anti-mouse Hashtag 4 Antibody, TotalSeq-B0305 anti-mouse Hashtag 5 Antibody


title: testis, d26_wt_rep2

extract_protocol:
Spermatogenic cell fraction purification was performed as previously described (Shiota et al. 2018).
For each sample, one µg of RNA (RIN = 10) was used for library preparation with TruSeq Stranded Total RNA (RiboZero Human/Mouse/Rat) Library Prep (Illumina, Cat#RS-122-2201) according to the manufacturer’s instructions. Each library was quantified on Qubit with the Qubit® dsDNA HS Assay Kit (Life Technologies) and the size distribution was examined on the Fragment Analyzer with High Sensitivity NGS Fragment Analysis kit (Agilent).
The libraries were then sequenced on the Illumina NextSeq 500 (paired-end 75) at the TGML Platform of Aix-Marseille University (France).

value: testis

value: wt

tag: day

tag: replicate


title: AA263-3

description:
Library name: Sample 6
AA263


title: testis, d26_wt_rep1


title: testis, d26_ko_rep2

value: ko


title: testis, d24_wt_rep2


title: testis, d26_ko_rep1


title: AA263yne-1

description:
Library name: Sample 7
AA263yne


title: testis, d24_wt_rep1


title: Gene Expression Library

description:
Library name: SLC_184_GELib
GEX (3' mRNA) library: Read1 contains 10x cell barcode and UMI, Read2 contains transcript

data_processing:
CITE-seq and Multiome were processed with CellRanger v9.0.0 using 10X Genomics Cloud Analysis
Assembly: Mouse GRCm39 2024-A
Supplementary files format and content: CellRanger Output File: filtered_feature_bc_matrix.tar.gz


title: testis, d22_wt_rep4


title: s07_T_mm

description: Library name: s07_T_mm

data_processing:
Timming. The raw fastq files were processed by 5 prime trimming, keeping 30bp-length fragments, using fastx_trimmer [http://hannonlab.cshl.edu/fastx_toolkit/. Accessed 28 Feb. 2022.], with options -l 30 -Q33.
Alignment. The trimmed fastq files were aligned on the UCSC Mus_musculus mm10 genome using the Bowtie2 aligner (Langmead and Salzberg 2012) [PMID: 22388286], with options –end-to-end, –no-mixed, –no-discordant.
big wig files (.bw) containing normalized integrated aligned read count signals.
Assembly: UCSC Mus_musculus mm10 genome
Supplementary files format and content: big wig files (.bw) containing normalized integrated aligned read count signals.

extract_protocol:
Round and total germ cell fractions were washed in cold PBS and lysed on ice using Lysis Buffer (0.06 M KCl, 0.015 M NaCl, 0.015 M Tris-HCl pH 7.4, 0.34 M sucrose, 2 mM EDTA, 0.5 mM EGTA, 0.65 mM spermidine, 1 mM DTT, 0.03% Triton X-100, 1% glycerol, and 1X Complete Protease Inhibitor). Lysates were centrifuged at 225g for 5 minutes at 4°C, and the nuclei pellet was resuspended in Nuclei Buffer (same composition as Lysis Buffer without Triton X-100, EDTA, or EGTA).
Nuclei were processed using the ATAC-seq Kit (Active Motif, Catalog No. 53150) following the manufacturer’s protocol. Libraries were purified with AMPure XP beads (Beckman Coulter, Catalog No. A63881) using double size selection (100–800 bp). Quality control was performed with Qubit and Fragment Analyzer, and paired-end sequencing was conducted on a NextSeq 2000 with a 200-cycle P2 flow cell.

value: total testis

value: Atad2 -/-


title: AA263-1

description:
Library name: Sample 4
AA263


title: s12_R_mm

description: Library name: s12_R_mm

value: round spermatids


title: s02_R_pp

description: Library name: s02_R_pp

value: Atad2 +/+


title: s06_T_pp

description: Library name: s06_T_pp


title: s01_R_pp

description: Library name: s01_R_pp


title: s04_R_pp

description: Library name: s04_R_pp


title: s10_R_mm

description: Library name: s10_R_mm


title: s03_R_pp

description: Library name: s03_R_pp


title: s08_T_mm

description: Library name: s08_T_mm


title: s09_R_mm

description: Library name: s09_R_mm


title: s11_R_mm

description: Library name: s11_R_mm


title: s05_T_pp

description: Library name: s05_T_pp


title: testis, d24_ko_rep1


title: testis, d22_wt_rep3


title: AA263-2

description:
Library name: Sample 5
AA263


title: scTCR-seq of Tet2KO NOD mice set 1

city: Farmington

first: Madhav

last: Kothari

state: CT

address: 10 Discovery Drive

institute: The Jackson Lab

description: Library name: scTCR-seq KO 1

data_processing:
scTCR-seq samples were processed using the "cellranger v7.0.1" vdj function with "refdata-cellranger-vdj-GRCm38-alts-ensembl-7.0.0" as the reference.
Assembly: mm10
Supplementary files format and content: contif files is a comma seperated text file containing info from scTCR-seq results
Library strategy: TCR-Seq

molecule: other

source_name: Pancreatic Islet

extract_protocol:
Islets were harvested from mice at 10-13 weeks post BTM. The islets from 4-6 mice per genotype from each experimental condition were pooled and analyzed together. There were 2-3 pools of the mice used for the RNAseq or ATACseq studies. Cells were lysed for between 3-5 minutes depending on the sample [SC2200283/84 were 3 min, SC2200373-76 were 5 min] according to the 10x Genomics demonstrated protocol CG000169 (Rev D). Nuclei were washed and suspended in PBS containing 0.04% BSA and immediately processed as follows. Nuclei quality was assessed via brightfield imaging and counted via Trypan Blue and a Countess II automated cell counter (ThermoFisher), and up to 12,000 nuclei were loaded onto one lane of a 10x Genomics Chromium chip H.
Single nuclei capture, barcoding and library preparation were performed using the 10x Genomics Chromium X platform and according to the manufacturer’s protocol (#CG000209 Rev F).  Libraries were checked for quality on Agilent 4200 Tapestation, quantified by KAPA qPCR, and pooled at 12.5% of an Illumina NovaSeq 6000 S4 100 cycle flow cell lane, targeting 6,000 barcoded nuclei with an average sequencing depth of 50,000 read pairs per nucleus. Illumina base call files for all libraries were demultiplexed and converted to FASTQ files using Illumina bcl2fastq 2.20.0.422.  A filtered digital gene expression matrix was generated for each gene expression library against the 10x Genomics mm10 Multiome reference build (version 2020-A, Assembly: GRCm38, release 98; Annotations: Gencode vM23; Motifs:  JASPAR2018 CORE) using 10X Genomics CellRanger-ATAC count version 2.1.0 for all samples.

treatment_protocol: Female NOD mice for backcross or used as donors for bone marrow transplant were all obtained from The Jackson Laboratory. Tet2−/−(Strain #:023359) male breeders under B6 background were originally purchased from The Jackson Laboratory and backcrossed with NOD females for over 14 generations for the study. All animals were maintained under pathogen-free conditions. All protocols were approved by the Yale Institutional Animal Care and Use Committee. Animals were housed under the following facility conditions: Temperatures: 21–23 °C; Humidity:50–60%. Lighting: 12:12 (i.e., 12 h of light from 7 a.m.–7 p.m. then 12 h of dark from 7 p.m.–7 a.m.).

value: Pancreatic Islet

value: KO


title: testis, d24_ko_rep2


title: scTCR-seq of Tet2KO NOD mice set 2

description: Library name: scTCR-seq KO 2


title: testis, d22_wt_rep1


title: testis, d22_ko_rep4


title: testis, d22_wt_rep2


title: Veh-3

description:
Library name: Sample 3
Veh

value: 6h DMSO


title: Veh-1

description:
Library name: Sample 1
Veh


title: testis, d20_wt_rep2


title: Veh-2

description:
Library name: Sample 2
Veh


title: testis, d20_wt_rep3


title: testis, d22_ko_rep3


title: Npc1-/-, Hippocampus, DIP, rep3

city: Rome

first: Sabrina

last: Tait

state: Italy

address: Viale Regina Elena 299

department: Dpt. Infectious Diseases

country: Italy

institute: Istituto Superiore di Sanità

description: Library name: hippo13_KO-D

data_processing:
quality check with FastQC v0.11.9
Trimming of low-quality sequences with Trimmomatic v0.39
Mapping versus the mouse genome (Ensemble GRCh39) using STAR v2.7.9a
Read count extraction with featureCounts v2.0.3
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: Hippocampus 13

growth_protocol: Npc1-/- and Npc1+/+ littermates were housed separately 2-4 per cage with corn cob as bedding material, which was changed twice weekly. A cardboard mouse house was inserted inside each cage as an environmental enrichment. They were housed under standard laboratory conditions (25 ± 2°C, 45%–50% humidity) with a 12 h light–dark cycle (lights on 7:00 am) and free access to water and food

extract_protocol:
Total RNA was extracted from hippocampi and cerebella of mice (N=4/group) at PND 63-65 using the RNeasy Lipid Tissue Mini Kit (#74804, QIAGEN) following manufacture’s instruction. DNase was also included to remove genomic DNA, and RNA quality and purity was assessed for each sample with Agilent 2100 Bioanalyzer.
The selected RNA samples were quantified using Qubit™ RNA HS Assay Kit and 10 ng were reverse-transcribed using SuperScript™ VILO™ cDNA+ Synthesis Kit (ThermoFisher Scientific). Transcriptome analysis was performed using the Ion S5™ System and the Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit (ThermoFisher Scientific) that provides gene-level expression information from a single multiplexed panel targeting over 20,000 genes.

treatment_protocol: Mice receiving DIP or vehicle (PBS:PEG400) by intraperitoneal injection every day for 5 days/week at the dose of 30mg/kg in a sterile PBS:PEG400 solution starting from post-natal day 28 (PND28) until PND63-65

value: BALB/cNctr-Npc1m1N/J (JAX#3092)

value: Hippocampus 13

tag: age

value: Female

value: Dipyridamole 30mg/kg/day

value: Ion code #129


title: testis, d22_ko_rep2


title: testis, d20_wt_rep4


title: Npc1-/-, Hippocampus, DIP, rep4

description: Library name: hippo29_KO-D

source_name: Hippocampus 29

value: Hippocampus 29

value: Ion code #124


title: testis, d20_wt_rep1

value: testis


title: Npc1-/-, Hippocampus, DIP, rep2

description: Library name: hippo12_KO-D

source_name: Hippocampus 12

value: Hippocampus 12

value: Male

value: Ion code #128


title: testis, d20_ko_rep3

value: ko


title: HepG2_si-CPSF6_6h_rep1

city: Guangzhou

first: Keren

last: Zhou

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

country: China

institute: Sun Yat-sen University

data_processing:
For RNA-seq, we mapped reads to the human hg38 genome by STAR with Genecode V37 annotations
We then quantified the raw read counts of gene/transcripts by RSEM, removed the hidden and unwanted batch effects by RUVSeq and then convert gene read counts to transcript per million (TPM) for downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix tables with normalized gene counts and TPM for every gene and every sample

growth_protocol: HepG2 cells were transfected with CPSF6 siRNAs which were purchased from RiboBio (China) into 12 well plates and cultured for 48h to get 80% confluence.

extract_protocol: ERCC spike-in RNA (Thermo Fisher) were added into 5μg total RNA following with construction for mRNA sequencing libraries with NEBNext Ultra Directional RNA library Prep Kit

treatment_protocol: Then cells were treated with 5ug/ml Actinomycin D (Selleck, America) and harvested at 0h, 3h and 6h with Trizol.

tag: time point


title: testis, d20_ko_rep4


title: Npc1-/-, Hippocampus, DIP, rep1

description: Library name: hippo10_KO-D

source_name: Hippocampus 10

value: Hippocampus 10

value: Ion code #126


title: testis, d20_ko_rep2


title: testis, d22_ko_rep1


title: testis, d20_ko_rep1


title: Npc1-/-, Cerebellum, DIP, rep3

description: Library name: cerv13_KO-D

source_name: Cerebellum 13

value: Cerebellum 13

value: Ion code #121


title: Npc1-/-, Cerebellum, DIP, rep4

description: Library name: cerv29_KO-D

source_name: Cerebellum 29

value: Cerebellum 29


title: HepG2_si-CPSF6_0h_rep2


title: HepG2_si-CPSF6_6h_rep2


title: HepG2_si-NC_6h_rep1

value: si-NC


title: HepG2_si-CPSF6_3h_rep1


title: HepG2_si-CPSF6_3h_rep2


title: HepG2_si-CPSF6_0h_rep1


title: HepG2_si-NC_6h_rep2


title: Npc1-/-, Cerebellum, DIP, rep1

description: Library name: cerv10_KO-D

source_name: Cerebellum 10

value: BALB/cNctr-Npc1m1N/J (JAX#3092)

value: Cerebellum 10

value: Ion code #118


title: pan02-chi-25-LGM27199_L3_1.fq.gz

city: Suzhou

first: Mengyao

last: Wu

state: Jiangsu

address: No.899 Pinghai Road

institute: The First Affiliated Hospital of Soochow University

description: Library name: Sample 3

data_processing:
The raw sequencing data was processed by Fastp to trim primer sequence and low quality bases. And then cellranger was used to process sequence data and aligned to human GRCh38 in order to obtain gene expression matrix. We used Seurat (version 4.0.0) to filter low quality cells, cells with number of detected genes <200 or >5000 were omitted, and use MAD variance normal to remove cells affected by mitochondrial genes. After quality control and filtering, library-size normalization to each cell was performed by NormalizeData of Seurat. The variable genes were calculated by FindVariableGenes. Then, all libraries were combined together using FindIntegrationAnchors and IntegrateData with default parameters, and using ScaleData to regress out the variability of the numbers of UMIs. Then the RunPCA and RunUMAP was used to reduce dimensions. FindClusters was used to cluster cells using the 20 dims at a resolution of 0.8.
Assembly: mouse mm10
Supplementary files format and content: Cell Ranger software output H5 file

source_name: subcutaneous pancreatic cancer

extract_protocol:
The tissue is washed with preconfigured PBS solution, sterilized mechanically spliced, and digested with preconfigured digestion solution for 30-60 minutes (depending on the type of tissue). After digestion is terminated, centrifugation, supernatant removal, and resuspension are performed. The suspension is collected by centrifugation through a 70 nm sieve and subjected to cell lysis red (depending on the type of tissue, lysis red treatment is selected). After lysis red is completed, centrifugation and resuspension are performed through a 40 nm sieve. Finally, counting cell number and viability to observe and judge whether the cell suspension was qualified. After collection of cells, centrifuge at a speed not exceeding 400rcf (adjust the speed and centrifugation time according to the cell types). Carefully discard the supernatant and retain the cell precipitation. The cell pellet was resuspended by 1mL 1x PBS containing 0.04% BSA and the washing procedure was repeated twice. After washing, appropriate volume PBS was added to the cell precipitation to obtain single-cell dispersion suspension with a concentration close to the goal number. A type of wide-bore pipette tip was used in cell resuspension for a lower cell damage. If necessary, cell filter should be applied to remove cell debris and clusters (eg.30µm MACS SmartStrainers and 40µm FlowmiTM Cell Strainer). Automatic cytometry was used to determine the cell concentration. And the sample volume was calculated based on the optimal cell sampling concentration supplied by 10X official website and the target capture number. If the calculated concentration is too high, adjust the liquid volume to the appropriate concentration and repeat counting once more. Once the desired cell suspension was obtained, immediately place the samples on ice for subsequent GEMs preparation and reverse transcription.
After cell counts and viability were determined, cell suspensions were adjusted to a concentration of 1,000 cells/ml in PBS supplemented with 0.04% BSA. The 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 was used according to the manufacturer's instructions. Agilent 4200 TapeStation was used to detect the fragment length distribution of the library. Also, Qubit HS DNA Kit was used to accurately quantify the effective concentration of the library ( > 10nmol/L).The qualified library was sequenced on the DNBSEQ T7 platform at the illumina NovaSeq 6000 with PE150 read length.

value: subcutaneous pancreatic cancer

value: chidamide at 25 mg/mL


title: Splenic CD45+ immune cells from TPflox/flox mice, CLP, 3 days, rep1

city: Tianjin

first: Ying

last: Yu

address: 22 Qixiangtai Road, Heping District

institute: Tianjin Medical University

description: Library name: TP_FF_1

data_processing:
Raw sequencing data were processed using the Cell Ranger pipeline (v7.2.0, 10X Genomics) for alignment, barcode assignment, and UMI quantification. Low-quality cells were removed based on the following criteria: retained cells expressing between 200 and 7,500 genes; cells with >20% mitochondrial gene expression; and doublets were identified and filtered using the DoubletFinder package.
Data were normalized using the LogNormalize function in the Seurat (v4.4.0) package. PCA was conducted using the RunPCA function, and batch effects were corrected using the Harmony (v1.2.0) package. Cells were clustered based on the top 20 PCs and visualized using t-SNE via the RunTSNE, FindNeighbors, and FindClusters functions in Seurat.
Differentially expressed genes (DEGs) were identified using FindMarker in Seurat software. The selection criteria for significant DEGs were: Adjusted p-value < 0.05; Absolute log2 fold change (|log2FC|) ≥ 0.5.
For functional enrichment analysis, gene ontology analysis was conducted using the enrichGO function from the clusterProfiler package (v4.6.2), focusing on biological processes enriched in significantly upregulated genes.
Assembly: GRCm39 mouse reference genome
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: spleen

extract_protocol:
Splenic CD45+ immune cells from TPflox/flox and TPflox/floxCD11cCre mice subjected to cecal ligation and puncture (CLP) were sorted for droplet-based single-cell RNA-seq (10x Genomics platform).
Single-cell RNA-seq libraries were generated using the Chromium Controller and the Chromium NextGEM Single Cell 3’ HT Kit v3.

value: spleen

value: CD45+ immune cells

value: TP flox/flox


title: chi_0_LGM27197_L3_1.fq.gz

description: Library name: Sample 1

value: chidamide at 0mg/mL


title: Splenic CD45+ immune cells from TPflox/floxCD11cCre mice, CLP, 3 days, rep1

description: Library name: TP_FF_CD11cCre_1

value: TP flox/flox; CD11c Cre


title: Splenic CD45+ immune cells from TPflox/flox mice, CLP, 3 days, rep2

description: Library name: TP_FF_2


title: pan02_chi_12_5_LGM27198_L3_1.fq.gz

description: Library name: Sample 2

value: chidamide at 12.5mg/mL


title: HepG2_si-NC_3h_rep2


title: Npc1-/-, Hippocampus, vehicle, rep4

description: Library name: hippo21_KO

source_name: Hippocampus 21

value: Hippocampus 21

value: Male

value: Veh

value: Ion code #131


title: HepG2_si-NC_0h_rep2


title: Splenic CD45+ immune cells from TPflox/floxCD11cCre mice, CLP, 3 days, rep2

description: Library name: TP_FF_CD11cCre_2


title: HepG2_si-NC_0h_rep1


title: Kidney cells, Dicer1 control mice, FACS-sorted, 13 days after tamoxifen treatment.

city: Vancouver

first: David

last: Huntsman

state: BC

address: 675 W 10th Ave

department: Molecular Oncology

institute: BC Cancer Research Centre

description:
Library name: HDT1106_1107_1108
10X Genomics

data_processing:
Raw fastq files were processed together for each sample, using the 10X Cell Ranger count tool, v7.10.
Assembly: Mouse, mm10 plus tdTomato
Supplementary files format and content: Tab-separate values files of genes and barcodes, and matrix files.

source_name: Kidney

extract_protocol:
Tumour and normal kidney tissues were minced to 1mm3 with forceps and incubated at 37 degrees C with Stemcell 10X Collagenase/hyaluronidase in DMEM (10X Genomics, C#07912) in HBSS for 30 minutes. The minced tissues were subsequently incubated in Trypsin-EDTA (0.25%) for 5 min at 37 degrees C. Cells were then filtered through a 70 μm cell strainer. Live cells were enriched with Miltenyi Biotec Dead Cell Removal Kit. Mesenchymal cell populations were then isolated by FACS sorting with tdTomato positive enrichment and antibody depletion of Epcam, CD45,493 CD31, CD11b and F4/80.
Libraries were prepared according to the 10X Genomics Chromium Single Cell Universal 3‘ Gene Expression kit protocol.

treatment_protocol: Mice were injected intraperitoneally with tamoxifen (dose: 1 mg/kg, 5 consecutive days for mice > 3 weeks old; 2 mg/kg, 3 consecutive days for mice <2 weeks old). The cohort received a tamoxifen injection within first 2 months of birth (<=61 days).

value: Kidney

value: Hic1+ cells

value: Dicer1 control

value: tamoxifen

tag: days post-injection

value: 1 month


title: HepG2_si-NC_3h_rep1

value: si-NC


title: Npc1-/-, Cerebellum, DIP, rep2

description: Library name: cerv12_KO-D

source_name: Cerebellum 12

value: BALB/cNctr-Npc1m1N/J (JAX#3092)

tag: tissue

value: Cerebellum 12

value: Dipyridamole 30mg/kg/day

value: Ion code #120


title: Kidney cells, Dicer1 control mice, FACS-sorted, 43 days after tamoxifen treatment.

description:
Library name: HDT967_968
10X Genomics


title: scTCR-seq of NOD mice set 1

description: Library name: scTCR-seq WT 1

value: Pancreatic Islet

value: WT


title: snATAC-seq of Tet2KO NOD mice set 1

description: Library name: snATAC-seq KO 1

library_source: genomic single cell

data_processing:
snATAC-seq reads (3 WT, 3 KO, Supplemental Table 2) were aligned to the mm10 genome build using the "cellranger-atac v2.1.0" count function. Aligned profiles were further processed and visualized using the "Signac v1.7.0" package in R. Doublets were identified by "Amulet v1" and removed from further consideration. snATAC-seq profiles were filtered based on the following criteria: number of fragments per peak < 2500 or > 25000, percent of reads in peaks < 30%, nucleosome signal > 1.5, TSS enrichment < 1, and blacklist ratio > 0.05.
Assembly: mm10
Supplementary files format and content: .h5 files contain the counts from the snATAC-seq and scRNA-seq file outputs from cellranger

value: KO


title: 5' scRNA-seq of NOD mice set 1

description: Library name: scRNA-seq 5_ WT 1

data_processing:
scRNA-seq reads (10X Genomics) were aligned to the mm10 genome build using the "cellranger v7.0.1" count function. The data was cleaned by removing ambient RNA using "SoupX v1.6.2" with the contamination factor set to 20%. Doublets were identified and removed using "Scrublet v0.2.3". scRNA-seq profiles with 250-4000 features and <25% mitochondrial percentage were retained for further analysis. The resulting counts matrix was processed using "Seurat v4.3.0.1".
Assembly: mm10
Supplementary files format and content: .h5 files contain the counts from the snATAC-seq and scRNA-seq file outputs from cellranger


title: snATAC-seq of NOD mice set 1

description: Library name: snATAC-seq WT 1


title: 5' scRNA-seq of NOD mice set 2

description: Library name: scRNA-seq 5_ WT 2


title: 3' scRNA-seq of NOD mice set 1

description: Library name: scRNA-seq 3_ WT


title: scTCR-seq of NOD mice set 2

description: Library name: scTCR-seq WT 2


title: snATAC-seq of NOD mice set 3

description: Library name: snATAC-seq WT 3


title: 5' scRNA-seq of Tet2 KO NOD mice set 2

description: Library name: scRNA-seq 5_ KO 2


title: snATAC-seq of NOD mice set 2

description: Library name: snATAC-seq WT 2


title: 3' scRNA-seq of Tet2 KO NOD mice set 1

description: Library name: scRNA-seq 3_ KO


title: Npc1-/-, Hippocampus, vehicle, rep2

description: Library name: hippo11_KO

source_name: Hippocampus 11

value: Hippocampus 11

tag: Sex

value: Ion code #127


title: snATAC-seq of Tet2KO NOD mice set 2

description: Library name: snATAC-seq KO 2


title: 5' scRNA-seq of Tet2 KO NOD mice set 1

description: Library name: scRNA-seq 5_ KO 1


title: Renal tumor cells, Dicer1 mutant mouse, FACS-sorted, 444 days after tamoxifen treatment.

description:
Library name: HDT339
10X Genomics

source_name: Renal tumor

value: Renal tumor

value: Dicer1 -/D1693N

value: 15 months


title: Kidney cells, Dicer1 control mice, FACS-sorted, 190 days after tamoxifen treatment.

description:
Library name: HDT789_799
10X Genomics

value: Kidney

value: Hic1+ cells

value: 6 months


title: wild type mice 7 day after born rep1

city: Yinchuan

first: Xin

last: Qian

state: Ningxia

address: 804 Shengli Street

department: Department of Neurosurgery

institute: General Hospital of Ningxia Medical University

description: Library name: WTP7_1

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression AnalysisExpression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene AnnotationTo take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cerebral cortex

extract_protocol:
1. Experimental Procedures1.1 Sample Lysis1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107).1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min.1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column.1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification.1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification.1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate.1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate.1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube.1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min.1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA.1.3 RNA Purification1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting.1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow.1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate.1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube.1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min.1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: cerebral cortex

value: wild type mice 7 day after born rep1


title: Renal tumor cells, Dicer1 mutant mouse, FACS-sorted, 272 days after tamoxifen treatment.

description:
Library name: HDT546
10X Genomics

value: tamoxifen

value: 9 months


title: snATAC-seq of Tet2KO NOD mice set 3

description: Library name: snATAC-seq KO 3


title: wild type mice 7 day after born rep3

description: Library name: WTP7_3

value: wild type mice 7 day after born rep3


title: Npc1-/-, Hippocampus, vehicle, rep3

description: Library name: hippo14_KO

source_name: Hippocampus 14

tag: strain

value: BALB/cNctr-Npc1m1N/J (JAX#3092)

value: Hippocampus 14

value: Female

value: Veh

value: Ion code #130


title: Npc1-/-, Hippocampus, vehicle, rep1

description: Library name: hippo9_KO

source_name: Hippocampus 9

value: Hippocampus 9

value: Male

tag: treatment

value: Ion code #125


title: Npc1+/+, Hippocampus, vehicle, rep4

description: Library name: hippo4_WT

source_name: Hippocampus 4

value: Hippocampus 4

value: Ion code #112


title: Npc1-/-, Cerebellum, vehicle, rep2

description: Library name: cerv11_KO

source_name: Cerebellum 11

value: Cerebellum 11

value: Ion code #119


title: wild type mice 30 day after born rep3

description: Library name: WTP30_3

value: cerebral cortex

value: wild type mice 30 day after born rep3


title: wild type mice 30 day after born rep2

description: Library name: WTP30_2

value: wild type mice 30 day after born rep2


title: Npc1+/+, Hippocampus, vehicle, rep3

description: Library name: hippo3_WT

source_name: Hippocampus 3

value: Hippocampus 3

value: Ion code #110


title: Ndufs2-KO-3

city: Chicago

first: Joseph

last: Bass

state: IL

address: 303 E Superior St, Lurie 7-220

institute: Northwestern University

data_processing:
Samples aligned to mm39 using STAR
Gene Counts obtained using RSEM
Counts Normalized using DESeq2
Assembly: mm39
Supplementary files format and content: DESeq2 Normalized Counts for all samples in this study

source_name: gonadal white adipose tissue

extract_protocol:
Fresh gonadal white adipose tissue was minced in digestion buffer (2.5 units/ml collagenase D, 2.4 units/ml Dispase II, 10 mM CaCl2 in PBS) followed by incubation in a shaking water bath at 37C. The homogenate was then filtered through a 100 um cell strainer, followed by centrifugation at 600g for 5 minutes. The floating adipocyte fraction was isolated with a 1 mL pipette, washed with PBS, and then added to Trizol followed by RNA isolation using the Qiagen RNeasy mini kit.
Libraries were constructed from 250 ng of RNA using the NEBNext RNA Ultra Directional library prep kit with poly(A) enrichment. Average library size and concentration were determined by Bioanalyzer and qPCR (NEBNext Library Quant kit)

value: gonadal white adipose tissue

value: 3 months


title: MSI2-KO + ASXL1 edited, replicate 1

city: Boston

first: Gaurav

last: Agarwal

state: MA

address: 1 Blackfan Circle

department: Division of Hematology/Oncology

institute: Boston Children's Hospital

description:
Library name: KO-ASXL1-rep1
Genewiz Ultra-Low Input RNA-Seq

data_processing:
Salmon (v1.5.2) was used to align reads to the reference transcriptome (GRCh38, Ensembl v104), to quantify gene expression levels.
Assembly: GRCh38
Supplementary files format and content: Tab-separated file containing transcript-level expression quantification (output by Salmon v1.5.2 package). Columns include: Name (transcript ID), Length (transcript length), EffectiveLength (bias-corrected transcript length), TPM (Transcripts Per Million, normalized expression), and NumReads (estimated number of mapped reads).

source_name: Primary Human HSPC

growth_protocol: Serum-free HSPC expansion media

extract_protocol:
6 days after editing, CD34+CD45RA-CD90+ HSPCs were sorted, and total RNA was extracted (using Norgen Total RNA Purification Micro Kit).
Samples were send to Genewiz for Processing. RNA sequencing (RNA-seq) was carried out by Genewiz using an ultra-low input RNA-seq package. Sequencing was performed with an Illumina HiSeq, with ~30M reads per sample.

treatment_protocol: Primary human CD34+ HSPCs were edited (on day 1 of culture) using CRISPR/Cas9 at dual loci: i) AAVS1 + AAVS1-guide2; ii) AAVS1 + ASXL1; iii) ENH-1 microdeletion + ASXL1; iv) MSI2-KO + ASXL1.

value: Primary Human HSPC

value: CD34+CD45RA-CD90+ HSPCs

value: CRISPR/Cas9 editing at MSI2-knockout and ASXL1-exon12


title: Npc1+/+, Hippocampus, vehicle, rep2

description: Library name: hippo2_WT

source_name: Hippocampus 2

value: BALB/cNctr-Npc1m1N/J (JAX#3092)

value: Hippocampus 2

value: Female

value: Veh

value: Ion code #104


title: Bmal1-KO-3


title: Renal tumor cells, Dicer1 mutant mouse, FACS-sorted, 384 days after tamoxifen treatment.

description:
Library name: HDT375
10X Genomics

value: Renal tumor

value: Hic1+ cells

value: Dicer1 -/D1693N

value: tamoxifen

value: 13 months


title: wild type mice 30 day after born rep1

description: Library name: WTP30_1

value: cerebral cortex

value: wild type mice 30 day after born rep1


title: Renal tumor cells, Dicer1 mutant mouse, FACS-sorted, 238 days after tamoxifen treatment.

description:
Library name: HDT563
10X Genomics

value: 8 months


title: MSI2-KO + ASXL1 edited, replicate 2

description:
Library name: KO-ASXL1-rep2
Genewiz Ultra-Low Input RNA-Seq


title: wild type mice 7 day after born rep2

description: Library name: WTP7_2

value: wild type mice 7 day after born rep2


title: Npc1-/-, Cerebellum, vehicle, rep4

description: Library name: cerv21_KO

source_name: Cerebellum 21

value: Cerebellum 21

value: Male

value: Ion code #123


title: wild type mice 1 day after born rep2

description: Library name: WTP1_2

value: wild type mice 1 day after born rep2


title: Renal tumor cells, Dicer1 mutant mouse, FACS-sorted, 391 days after tamoxifen treatment.

description:
Library name: HDT340
10X Genomics


title: Bmal1-KO-4

value: gonadal white adipose tissue

value: 3 months


title: Npc1-/-, Cerebellum, vehicle, rep3

description: Library name: cerv14_KO

source_name: Cerebellum 14

value: BALB/cNctr-Npc1m1N/J (JAX#3092)

value: Cerebellum 14

value: Female

value: Veh

value: Ion code #122


title: AAVS1 + ASXL1 edited, replicate 2

description:
Library name: AAVS1-ASXL1-rep2
Genewiz Ultra-Low Input RNA-Seq

value: Primary Human HSPC

value: CD34+CD45RA-CD90+ HSPCs

value: CRISPR/Cas9 editing at AAVS1 and ASXL1-exon12


title: Ndufs2-KO-2


title: wild type mice 1 day after born rep3

description: Library name: WTP1_3

value: cerebral cortex

value: wild type mice 1 day after born rep3


title: Alg13 knockout mice 7 day after born rep3

description: Library name: KOP7_3


title: AAVS1 + ASXL1 edited, replicate 1

description:
Library name: AAVS1-ASXL1-rep1
Genewiz Ultra-Low Input RNA-Seq


title: Ndufs2-KO-1


title: ENH-1 microdeletion + ASXL1 edited, replicate 1

description:
Library name: ENH1-ASXL1-rep1
Genewiz Ultra-Low Input RNA-Seq

value: CRISPR/Cas9 editing at ENH-1 microdeletion at MSI2 enhancer and ASXL1-exon12


title: ENH-1 microdeletion + ASXL1 edited, replicate 2

description:
Library name: ENH1-ASXL1-rep2
Genewiz Ultra-Low Input RNA-Seq


title: scRNAseq, HCMV-infected fibroblasts

city: Ulm

first: Thomas

last: Stamminger

address: Albert Einstein Allee 11

country: Germany

institute: Institute of Virology, Ulm University

description:
Library name: Sample 1
10xGenomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mtx

source_name: connetive tissue

extract_protocol:
For single cell RNA sequencing, confluent HFF cells were infected with HCMV in T175 cm2 cell culture flasks. 6 hpi, cells were harvested and washed following instructions of the scRNAseq 10x Genomics Sample Preparation Demonstrated Protocol. From the cell suspension, 10000 live cells were subjected to single cell library preparation with a target cell count of 6000.
Libraries were generated with the 10x Chromium Single Cell 3’ Gene Expression v3 kit (10x Genomics) according to the manufacturer’s instructions.

value: connetive tissue

value: primary human foreskin fibroblasts

value: infected with human cytomegalovirus strain AD169


title: Npc1-/-, Cerebellum, vehicle, rep1

description: Library name: cerv9_KO

source_name: Cerebellum 9

value: Cerebellum 9

value: Male

value: Ion code #117


title: Ndufs2-KO-4

value: gonadal white adipose tissue

value: 3 months


title: Npc1+/+, Hippocampus, vehicle, rep1

description: Library name: hippo1_WT

source_name: Hippocampus 1

value: BALB/cNctr-Npc1m1N/J (JAX#3092)

value: Hippocampus 1

value: Female

value: Ion code #102


title: Npc1+/+, Cerebellum, vehicle, rep1

description: Library name: cerv1_WT

source_name: Cerebellum 1

value: Cerebellum 1

value: Veh

value: Ion code #101


title: Bmal1-KO-2


title: Npc1+/+, Cerebellum, vehicle, rep4

description: Library name: cerv4_WT

source_name: Cerebellum 4

value: Cerebellum 4

value: Ion code #111


title: Bmal1-KO-1


title: Npc1+/+, Cerebellum, vehicle, rep3

description: Library name: cerv3_WT

source_name: Cerebellum 3

value: Cerebellum 3

value: Ion code #109


title: Alg13 knockout mice 30 day after born rep3

description: Library name: KOP30_3

source_name: cerebral cortex

value: cerebral cortex


title: Carya, TP, biol rep4

city: Chengdu

first: Xiaoping

last: Zhang

state: Sichuan

address: Huimin Road, Chengdu, 611130, China

department: College of Resources

institute: Sichuan Agricultural University

description: Library name: C_T4_TP4

data_processing:
Processed with Trimmomatic software to perform the quality control
Clean reads were assembled into expressed sequence tag clusters (contigs) and then de novo assembled into transcript by Trinity (version 2.4) using paired end method
CD-HIT software was used to cluster and remove redundancy to obtain a final set of unigenes.
Assembly: de novo assembled transcripts
Supplementary files format and content: xls files including FPKM values for samples of C. illinoinensis
Supplementary files format and content: xls files including FPKM values for samples of P. armandii

organism: Carya illinoinensis

source_name: Leaf

extract_protocol:
Total RNA  was extracted using TRIzol reagent according to the manufacturer’s protocol.
The libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (NR604-01, Vazyme, China) according to the manufacturer’s instructions.

value: Leaf

tag: time

value: 30 months after inoculation

value: T. panzhihuanense inoculation


title: wild type mice 1 day after born rep1

description: Library name: WTP1_1

value: wild type mice 1 day after born rep1


title: Control-4

value: gonadal white adipose tissue

value: 3 months

value: Wildtype


title: Carya, TP, biol rep3

description: Library name: C_T4_TP3


title: Alg13 knockout mice 7 day after born rep2

description: Library name: KOP7_2


title: Npc1+/+, Cerebellum, vehicle, rep2

description: Library name: cerv2_WT

source_name: Cerebellum 2

value: BALB/cNctr-Npc1m1N/J (JAX#3092)

value: Cerebellum 2

value: Female

value: Ion code #103


title: Control-3


title: AAVS1 + AAVS1-guide2 edited, replicate 2

description:
Library name: AAVS1-g2-rep2
Genewiz Ultra-Low Input RNA-Seq

value: Primary Human HSPC

tag: cell type

value: CD34+CD45RA-CD90+ HSPCs

value: CRISPR/Cas9 editing at AAVS1 and AAVS1-g2


title: Control-2

tag: genotype


title: Carya, TP, biol rep1

description: Library name: C_T4_TP1


title: Alg13 knockout mice 7 day after born rep1

description: Library name: KOP7_1


title: AAVS1 + AAVS1-guide2 edited, replicate 1

description:
Library name: AAVS1-g2-rep1
Genewiz Ultra-Low Input RNA-Seq


title: Alg13 knockout mice 30 day after born rep2

description: Library name: KOP30_2


title: Carya, Ti, biol rep4

description: Library name: C_T4_Ti4

value: T. indicum inoculation


title: hKLF6 RnD Antibody ChIP

city: Cincinnati

first: Artem

last: Barski

state: OH

address: 3333 Burnet Av

department: Allergy

institute: Cincinnati Children's Hospital

description:
Library name: ABSP97
pooled_peaks.bed

data_processing:
Bigwigs: Data analysis of the raw sequencing data from each of the paired-end ChIP-Seq experiments was performed using the "Trim Galore ChIP-Seq pipeline paired-end" (https://github.com/Barski-lab/workflows-datirium/blob/master/workflows/trim-chipseq-pe.cwl) data analysis pipeline on the SciDAP platform (https://www.scidap.com/). The workflow was run with the following parameters: trimmed sequencing adapters, removed PCR duplicates.
Bed: Reads were trimmed from the raw fastq files using TrimGalore v0.6.6. Trimmed fastqs were then aligned using Bowtie2 v2.4.2 (additional params: --very-sensitive --maxins = 2000 --B). Aligned bam files were deduplicated using samtools markdup (additional params: -r) and then indexed with samtools. Finally, peak calling was performed with macs2 v2.1.4 (addional params --nomodel --extsize 147 –q 0.01)
Assembly: GRCh38
Supplementary files format and content: CPM-normalized genome coverage files in bigWig format.
Supplementary files format and content: Bed file containing called peaks based on combined sample.

source_name: Peripheral Blood

growth_protocol: Human CD4+ T cells were enriched from ficoll isolated human PBMC by negative magnetic selection (Invitrogen; 11346D) and plated at 10 million in 1 mL per 6 well flat bottom plate.

extract_protocol:
Cells were spun down at 500 x g for 5 minutes in a refrigerated eppendorf centrifuge and crosslinked at a concentration of 10 million cells per 5 mL in freshly made 1x phosphate buffered saline without magnesium or calcium with formaldehyde-containing buffer (50 mM HEPES-KOH, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 8.8% formaldehyde in 10% FBS RPMI) added at 1/11 ratio to cell suspension. Crosslinking performed by incubating for 3 minutes on ice. After the crosslinking reaction, a 2.5 M glycine solution was added to make a final concentration of 125 mM, which were incubated at room temperature for 5 minutes to stop fixation. Cells were pelleted at 2000 x g for 10 minutes in a refrigerated eppendorf centrifuge, the formaldehyde-glycine supernatant was removed, and the cells were washed (resuspended and then pelleted at 2000 x g for 10 minutes in a refrigerated eppendorf centrifuge) in cold PBS twice. The fixed cell pellets were stored at -80 °C until the ChIPmentation protocol was performed. The fixed cell pellet was resuspended in 5 mL of L1 buffer (50 mM HEPES-KOH, pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 5 mM sodium butyrate and 1:100 dilution of 1 tablet/1 mL protease inhibitor (P8340; Sigma) and rotated at 4 °C for 10 minutes to lyse the cells. The cell solution was centrifuged at 2000 x g for 8 minutes in a refrigerated table-top centrifuge, the supernatant was removed, and the cell pellet was subjected to nuclei isolation from cytoplasm via incubation with 5 mL L2 buffer (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA, 5 mM sodium butyrate, and 1:100 dilution of 1 tablet/mL  protease inhibitor (P8340; Sigma) with rotation for 10 minutes at room temperature (RT). The cell solution was centrifuged at 2000 x g for 8 minutes in a refrigerated table-top centrifuge, the supernatant was removed, and the isolated nuclei pellets were carefully washed twice and resuspended in a 1X Tris-EDTA (TE) + 0.1% NP40 0.1% Triton X100 solution. The cells were sonicated (peak power 175.0, duty factor 10.0, cycle/burst 200) for 300 s in large 1 mL microtubes at 4 °C using a S220 focused ultrasonicator (Covaris) to obtain the 200- to 500-bp fragments of chromatin.
The ChIP procedure was performed by the Diagenode IP-Star Compact automation system.Antibodies against KLF6 (2 µg; 39-6900; Invitrogen or AF3499; R&D systems) were bound to 4.5 uL of Protein G Dynabeads were incubated with 2 µg of chromatin for 1 hour in PBS + 0.04% NP-40 followed by sequential washes of with RIPA-150 buffer 1 (10 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, and 1% Triton X-100 in DI water), RIPA-300 buffer 2 (10 mM Tris-HCl, pH 7.5, 300 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, and 1% Triton X-100 in DI water), LiCl buffer 3 (250 mM LiCl, 0.5% sodium deoxycholate, and 0.5% NP-40 in TE buffer), and Wash buffer 4 (TE + 0.2% Triton X-100). Samples were eluted in 10 mM Tris-HCl containing 0.25 M NaCl to be processed via ChIPmentation. Washed Dynabeads were processed with loaded Tn5 transposase (C01070012; Hologic Diagenode) per an established ChIPmentation protocol to accomplish tagmentation of ChIPed DNA (Schmidl et al., 2015). The tagmented ChIPed DNA were washed with cold 10 mM Tris-HCl and incubated with proteinase K in elution buffer (TE with 250 mM NaCl and 0.3% SDS) for a cycle of 15 minutes at 42 °C, 4 hours at 60 °C, and 10 minutes at 15 °C. Lastly, the tagmented ChIPed DNA was purified from beads using the Qiagen MinElute DNA kit per the manufacturer’s instructions. The library was amplified using a cycle number based on side reaction to stop amplification prior to saturation. The product was cleaned with AMPure beads and the size and distribution were checked on TapeStation (Agilent).

treatment_protocol: CD4+ T cells were stimulated with plate bound anti-CD3 (2 µg/mL BE0001-2; Bio X Cell) and soluble anti-CD28 antibodies (2 µg/mL; BE0248; Bio X Cell) in RPMI containing 10% FBS for 5 hours.

value: Peripheral Blood

value: CD4+ T cells

value: 5h stimulated with aCD3 (plate bound) and aCD28 (soluble)

tag: chip antibody

value: AF3499; R&D systems

tag: chromatin

value: ab ratio:01:01


title: C6_Baseline_Input

city: Cambridge

first: Jason

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

description: Library name: jc6528

data_processing:
Reads were mapped to hg38 using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
Peaks were called with MACS2 version 2.1.1.20160309 (Zhang Y1 at al., 2008) using sequences from the corresponding input as a background control
Peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.  For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Assembly: GRCh38
Supplementary files format and content: bed/text

source_name: breast cancer

extract_protocol:
ChIP-Seq was performed at described in Ross-Innes CS et al. Nature. 2012 and in the materials and methods of Burrell et al. Antibodies used are a 50:50 mixture of Millipore: 06-935, Abcam: ab3575, as validated in Glont et al. PloS One 2019.
DNA was prepared for Illumina sequencing on the HiSeq 4000 using the ThruPLEX DNA-seq kit according to the manufacturer's instructions.

treatment_protocol: samples are either baseline biopsies from untreated patients enrolled in the PIONEER trial, or end of treatment biopsies after 15 days of trial treatment (either letrozole only (Arm A), letrozole + megestrol 40mg (Arm B), or letrozole + megestrol 160mg (Arm C))

value: breast cancer

tag: sample type

value: breast core biopsy

value: Letrozole + Megestrol 160mg

tag: timepoint

value: baseline

value: Input

tag: antibody lot_number


title: NDI1-BMAL1KO_snRNASeq

description: 10X Genomics

data_processing:
The demultiplexing and barcoded processing were performed using Cell Ranger v7.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Reads were aligned to mm39 genome using Cell Ranger v7.2.0 with updated annotations to include Ndi1 transgene
Nuclei were filtered using Seurat (v5) based on the total number of genes and molecules, as well as percent of mitochondrial reads (500 < nFeature_RNA < 6000; 1000 < nCount_RNA < 25000; percent.mt < 15%)
Dimensiionality reduction and cluserting (UMAP) were performed in Seurat v5
Pathway analysis was run using limma and biomaRt (2.28.2)
Assembly: mm39 updated to include Ndi1 gene sequence
Supplementary files format and content: Raw counts produced from Seurat object in R

extract_protocol:
Fresh gonadal WAT was minced in nucleus preparation buffer (NPB; 10 mM HEPES, 1.5 mM MgCl2, 10 mM KCl, 250 mM sucrose, 0.001% NP-40) with 0.2 U/ul Roche Protector RNase inhibitor followed by dounce homogenization. The homogenate was filtered through a 70 mM cell strainer and centrifuged at 1000 xg for 10 minutes at 4°C, then the nuclear pellet was washed once in NPB followed by resuspension in PBS with 1% BSA and 0.2 U/ul Roche Protector RNase inhibitor.
Single-nuclei RNA-seq libraries were prepared using Chromium Next GEM Single Cell 3’ Reagent Kits v.3.1 (10x Genomics) according to the manufacturer's instructions.

value: gonadal white adipose tissue

value: 3 months

value: Bmal1-KO + NDI1 (Adiponectin-Cre;Bmal1-flox;LSL-NDI1)


title: CAR11-3 T cells, GAS-4h

city: Beijing

first: Shuai

last: Huang

address: yangfangdianxi 1

institute: beijingshijiytan hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg18
Supplementary files format and content: counts and normalized counts

source_name: T Lymphocyte

growth_protocol: NT and CAR-T cells were activated and expanded in X-Vivo15 medium supplemented with 5 % GemcellTM Human serum AB, 100 U/L IL-2 and 1 % penicillin-streptomucin (EallBio Life Science）at 37 °C with 0.5 % CO2

extract_protocol:
RNA was harvested using Trizol regent (Ambion). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit (#E7530L, NEB) following the manufacturer protocols.

treatment_protocol: GAS treated CAR11-3 cells for 30 min or 4 h, DMSO as vehicle control.

tag: cell line

value: IL-13Ralpha2-chimeric antigen receptor T cell

value: GAS for 4h


title: Control-1

source_name: gonadal white adipose tissue

value: Wildtype


title: CAR11-3 T cells, GAS-0_5h

value: GAS for 30 min


title: Carya, TP, biol rep2

description: Library name: C_T4_TP2

value: Leaf

value: 30 months after inoculation

value: T. panzhihuanense inoculation


title: Alg13 knockout mice 30 day after born rep1

description: Library name: KOP30_1

value: cerebral cortex

tag: batch


title: WT_snRNASeq

description: 10X Genomics

tag: age


title: Carya, Ti, biol rep2

description: Library name: C_T4_Ti2

value: T. indicum inoculation


title: T23-015_Rucaparib_Low_9

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

description: GeoMX Nanostring

data_processing:
Sequenced data was analysed using the GeoMx NGS pipeline v2.3.3.10. Quality control thresholds: 100,000 raw reads and 50% sequencing saturation.
Quartile3 normalisation was applied across all targets to account for differing ROI size and cellularity which impact transcript abundance.
Data analysis performed wuthin R-environment, and differential gene expression analysed based on Linear Mixed Model. Significant genes defined as FDR<0.05
Assembly: GRCh38
Supplementary files format and content: DCC files produced by GeoMX NGS Pipeline
Library strategy: Spatial Transcriptomics

growth_protocol: PDEs were placed onto inserts (0.4 μm porosity, Millipore PICM01250) within 6-well plates and just submerged in media before acclimatising overnight in complete medium (RPMI 1640, 20% FCS (foetal calf serum), 2 mM sodium pyruvate, 100 U/mL penicillin, 100 μg/mL streptomycin, 2.5 μg/mL insulin) at 37°C, 5% CO2.

extract_protocol:
sample processing step: To aid cryosection, frozen PDEs were embedded in a hydrogel (7.5% hydroxypropyl methylcellulose, 2.5% PVP)60. Polymer blocks were snap-frozen using dry ice-chilled isopropyl alcohol. 10-12 μm serial sections of were cut using a Leica CM3050s cryostat (-17°C), thaw-mounted onto slides (Thermo Fisher, 12-550-15) prior to storage at -80°C.
Adjacent tissue sections to those used for MSI were processed as recommended by Nanostring. In average, 5 high- and 5 low-drug  areas  were selected per sample,  inferred differential drug accumulation according to mass spectrometry imaging data.
PCR amplification/library preparations was carried out according to manufacturer’s instructions. Pooled libraries were purified using AMPure XP beads (Beckman Coulter), and final library quality and quantity assessed using the Agilent 2100 High Sensitivity DNA, and Qubit High-Sensitivity DNA assays. Sequencing was performed using the Illumina NextSeq2000 platform (Paired End 27bp + dual 8bp indexing).

treatment_protocol: Explants were treated with Niraparib, Olaparib and Rucaparib at 20 μM in complete media or with 0.1% DMSO as vehicle. PDEs were incubated with drug (37°C, 5% CO2) for 24 hours.

value: Cancer

tag: patient id

tag: drug treatment

value: Rucaparib

tag: absorbtion

value: Low


title: Alg13 knockout mice 1 day after born rep3

description: Library name: KOP1_3

tag: tissue


title: hKLF6 Invitrogen Antibody ChIP

description:
Library name: ABSP96
pooled_peaks.bed

value: Peripheral Blood

value: CD4+ T cells

value: 5h stimulated with aCD3 (plate bound) and aCD28 (soluble)

value: 39-6900; Invitrogen

value: ab ratio:01:01


title: CAR11-3 T cells, DMSO-0_5h

value: IL-13Ralpha2-chimeric antigen receptor T cell

value: NT, 0h


title: CAR11-3 T cells, DMSO-4h

value: NT, 4h


title: BMAL1KO_snRNASeq

description: 10X Genomics

value: gonadal white adipose tissue

value: 3 months

tag: strain

value: Bmal1-KO (Adiponectin-Cre;Bmal1-flox)


title: C6_EOT_Input

description: Library name: jc6529

value: breast cancer

value: breast core biopsy

tag: treatment

value: Letrozole + Megestrol 160mg

value: end of treatment

value: Input


title: Carya, Ti, biol rep3

description: Library name: C_T4_Ti3

value: Leaf

tag: time

value: 30 months after inoculation

value: T. indicum inoculation


title: Alg13 knockout mice 1 day after born rep2

description: Library name: KOP1_2

value: cerebral cortex


title: Alg13 knockout mice 1 day after born rep1

description: Library name: KOP1_1


title: T23-015_Rucaparib_Low_7

description: GeoMX Nanostring

tag: cell type

value: Cancer

value: Rucaparib

value: Low


title: C5_EOT_Input

description: Library name: jc6284


title: C6_EOT_ER

description: Library name: jc6523

value: Millipore:06-935, Abcam:ab3575


title: Foxl1KO-heterozygous rep6

city: Philadelphia

first: Klaus

last: Kaestner

state: PA

address: 3400 Civic Center Blvd

department: Perelman School of Medicine

institute: University of Pennsylvania

description:
Library name: Sample_6
Proximal half of E15.5 small intestine from Foxl1-CreERT2-tdTomato heterozygous mouse (control)

data_processing:
Raw FASTQ files from 10X were processed with CellRanger 7.0.0 using mm10 as the reference genome
Assembly: mm10
Supplementary files format and content: TAR-gzipped folder with filtered CellRanger output: the cell-gene read counts matrix

extract_protocol:
Proximal half of the embryonic small intestine (E15.5) was dissected, minced, and digested enzymatically using collagenase type II and DNase I to obtain single-cell suspensions. Cells were filtered, resuspended in PBS with 0.05% BSA, and live cells were enriched by FACS sorting. Viability and concentration were assessed using Trypan blue staining. The extracted single-cell suspension was immediately processed for library construction.
Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3' Library & Gel Bead Kit v2 according to the manufacturer’s protocol. Approximately 5,000 cells per sample were loaded onto a 10x Genomics Chromium Single Cell Controller. The resulting cDNA libraries were quantified and quality-checked using an Agilent 2100 Bioanalyzer and Qubit Fluorometer, then sequenced on an Illumina NovaSeq 6000 instrument.

value: Foxl1-positive mesenchymal telocyte progenitors, mesenchymal stromal cells, intestinal epithelial cells, immune cells, endothelial cells, and other intestinal cell types.

tag: genotype

value: Foxl1-tdTomat-P2A-CreERT2 Heterozygote


title: Foxl1KO-homozygous rep3

description:
Library name: Sample_3
Proximal half of E15.5 small intestine from Foxl1-CreERT2-tdTomato homozygous null mouse

source_name: Proximal half of the embryonic small intestine (E15.5)

value: Foxl1-tdTomat-P2A-CreERT2 Homozygous


title: T23-015_Rucaparib_Low_6

description: GeoMX Nanostring


title: Carya, CK, biol rep3

description: Library name: C_T4_CK3

value: control


title: T23-015_Rucaparib_High_5

description: GeoMX Nanostring

value: High


title: Carya, CK, biol rep4

description: Library name: C_T4_CK4


title: T23-015_Rucaparib_Low_8

description: GeoMX Nanostring


title: Carya, Ti, biol rep1

description: Library name: C_T4_Ti1


title: Foxl1KO-heterozygous rep4

description:
Library name: Sample_4
Proximal half of E15.5 small intestine from Foxl1-CreERT2-tdTomato heterozygous mouse (control)

value: Proximal half of the embryonic small intestine (E15.5)


title: Foxl1KO-homozygous rep1

description:
Library name: Sample_1
Proximal half of E15.5 small intestine from Foxl1-CreERT2-tdTomato homozygous null mouse


title: C6_Baseline_ER

last: Carroll

description: Library name: jc6522

value: breast cancer

value: breast core biopsy

value: Letrozole + Megestrol 160mg

value: baseline

tag: chip antibody


title: C5_EOT_ER

description: Library name: jc6277

value: end of treatment


title: T23-015_Rucaparib_High_4

description: GeoMX Nanostring


title: 20842x3 DEN CDHFD 36 week old Female miR146-/- Ccl5-/- Liver Immune Cells

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah

description: Library name: 20842X3

data_processing:
The Fastq files were aligned to the refdata-gex-mm10-2020-A mouse reference dataset from 10x Genomics.
Cellranger count 7.0.1 was used to create quality control metrics, Loupe Browser files and filtered gene barcode matrices.
Assembly: mm10
Supplementary files format and content: Filtered feature barcode matrices in MEX format

source_name: Liver miR146-/- Ccl5-/-, aged

growth_protocol: All WT, miR-146a-/-, and Ccl5-/- mice were on a C57BL/6 background and were bred and housed in a specific pathogen-free mouse facility at the University of Utah, USA, according to approved IACUC protocols. HCC Mice were weaned at 21 days and placed on a 60% high-fat, choline-deficient diet (CDHFD, Research Diets, # D05010403i). Aging, cancer-free mice (miR-146a-/- and WT) were maintained on a standard diet and sacrificed at 43-60 weeks for analysis.

extract_protocol:
Mouse liver was processed into a single-cell suspension and then stained with DAPI and FITC-conjugated anti-CD45 antibody. Following staining, cells were washed twice with 1X DPBS with 0.4% BSA (Miltenyi) and FACS sorted on the BD FACSAria Cell Sorter. Sorted cells were washed in 1X DPBS with 0.4% BSA and processed for scRNAseq by the University of Utah High-throughput Genomics Core.
10x Genomics Chromium Next GEM Single Cell  5' v2 Gene Expression Library Preparation

treatment_protocol: Experimental HCC mice were given intraperitoneal (i.p.) injections at 14 days old, of 25 mg/kg diethylnitrosamine (DEN), then weaned at 21 days and placed on a 60% high-fat, choline-deficient diet (CDHFD) for the indicated duration of the experiment.

value: Liver miR146-/- Ccl5-/-, aged

value: CD45+ immune

value: aging, DEN, CDHFD


title: C4_EOT_Input

description: Library name: jc6279

value: Input


title: Carya, CK, biol rep1

description: Library name: C_T4_CK1

value: Leaf

value: 30 months after inoculation


title: Carya, CK, biol rep2

description: Library name: C_T4_CK2


title: T23-015_Rucaparib_High_2

description: GeoMX Nanostring

value: Cancer

value: Rucaparib


title: Foxl1KO-homozygous rep5

description:
Library name: Sample_5
Proximal half of E15.5 small intestine from Foxl1-CreERT2-tdTomato homozygous null mouse

value: Foxl1-positive mesenchymal telocyte progenitors, mesenchymal stromal cells, intestinal epithelial cells, immune cells, endothelial cells, and other intestinal cell types.

value: Foxl1-tdTomat-P2A-CreERT2 Homozygous


title: Foxl1KO-heterozygous rep2

description:
Library name: Sample_2
Proximal half of E15.5 small intestine from Foxl1-CreERT2-tdTomato heterozygous mouse (control)

value: Foxl1-tdTomat-P2A-CreERT2 Heterozygote


title: T23-015_Rucaparib_High_3

description: GeoMX Nanostring

value: High


title: C5_Baseline_Input

description: Library name: jc6283

value: breast cancer


title: 20842x4  Young (~8 week old) Female WT Liver Immune Cells

description: Library name: 20842X4

source_name: Liver WT, young

value: Liver WT, young

value: WT


title: C5_Baseline_ER

description: Library name: jc6276

value: breast core biopsy

value: Letrozole + Megestrol 160mg

value: baseline

value: Millipore:06-935, Abcam:ab3575


title: Bronchoalveolar lavage fluid from patients with intermediate-stage lung injury

city: chengdu

first: zeng

last: wanqin

state: chengdu

address: No17 renming

institute: Sichuan University

description: Library name: BALF9618

data_processing:
Raw FASTQ files were processed using Cell Ranger (v3.1.0, 10× Genomics) to demultiplex, align to the mouse reference genome (mm10), and generate gene-barcode matrices. Downstream quality control, normalization, dimensionality reduction, clustering, and differential gene expression analysis were performed using the Seurat R package (v4.4.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files including genes normalized data.

source_name: bronchoalveolar lavage fluid (BALF)

extract_protocol:
Aortic leukocytes were lysed using TRIzol reagent (Thermo Fisher Scientific) following repeated pipetting to achieve a single-cell suspension without visible clumps, then snap-frozen in liquid nitrogen for RNA extraction.
Single-cell RNA-seq libraries were constructed using the Chromium Single Cell 3’ Library & Gel Bead Kit v2 (10× Genomics) following the manufacturer’s protocol. Barcoded cDNAs were amplified, purified with the SPRIselect reagent (Beckman Coulter), and assessed for quality using the Agilent 5400 system.

value: bronchoalveolar lavage fluid (BALF)

value: bronchoalveolar lavage fluid cells / BALF cells


title: 20842x2 DEN CDHFD 36 week old Female miR146-/- Liver Immune Cells

description: Library name: 20842X2

source_name: Liver miR146-/-, aged

value: Liver miR146-/-, aged

value: CD45+ immune

value: aging, DEN, CDHFD


title: T23-015_Rucaparib_Low_10

description: GeoMX Nanostring

value: Cancer

value: Rucaparib

value: Low


title: C4_Baseline_Input

description: Library name: jc6278

value: Input


title: C4_EOT_ER

description: Library name: jc6273

value: end of treatment


title: Bronchoalveolar lavage fluid from patients with advanced-stage lung injury

description: Library name: BALF5483


title: 20842x1 DEN CDHFD 36 week old Female WT Liver Immune Cells

description: Library name: 20842X1

source_name: Liver WT, aged

value: Liver WT, aged


title: C4_Baseline_ER

description: Library name: jc6272

value: breast cancer


title: C3_EOT_Input

description: Library name: jc6706


title: T23-015_Rucaparib_High_1

description: GeoMX Nanostring

value: High


title: T23-071_Rucaparib_High_9

description: GeoMX Nanostring

source_name: Omentum

value: Omentum


title: C3_Baseline_Input

description: Library name: jc6705

value: breast core biopsy

value: Letrozole + Megestrol 160mg


title: T23-071_Rucaparib_High_8

description: GeoMX Nanostring


title: scRNA-seq of Mus musculus: Lung,MCZ_ip

city: Hangzhou

first: Yicheng

last: Xie

address: 3333 Binsheng Rd

institute: Children’s Hospital Zhejiang University School of Medicine

description: Library name: MCZ_ip

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software (version2.20).
Sample demultiplexing, barcode processing and single-cell 3’gene counting by using the Cell Ranger pipeline(https://support.10xgenomics.com/single-cell-geneexpression/ software/pipelines/latest/what-is-cell-ranger，version 3.1.0) .
Assembly: mm10
Supplementary files format and content: matrix.mtx file, store the gene expression matrix in sparse format, representing counts of UMIs (unique molecular identifiers) for each gene (row) in each cell barcode (column).
Supplementary files format and content: features.tsv file, feature annotations (rows of matrix: gene ID, name, type).

source_name: Lung

growth_protocol: Male ICR mice, aged 6-8 weeks, were purchased from Shanghai SLAC Laboratory Animal Co., Ltd. (Production License No. SCXK (Hu) 2017-0005). All animals were housed in the Experimental Animal Center of Zhejiang University, under controlled environmental conditions (20-26°C, 40-70% humidity, and a 12-hour light/dark cycle), with ad libitum access to food and water.

extract_protocol:
Lung tissue samples from all mice in the LPS group and the LPS + MCZ group   (LPS + 1 mg/kg MCZ) were collected and pooled for analysis. The left lower lobe of the lung was rapidly excised, placed in cold PBS, and cut into small fragments.  These fragments were washed three times before being immersed in a digestive mixture containing collagenase I, collagenase II, and Dispase® (all from Sigma, USA). After digestion, the mixture of liquid and tissue was transferred to a centrifuge tube, rinsed with DMEM, and centrifuged at 4°C at 350 g for 7 minutes. Next, 1-2 mL of trypsin was added, and the mixture was incubated at room temperature for 3-5 minutes before resuspension. After digestion, the cell suspension was strained through a 70 µm sieve (Miltenyi, GER). The resulting filtrate was centrifuged at 350 g for 7 minutes at 4°C, and the supernatant was discarded. The pellet was treated with a lysis reagent, resuspended, and chilled on ice for 2-3 minutes. To halt the lysis, 5 mL of DMEM containing 10% FBS was added, followed by centrifugation at 350 g for 7 minutes at 4°C. The pellet was then washed and resuspended according to its volume. Single cells were isolated using the 10× Genomics Chromium Single Cell 3′ Solution (10× Genomics, USA).
Single-cell suspensions were loaded to 10x Chromium to capture single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by CapitalBio Technology at a minimum depth of 20,000 reads per cell.

value: Lung

value: LPS administration and treated with intraperitoneal injection of 0.2 mg/kg MCZ.

tag: Sex

value: Male

value: ICR


title: scRNA-seq of Mus musculus: Lung, LPS

description: Library name: LPS

value: LPS administration


title: SINUS

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 35/GF-127, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description:
Library name: SINUS
10x Genomics

data_processing:
Post sequencing, an average of 35,000 reads per cell were generated. The bcl files were demultiplexed into a FASTQ, aligned to Mouse_genome mm10-2020-A, and single-cell 3′ gene counting were performed by the standard 10X Genomics’ CellRanger mkfastq software v7.1.0. The single-cell QC was generated by 10X Genomics CellRanger and visualized using 10X Genomics’ LoupeTM Cell Browser and Partek Flow. Valid barcode reads in all samples were >95%. Reads aligned to mm10-2020-A genome were >90% in all samples, while anti-sense reads were <6% in all samples. All key metrics were within the expected range and did not trigger any errors or warnings in the Cell Ranger web summaries.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Sinus endothelial cells (SECs)

growth_protocol: All mice used in this study were handled in accordance with the guidelines established by the NIH Animal Care and Use Committee and the recommendations of AAALAC for the Care and Use of Laboratory Animals. The animal study protocol was approved by the NINDS Animal Care and Use Committee. Mice were bred and maintained within individually ventilated cages in the specific pathogen-free animal facilities at the NIH.

extract_protocol:
Samples were then enzymatically and mechanically digested using the mouse tumor dissociation kit (Miltenyi Biotec) and the gentleMACs Octo Dissociator (Miltenyi Biotec). Following dissociation, samples were passed through a 100-micron cell strainer and were washed with RMPI containing 2% fetal bovine serum. Samples were then resuspended in buffer containing 0.05% BSA in PBS. Single cell suspensions quality, number and viability were assessed with a dual fluorescence cell counter LUNA-FX7TM (Logos Biosystems).
10,000 cells were targeted from each sample cell suspension. The cells were washed twice with PBS+0.04% BSA and resuspended in about 500 cells µl-1.10X Genomics’ Chromium instrument and Dual index Single-Cell 3′ Reagent kit (V3.1) were used to prepare the individually barcoded single-cell RNA-Seq libraries following the manufacturer’s protocol.  Quality of the libraries were assessed by the TapeStation-4200 traces (Agilent BioAnalyzer High Sensitivity Kit) and quantitated by the Qubit system. Sequencing was done on the Illumina NextSeq-2000 machine using the P3 sequencing Kit (Illumina).

treatment_protocol: Lower sagittal sinus and rostral-rhinal hub samples were prepared for single cell RNA sequencing, as previously described (PMID: 38509366).

value: Sinus endothelial cells (SECs)

value: lower superior sagittal sinus


title: T23-071_Rucaparib_High_7

description: GeoMX Nanostring

value: Cancer

value: Rucaparib


title: C3_Baseline_ER

description: Library name: jc6673

tag: sample type

value: baseline

value: Millipore:06-935, Abcam:ab3575


title: HUB

description:
Library name: HUB
10x Genomics

value: rostral-rhinal hub


title: bone and BM, control, lane2

city: Tokorozawa

first: Masahiro

last: Shinohara

state: Saitama

address: 4-1 Namiki

country: Japan

institute: National Rehabilitation Center for Persons with Disabilities

description:
Library name: 4_Control_L2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone, bone marrow

extract_protocol:
Femurs and tibias from Tnfsf11tTA/+; LC1; Rosa26LSL-tdTomato mice were isolated from both limbs, and bone marrow was flushed out with PBS. The remaining bones were minced using scissors and forceps, then incubated in 5 mM EDTA in PBS at room temperature for 1 hour. Dissociated cells were collected every 30 minutes and pooled with the bone marrow cells isolated from the same mouse. Cells were collected by centrifugation and treated with Red Blood Cell Lysis Buffer, followed by incubation in DMEM containing 1 mg/mL Collagenase P, 0.025 mg/mL Liberase TH and 0.1 mg/mL DNase I at 37ºC with gentle shaking for 1 hour. Dissociated cells were collected every 20 minutes and passed through a 100 μm nylon mesh. The cells were then collected by centrifugation, resuspended in 2% FBS/2 mM EDTA/PBS. The isolated cells were stained with antibodies against Ter119 and CD45.2. Fixable Viability Dye (eBioscience) was used to stain dead cells. Live CD45.2-Ter119-tdTomato+ cells were sorted for single cell 3' gene expression library construction.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics) with slight modification.  Cells up to 10,000 were directly sorted into the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM).

value: bone, bone marrow

value: Control