title: ESC_Cbs_OE_input_r2

description: Library name: 11ESC_Cbs_OE_input_r2


title: marmoset neonate female PFC, rep 21-197 rep1

status: Public on Nov 20 2025

type: SRA

city: Cambridge

first: Margaret

last: Schroeder

state: MA

address: 77 Massachusetts Avenue

department: Brain and Cognitive Sciences

country: USA

institute: Massachusetts Institute of Technology

description:
Library name: Exp057_cjneo_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

library_source: transcriptomic single cell

data_processing:
Demultiplexed fastq files were generated by the Broad Institute Genomics Platform using Illumina software. 10x Genomics Cell Ranger software version 7.1 was used for alignment and counting via the 10x Genomics Cloud Analysis platform. For samples that were sequenced across several library pools, fastq files were grouped prior to alignment to create one cell-by-gene (cell x gene) counts matrix per sample. CellBender (v0.2.0) remove-background (Fleming et al., 2023) was used to remove ambient RNA and call nuclei with default parameters and expected_cells = 10,000, total-droplets-included = 40,000 and the –cuda flag. CellBender-cleaned cell x gene matrix .h5 files were read into Python in the anndata format using a custom function written by Stephen Fleming (https://github.com/broadinstitute/CellBender/issues/57).
Assembly: Reads were aligned to an optimized mouse reference genome based on the mouse GRCm38 primary sequence assembly (version 2, Pool et al. 2024) or or a modified marmoset mCalja1.2.pat.X assembly (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_011100555.1/) provided courtesy of Michael DeBerardine and Fenna Krienen (Princeton Neuroscience Institute) in which mitochondrial genes from CM021961.1 (https://www.ncbi.nlm.nih.gov/nuccore/1820101357/) were annotated using MITOS2113. The marmoset reference genome was generated from the .fasta and .gtf files using Cell Ranger “mkref” v7.1.0 using default parameters without filtering for any gene/transcript biotype and is available at: https://doi.org/10.5281/zenodo.16915694.
Supplementary files format and content: Processed data files are cell x gene count matrices in .h5 format without ambient RNA removal.

molecule: polyA RNA

organism: Callithrix jacchus

source_name: PFC

growth_protocol: Common marmosets were housed in AAALAC-accredited facilities at MIT, in spacious holding rooms with a 12 hour light/dark cycle, temperature 74.0 ± 2.0°F (23.3 ± 1.1°C), relative humidity of 50 ± 20 %, and unrestricted access to food and water. Cages contained a variety of perches and enrichment devices. Procedures were conducted with prior approval by the MIT Committee for Animal Care (CAC) and following veterinary guidelines. Animal work was performed in accordance with protocols approved by MIT’s Committee on Animal Care and NIH guidelines. All postnatal mice were wild-type C57BL/6J originally obtained from Jackson Laboratories and bred in-house. Timed pregnant C57BL/6J females were either obtained from Jackson Laboratories to arrive between gestation day 11 and 15 or were impregnated in house by setting up overnight mating pairs with females in proestrus or estrus phase. Embryos were harvested at E18.5 (18 days after the plug date). Mice were housed in a facility with a light cycle running from 07:00 to 19:00,  temperature 20-22.2°C, humidity 30-70%, and food and water available ad libitum. Postnatal mice were not derived from timed pregnant females. Instead, age was determined during regular pup checks by experienced researchers based on the Jax Mice Pup Appearance Chart.

extract_protocol:
Nuclei were extracted from frozen tissue using the 10x Genomics Chromium Nuclei Isolation Kit (Protocol CG000505, Rev A).
snRNAseq libraries were prepared using 10x Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Protocol CG000315 Rev C or Rev D) following manufacturer instructions.

treatment_protocol: None; animals were wild-type and allowed to develop normally.

tag: tissue

value: PFC

tag: cell type

value: nuclei


title: ESC_Cbs_OE_H3k9ac_r1

city: Mannheim

first: Gergana

last: Dobreva

state: Baden Württemberg

address: Ludolf-Krehl-Str. 7-11

department: Cardiovascular Genomics and Epigenomics

country: Germany

institute: Medical Faculty Mannheim/University of Heidelberg

description: Library name: 03ESC_Cbs_OE_H3k9ac_r1

library_source: genomic

data_processing:
High quality trimmed reads were mapped to the mm10 reference genome using STAR (v. 2.7.10a) (−alignIntronMin 20 −alignIntronMax 500000) (Dobin et al., 2013).
Mapped sam files were used to create makeTaglibraries using makeTagDirectory (default settings).
analyzeRepeats.pl function (rna mm10 -strand both -count genes –noadj) from HOMER (Heinz et al., 2010) was used to quantify the mapped reads.
Differential expression was quantified and normalized by Deseq2 (v. 1.40.1). rpkm.default (defaults) from EdgeR (v. 3.42.4) was used to calculate the reads per kilobase of millon reads (RPKM).
Bam files were merged with bamtools merge (v. 2.5.1) (default settings) and converted to BigWig files with the help of bamCoverage (v. 3.5.1) settings (-bs 20 --smoothLength 40 -p max --normalizeUsing RPKM -e 150)
Assembly: Assembly: mm10 from UCSC genome
Supplementary files format and content: Supplementary files format and content: BigWig files and normalized DESEQ2 excel file

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic stem cells

growth_protocol: ESCs were maintained on 0.2% gelatin coated plate in Knockout DMEM medium (Thermo Fisher Scientific, 10829018) containing 4.5 mg/ml D-glucose, supplemented with 10% serum replacement (Thermo Fisher Scientific, 10828028), 2 mM L-glutamine, 0.1 mM 2-mercaptoethanol, 1 mM sodium pyruvate, 1% penicillin-streptomycin and 1000 U/ml leukemia inhibitory factor.

extract_protocol:
Total RNA was isolated using QiaZOl RNA extraction kit from Qiagen
RNA libraries for RNA-seq were preced using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: mouse embryonic stem cells

tag: cell line

tag: genotype

tag: treatment

value: CBS_OE viral transfection

tag: antibody

value: Cell Signaling Technology, 9649S


title: ESC_Cth_OE_input_r1

data_processing:
trimmed of the raw reads using Trimmomatic (Bolger et al. 2014), min lengh of 60 bp and Quality score of minimum 15, remove Illumina Adapters TruSeq3
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 default settings
mapped bam files were merged with bamtools merge (default settings)
Bam files were merged with bamtools merge (v. 2.5.1) (default settings) and converted to BigWig files with the help of bamCoverage (v. 3.5.1) settings (-bs 20 --smoothLength 40 -p max  --normalizeUsing RPKM -e 150)
Assembly: mm10 from UCSC genome version
Supplementary files format and content: bigWig files

growth_protocol: Control , Lmna KO and CTH OE Nkx2-5-GFP mES cell lines were cultured on feeder condition in DMEM high glucose supplemented with 15% FCS and 1000 U/ml LIF for 2 days. mESC were preplated for 50min and collected for RNA extraction.

extract_protocol:
ESCs were dissociated by 0.05% trypsin-EDTA followed by preplating for 50min to obtain single mESCs and 1million mESCs were collected for H3K9ac and H3k27ac chip-seq
Libraries were constructed with the NEB Ultra DNA II Library Kit for Illumina (#E7103S/L)


title: ESC_Lmna_KO_input_r2


title: ESC_Cbs_OE_H3K27ac_r1

description: Library name: 07ESC_Cbs_OE_H3K27ac_r1

value: Active motif, 39135


title: ESC_Lmna_KO_input_r1


title: ESC_Ctr_input_r2

value: Ctr


title: ESC_Cth_OE_H3K27ac_ChIPseq_r2


title: ESC_Cth_OE_H3K27ac_ChIPseq_r1


title: ESC_Ctr_H3K27ac_ChIPseq_r2


title: marmoset neonate female MO, rep 21-197 rep2

description:
Library name: Exp057_cjneo_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

source_name: MO

value: MO


title: ESC_Lmna_KO_H3K27ac_ChIPseq_r1


title: ESC_Ctr_H3K27ac_ChIPseq_r1


title: ESC_Lmna_KO_H3K27ac_ChIPseq_r2


title: ESC_Cth_OE_H3K9ac_ChIPseq_r1


title: ESC_Cth_OE_H3K9ac_ChIPseq_r2


title: ESC_Lmna_KO_H3K9ac_ChIPseq_r2


title: ESC_Lmna_KO_H3K9ac_ChIPseq_r1


title: ESC_Ctr_H3K9ac_ChIPseq_r2


title: mus_Ctr1_UUO

city: Shanghai

first: Qianyi

last: Bao

address: 800 Dongchuan RD. Minhang District, Shanghai, China

country: China

institute: Bio-X Institutes, Shanghai Jiao Tong University

library_source: transcriptomic

data_processing:
DNBs were transformed to single end 50 bases reads and sequencing on BGISEQ-500 platform (BGI-Shenzhen, China).
In GO analysis and pathway analysis, DEGs were classified according to official classification with the GO or KEGG annotation results and phyper (a function of R) was performed in GO and pathway functional enrichment.
Assembly: mm9
Supplementary files format and content: Tab-delimited text file includes FPKM values.

molecule: total RNA

source_name: kidney

extract_protocol:
Total RNA was extracted from cells and kidney tissue by using TRIzol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: kidney

value: renal cells

value: WT

tag: Sex

value: male

value: UUO


title: ESC_Ctr_H3K9ac_ChIPseq_r1


title: mus_KO2_UUO

value: c-Abl knockdown


title: mus_KO3_UUO


title: Cal51R_2

city: Tian Jin

first: Yang

last: Ou

address: Weijin road

institute: Nankai university

data_processing:
Data filtering: The raw data was filtered with SOAPnuke (v1.5.2) by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 10%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 50%, afterwards clean reads were obtained and stored in FASTQ format.
Reference genome mapping： The clean data were mapped to the reference genome by HISAT (v2.1.0)
Reference gene mapping: The clean data were mapped to the assembled unique gene by Bowtie2 (v2.2.5) . The expression level of genes was calculated by RSEM (v1.2.8)
Gene Annotation: Annotating assembled Unigene with seven major functional databases (KEGG, GO, NR, NT, SwissProt, Pfam, and KOG), and predicting the transcription factors;Time Series and WGCNA analysis: Time Series analysis was performed by Mfuzz (v2.34.0), and gene co-expression network analysis was performed by WGCNA (v1.48).
Differential Gene Expression: Within-group differential gene analysis was performed using DESeq [6] under the conditions of Fold Change ≥ 2 and Adjusted P value ≤ 0.001. PossionDis was performed between-group differential gene analysis under the conditions of Fold Change ≥ 2 and FDR ≤ 0.001.
Assembly: hg38
Supplementary files format and content: xls files include FPKM values for each sample

organism: Homo sapiens

extract_protocol:
RNA was harvested using Trisol(Solarbio).
Experimental Procedure 1 Sample QC Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads. 3 mRNA Fragmentation The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented. 4 cDNA Synthesis Prepare the first-strand synthesis reaction system, and set up the reaction program, synthesize the first- strand cDNA, prepare the second-strand synthesis reaction system, and set up the reaction program to synthesize the second-strand cDNA. 5 End Repair, Add A and Adaptor Ligation After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs. 6 PCR The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC The corresponding library quality control protocol will be selected depending upon product requirements. 8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 9 Sequencing Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).


title: mus_KO1_UUO


title: ESC_Ctr_input_r1


title: Cal51R_1


title: Mtb, ECU, rep4

city: Camperdown

first: Daniel

last: Hesselson

state: NSW

address: Bldg 93, RPA Hospital, Missenden Rd

country: Australia

institute: Centenary Institute

description: Library name: ECU_R4_235VKJLT3

data_processing:
Raw paired-end FASTQ files were quality filtered and adapter-trimmed using fastp with default settings.
Trimmed reads were quantified directly against an Mtb H37Rv reference transcriptome supplemented with rRNA/tRNA features (gentrome index) using Salmon (version 1.10.3) in selective-alignment mode with sequence- and GC- bias correction enabled.
Transcript-to-gene mapping used the H37Rv transcript FASTA, and non-coding features (rRNA, tRNA, tmRNA, sRNA) were excluded from downstream gene-level analyses.
Gene-level counts were imported into R using tximport73 with counts scaled by transcript length and TPM.
Assembly: NC_000962, Mycobacterium tuberculosis H37Rv, complete genome
Supplementary files format and content: normalized_counts.tsv, DESeq2 size-factor normalized counts (gene x sample)
Supplementary files format and content: vsd_counts.csv, variance-stabilizing transformed matrix (gene x sample)

organism: Mycobacterium tuberculosis H37Rv

source_name: mycobacterium

growth_protocol: Mtb H37Rv cultures were grown in Middlebrook 7H9 media (Difco) supplemented with OAD (0.005% oleic acid, 0.5% bovine serum albumin, 0.2% dextrose), 0.01% tyloxapol (Sigma) and 0.2% Glycerol under BSL3 conditions. For all Mtb experiments, Mtb H37Rv was incubated at 37 ºC, 20% oxygen and 5% carbon dioxide without agitation until desired optical density at 600 nm (OD600) was reached. Each biological replicate was performed with a unique aliquot of a Mtb H37Rv glycerol stock.

extract_protocol:
The Mtb cells were then centrifuged at 3725 g for 10 min to pellet bacteria. Pellets were resuspended with 1 mL TRIzol and transferred to a 2 mL O-ring tube with 250 µL < 106 µm acid-washed glass beads. To disrupt the mycobacterial cell envelope, cells were subjected to six cycles of bead beating (20 s at 4600 rpm and 40 s on ice) with a (Biopec products) mini beadbeater. Samples were then clarified at 18000 g for 1 min. After a short room temp incubation, 200 µL of chloroform was added to each sample and samples were inverted by hand for 15 seconds and incubated at room temperature for 3 min. Samples were then centrifuged at 12000 g for 15 min at 4 °C. The upper aqueous phase containing RNA was collected. RNA was purified from the aqueous phase with the Isolate II RNA micro kit
Libraries were prepared using the (Illumina) Total RNA library kit with Ribo-Zero Plus chemistry for rRNA depletion and sequenced on an (Illumina) NovaSeq 6000 platform to generate 150 bp paired-end reads.

treatment_protocol: Exponentially growing Mtb H37Rv cultures were treated with MIC90 Ecu* and incubated for a further 48 h at 37°C.

value: mycobacterium

value: ECU


title: Mtb, ECU, rep3

description: Library name: ECU_R3_235VKJLT3


title: Cal51_2


title: Mtb, ECU, rep1

description: Library name: ECU_R1_235VKJLT3


title: Cal51_1


title: Mtb, DMSO, rep4

description: Library name: DMSO_R4_235VKJLT3

value: DMSO


title: Mtb, DMSO, rep3

description: Library name: DMSO_R3_235VKJLT3


title: Mtb, DMSO, rep2

description: Library name: DMSO_R2_235VKJLT3


title: Mtb, DMSO, rep1

description: Library name: DMSO_R1_235VKJLT3


title: rCD4_NMS_48h

city: Shenyang

first: Li

last: Zhao

address: Nanjing north street

department: Key Laboratory of AIDS Immunology of National Health and Family Planning Commission

institute: The First Affiliated Hospital of China Medical University

description: Library name: Sample 8

data_processing:
Raw sequencing images generated on the DNBSEQ-T7 platform were converted into FASTQ files using the standard basecalling pipeline provided by BasecallLite (version 2.0.1).
The raw reads were subjected to quality control and adaptor trimming using fastp (version 1.0.1), with default parameters unless otherwise specified.
High-quality reads were then collapsed to unique sequences with associated counts using the collapse_reads_md.pl script from the miRDeep2 (version 2.0.1.3) package.
The collapsed reads (in FASTA format) were then aligned to the human protein-coding transcriptome using Bowtie (version 1.3.1) with the GENCODE GRCh38 reference (GENCODE v43 protein-coding transcripts; cds-only index). The following parameters were used: -f -p 40 -v 1 -a --best --strata --norc. Reads mapping to coding sequence (CDS) transcripts were considered potential degradation products of mRNAs and were removed from further miRNA quantification.
High-quality reads were then collapsed to unique sequences with associated counts using the collapse_reads_md.pl script from the miRDeep2 package. The collapsed reads were quantified against human miRNA reference sequences using quantifier.pl (miRDeep2), with mature and precursor miRNA annotations obtained from miRBase (human, release 22). Quantifier.pl internally maps the collapsed reads to the miRNA reference and reports read counts for each known miRNA.
Assembly: GRCh38
Supplementary files format and content: csv file include raw counts and norm counts for each Sample

source_name: primary cells

growth_protocol: ustimulated CD4+ T cells were maintained in RPMI1640 supplemented with 10% fetalbovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from all samples using TRIzol reagent (Thermo Fisher Scientific, USA) following the manufacturer’s instructions. RNA concentration and purity were measured using a NanoDrop spectrophotometer (Thermo Fisher Scientific, USA), and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Only RNA samples with an RNA integrity number (RIN) > 7 were used for downstream library preparation.
Small RNA libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs, USA) according to the manufacturer’s protocol. Briefly, 3' and 5' adaptors were ligated to purified small RNAs, followed by first-strand cDNA synthesis and PCR amplification. The amplified libraries were purified using AMPure XP beads (Beckman Coulter, USA). Library quality and fragment size distribution were examined using an Agilent 2100 Bioanalyzer, and library concentration was quantified by qPCR. Sequencing was performed on the DNBSEQ-T7 platform generating 150-bp paired-end reads.

treatment_protocol: ustimulated CD4+ T cells were treated with or without 5μM PLK inhibitors (MCE) for 24h or 48h

value: peripheral blood

value: CD4+T cell

value: NMS-P937 5μM

tag: batch


title: rCD4_TAK_48h

description: Library name: Sample 7

value: TAK960 5μM


title: rCD4_GW_48h

description: Library name: Sample 6


title: rCD4_NMS_24h

description: Library name: Sample 4


title: rCD4_DMSO_48h

description: Library name: Sample 5


title: rCD4_TAK_24h

description: Library name: Sample 3


title: mus_Ctr3_UUO


title: rCD4_GW_24h

description: Library name: Sample 2


title: rCD4_DMSO_24h

description: Library name: Sample 1


title: rCD4_NMS_48h

description: Library name: Sample 8

data_processing:
Raw sequencing images generated on the DNBSEQ-T7 platform were converted into FASTQ files using the standard basecalling pipeline provided by BasecallLite (version 2.0.1).
The raw reads were subjected to quality control and adaptor trimming using fastp (version 1.0.1), with default parameters unless otherwise specified.
Clean reads were aligned to the reference genome GRCh38.gencode.p13.V43 using HISAT2 (version 2.2.1).
Transcript assembly and quantification were performed using StringTie (version 3.0.1) to obtain expression values at gene levels.
Assembly: GRCh38
Supplementary files format and content: csv file include raw counts for each Sample

extract_protocol:
Total RNA was extracted from all samples using TRIzol reagent (Thermo Fisher Scientific, USA) following the manufacturer’s instructions. RNA concentration and purity were measured using a NanoDrop spectrophotometer (Thermo Fisher Scientific, USA), and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). Only RNA samples with an RNA integrity number (RIN) > 7 were used for downstream library preparation.
Comprehensive RNA libraries, including long non-coding RNAs and mRNAs, were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, USA). Ribosomal RNA was removed from total RNA using the Ribo-Zero rRNA Removal Kit (Illumina, USA). The rRNA-depleted RNA was fragmented and reverse-transcribed into cDNA, followed by end repair, adaptor ligation, and PCR amplification according to the manufacturer’s protocol. The resulting libraries were purified using AMPure XP beads (Beckman Coulter, USA). Library quality was assessed using an Agilent 2100 Bioanalyzer, and concentrations were measured by qPCR. Sequencing was performed on the DNBSEQ-T7 platform generating 150-bp paired-end reads.


title: rCD4_GW_48h

description: Library name: Sample 6


title: Mtb, ECU, rep2

description: Library name: ECU_R2_235VKJLT3


title: rCD4_DMSO_24h

description: Library name: Sample 1


title: mus_Ctr2_UUO


title: rCD4_DMSO_48h

description: Library name: Sample 5


title: rCD4_TAK_48h

description: Library name: Sample 7


title: sgPB2R2

city: Guangzhou

first: Siyao

last: Guo

address: No.58 Zhongshan Er Road

institute: The First Affiliated Hospital, Sun Yat-sen University

description: Library name: Sample5

data_processing:
The sequencing data was filtered with SOAPnuke.
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: GRCh38
Supplementary files format and content: FPKM value of genes calculated by RSEM.

source_name: HCC cells

extract_protocol: The RNA-seq library was prepared by Poly(A)+ RNA preparation, GI tailing of RNA, cDNA synthesis, cDNA library amplification and Sequencing library preparation. Libraries were prepared for sequencing according to SMRTbell Template Prep Kit protocol.

value: HCC cells


title: sgPB2R3

description: Library name: Sample6


title: rCD4_GW_24h

description: Library name: Sample 2


title: NCR3

description: Library name: Sample3

value: NCR


title: sgPB2R1

description: Library name: Sample4


title: rCD4_TAK_24h

description: Library name: Sample 3


title: NCR2

description: Library name: Sample2


title: NCR1

description: Library name: Sample1


title: WT FAC-sorted neuron 40

city: Boston

first: Elisabetta

last: Furlanis

address: Longwood avenue

institute: Harvard Medical School

description:
Library name: Cell 40
G5_2

data_processing:
Reads were mapped using STAR (v.2.7.10) against the GRCm38/mm10 reference genome, where GFP and mCherry sequences were added
Assembly: mm10
Supplementary files format and content: FPKM values for each neuron

source_name: brain

extract_protocol:
FAC-sorted neurons were sorted directly in CSS buffer from the SMART-Seq mRNA Single Cell LP kit (Takara Bio)
RNA library preparation from individually neurons was performed using the SMART-Seq mRNA Single Cell LP kit following manufacturer’s instructions

treatment_protocol: dissection media and pre-sort buffer were supplemented with the transcriptional inhibitor actinomycin D 5 μg/ml

value: brain

value: neuron

tag: fac-sorted cell

value: CRN

value: wild-type

value: actinomycin-D


title: WT FAC-sorted neuron 39

description:
Library name: Cell 39
G3_2


title: WT FAC-sorted neuron 41

description:
Library name: Cell 41
G8_2


title: rCD4_NMS_24h

description: Library name: Sample 4

value: WT


title: UVB 200 mJ/cm2 (2)

type: RNA

city: Birmingham

first: Hui

last: Xu

state: AL

address: VH566B 1670 University Blvd.

department: Dermatology

institute: The University of Alabama at Birmingham

hyb_protocol: Hybridization was done in the UAB Department of Radiation Oncology Nanostring Laboratory using their established protocols.

scan_protocol: Data collection was done in the UAB Department of Radiation Oncology Nanostring Laboratory using their established protocols.

data_processing: Data processing was done in the UAB Department of Radiation Oncology Nanostring Laboratory using their established protocols.

source_name: UVB irradiated mouse back skin

extract_protocol: RNA was extracted from irradiated back skin tissues or non irradiated back skin tissues.

treatment_protocol: The back skin of C57BL/6 mice was irradiated for 4 consecutive days with 200 mJ/cm2 of UVB light. Non irradiated mice were used as control. UVB-irradiated skin was collected after 24 hours of the last UVB light exposure.

value: Mouse back skin


title: UVB 200 mJ/cm2 (1)


title: UVB 200 mJ/cm2 (3)


title: WT FAC-sorted neuron 36

description:
Library name: Cell 36
F6


title: WT FAC-sorted neuron 37

description:
Library name: Cell 37
F8_2


title: WT FAC-sorted neuron 35

description:
Library name: Cell 35
F4_2


title: no UVB control (3)

source_name: Control mouse back skin


title: WT FAC-sorted neuron 38

description:
Library name: Cell 38
G2_2


title: WT FAC-sorted neuron 34

description:
Library name: Cell 34
F3


title: no UVB control (1)


title: no UVB control (2)


title: WT FAC-sorted neuron 32

description:
Library name: Cell 32
F2_2


title: WT FAC-sorted neuron 33

description:
Library name: Cell 33
F3_2


title: WT FAC-sorted neuron 31

description:
Library name: Cell 31
E9


title: WT FAC-sorted neuron 29

description:
Library name: Cell 29
E7


title: WT FAC-sorted neuron 27

description:
Library name: Cell 27
E4_2


title: WT FAC-sorted neuron 28

description:
Library name: Cell 28
E4


title: WT FAC-sorted neuron 30

description:
Library name: Cell 30
E8


title: WT FAC-sorted neuron 25

description:
Library name: Cell 25
D8_2

value: CPN


title: WT FAC-sorted neuron 23

description:
Library name: Cell 23
D5_2


title: WT FAC-sorted neuron 22

description:
Library name: Cell 22
D4


title: WT FAC-sorted neuron 21

description:
Library name: Cell 21
D4_2


title: WT FAC-sorted neuron 26

description:
Library name: Cell 26
E2_2


title: WT FAC-sorted neuron 24

description:
Library name: Cell 24
D6_2


title: WT FAC-sorted neuron 20

description:
Library name: Cell 20
D3


title: WT FAC-sorted neuron 19

description:
Library name: Cell 19
D2_2


title: WT FAC-sorted neuron 18

description:
Library name: Cell 18
C11


title: WT FAC-sorted neuron 17

description:
Library name: Cell 17
C7


title: WT FAC-sorted neuron 15

description:
Library name: Cell 15
C6


title: WT FAC-sorted neuron 16

description:
Library name: Cell 16
C7_2


title: WT FAC-sorted neuron 10

description:
Library name: Cell 10
B11


title: WT FAC-sorted neuron 9

description:
Library name: Cell 9
B10


title: WT FAC-sorted neuron 14

description:
Library name: Cell 14
C5


title: WT FAC-sorted neuron 11

description:
Library name: Cell 11
C2


title: WT FAC-sorted neuron 5

description:
Library name: Cell 5
B6


title: WT FAC-sorted neuron 12

description:
Library name: Cell 12
C3


title: WT FAC-sorted neuron 6

description:
Library name: Cell 6
B7_2


title: WT FAC-sorted neuron 3

description:
Library name: Cell 3
B5_2


title: WT FAC-sorted neuron 8

description:
Library name: Cell 8
B9


title: WT FAC-sorted neuron 4

description:
Library name: Cell 4
B5


title: WT FAC-sorted neuron 2

description:
Library name: Cell 2
B4


title: mouse E18.5 mixed thalamus, rep litter1_set1

description:
Library name: Exp110_mmE18.5_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

source_name: thalamus

value: thalamus

value: nuclei


title: mouse 90wks male MO, rep 230130_aged_10M

description:
Library name: Exp106_mmaged_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

value: MO


title: WT FAC-sorted neuron 7

description:
Library name: Cell 7
B8_2


title: mouse P14 female MO, rep 220411_P14_F

description:
Library name: Exp090_mmP14_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse 90wks male thalamus, rep 221022_aged_1M

description:
Library name: Exp094_mmaged_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse 90wks female MO, rep 221022_aged_3F

description:
Library name: Exp094_mmaged_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse 90wks male striatum, rep 221022_aged_1M

description:
Library name: Exp094_mmaged_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

source_name: striatum

value: striatum


title: mouse 90wks female thalamus, rep 221022_aged_3F

description:
Library name: Exp094_mmaged_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: WT FAC-sorted neuron 13

description:
Library name: Cell 13
C4


title: mouse P14 male striatum, rep 220819_P14_13M

description:
Library name: Exp090_mmP14_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P14 male PFC, rep 220819_P14_13M

description:
Library name: Exp090_mmP14_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq

value: PFC


title: mouse 90wks female PFC, rep 221022_aged_3F

description:
Library name: Exp090_mmaged_3A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse 90wks male striatum, rep 221022_aged_2M

description:
Library name: Exp089_mmaged_2D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: WT FAC-sorted neuron 1

description:
Library name: Cell 1
B3_2


title: mouse 90wks female striatum, rep 221022_aged_3F

description:
Library name: Exp094_mmaged_2D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P90 male thalamus, rep 220822_P90_5M

description:
Library name: Exp086_mmP90_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P90 male striatum, rep 220822_P90_5M

description:
Library name: Exp086_mmP90_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse 90wks female PFC, rep 221022_aged_4F

description:
Library name: Exp089_mmaged_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P4 male striatum, rep 220519_P4_M

description:
Library name: Exp086_mmP4_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P4 female thalamus, rep 220519_P4_F

description:
Library name: Exp074_mmP4_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P14 female thalamus, rep 220808_P14_12F

description:
Library name: Exp086_mmP14_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P4 female MO, rep 220412_P4_F

description:
Library name: Exp074_mmP4_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P32 male striatum, rep 220406_P32_1M

description:
Library name: Exp074_mmP35_2D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P4 female striatum, rep 220519_P4_F

description:
Library name: Exp074_mmP4_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P14 female striatum, rep 220808_P14_12F

description:
Library name: Exp086_mmP14_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P14 female PFC, rep 220808_P14_12F

description:
Library name: Exp086_mmP14_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P32 male PFC, rep 220406_P32_1M

description:
Library name: Exp074_mmP35_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P32 male thalamus, rep 220406_P32_1M

description:
Library name: Exp074_mmP35_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P90 female striatum, rep 220311_P90_3F

description:
Library name: Exp073_mmP90_2D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P4 female PFC, rep 220519_P4_F

description:
Library name: Exp074_mmP4_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P90 female thalamus, rep 220311_P90_3F

description:
Library name: Exp073_mmP90_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P90 female MO, rep 220311_P90_3F

description:
Library name: Exp073_mmP90_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P90 female PFC, rep 220311_P90_3F

description:
Library name: Exp073_mmP90_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P14 male MO, rep 220819_P14_13M

description:
Library name: Exp090_mmP14_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P14 male striatum, rep 220808_P14_10M

description:
Library name: Exp073_mmP14_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P14 male thalamus, rep 220819_P14_13M

description:
Library name: Exp090_mmP14_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P14 male thalamus, rep 220808_P14_10M

description:
Library name: Exp073_mmP14_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P14 male MO, rep 220808_P14_10M

description:
Library name: Exp073_mmP14_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P14 male PFC, rep 220808_P14_10M

description:
Library name: Exp073_mmP14_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P32 female striatum, rep 220406_P32_4F

description:
Library name: Exp070_mmP35_2D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P32 female thalamus, rep 220406_P32_4F

description:
Library name: Exp070_mmP35_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P32 male MO, rep 220406_P32_1M

description:
Library name: Exp074_mmP35_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P32 female MO, rep 220406_P32_4F

description:
Library name: Exp070_mmP35_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P32 male MO, rep 220406_P32_3M

description:
Library name: Exp070_mmP35_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P32 female PFC, rep 220406_P32_4F

description:
Library name: Exp070_mmP35_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P90 female striatum, rep 220311_P90_4F

description:
Library name: Exp068_mmP90_2D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P32 male striatum, rep 220406_P32_3M

description:
Library name: Exp070_mmP35_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P32 male PFC, rep 220406_P32_3M

description:
Library name: Exp070_mmP35_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P90 female PFC, rep 220311_P90_4F

description:
Library name: Exp068_mmP90_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P90 male MO, rep 220214_P90_1M

description:
Library name: Exp068_mmP90_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P4 female striatum, rep 220408_P4_2F

description:
Library name: Exp062_mmP4_1D
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P4 male MO, rep 220430_P4_M

description:
Library name: Exp062_mmP4_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P4 male thalamus, rep 220430_P4_M

description:
Library name: Exp062_mmP4_2C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P4 female PFC, rep 220408_P4_2F

description:
Library name: Exp062_mmP4_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P4 male PFC, rep 220430_P4_M

description:
Library name: Exp062_mmP4_2A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P90 female MO, rep 220311_P90_4F

description:
Library name: Exp068_mmP90_2B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: mouse P90 male thalamus, rep 220214_P90_1M

description:
Library name: Exp068_mmP90_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: GSDME KO treated BRAFi MEKi

city: Philadelphia

first: Andrew

middle: E

last: Aplin

state: PA

address: 233 South 10th St.

institute: Thomas Jefferson University

description: Library name: GSDME_KO_treated_BRAFi_MEKi

data_processing:
CellRanger v5.0.0 was used to align raw sequencing data to the CellRanger mm10-3.0.0 reference transcriptome, quantify gene expression levels, aggregate data and filter empty cell barcodes for 10x Genomics samples
Assembly: mm10
Supplementary files format and content: h5, CellRanger filtered_feature_bc_matrix.h5 files

source_name: tumor

growth_protocol: 3x10^5 YUMM1.7 WT and GSDME KO cells were injected intradermally into C57BL/6J mice.

extract_protocol:
On day 4, 5 BRAFi+MEKi treated tumors and 2 control treated tumors were harvested, homogenized, and pooled into individual samples. Live cells were enriched using the Miltenyi Biotech dead cell removal kit followed by sorting the Annexin V negative population. Cell suspensions were adjusted to 1000 cells/μL and loaded onto a Chromium Controller (10x Genomics).
scRNA-seq libraries were prepared using the Chromium Single Cell 3’ & Gel Bead kit v3.1 (10x Genomics) according to the manufacturer’s instructions. Reverse transcription and amplification were performed on a C1000 Touch Thermal Cycler (BioRad). The quality of cDNA and the final libraries were checked using the 4200 TapeStation System (Agilent). Libraries were pooled and sequenced at 400pM as the final loading concentration using the Illumina NovaSeq 6000.

treatment_protocol: When tumors reached approximately 100-200mm3, animals were administered BRAFi+MEKi or vehicle control chow.

value: tumor

value: GSDME KO

value: BRAFi MEKi


title: WT control

description: Library name: WT_control

value: Control


title: mouse P4 female MO, rep 220519_P4_F

description:
Library name: Exp062_mmP4_1B
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: WT treated BRAFi MEKi

description: Library name: WT_treated_BRAFi_MEKi


title: GSDME KO control

description: Library name: GSDME_KO_control


title: Male mutant #2

city: Rockville

first: Carlos

middle: Raul

last: Ferreira

state: Maryland

address: 10 Center Drive, Building 10, Room 2-5142

institute: NICHD

description: Library name: 10_SAf1-255

data_processing:
Alignment was performed using STAR v2.5.2b aligner. Data normalization was performed by the median of ratios method using DESeq2 v.1.14.1.
Assembly: mm10
Supplementary files format and content: Microsoft Excel Worksheet containing DESe2-normalized gene counts for each sample

source_name: Bone

extract_protocol:
Total RNA from pulverized bone was extracted using TRIzol Reagent (Thermo Fisher Scientific) and further purified by phenol-chloroform precipitation.
Total RNA (10 μg) was subjected to rRNA depletion–based library preparation and Illumina sequencing (Active Motif, CA, USA).

value: Bone


title: Male WT #2

description: Library name: 09_SAf1-254


title: mouse P32 male thalamus, rep 220406_P32_3M

description:
Library name: Exp070_mmP35_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: Male mutant #1

description: Library name: 07_SAf1-238


title: Female WT #3

description: Library name: 06_S13-Fgfr1pp


title: Female WT #2

description: Library name: 05_S12-Fgfr1pp


title: mouse P90 male PFC, rep 220214_P90_1M

description:
Library name: Exp068_mmP90_1A
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: Female mutant #3

description: Library name: 03_S10-Fgfr1


title: mouse P4 female thalamus, rep 220408_P4_2F

description:
Library name: Exp062_mmP4_1C
10x Genomics Chromium Next GEM Single Cell 3' v3.1 snRNA-seq


title: Female mutant #1

description: Library name: 01_S8-Fgfr1


title: Pro_CTCF-Nm_rep1

city: East Lansing

first: Yu

last: Zhang

state: MI

address: 567 Wilson Rd, Biomedical and Physical Sciences Building, Rm 5176

department: Microbiology, Genetics and Immunology

institute: Michigan State University

description: Library name: Sample 4

data_processing:
Reads were aligned using bowtie 2.2.8 with --non-deterministic flag.
Duplicate reads were removed using samtools markdup.
Libraries were strand-separated based on alignment orientation and normalized to reads per million.
Assembly: mm9
Supplementary files format and content: bigWig including germline expression information for samples.
Library strategy: PRO-Seq

molecule: nuclear RNA

source_name: v-Abl transformed pro-B cell line

growth_protocol: v-Abl pro-B lines were maintained in RPIM1640 medium supplemented with 10% FBS, 50 uM 2-Mercaptoethanol, 100 U/ml Penicillin-Streptomycin and 2 mM L-Glutamine.

extract_protocol:
5 million nuclei were collected by sucrose gradient centrifugation. Nuclear run-on was performed at 37 °C for 5 min by mixing nuclei with 2 X run-on master mix (10 mM Tris-HCl pH 8.0, 5 mM MgCl₂, 1 mM DTT, 300 mM KCl, 50 uM Biotin-11-CTP, 0.5 uM CTP, 250 uM each ATP/CTP/UTP, 10 U RNase inhibitor, 1% sarkosyl), followed by Trizol total RNA extraction.
RNA was hydrolyzed with 0.2 N NaOH on ice for 12 min, neutralized with 0.55 M Tris-HCl pH 6.8, and buffer-exchanged with Bio-Rad P30 columns. Biotin-labeled RNA was enriched using Dynabeads MyOne Streptavidin C1 beads, treated with RppH (NEB) and T4 PNK (NEB), and sequentially ligated to 5’ and 3’ RNA adaptors with Streptavidin bead enrichments after each ligation. Reverse transcription was followed by PCR with indexed Illumina adaptors (8 cycles). 200-500 bp products were selected by SPRIselect beads (Beckman Coulter) to remove adaptor dimers. Libraries were then amplified to full scale with cycle number determined by test PCR, SPRIselect beads-purified, and sequenced via Illumina paired-end 150 bp sequencing.

treatment_protocol: 3 uM STI571 induced G1 arrest for 4 days.

value: v-Abl transformed pro-B cell line

value: 3 uM STI-571 treated for 4 days


title: Pro_WT_rep1

description: Library name: Sample 1

value: Emu-Bcl2+, RAG1(D708A)


title: Pro_CTCF-Nm_rep3

description: Library name: Sample 6


title: Astrocytes, TDP-43_Q331K, omomyc, rep1

city: Trento

first: Manuela

last: Basso

address: via sommarive 9

department: CIBIO

country: Italy

institute: University of Trento

description:
Library name: TG_omomyc_REP1
Omomyc_normalized_counts.tsv
Omomyc_raw_counts.tsv

data_processing:
The raw RNA-sequencing data from astrocytes and oligodendrocytes were analyzed using the standard pipeline provided by Lexogen for the Corall and Corall v2 library preparation kits. The pipeline is available on GitHub here. Gene expression quantification (read counts) was performed using featureCounts v2.0.1 with the parameters -s 0 -t exon -g gene_name. Samples with fewer than 5 million reads assigned by featureCounts were excluded from further analysis.
For microglia samples, RNA sequencing was performed using the Lexogen QuantSeq protocol. Unique Molecular Identifiers (UMIs) were removed with UMI-tools v1.0.1. Gene quantification was done with STAR v2.7.7a, using the Ensembl GRCm39 genome (accessed March 2021). The resulting gene counts were analyzed using the DESeq2 package in R, and normalized counts were obtained via variance stabilizing transformation (VST) as implemented in DESeq2.
For the analysis of the Omomyc bulk RNA-seq data, we used the standard nf-core/rnaseq pipeline (v3.18). The used reference genome was GRCm38.p6, with the Gencode annotation file (vM25). Furthermore, we set the additional parameters defined in the documentation for the Watchmaker mRNA Library Prep Kit with Twist UMI Adapter System to improve the accuracy of the quantification. For the trimming, fastp was set. Other parameters were left to default.
Assembly: mm10
Supplementary files format and content: Tab-delimited file (tsv) with raw counts (samples on columns) for Oligo
Supplementary files format and content: Tab-delimited file (tsv) with raw counts (samples on columns) for Astro
Supplementary files format and content: Tab-delimited file (tsv) with TPM (samples on columns) for Oligo
Supplementary files format and content: Tab-delimited file (tsv) with TPM (samples on columns) for Astro
Supplementary files format and content: Tab-delimited file (tsv) with raw counts (samples on columns) for Microglia
Supplementary files format and content: Tab-delimited file (tsv) with DESeq2 norm. counts (samples on columns) for Microglia
Supplementary files format and content: Tab-delimited file (tsv) with raw counts (samples on columns) for purified astrocytes vehicle and treated with Omomyc
Supplementary files format and content: Tab-delimited file (tsv) with DESeq2 norm. counts (samples on columns) for purified astrocytes vehicle and treated with Omomyc

source_name: Astrocytes

extract_protocol:
To obtain a high RNA quality and yield with small cell amounts, we used the Single Cell RNA Purification Kit (Norgen Biotek Corporation, Thorold, ON, Canada) according to the manufacturer’s instructions. RNA was quantified with Qubit fluorometer (Thermo Fisher Scientific, Inc.). Finally, RNA quality was assessed with Agilent 2100 Bioanalyzer HS for RNA. Omomyc: After 14 days, primary astrocytes were replated (4 × 10⁵ cells/well), treated the next day with 40 μM Omomyc for 48 h, and harvested for RNA extraction (Total RNA Purification Kit, Norgen Biotek).
Astrocytes and oligodendrocytes: Poly(A) RNA-seq library prep was performed according to the manufacturer’s protocol (Lexogen CORALL mRNA-Seq V2 Library Prep Kits with UDIs cat. N. 177-182), adding Unique Molecular Identifier during the linker ligation step. Microglia: Poly(A) RNA-seq Lexogen QuantSeq 3‘ mRNA-Seq Library Prep Kit for Illumina. For Omomyc-treated and control cells, 1000ng of total RNA was used for Poly(A) enrichment and RNA-seq library preparation according to the Watchmaker mRNA Library Prep Kit protocol. For library construction, the Twist UMI Adapter System (Twist Bioscience) was included in the protocol. Final sequencing libraries were quantified with Qubit DNA HS Kit, analyzed on a Perkin Elmer LabChip GXII, pooled in equimolar amounts, and sequenced on a lane of SP Novaseq6000 flow cell, obtaining an average of 40 million PE150 reads (clusters) per sample.

value: Astrocytes

value: omomyc


title: Pro_WT_rep2

description: Library name: Sample 2


title: Astrocytes, TDP-43_Q331K, omomyc, rep2

description:
Library name: TG_omomyc_REP2
Omomyc_normalized_counts.tsv
Omomyc_raw_counts.tsv


title: Astrocytes, TDP-43_Q331K, vehicle, rep3

description:
Library name: TG_vehicle_REP3
Omomyc_normalized_counts.tsv
Omomyc_raw_counts.tsv

value: vehicle


title: Astrocytes, TDP-43_Q331K, omomyc, rep3

description:
Library name: TG_omomyc_REP3
Omomyc_normalized_counts.tsv
Omomyc_raw_counts.tsv


title: Pro_WT_rep3

description: Library name: Sample 3


title: Astrocytes, TDP-43_Q331K, vehicle, rep2

description:
Library name: TG_vehicle_REP2
Omomyc_normalized_counts.tsv
Omomyc_raw_counts.tsv


title: Male WT #1

description: Library name: 08_SAf1-253

value: WT


title: Ginigival mucosa, diabetic CD11c.Cre+/-.Akt1L/L

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

description: Library name: Akt1KO_Diab

data_processing:
CellRanger Software version 6.0.2 was use to generate the FASTQ files, aligned fastq files to the mouse reference genome (refdata-gex-mm10-2020-A)
Data filtering: mRNA contamination was moved using Soupx v1.3.0, nCount_RNA >= 500 & nFeature_RNA > 200 & nFeature_RNA < 6500 & percent.mt < 15
Assembly: mm10
Supplementary files format and content: Barcodes, features and matrix for each sample

source_name: Gingival tissue

extract_protocol:
Chromium Single Cell 3' Reagent Kits v3-10x scRNA-Seq 3p v3-CSCC_3pCapture
Chromium Single Cell 3' Reagent Kits v3-10x scRNA-Seq 3p v3-CSCC_3pLibraryPrep

treatment_protocol: Type-I diabetes mellitus was induced in mice using streptozotocin. Bacterial-induced inflammation was maintained for two weeks, followed by a two-week waiting period. Cells were isolated from the gingiva, pooled from 4 mice per group. Negative selection was performed to remove dead cells (DAPI+), endothelial cells (CD31+), and red blood cells (Ter-119+). Positive selection for CD45+ cells was conducted, with 20% enrichment of CD11c+CD45+ cells by FACS sorting. 10,000 FACS-sorted cells were loaded per lane of a 10x Genomics Chromium instrument for scRNA-seq analysis. For each experimental condition, a pool of four mice was used, with no replicates.

value: Gingival tissue


title: BMDMs, KO rep2

city: shang hai

last: Fan

address: song jiang qu

institute: Shanghai jiao tong university

description: Library name: Pfkfb1 KO-5

data_processing:
Illumina adapter sequences were trimmed using Skewer (v0.2.2). And the quality checking was performed using FastQC (v0.11.5)
Then clean reads were mapped to mouse genome version GRCm38 using STAR (v2.5.3a)
StringTie (v1.3.1c) was used to generate gene expression data and differential gene expression
Differentially expression analysis between matched case and control samples were performed by the R package DESeq2 version 1.16.1 with the likelihood ratio test option
Gene ontology analysis was performed using TopGO (https://www.bioconductor.org/packages/release/bioc/html/topGO.html); pathway analysis was performed using the KEGG PATHWAY Database (https://www.genome.jp/kegg/pathway.html); Gene Set Enrichment Analysis was performed using the R package clusterProfiler (v3.14.3, http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html), The gmt file used is the kegg.gmt file corresponding to the species, and the filtering standard is Pvalue<0.05.
Assembly: GRCm38
Supplementary files format and content: txt file includes FPKM values for each sample

source_name: BMDMs

growth_protocol: BMDMs were cultured in DMEM/high glucose medium (HyClone) supplemented with 10% fetal bovine serum (FBS) (Gibco), 55 μM 2-Me (Gibco), 1% Penicillin/streptomycin/Amphotericin B (Solarbio), 100 μM Non-Essential amino acids (Solarbio), 10 mM HEPES (Solarbio), 1 mM Sodium pyruvate (Solarbio) and 20 ng/ml macrophage colony-stimulating factor (M-CSF) (PeproTech) for 7 days, at 37℃, 5% CO2. The culture medium was partially replaced every 2 days.

extract_protocol:
Samples were washed twice with PBS, and RNA was extracted with RNAiso Plus (Takara Bio).
RNA libraries were prepared using the VVAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina (NR605-0, Vazyme)

value: BMDMs

value: Pfkfb1 KO


title: BMDMs, KO rep1

description: Library name: Pfkfb1 KO-4


title: BMDMs, WT rep2

description: Library name: WT-2


title: BMDMs, WT rep3

description: Library name: WT-6


title: BMDMs, WT rep1

description: Library name: WT-1


title: Female WT #1

description: Library name: 04_S11-Fgfr1pp


title: Blood_NLGF_W3_WGBS_Female2

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

description: Library name: T3_NLGF_F2_blood_WGBS

data_processing:
Raw reads were QC’d using FastQC and trimmed with TrimGalore.
Trimmed reads were aligned to the mm10 reference genome with Bismark using default parameters.
Deduplication was performed with deduplicate_bismark, followed by bismark_methylation_extractor with parameters –ignore 2, --ignore_r2 2, and --ignore_3prime_r2 2.
Differential methylation analysis was performed with methylKit using the coverage files from Bismark methylation extractor data as input (overdispersion = “MN” and test = ”Chisq”). The genome was tiled into non-overlapping 1kb tiles, that were merged based on the following parameters: CpG coverage threshold > 5, covered CpGs in the tile > 10, and tile present in > 3 samples per group.
Assembly: mm10
Supplementary files format and content: A txt file containing the coordinates and statistical metrics of all significant differentialy methylated reagions or DMRs

source_name: Blood

extract_protocol:
DNA from 60 hippocampus samples was extracted using the NEB Monarch Genomic DNA Purification Kit (Cat T3010, New England Biolabs) according to manufacturer's protocol. DNA from 60 blood samples was extracted using the Purgene Genomic DNA Purification from Blood kit (Cat D-5500, Qiagen) based on a modified version of the Puregene DNA purification from blood protocol (Gentra Systems). Briefly, cell lysis solution was added directly to the frozen blood at a 5:1 ratio and incubated at 55 °C overnight, followed by 40 min or 1,000 rpm agitation. The samples were cooled on ice and protein precipitation solution was added (1:3 ratio) followed by 1,000 rpm agitation and 16,000 g centrifugation for 1 min. The lysate was moved to a 1:1 ratio of isopropyl alcohol and centrifuged to pellet the DNA. Pellets were washed with 80% ethanol, air dried, and resuspended at 65 °C with 1,000 rpm agitation. The gDNA samples were then quantified with Qubit (Thermofisher) and Nanodrop (Thermofisher) and stored at -80 °C.
To generate whole genome bisulfite sequencing (WGBS) libraries for both hippocampus and blood,100 ng of gDNA was randomly sheared per sample with a Bioruptor Pico Sonicator (Diagenode) at 30:30 on/off for 15 cycles. Libraries were prepared with the NEBNext Ultra II Modules (New England Biolabs) and the NEBNext Methylated Adaptor (New England Biolabs), with size-selection to 200bp using Ampure beads (Beckman Coulter). Bisulfite conversion and subsequent cleanup was performed with the EZ DNA Methylation-Gold Kit (Zymo Research). The converted libraries were PCR amplified using NEBNext Q5U polymerase and the NEBNext Multiplex Oligos for Illumina (New England Biolabs) for unique library barcoding.

value: Blood

value: APP-nlgf


title: Blood_NLGF_W3_WGBS_Female1

description: Library name: T3_NLGF_F1_blood_WGBS


title: Pro_CTCF-Nm_rep2

description: Library name: Sample 5


title: Blood_NLGF_W3_WGBS_Female3

description: Library name: T3_NLGF_F3_blood_WGBS


title: Blood_NLGF_W3_WGBS_Female4

description: Library name: T3_NLGF_F4_blood_WGBS


title: Female mutant #2

description: Library name: 02_S9-Fgfr1


title: Blood_NLGF_W3_WGBS_Female5

description: Library name: T3_NLGF_F5_blood_WGBS


title: Blood_NLGF_W3_WGBS_Male1

description: Library name: T3_NLGF_M1_blood_WGBS


title: Astrocytes, TDP-43_Q331K, vehicle, rep1

description:
Library name: TG_vehicle_REP1
Omomyc_normalized_counts.tsv
Omomyc_raw_counts.tsv


title: Blood_NLGF_W3_WGBS_Male2

description: Library name: T3_NLGF_M2_blood_WGBS


title: Blood_NLGF_W3_WGBS_Male3

description: Library name: T3_NLGF_M3_blood_WGBS


title: Blood_NLGF_W3_WGBS_Male5

description: Library name: T3_NLGF_M5_blood_WGBS


title: Blood_WT_W3_WGBS_Female2

description: Library name: T3_W_F2_blood_WGBS

value: Wild-type


title: BMDMs, KO rep3

description: Library name: Pfkfb1 KO-13


title: Blood_WT_W3_WGBS_Female3

description: Library name: T3_W_F3_blood_WGBS


title: Blood_WT_W3_WGBS_Male1

description: Library name: T3_W_M1_blood_WGBS


title: Blood_WT_W3_WGBS_Female4

description: Library name: T3_W_F4_blood_WGBS


title: Blood_NLGF_W3_WGBS_Male4

description: Library name: T3_NLGF_M4_blood_WGBS


title: Blood_WT_W3_WGBS_Male2

description: Library name: T3_W_M2_blood_WGBS


title: Blood_WT_W3_WGBS_Male4

description: Library name: T3_W_M4_blood_WGBS


title: Blood_WT_W3_WGBS_Male5

description: Library name: T3_W_M5_blood_WGBS


title: Blood_WT_W3_WGBS_Male3

description: Library name: T3_W_M3_blood_WGBS


title: Blood_NLGF_W8_WGBS_Female3

description: Library name: T8_NLGF_F3_blood_WGBS


title: Blood_NLGF_W8_WGBS_Female2

description: Library name: T8_NLGF_F2_blood_WGBS


title: Blood_NLGF_W8_WGBS_Female4

description: Library name: T8_NLGF_F4_blood_WGBS


title: Blood_NLGF_W8_WGBS_Female1

description: Library name: T8_NLGF_F1_blood_WGBS


title: Blood_NLGF_W8_WGBS_Male1

description: Library name: T8_NLGF_M1_blood_WGBS


title: Blood_NLGF_W8_WGBS_Male3

description: Library name: T8_NLGF_M3_blood_WGBS


title: Blood_NLGF_W8_WGBS_Male2

description: Library name: T8_NLGF_M2_blood_WGBS


title: Blood_NLGF_W8_WGBS_Female5

description: Library name: T8_NLGF_F5_blood_WGBS


title: Blood_NLGF_W8_WGBS_Male5

description: Library name: T8_NLGF_M5_blood_WGBS


title: Blood_NLGF_W8_WGBS_Male4

description: Library name: T8_NLGF_M4_blood_WGBS


title: Blood_WT_W8_WGBS_Female1

description: Library name: T8_W_F1_blood_WGBS


title: Blood_WT_W8_WGBS_Female2

description: Library name: T8_W_F2_blood_WGBS


title: Blood_WT_W3_WGBS_Female5

description: Library name: T3_W_F5_blood_WGBS


title: Blood_WT_W8_WGBS_Female4

description: Library name: T8_W_F4_blood_WGBS


title: Blood_WT_W3_WGBS_Female1

description: Library name: T3_W_F1_blood_WGBS


title: Blood_WT_W8_WGBS_Female3

description: Library name: T8_W_F3_blood_WGBS


title: Blood_WT_W8_WGBS_Male3

description: Library name: T8_W_M3_blood_WGBS


title: Blood_WT_W8_WGBS_Male1

description: Library name: T8_W_M1_blood_WGBS


title: Blood_WT_W8_WGBS_Male2

description: Library name: T8_W_M2_blood_WGBS


title: Blood_NLGF_W24_WGBS_Female1

description: Library name: T24_NLGF_F1_blood_WGBS


title: Blood_WT_W8_WGBS_Male4

description: Library name: T8_W_M4_blood_WGBS


title: Blood_WT_W8_WGBS_Male5

description: Library name: T8_W_M5_blood_WGBS


title: Blood_NLGF_W24_WGBS_Female3

description: Library name: T24_NLGF_F3_blood_WGBS


title: Blood_NLGF_W24_WGBS_Female5

description: Library name: T24_NLGF_F5_blood_WGBS


title: Blood_NLGF_W24_WGBS_Male1

description: Library name: T24_NLGF_M1_blood_WGBS


title: Blood_NLGF_W24_WGBS_Male2

description: Library name: T24_NLGF_M2_blood_WGBS


title: Blood_NLGF_W24_WGBS_Male5

description: Library name: T24_NLGF_M5_blood_WGBS


title: Blood_NLGF_W24_WGBS_Male4

description: Library name: T24_NLGF_M4_blood_WGBS


title: Blood_WT_W24_WGBS_Female2

description: Library name: T24_W_F2_blood_WGBS


title: Blood_WT_W24_WGBS_Female4

description: Library name: T24_W_F4_blood_WGBS


title: Blood_WT_W24_WGBS_Female3

description: Library name: T24_W_F3_blood_WGBS


title: Blood_NLGF_W24_WGBS_Female4

description: Library name: T24_NLGF_F4_blood_WGBS


title: Blood_WT_W24_WGBS_Female5

description: Library name: T24_W_F5_blood_WGBS


title: Blood_WT_W24_WGBS_Female1

description: Library name: T24_W_F1_blood_WGBS


title: Blood_WT_W24_WGBS_Male1

description: Library name: T24_W_M1_blood_WGBS


title: Blood_WT_W24_WGBS_Male2

description: Library name: T24_W_M2_blood_WGBS


title: Blood_WT_W8_WGBS_Female5

description: Library name: T8_W_F5_blood_WGBS


title: Blood_WT_W24_WGBS_Male3

description: Library name: T24_W_M3_blood_WGBS


title: Blood_WT_W24_WGBS_Male4

description: Library name: T24_W_M4_blood_WGBS


title: Blood_NLGF_W24_WGBS_Male3

description: Library name: T24_NLGF_M3_blood_WGBS


title: Hippocampus_NLGF_W3_WGBS_Female1

description: Library name: T3_NLGF_F1_Hipp_WGBS

source_name: Hippocampus

value: Hippocampus


title: Blood_NLGF_W24_WGBS_Female2

description: Library name: T24_NLGF_F2_blood_WGBS


title: Hippocampus_NLGF_W3_WGBS_Female4

description: Library name: T3_NLGF_F4_Hipp_WGBS


title: Hippocampus_NLGF_W3_WGBS_Female3

description: Library name: T3_NLGF_F3_Hipp_WGBS


title: Hippocampus_NLGF_W3_WGBS_Female2

description: Library name: T3_NLGF_F2_Hipp_WGBS


title: Hippocampus_NLGF_W3_WGBS_Female5

description: Library name: T3_NLGF_F5_Hipp_WGBS


title: Hippocampus_NLGF_W3_WGBS_Male3

description: Library name: T3_NLGF_M3_Hipp_WGBS


title: Hippocampus_NLGF_W3_WGBS_Male4

description: Library name: T3_NLGF_M4_Hipp_WGBS


title: Hippocampus_NLGF_W3_WGBS_Male1

description: Library name: T3_NLGF_M1_Hipp_WGBS


title: Hippocampus_NLGF_W3_WGBS_Male2

description: Library name: T3_NLGF_M2_Hipp_WGBS


title: Hippocampus_NLGF_W3_WGBS_Male5

description: Library name: T3_NLGF_M5_Hipp_WGBS


title: Hippocampus_WT_W3_WGBS_Female3

description: Library name: T3_W_F3_Hipp_WGBS


title: Hippocampus_WT_W3_WGBS_Female4

description: Library name: T3_W_F4_Hipp_WGBS


title: Hippocampus_WT_W3_WGBS_Female2

description: Library name: T3_W_F2_Hipp_WGBS


title: Hippocampus_WT_W3_WGBS_Female5

description: Library name: T3_W_F5_Hipp_WGBS


title: Hippocampus_WT_W3_WGBS_Male2

description: Library name: T3_W_M2_Hipp_WGBS


title: Hippocampus_WT_W3_WGBS_Male3

description: Library name: T3_W_M3_Hipp_WGBS


title: Hippocampus_WT_W3_WGBS_Male4

description: Library name: T3_W_M4_Hipp_WGBS


title: Hippocampus_WT_W3_WGBS_Male1

description: Library name: T3_W_M1_Hipp_WGBS


title: Hippocampus_WT_W3_WGBS_Male5

description: Library name: T3_W_M5_Hipp_WGBS


title: Hippocampus_NLGF_W8_WGBS_Female2

description: Library name: T8_NLGF_F2_Hipp_WGBS


title: Blood_WT_W24_WGBS_Male5

description: Library name: T24_W_M5_blood_WGBS


title: Hippocampus_NLGF_W8_WGBS_Female4

description: Library name: T8_NLGF_F4_Hipp_WGBS


title: Hippocampus_NLGF_W8_WGBS_Female3

description: Library name: T8_NLGF_F3_Hipp_WGBS


title: Hippocampus_NLGF_W8_WGBS_Male2

description: Library name: T8_NLGF_M2_Hipp_WGBS


title: Hippocampus_NLGF_W8_WGBS_Male3

description: Library name: T8_NLGF_M3_Hipp_WGBS


title: Hippocampus_NLGF_W8_WGBS_Female5

description: Library name: T8_NLGF_F5_Hipp_WGBS


title: Hippocampus_WT_W3_WGBS_Female1

description: Library name: T3_W_F1_Hipp_WGBS


title: Hippocampus_NLGF_W8_WGBS_Male4

description: Library name: T8_NLGF_M4_Hipp_WGBS


title: Hippocampus_NLGF_W8_WGBS_Male1

description: Library name: T8_NLGF_M1_Hipp_WGBS


title: Hippocampus_NLGF_W8_WGBS_Male5

description: Library name: T8_NLGF_M5_Hipp_WGBS


title: Hippocampus_WT_W8_WGBS_Female1

description: Library name: T8_W_F1_Hipp_WGBS


title: Hippocampus_WT_W8_WGBS_Female2

description: Library name: T8_W_F2_Hipp_WGBS


title: Hippocampus_WT_W8_WGBS_Female3

description: Library name: T8_W_F3_Hipp_WGBS


title: Hippocampus_WT_W8_WGBS_Female4

description: Library name: T8_W_F4_Hipp_WGBS


title: Hippocampus_WT_W8_WGBS_Male1

description: Library name: T8_W_M1_Hipp_WGBS


title: Hippocampus_WT_W8_WGBS_Male2

description: Library name: T8_W_M2_Hipp_WGBS


title: Hippocampus_WT_W8_WGBS_Male5

description: Library name: T8_W_M5_Hipp_WGBS


title: Hippocampus_WT_W8_WGBS_Male3

description: Library name: T8_W_M3_Hipp_WGBS


title: Hippocampus_NLGF_W24_WGBS_Female1

description: Library name: T24_NLGF_F1_Hipp_WGBS


title: Hippocampus_NLGF_W24_WGBS_Female5

description: Library name: T24_NLGF_F5_Hipp_WGBS


title: Hippocampus_NLGF_W24_WGBS_Female4

description: Library name: T24_NLGF_F4_Hipp_WGBS


title: Hippocampus_NLGF_W24_WGBS_Male1

description: Library name: T24_NLGF_M1_Hipp_WGBS


title: Hippocampus_WT_W8_WGBS_Male4

description: Library name: T8_W_M4_Hipp_WGBS


title: Hippocampus_NLGF_W24_WGBS_Female2

description: Library name: T24_NLGF_F2_Hipp_WGBS


title: Hippocampus_NLGF_W24_WGBS_Male3

description: Library name: T24_NLGF_M3_Hipp_WGBS


title: Hippocampus_NLGF_W24_WGBS_Female3

description: Library name: T24_NLGF_F3_Hipp_WGBS


title: Hippocampus_NLGF_W24_WGBS_Male5

description: Library name: T24_NLGF_M5_Hipp_WGBS


title: Hippocampus_NLGF_W24_WGBS_Male2

description: Library name: T24_NLGF_M2_Hipp_WGBS


title: Hippocampus_NLGF_W8_WGBS_Female1

description: Library name: T8_NLGF_F1_Hipp_WGBS


title: Hippocampus_NLGF_W24_WGBS_Male4

description: Library name: T24_NLGF_M4_Hipp_WGBS


title: Hippocampus_WT_W24_WGBS_Female1

description: Library name: T24_W_F1_Hipp_WGBS


title: Hippocampus_WT_W24_WGBS_Female2

description: Library name: T24_W_F2_Hipp_WGBS


title: Hippocampus_WT_W8_WGBS_Female5

description: Library name: T8_W_F5_Hipp_WGBS


title: Hippocampus_WT_W24_WGBS_Male2

description: Library name: T24_W_M2_Hipp_WGBS


title: Hippocampus_WT_W24_WGBS_Male3

description: Library name: T24_W_M3_Hipp_WGBS


title: Hippocampus_WT_W24_WGBS_Female4

description: Library name: T24_W_F4_Hipp_WGBS


title: Hippocampus_WT_W24_WGBS_Female5

description: Library name: T24_W_F5_Hipp_WGBS


title: Hippocampus_WT_W24_WGBS_Female3

description: Library name: T24_W_F3_Hipp_WGBS


title: Hippocampus_NLGF_W3_RNAseq_Female3

description: Library name: T3_NLGF_F3_RNA

data_processing:
Raw reads were QC’d using FastQC and aligned to the mm10 genome using STAR.
The raw gene counts table was generated using custom bash scripts and filtered by the filterByExpr function from edgeR with default parameters and defining group membership as the combination of age and genotype.
DESeq2 was used to perform differential analysis, to compare gene expression between wild-type and AppNL-G-F at each age separately with sex as a covariate.
Assembly: mm10
Supplementary files format and content: A text file containing all the differentially expressed genes (p-adjusted<0.05) between WT and APP-NLGF mice at three time points.

extract_protocol:
RNA was extracted from 60 fresh frozen hippocampus aliquotes using the NEB Monarch Total RNA Miniprep Kit (Cat T2010S, New England Biolabs)
RNA-seq libraries were generated from 1ug of total RNA using the NEBNext rRNA Depletion Kit v2 for human/mouse/rat (New England Biolabs) according to manufacturer's protocol.

tag: age

value: 3 weeks


title: Hippocampus_WT_W24_WGBS_Male5

description: Library name: T24_W_M5_Hipp_WGBS


title: Hippocampus_NLGF_W3_RNAseq_Female1

description: Library name: T3_NLGF_F1_RNA


title: Hippocampus_NLGF_W3_RNAseq_Female5

description: Library name: T3_NLGF_F5_RNA


title: Hippocampus_NLGF_W3_RNAseq_Female4

description: Library name: T3_NLGF_F4_RNA


title: Hippocampus_WT_W24_WGBS_Male1

description: Library name: T24_W_M1_Hipp_WGBS


title: Hippocampus_NLGF_W3_RNAseq_Female2

description: Library name: T3_NLGF_F2_RNA


title: Hippocampus_NLGF_W3_RNAseq_Male4

description: Library name: T3_NLGF_M4_RNA


title: Hippocampus_NLGF_W3_RNAseq_Male2

description: Library name: T3_NLGF_M2_RNA


title: Hippocampus_NLGF_W3_RNAseq_Male3

description: Library name: T3_NLGF_M3_RNA


title: Hippocampus_WT_W3_RNAseq_Female1

description: Library name: T3_W_F1_RNA


title: Hippocampus_NLGF_W3_RNAseq_Male1

description: Library name: T3_NLGF_M1_RNA


title: Hippocampus_WT_W3_RNAseq_Female5

description: Library name: T3_W_F5_RNA


title: Hippocampus_WT_W24_WGBS_Male4

description: Library name: T24_W_M4_Hipp_WGBS


title: Hippocampus_WT_W3_RNAseq_Female3

description: Library name: T3_W_F3_RNA


title: Hippocampus_WT_W3_RNAseq_Female2

description: Library name: T3_W_F2_RNA


title: Hippocampus_NLGF_W3_RNAseq_Male5

description: Library name: T3_NLGF_M5_RNA


title: Hippocampus_WT_W3_RNAseq_Female4

description: Library name: T3_W_F4_RNA


title: Hippocampus_WT_W3_RNAseq_Male1

description: Library name: T3_W_M1_RNA


title: Hippocampus_WT_W3_RNAseq_Male3

description: Library name: T3_W_M3_RNA


title: Hippocampus_WT_W3_RNAseq_Male5

description: Library name: T3_W_M5_RNA


title: Hippocampus_WT_W3_RNAseq_Male4

description: Library name: T3_W_M4_RNA


title: Hippocampus_NLGF_W8_RNAseq_Female1

description: Library name: T8_NLGF_F1_RNA


title: Hippocampus_NLGF_W8_RNAseq_Female5

description: Library name: T8_NLGF_F5_RNA

value: 8 weeks


title: Hippocampus_NLGF_W8_RNAseq_Female3

description: Library name: T8_NLGF_F3_RNA


title: Hippocampus_NLGF_W8_RNAseq_Male2

description: Library name: T8_NLGF_M2_RNA


title: Hippocampus_NLGF_W8_RNAseq_Male4

description: Library name: T8_NLGF_M4_RNA


title: Hippocampus_NLGF_W8_RNAseq_Male5

description: Library name: T8_NLGF_M5_RNA


title: Hippocampus_WT_W8_RNAseq_Male3

description: Library name: T8_W_M3_RNA


title: Hippocampus_WT_W8_RNAseq_Male4

description: Library name: T8_W_M4_RNA


title: Hippocampus_NLGF_W8_RNAseq_Female2

description: Library name: T8_NLGF_F2_RNA


title: Hippocampus_NLGF_W8_RNAseq_Male3

description: Library name: T8_NLGF_M3_RNA


title: Hippocampus_WT_W8_RNAseq_Male2

description: Library name: T8_W_M2_RNA


title: Hippocampus_WT_W8_RNAseq_Female3

description: Library name: T8_W_F3_RNA


title: Hippocampus_WT_W3_RNAseq_Male2

description: Library name: T3_W_M2_RNA


title: Hippocampus_WT_W8_RNAseq_Female4

description: Library name: T8_W_F4_RNA


title: Hippocampus_NLGF_W24_RNAseq_Female1

description: Library name: T24_NLGF_F1_RNA

value: 24 weeks


title: Hippocampus_NLGF_W24_RNAseq_Female3

description: Library name: T24_NLGF_F3_RNA


title: Hippocampus_WT_W8_RNAseq_Female5

description: Library name: T8_W_F5_RNA


title: Hippocampus_NLGF_W24_RNAseq_Female2

description: Library name: T24_NLGF_F2_RNA


title: Hippocampus_WT_W8_RNAseq_Male1

description: Library name: T8_W_M1_RNA


title: Hippocampus_WT_W8_RNAseq_Male5

description: Library name: T8_W_M5_RNA


title: Hippocampus_WT_W8_RNAseq_Female1

description: Library name: T8_W_F1_RNA


title: Hippocampus_NLGF_W24_RNAseq_Female4

description: Library name: T24_NLGF_F4_RNA


title: Hippocampus_NLGF_W8_RNAseq_Male1

description: Library name: T8_NLGF_M1_RNA


title: Hippocampus_NLGF_W8_RNAseq_Female4

description: Library name: T8_NLGF_F4_RNA


title: Hippocampus_NLGF_W24_RNAseq_Female5

description: Library name: T24_NLGF_F5_RNA


title: Hippocampus_NLGF_W24_RNAseq_Male2

description: Library name: T24_NLGF_M2_RNA


title: Hippocampus_NLGF_W24_RNAseq_Male1

description: Library name: T24_NLGF_M1_RNA


title: Hippocampus_WT_W8_RNAseq_Female2

description: Library name: T8_W_F2_RNA


title: Hippocampus_NLGF_W24_RNAseq_Male3

description: Library name: T24_NLGF_M3_RNA


title: Hippocampus_NLGF_W24_RNAseq_Male5

description: Library name: T24_NLGF_M5_RNA


title: Hippocampus_NLGF_W24_RNAseq_Male4

description: Library name: T24_NLGF_M4_RNA


title: Hippocampus_WT_W24_RNAseq_Female1

description: Library name: T24_W_F1_RNA


title: Hippocampus_WT_W24_RNAseq_Female3

description: Library name: T24_W_F3_RNA


title: Hippocampus_WT_W24_RNAseq_Female2

description: Library name: T24_W_F2_RNA


title: Hippocampus_WT_W24_RNAseq_Male1

description: Library name: T24_W_M1_RNA


title: Hippocampus_WT_W24_RNAseq_Female5

description: Library name: T24_W_F5_RNA


title: Hippocampus_WT_W24_RNAseq_Male2

description: Library name: T24_W_M2_RNA


title: Hippocampus_WT_W24_RNAseq_Male3

description: Library name: T24_W_M3_RNA


title: Hippocampus_WT_W24_RNAseq_Male5

description: Library name: T24_W_M5_RNA


title: Hippocampus_WT_W24_RNAseq_Female4

description: Library name: T24_W_F4_RNA


title: Hippocampus_WT_W3_scATAC_Female.pool

description: Library name: T3_W_Fpool_scATAC

library_source: genomic single cell

data_processing:
Raw scATAC-seq data was processed using the scitools package, with reads demultiplexed, mapped to mm10, and filtered for quality.
ArchR was used for cell filtering, clustering via LSI, and UMAP visualization, identifying 21 clusters, four of which remained unclassified. Gene activity scores determined marker genes, aiding manual cluster annotation.
Peaks were called at the pseudo-bulk level by age, genotype, and cell type. Excitatory and inhibitory neurons were further analyzed for differential chromatin accessibility between WT and AppNL-G-F across ages, using ArchR.
Assembly: mm10
Supplementary files format and content: bed files, and corresponding index files, containing genome coordinates of all scATAC fragments.

extract_protocol:
Hippocampal nuclei were isolated by pooling tissue from five male and five female replicates per age/genotype group, yielding 12 pools. Nuclei were extracted via homogenization, filtration, and centrifugation.
Extracted nuclei were tagmented with Tn5 transposase and washed. Multiplexed nuclei were processed using the 10x Genomics Single Cell ATAC v2 Kit, incorporating ScaleBio indexing. Libraries were quantified and sequenced on the Illumina NextSeq2000 with paired-end reads.


title: Hippocampus_NLGF_W3_scATAC_Female.pool

description: Library name: T3_N_Fpool_scATAC


title: Hippocampus_NLGF_W8_scATAC_Female.pool

description: Library name: T8_N_Fpool_scATAC


title: Hippocampus_WT_W24_RNAseq_Male4

description: Library name: T24_W_M4_RNA


title: Hippocampus_NLGF_W3_scATAC_Male.pool

description: Library name: T3_N_Mpool_scATAC


title: sen1-md (mutant), 2hr after Spo medium, Rep2

city: Stony Brook

first: Ed

last: Luk

state: NY

address: 100 Nicolls Rd, Life Sciences Building

department: Biochemistry and Cell Biology

institute: Stony Brook University

description: Library name: sen1-md_Rep2_dRNA-seq

data_processing:
FASTQ files were processed using the wf-transcriptomes pipeline implemented in nextflow (Epi2Me Labs, version 25.04.06)( https://nanoporetech.com/products/analyse/epi2me) with the -direct_rna option enabled.  Reads were aligned to the SK1 reference genome using minimaps2 with a preset override of -x splice -uf -k 14 -G1k, optimized for direct RNA reads with short introns.  The reference genome was indexed in minimap2 with the -k 15 setting. The workflow produced aligned BAM files for downstream analysis.
The genomic coordinates of CUTs, SUTs, and ORF-T were originally annotated based on the S288C genome (version V56, 2007-04-06) (XU et al. 2009). These coordinates were first converted to genome version V64 (2011-02-3) using liftOver and subsequently remapped to the SK1 genome. This was achieved by retrieving the DNA sequences corresponding to the annotated regions with bedtools getfasta and aligned to the SK1 genome using minimap2. The resulting SAM alignment files were converted to sorted and indexed BAM files with samtools, which were then transformed to BED format using bedtools bamtobed for downstream analysis.
Differential gene expression was performed as follows. Read count quantification was determined using featureCounts (v2.1.1; Subread package). Reads were assigned to annotated ORF-T features defined in the SK1 genome using the following options: -F SAF-format annotation) and -O (minimum MAPQ > 20). The resulting count matrix was analyzed in R Studio (version 2025.09.1) with the DESeq2 package. Raw counts from two SEN1 and two sen1-md dRNA-seq replicates were normalized for library size, and differential expression analysis was performed using DESeq2’s negative binomial model with Wald test statistics. Genes with a false discovery rate (FDR) < 0.01 and an absolute log2 fold change > 1 were considered significantly differentially expressed.
Assembly: SK1 genome assembly (PacBio 2016) (https://yjx1217.github.io/Yeast_PacBio_2016/data/)
Supplementary files format and content: BAM files

organism: Saccharomyces cerevisiae

growth_protocol: Two biological replicates of SEN1 and sen1-md were incubated for two hours after transfer to Spo medium. Five ml cells (approximately 1.5x108 cells) were harvested by centrifugation at 2851 x g for 5 minutes at 4°C. The cell pellets were washed with 1 mL Molecular Grade water to remove any residual medium. Cells were then centrifuged at 16,000 x g for 15 seconds at 4°C and the supernatants were removed. Pellets were flash frozen in liquid nitrogen and stored at -80°C.

extract_protocol:
Total RNA was extracted using the RiboPure RNA Purification Yeast kit (Cat#: AM1926; Life Technologies).
Total RNA (12.5 ug) was subjected to ribosomal RNA (rRNA) depletion using magnetic beads coated with antisense probes targeting the 25S, 18S, 5.8S, and 5S rRNAs. The resulting rRNA-depleted samples were purified using RNAClean XP beads, followed by polyadenylation with the E.coli Poly(A) Polymerase. Reactions were quenched using EDTA and purified again with the RNAClean XP beads before proceeding to library preparation using the Oxford Nanopore Techonlogy direct RNA-sequencing kit, according to the manufacturer protocol.


title: Hippocampus_WT_W3_scATAC_Male.pool

description: Library name: T3_W_Mpool_scATAC


title: sen1-md (mutant), 2hr after Spo medium, Rep1

description: Library name: sen1-md_Rep1_dRNA-seq


title: Hippocampus_WT_W8_scATAC_Male.pool

description: Library name: T8_W_Mpool_scATAC


title: SEN1 (wild type), 2hr after Spo medium, Rep2

description: Library name: SEN1_Rep2_dRNA-seq


title: Hippocampus_NLGF_W8_scATAC_Male.pool

description: Library name: T8_N_Mpool_scATAC


title: SEN1 (wild type), 2hr after Spo medium, Rep1

description: Library name: SEN1_Rep1_dRNA-seq


title: Hippocampus_WT_W8_scATAC_Female.pool

description: Library name: T8_W_Fpool_scATAC


title: 100% Mouse Spleen [205041760090_R06C01]

type: genomic

first: Wanding

last: Zhou

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe software v1.22, openSesame and IDATs are de-identified to mask SNP probe readings using the deIdentifiy() function.
Normalized average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: 100% Mouse Spleen

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using commercially available QIAGEN QIAamp Mini Kit (QIAGEN, 51304), following the manufacturer’s protocol.

tag: mousepercent


title: 100% Mouse Fat [205041760090_R05C01]

source_name: 100% Mouse Fat


title: Hippocampus_NLGF_W24_scATAC_Female.pool

description: Library name: T24_N_Fpool_scATAC


title: 5% Human Blood, 95% Mouse Spleen [205041760090_R04C01]

organism:
Homo sapiens
Mus musculus

source_name: 5% Human Blood, 95% Mouse Spleen


title: Hippocampus_WT_W24_scATAC_Female.pool

description: Library name: T24_W_Fpool_scATAC


title: Hippocampus_NLGF_W24_scATAC_Male.pool

description: Library name: T24_N_Mpool_scATAC


title: 10% Human Blood, 90% Mouse Spleen [205041760090_R03C01]

source_name: 10% Human Blood, 90% Mouse Spleen


title: 15% Human Blood, 85% Mouse Spleen [205041760090_R02C01]

source_name: 15% Human Blood, 85% Mouse Spleen


title: 25% Human Blood, 75% Mouse Spleen [205041760090_R01C01]

source_name: 25% Human Blood, 75% Mouse Spleen


title: PC Scar

city: Houston

first: Jinho

last: Jang

state: Texas

address: 1755 Wyndale Street

institute: MD Anderson Cancer Center

description:
Library name: Scar
Organoid

data_processing:
Cell Ranger (cloud version, 10x Genomics) was used to align the raw sequencing reads to the mouse reference genomes (mm10) to generate the 10x matrices.Then, Scanpy (v1.8.2) was used for processing the 10x matrices
Assembly: mm10 mouse reference genome.
Supplementary files format and content: files included in filtered_feature_bc_matrix from cellranger output

source_name: Esophageal Cancer

extract_protocol:
PC cells with constitutive Cas9 expression were transfected with a barcode library using Lipofectamine 3000, expanded for three passages, sorted via flow cytometry to isolate RFP-positive live cells (~1 million sorted, ~20,000 recovered), and processed for scRNA-seq.
DNA libraries were generated for gene expression (10× Genomics 3' v2 kit), barcode, and scar regions, with barcodes amplified using root and nested PCR, purified via AMPure XP beads, indexed with dual-index primers, and sequenced on Illumina NovaSeq, followed by mapping with CellRanger.

value: Esophageal Cancer


title: 50% Human Blood, 50% Mouse Spleen [205041760124_R08C01]

source_name: 50% Human Blood, 50% Mouse Spleen


title: PC GEX

description:
Library name: GEX
Organoid


title: PC barcodes

description:
Library name: PC
Organoid


title: 75% Human Blood, 25% Mouse Spleen [205041760124_R07C01]

source_name: 75% Human Blood, 25% Mouse Spleen


title: 90% Human Blood, 10% Mouse Spleen [205041760124_R05C01]

source_name: 90% Human Blood, 10% Mouse Spleen


title: CD4+ T cells, AAV-PHP.eB-Gdf15, EAE, Rep5

city: Hamburg

first: Jana

last: Sonner

state: Hamburg

address: Martinistr. 52

department: ZMNH

institute: UKE

description: Library name: Id46_AE_GDF_5

data_processing:
Read quality was evluated with fastqc v0.11.5
Reads were alligned with STAR-2.7.9a
Gene counts were calculated with featureCounts v1.5.1
Assembly: GRCm39r108
Supplementary files format and content: Raw counts as tab seperated values
Supplementary files format and content: DESeq2 normalized counts as tab seperated values

source_name: spleen

extract_protocol:
Qiagen Rneasy Mini Kit, Dnase I treatment on column
Illumina TruSeq stranded mRNA Library Prep Kit

value: spleen

value: CD4+ T cell

tag: disease state

value: EAE day 9


title: CD4+ T cells, AAV-PHP.eB-Gdf15, EAE, Rep1

description: Library name: Id38_AE_GDF_1


title: CD4+ T cells, AAV-PHP.eB-eGFP, EAE, Rep5

description: Library name: Id45_AE_GFP_5


title: CD4+ T cells, AAV-PHP.eB-Gdf15, EAE, Rep4

description: Library name: Id43_AE_GDF_4


title: CD4+ T cells, AAV-PHP.eB-eGFP, EAE, Rep4

description: Library name: Id44_AE_GFP_4


title: 95% Human Blood, 5% Mouse Spleen [205041760124_R04C01]

source_name: 95% Human Blood, 5% Mouse Spleen


title: 50% Human Blood, 50% Mouse Fat [205041760003_R07C01]

source_name: 50% Human Blood, 50% Mouse Fat


title: CD4+ T cells, AAV-PHP.eB-Gdf15, EAE, Rep2

description: Library name: Id40_AE_GDF_2


title: 10% Human Blood, 90% Mouse Fat [205041760124_R02C01]

source_name: 10% Human Blood, 90% Mouse Fat


title: CD4+ T cells, AAV-PHP.eB-eGFP, EAE, Rep3

description: Library name: Id41_AE_GFP_3


title: CD4+ T cells, AAV-PHP.eB-Gdf15, EAE, Rep3

description: Library name: Id42_AE_GDF_3


title: 15% Human Blood, 85% Mouse Fat [205041760124_R01C01]

source_name: 15% Human Blood, 85% Mouse Fat


title: 25% Human Blood, 75% Mouse Fat [205041760003_R08C01]

source_name: 25% Human Blood, 75% Mouse Fat


title: CD4+ T cells, AAV-PHP.eB-eGFP, EAE, Rep2

description: Library name: Id39_AE_GFP_2


title: 75% Human Blood, 25% Mouse Fat [205041760003_R06C01]

source_name: 75% Human Blood, 25% Mouse Fat


title: CD4+ T cells, AAV-PHP.eB-eGFP, EAE, Rep1

description: Library name: Id37_AE_GFP_1


title: Hippocampus_WT_W24_scATAC_Male.pool

description: Library name: T24_W_Mpool_scATAC

source_name: Hippocampus


title: 90% Human Blood, 10% Mouse Fat [205041760003_R04C01]

source_name: 90% Human Blood, 10% Mouse Fat


title: CD4+ T cells, AAV-PHP.eB-Gdf15, no EAE, Rep5

description: Library name: Id36_A_GDF_5

value: healthy


title: CD4+ T cells, AAV-PHP.eB-Gdf15, no EAE, Rep4

description: Library name: Id34_A_GDF_4


title: 95% Human Blood, 5% Mouse Fat [205041760003_R03C01]

source_name: 95% Human Blood, 5% Mouse Fat


title: 5% Human Blood, 95% Mouse Fat [205041760124_R03C01]

source_name: 5% Human Blood, 95% Mouse Fat


title: 85% Human Blood, 15% Mouse Spleen [205041760124_R06C01]

source_name: 85% Human Blood, 15% Mouse Spleen


title: 100% Human Blood [205041760003_R02C01]

source_name: 100% Human Blood


title: CD4+ T cells, AAV-PHP.eB-Gdf15, no EAE, Rep2

description: Library name: Id30_A_GDF_2


title: CD4+ T cells, AAV-PHP.eB-Gdf15, no EAE, Rep1

description: Library name: Id29_A_GDF_1


title: 100% Mouse Fat [204361720056_R07C01]

source_name: 100% Mouse Fat


title: CD4+ T cells, AAV-PHP.eB-Gdf15, no EAE, Rep3

description: Library name: Id32_A_GDF_3


title: 100% Human Blood [205041760090_R08C01]


title: CD4+ T cells, AAV-PHP.eB-eGFP, no EAE, Rep3

description: Library name: Id31_A_GFP_3


title: 100% Mouse Spleen [204361720056_R06C01]

source_name: 100% Mouse Spleen


title: 25% Human Blood, 75% Mouse Fat [204361720056_R04C01]


title: 100% Human Blood [205041760090_R07C01]


title: CD4+ T cells, AAV-PHP.eB-eGFP, no EAE, Rep1

description: Library name: Id27_A_GFP_1


title: CD4+ T cells, AAV-PHP.eB-eGFP, no EAE, Rep2

description: Library name: Id28_A_GFP_2


title: 50% Human Blood, 50% Mouse Fat [204361720056_R03C01]


title: CD4+ T cells, AAV-PHP.eB-eGFP, no EAE, Rep5

description: Library name: Id35_A_GFP_5


title: 75% Human Blood, 25% Mouse Fat [204361720056_R02C01]


title: 90% Human Blood, 10% Mouse Fat [204361720056_R01C01]


title: 85% Human Blood, 15% Mouse Fat [205041760003_R05C01]

source_name: 85% Human Blood, 15% Mouse Fat


title: 10% Human Blood, 90% Mouse Fat [204361720056_R05C01]


title: CD4+ T cells, AAV-PHP.eB-eGFP, no EAE, Rep4

description: Library name: Id33_A_GFP_4


title: 10% Human Blood, 90% Mouse Spleen [204339380081_R08C01]

source_name: 10% Human Blood, 90% Mouse Spleen


title: small extracellular vesicles from myotubes of type 2 diabetes donor, biological rep3

status: Public on Nov 21 2025

city: Oslo

first: Stian

last: Christiansen

address: Folke Bernadottes Vei 13D

country: Norway

institute: OsloMet

description:
micro-RNA from small extracellular vesicles from cultured myotubes of donor with type 2 diabetes
T2D_EO46

hyb_protocol: Samples were hybridized for 18 h at 48 °C on the Genechip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G30007.

data_processing: Normalization of signal intensities and quality control were done using the Affymetrix® GeneChip™ Command Console software

label: biotin

source_name: small extracellular vesicles from cultured human myotubes of a donor with type 2 diabetes

label_protocol: A total of 5 ng RNA was subjected to poly-A tailing, and biotin labelling using FlashTag Biotin HSR RNA Labeling kit (Thermo Fisher Scientific, Waltham, USA) following the manufacturer’s instructions.

growth_protocol: Human skeletal muscle cells were differentiated for 7 days in DMEM (5.5 mM glucose) containing 2% fetal bovine serum, 25 pM insulin, 50 µg/mL gentamicin, and 1.25 µg/mL amphotericin B in a humidified CO2 (5%) atmosphere at 37°C, with medium changed every two to three days.

extract_protocol: RNA was isolated from sEV samples using the miRNeasy Micro kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.

treatment_protocol: On day 6 of differentiation, cell medium was changed to serum free DMEM (5.5 mM glucose) with 25 pM insulin, gentamicin (50 µg/mL) and amphotericin B (1.25 µg/mL). The cells were incubated for another 24 h for synthesis and secretion of EVs, before media were collected, remnant cells and cell debris were removed by centrifugation at 450 g for 5 min. Next, the media underwent an initial centrifugation at 17 000 g for 30 min, before the supernatant was filtered through a 0.22 µm filter. The supernatant was transferred to Centricon-70 Plus 100 kDa Centrifugal Filter Columns and centrifuged at 3 500 g for 15 min. The filters were washed with phosphate buffered saline and further centrifuged at 3 500 g for 10 min. Finally, the filters were turned upside down, centrifuged at 1 000 g for 2 min, and the sEV filtrates were collected.

value: small extracellular vesicles from human myotubes

value: type 2 diabetes


title: 25% Human Blood, 75% Mouse Spleen [204339380081_R07C01]

source_name: 25% Human Blood, 75% Mouse Spleen


title: 50% Human Blood, 50% Mouse Spleen [204339380081_R06C01]

source_name: 50% Human Blood, 50% Mouse Spleen


title: 100% Human Blood [205041760003_R01C01]


title: 90% Human Blood, 10% Mouse Spleen [204339380081_R04C01]

source_name: 90% Human Blood, 10% Mouse Spleen


title: HEK293 eGFP-YAPdTAD sorbitol replicate 1 Hi-C

city: Chapel Hill

first: John Patrick

last: Flores

state: NC

address: 104 Manning Dr

institute: UNC Chapel Hill

description:
Library name: HEK293_eGFP_YAPdTAD_sorbitol_rep1
Hi-C of HEK293 cells at 1h

data_processing:
Adapters were trimmed using Trim Galore and read quality was assessed with FastQC and MultiQC. Transcript abundance was quantified using Salmon v1.10.0 with --validateMappings --seqBias --gcBias --posBias against the GENCODE hg38 transcriptome index. Quantifications were imported into R using tximeta, and counts were summarized to gene-level abundance using tximport. Genes with fewer than 10 counts in at least four samples were excluded. This GEO submission includes raw FASTQ files and gene-level expression matrices in both raw count and TPM formats.
Assembly: hg38 (GRCh38) human reference genome.
Supplementary files format and content: Hi-C contact matrices in .hic format (hg38 reference genome). Files include both individual biological replicates and merged replicates (megaMap) for each condition. Datasets include HCT116 wild-type cells (control and 1h sorbitol treatment), HEK293 wild-type cells from the Phanstiel lab (control and sorbitol treatment), HEK293 eGFP-YAP cells from the Cai lab (control and sorbitol treatment), HEK293 wild-type sorbitol timecourse (10m, 30m, 1h, 3h, 6h, 12h, 24h), and HEK293 eGFP-YAPdTAD cells from the Cai lab (control and sorbitol treatment). MegaMap files represent merged replicates for increased sequencing depth. Spike-in normalized loop calls at 5kb resolution are provided for eGFP-YAP and WT Phanstiel conditions. Differential loop analysis (diffLoops_WT_noDroso_10kb.rds) comparing control vs sorbitol treatment is provided for WT Phanstiel samples.

growth_protocol: HEK293T and HCT116 cells were cultured at 37 °C in a humidified incubator with 5% CO₂. HEK293T cells were maintained in DMEM supplemented with 10% FBS and penicillin/streptomycin. HCT116 cells were maintained in McCoy’s 5A medium supplemented with 10% FBS and penicillin/streptomycin. Cells were routinely monitored for mycoplasma contamination and maintained at ~70–80% confluence to ensure log-phase growth. Cells were harvested for experiments only when healthy and within 5–15 passages from thaw.

extract_protocol:
Cells were detached, counted, and pelleted at 4 °C. For RNA-seq, total RNA was extracted using a column-based RNA purification kit following the manufacturer’s instructions. For CUT&Tag and Hi-C, nuclei were isolated by gentle lysis in detergent-containing buffer prior to downstream processing.
In situ Hi-C libraries were prepared using MboI restriction digestion, fill-in with biotinylated nucleotides, proximity ligation, reverse crosslinking, and DNA purification. Libraries were size-selected and PCR-amplified prior to sequencing.

treatment_protocol: Hyperosmotic stress was induced by adding sorbitol to a final concentration of 200 mM for the indicated timepoints. Untreated samples were collected in parallel as controls. Cells were harvested at the specified time after treatment and processed immediately for downstream library preparation.

value: eGFP-YAPdTAD

value: 0.2M sorbitol for 1h


title: HEK293 eGFP-YAPdTAD control replicate 1 Hi-C

description:
Library name: HEK293_eGFP_YAPdTAD_control_rep1
Hi-C of HEK293 cells at 0h

value: untreated


title: HEK293 WT sorbitol 24h Hi-C

description:
Library name: HEK293_WT_timecourse_24h
Hi-C of HEK293 cells at 24h

value: wild type

value: 0.2M sorbitol for 24h


title: HEK293 WT sorbitol 12h Hi-C

description:
Library name: HEK293_WT_timecourse_12h
Hi-C of HEK293 cells at 12h

value: 0.2M sorbitol for 12h


title: tuNK, rep4

city: Lausanne

first: Yi

last: Wang

address: Rte Csntonale, Station9, MED1 2926

country: Switzerland

institute: EPFL

data_processing:
Raw reads underwent adapter trimming using BCL convert v3.9.3 (Illumina) and quality assessment using fastQC v0.11.9. Alignment and quantification of all RNA sequencing data were conducted using the STAR and Salmon methods via the nf-core v3.9 pipeline. Alignment was performed against the mouse genome GRCm38.
Assembly: mm10
Supplementary files format and content: salmon.merged.gene_counts.tsv
Supplementary files format and content: salmon.merged.gene_tpm.tsv

source_name: Spleen

extract_protocol:
Tissues (tumor and spleen) were dissected and dissected tissue were mechanically minced and digested through stirring in RPMI 1640 medium that contained collagenases Type IV (1 mg/mL, Thermo Fisher Scientific), dispase II (100 μg/mL, Sigma-Aldrich), hyaluronidase (100 μg/mL, Sigma-Aldrich), and DNase I (100 μg/mL, Sigma-Aldrich) at 37 °C for 60 min. Red blood cells were removed with ACK lysing buffer after digestion. TILs from tumor were enriched by density gradient centrifugation against Percoll (GE Healthcare) and resuspended in FACS buffer (1 × PBS containing 0.2 % BSA (wt / v), Sigma-Aldrich). Splenocytes and TILs were sorted by MACS (Miltenyi) and FACS (Sony). Total RNA extraction was carried out using the RNeasy Mini Kit (Qiagen), followed by quality assessment using TapeStation 4200 (Agilent Technologies) to ensure RNA integrity (scores > 7). High-quality RNA samples were then stored at −80°C until library preparation.
Libraries for mRNA-seq were prepared utilizing the NEBNext Ultra II Directional RNA Library Prep with PolyA method (NEB), starting from 20 ng RNA, in accordance with the NEBNext Ultra II Directional RNA Library Prep Kit, Version 4.0_4/21 (internal exp code CSX063). Each library, distinguished by unique dual indexes, was subsequently loaded onto a NovaSeq 6000 flow cell (Illumina) and sequenced following the manufacturer’s recommendations, yielding at least 40 million pairs of 60 nucleotides-long reads per sample.

value: Spleen

value: NK cell


title: HEK293 WT sorbitol 6h Hi-C

description:
Library name: HEK293_WT_timecourse_6h
Hi-C of HEK293 cells at 6h

value: 0.2M sorbitol for 6h


title: tuNK, rep3


title: HEK293 WT sorbitol 3h Hi-C

description:
Library name: HEK293_WT_timecourse_3h
Hi-C of HEK293 cells at 3h

value: 0.2M sorbitol for 3h


title: tuNK, rep1


title: HEK293 WT sorbitol 30min Hi-C

description:
Library name: HEK293_WT_timecourse_30min
Hi-C of HEK293 cells at 30min

value: 0.2M sorbitol for 30min


title: IL-15SA

data_processing:
Reads were demultiplexed according to cell barcodes and unique molecular identifiers (UMI), and poly-A tails and adaptor sequences were removed by Cutadapt using CeleScope v1.13.0. After quality control, reads were mapped to the reference genome (Mus_musculus_ensembl_92). Gene counts and UMI counts were acquired via feature Counts software. Gene expression matrix files for subsequent analyses were generated based on gene counts and UMI counts. Downstream data analysis was performed with the Seurat v4 pipeline and Scanpy pipeline78. Cells were first filtered based on three metrics: 1) the number of detected genes per cell between 500 to 5000; 2) the proportion of mitochondrial gene counts (UMIs from mitochondrial genes / total UMIs) must be less than 10 %; 3) the total counts of cells must between 1000 to 10000.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CT26_b2m-/- colon carcionma

extract_protocol:
Tumors were dissected and dissected tumors were mechanically minced and digested through stirring in RPMI 1640 medium that contained collagenases Type IV (1 mg/mL, Thermo Fisher Scientific), dispase II (100 μg/mL, Sigma-Aldrich), hyaluronidase (100 μg/mL, Sigma-Aldrich), and DNase I (100 μg/mL, Sigma-Aldrich) at 37 °C for 60 min. Red blood cells were removed with ACK lysing buffer after digestion. TILs were enriched by density gradient centrifugation against Percoll (GE Healthcare) and resuspended in FACS buffer (1 × PBS containing 0.2 % BSA (wt / v), Sigma-Aldrich), then sorted by MACS (Miltenyi) and FACS (Sony).
CD45.2+CD3-NKp46+ NK cells were sorted as described above, cells from the same treatment group were pooled together and resuspended at 3 × 105 cells/mL in PBS. Next, 100 µL cell resuspension was loaded onto a standard GEXSCOPE® microwell chip. scRNA-seq library was constructed using the GEXSCOPE® Single-Cell RNA Library Kit according to the manufacturer’s instructions (Singleron Biotechnologies GmbH). Individual libraries were diluted to equimolar and pooled for sequencing. Pools were sequenced on a lane of an S4 flow cell on an Illumina NovaSeq 6000 with 150 bp paired-end reads to a total depth of 90 GB per sample and an average read depth per cell of 50,000 reads. Raw reads were processed with FastQC to evaluate the quality of raw data.

value: CT26_b2m-/- colon carcionma


title: spNK, rep4

source_name: CT26_b2m-/- tumor

value: CT26_b2m-/- tumor


title: spNK, rep3


title: tuNK, rep2


title: HEK293 WT sorbitol 1h Hi-C

description:
Library name: HEK293_WT_timecourse_1h
Hi-C of HEK293 cells at 1h


title: HEK293 eGFP-YAP sorbitol replicate 4 Hi-C

description:
Library name: HEK293_eGFP_YAP_sorbitol_rep4
Hi-C of HEK293 cells at 1h

value: eGFP-YAP


title: HEK293 WT control 0h Hi-C

description:
Library name: HEK293_WT_timecourse_0h
Hi-C of HEK293 cells at 0h


title: HEK293 WT sorbitol 10min Hi-C

description:
Library name: HEK293_WT_timecourse_10min
Hi-C of HEK293 cells at 10min

value: 0.2M sorbitol for 10min


title: spNK, rep2


title: spNK, rep1


title: HEK293 eGFP-YAP control replicate 4 Hi-C

description:
Library name: HEK293_eGFP_YAP_control_rep4
Hi-C of HEK293 cells at 0h


title: HEK293 WT sorbitol replicate 3 Hi-C

description:
Library name: HEK293_WT_sorbitol_rep3
Hi-C of HEK293 cells at 1h


title: 75% Human Blood, 25% Mouse Spleen [204339380081_R05C01]

source_name: 75% Human Blood, 25% Mouse Spleen


title: 100% Human Blood [204339380081_R03C01]


title: HEK293 WT sorbitol replicate 2 Hi-C

description:
Library name: HEK293_WT_sorbitol_rep2
Hi-C of HEK293 cells at 1h