title: HeLa Nup88-GFP_48h_rep1

type: RNA

city: Kumamoto

first: Masaki

last: Makise

state: Kumamoto

address: 4-22-1 Ikeda, Nishi-ku

country: Japan

institute: Sojo University

description: Protein expression was induced for 48 hr in a culture medium containing 1 µg/mL DOX

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Ver.2.0 Microarray kit (Agilent, G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60k array slides (Scan Area 61×21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid 039494_D_F_20140813) to obtain background subtracted and spatially detrended Processed Signal intensities. The 75th percentile shift normalization was performed using Agilent GeneSpring GX 13.0.0.

source_name: HeLa Nup88-GFP, 48h, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer’s instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was prepared from cultured HeLa cells using the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

tag: cells

value: HeLa R19

tag: protein expression

value: tet on system


title: X32_PD_M_RT_matched_rnaseq_PD_g_ma_RT_M_73

status: Public on Mar 12 2026

type: SRA

city: Grand Rapids

first: Gerry

last: Coetzee

state: MI

address: 333 Bostwick Ave NE

department: CNS

country: USA

institute: Van Andel Research Institute

description:
202308001_2sampsremoved_ruvr_cpmmoretthanthird_contrastmatrix_model1.txt
202308001_2sampsremoved_ruvr_cpmmoretthanthird_limma_printfit_coefficients_model1.txt
202308001_2sampsremoved_ruvr_cpmmoretthanthird_limma_RNA_DE_Results_model1.txt
202308001_2sampsremoved_ruvr_cpmmoretthanthird_ruvnormcounts.txt

library_source: transcriptomic

data_processing:
RNA-seq: Following sequencing, fastq files were trimmed using Trimmomatic V0.36 and the settings: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
RNA-seq: Trimmed fastq files were aligned to HG19 using STAR v2.7 (Dobin and Gingeras, 2015).
RNA-seq: Alignments (bam files) were converted to feature counts using HTSeq v0.6.0 referenced against the ENSEMBLE annotation of HG19: Homo_sapiens.GRCh37.87.gtf counting against the feature “exon”, grouped by “gene_id”, and using the strand parameter “reverse”.  This set included exon locations for 57,905 genomic entities including pseudogenes, lncRNAs, and 20,356 protein coding genes.
RNA-seq: Alignments (bam files) were converted to .tdf files using  igvtools (V2.3.60) count -z 5 -w 25 -e 250
RNA-seq: The resulting gene_id map counts included 2 technical replicates for each sample. The 2 replicates were combined to generate 8 total samples which were normalized using edgeR (TMM) and tested for significant differential expression (either between 2 WT MCF-7 batches generated here or compared to existing HMEC expression data) with Limma and Voom, in R (v3.3.1) (Law et al., 2014; Ritchie et al., 2015; Robinson and Oshlack, 2010).
Assembly: Hg19
Supplementary files format and content: .txt file, contrast matrix defining contrasts for statistical testing
Supplementary files format and content: .txt file, Limma determined coeficients for each variable
Supplementary files format and content: .txt, counts in log2cpm for each gene
Supplementary files format and content: .txt, expression counts in RUVseq normalized counts for each gene

molecule: polyA RNA

organism: Homo sapiens

source_name: prefrontal cortex, sorted for NEUN+

growth_protocol: Human prefrontal cortex tissue for this study was obtained NIH NeuroBioBank with approval from the ethics committee of the Van Andel Research Institute (IRB #15025)

extract_protocol:
Neuronal nuclei were isolated from the human prefrontal cortex using flow cytometry and filtering for an anti-NeuN antibody.
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase. RNA was sheared to an average of 300 bp . Individually indexed libraries were pooled, and 75-bp single-end sequencing was performed on an Illumina NextSeq 500 sequencer. Base calling was done by Illumina NextSeq Control Software (NCS; v2.0), and the output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq (v1.9.0)

tag: tissue

value: prefrontal cortex, sorted for NEUN+

tag: cell line

tag: cod

value: Parkinson's Disease

tag: race

value: W

tag: rin

tag: pmi

value: Liz


title: Mouse, skin, PD0, scATAC, rep2

city: Seoul

first: Hanjae

last: Lee

address: 103, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

description: Library name: PD0_scATAC_Rep2

library_source: genomic single cell

data_processing:
Raw reads were processed using the CellRanger ATAC pipeline (v2.1.0) for scATAC-seq datasets and the CellRanger pipeline (v7.1.0) for scRNA-seq datasets.
Assembly: mm10 (2020-A provided by 10x Genomics)
Supplementary files format and content: The filtered_peak_bc_matrices and filtered_feature_bc_matrices files in H5 format, along with the fragments.tsv.gz files (for scATAC data), that were generated using the default parameters of the CellRanger pipeline.

molecule: genomic DNA

organism: Mus musculus

source_name: Skin

extract_protocol:
The entire back skin was harvested from sacrificed mice, and the epidermis was separated from the dermis by incubation with 1 mg/mL Dispase II (Roche) at 37°C for 30 minutes to 2 hours. The dermis was subsequently digested with 0.125 mg/mL Liberase TL (Roche) at 37°C for 30 minutes, while the epidermis was digested with 0.25% trypsin (Gibco) at 37°C for 15 minutes. Dissociated cells were filtered sequentially through 100-μm and 40-μm strainers, followed by a 1:1 matching of epidermal and dermal cells.
ScATAC-seq data were generated using 10x Chromium Single Cell ATAC Reagents Kits (v1 and v2), while scRNA-seq data were generated using the 10x Chromium Single Cell 3’ Kit (v3.1), following the manufacturer's instructions. Libraries were sequenced on a Novaseq system (Illumina), and two separate datasets, including replicates, were generated for each time point.

value: Skin


title: X30_PD_F_RT_un_rnaseq_PD_s_u_RT_F_81

value: Hypoxic Hypercapnic respiratory failure; Sepsis; Aspiration pneumonia; Parkinson's Disease


title: YTK1644-1-Input

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

institute: Yonsei University

description: Library name: YTK1644-1-Input

library_source: genomic

data_processing:
Paired-end 101-bp sequencing reads were mapped to the reference S. cerevisiae (sacCer3) genome assemblies using Bowtie2 with default settings.
Duplicated mapped reads were removed using SAMtools.
Assembly: R64-1-1/sacCer3
Supplementary files format and content: bigWig files were generated using makeBigWig tool (in HOMER suite)

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD media at 30℃ until O.D600nm was 0.5~0.6 and half of the cells were harvested.

extract_protocol:
Cells were harvested and immediately crosslinked. Then, cells were sonicated and proteins of interest were immunoprecipitated by antibodies.
Libraries were prepared with Accel-NGS 2S Plus DNA Library Kit (Swift BioSciences, 21096) following the manufacture’s instruction.

treatment_protocol: Half of the cells were subsequently shifted from YPD to 0.15x YP media for 4 hours at 30℃.

tag: strain

tag: chip antibody

tag: genotype

value: Wild type (Dot1-FLAG)

tag: treatment

value: YPD (Nutrient-rich, +N)


title: Mouse, skin, PD4, scATAC, rep1

description: Library name: PD4_scATAC_Rep1


title: Ileum, day 7, A109

city: Cerdanyola del Valles

first: Laia

last: Ferreres Serafini

state: Barcelona

address: Edifici V, Travessera dels Turons

country: Spain

institute: Autonomous University of Barcelona

description: Library name: A109

data_processing:
TrimGalore was used for quality filtering and adapter trimming; pseudo‑alignment and transcript quantification were performed using Kallisto against the Sus scrofa Sscrofa11.1 cDNA transcriptome; gene‑level counts were summarized and normalized using DESeq2 (median‑of‑ratios method).
Assembly: Sus scrofa reference genome Sscrofa11.1 (Ensembl).
Supplementary files format and content: Gene-level raw counts matrix, DESeq2 normalized counts, and sample metadata table (tab‑delimited or CSV).

organism: Sus scrofa

source_name: Ileum

extract_protocol:
RNA was extracted using Rneasy Mini Kit, Qiagen. RNA quantity and purity were assessed using NanoDrop spectrophotometry, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer to determine the RNA Integrity Number (RIN). The average RIN of samples used for library preparation was 7.8.
Libraries were prepared using poly‑A mRNA enrichment, RNA fragmentation, first‑ and second‑strand cDNA synthesis, end‑repair, A‑tailing, Illumina adapter ligation, size selection, and PCR amplification. Libraries were quality‑checked on an Agilent Bioanalyzer and sequenced as PE150 on an Illumina NovaSeq.

treatment_protocol: The two treatments were created based on growth, as average daily gain, from day 0 to 7 or  39.

value: Ileum

value: Low growth


title: HeLa-GFP_48h_rep1

molecule: total RNA

source_name: HeLa-GFP, 48h, replicate1


title: Ileum, day 7, A113

description: Library name: A113


title: Ileum, day 7, A110

description: Library name: A110

value: High growth


title: X35_PD_F_L_matched_rnaseq_PD_m_ma_L_F_76


title: Mouse, skin, PD0, scATAC, rep1

description: Library name: PD0_scATAC_Rep1


title: Hypothalamus, day 39, A036

description: Library name: A036

source_name: Hypothalamus

value: Hypothalamus


title: X3_PD_M_L_un_rnaseq_PD_t_u_L_M_81

value: Cancer


title: YTK1677-1-Dot1-FLAG

description: Library name: YTK1677-1-Dot1-FLAG

value: Anti-FLAG M2 (Sigma-Aldrich, F1804)

value: rad6del (Dot1-FLAG)


title: X29_PD_F_L_matched_rnaseq_PD_s_ma_L_F_81


title: Mouse, skin, E18.5, scATAC, rep2

description: Library name: E18.5_scATAC_Rep2


title: Hypothalamus, day 39, A035

description: Library name: A035


title: X27_PD_M_L_un_rnaseq_PD_z_u_L_M_88

value: JC


title: Mouse, skin, PD2, scATAC, rep1

description: Library name: PD2_scATAC_Rep1


title: YTK1644-2-Dot1-FLAG

description: Library name: YTK1644-2-Dot1-FLAG


title: Mouse, skin, E18.5, scATAC, rep1

description: Library name: E18.5_scATAC_Rep1


title: Hypothalamus, day 39, A034

description: Library name: A034


title: YF534-2-H3

description: Library name: YF534-2-H3

value: Anti-Histone H3 (Abcam, ab1791)


title: MEFs, P9, replicate 2, Input

city: Dongguan

first: Yuting Li

middle: Yuting

last: Li

address: Xin Cheng Avenue 1#, Songshan Lake,

country: China

institute: Guangdong Medical University

description: E-Input

data_processing:
The mapped reads represent enriched RNA fragments by MeRIP experiment.RNA methylation profiles of eachsample are saved as UCSC bedGraph format files,which can be visualized in IGV or UCSC Genome Browser.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and Visualization bedgraph data
Library strategy: meRIP-seq

source_name: Embryo

growth_protocol: Mouse embryonic fibroblasts (MEFs)were cultured in DMEM medium supplemented with 10% FBS and maintained in a CO2-incubator at 37 °C and 5% CO2.

extract_protocol:
IP group: RNA was extracted from MEFs and fragmented to ~150 nucleotides by RNA fragmentation reagents. Fragmented RNA was incubated with m6A primary antibody (Synaptic Systems, Germany) at 4°C for 2 h for immunoprecipitation. Eluted RNA was precipitated by 75% ethanol and treated with RNasin (Ambion, USA) according to the manufacturer’s instructions.Input group: total RNA was extracted from MEFs and TruSeq Stranded mRNA Sample Pre-Kit (Illumina, USA) was utilized to prepare the library.
TruSeq Stranded mRNA Sample Pre-Kit (Illumina, USA) was utilized to prepare the library from immunoprecipitated RNA.

value: Embryo

value: mouse embryonic fibroblasts

tag: cell type


title: X28_PD_M_RT_matched_rnaseq_PD_z_ma_RT_M_88

value: prefrontal cortex, sorted for NEUN+

value: Parkinson's Disease

value: W


title: YTK1644-1-Dot1-FLAG

description: Library name: YTK1644-1-Dot1-FLAG


title: YF534-1-H3

description: Library name: YF534-1-H3


title: MEFs, P9, replicate 3, Input

description: F-Input


title: Hypothalamus, day 39, A032

description: Library name: A032


title: X26rep_PD_M_RT_matched_rnaseq_PD_w_ma_RT_M_82

value: Cardiovascular/Respiratory Arrest

value: Liz


title: MEFs, P9, replicate 3, MeRIP

description:
MeRIP-Seq
F-IP

library_source: other

molecule: other


title: Hypothalamus, day 39, A033

description: Library name: A033


title: Hypothalamus, day 39, A031

description: Library name: A031


title: YTK1677-2-Dot1-FLAG

description: Library name: YTK1677-2-Dot1-FLAG

value: YPD (Nutrient-rich, +N)


title: Hypothalamus, day 39, A030

description: Library name: A030


title: MEFs, P9, replicate 2, MeRIP

description:
MeRIP-Seq
E-IP


title: X25rep_PD_M_L_un_rnaseq_PD_w_u_L_M_82


title: YF336-1-H3

description: Library name: YF336-1-H3

value: Wild type


title: YF336-2-H3

description: Library name: YF336-2-H3


title: X26_PD_M_RT_matched_rnaseq_PD_w_ma_RT_M_82


title: X25_PD_M_L_un_rnaseq_PD_w_u_L_M_82


title: Hypothalamus, day 39, A029

description: Library name: A029

value: Low growth


title: YF534-2-H3K79me1

description: Library name: YF534-2-H3K79me1

value: Anti-Histone H3K79me1 (Active motif, 39145)


title: MEFs, P9, replicate 1, Input

description: D-Input


title: X24_PD_F_RT_un_rnaseq_PD_x_u_RT_F_85

value: Failure to Thrive


title: MEFs, P9, replicate 1, MeRIP

description:
MeRIP-Seq
D-IP


title: YF534-1-H3K79me1

description: Library name: YF534-1-H3K79me1


title: YF336-2-H3K79me1

description: Library name: YF336-2-H3K79me1


title: Hypothalamus, day 39, A027

description: Library name: A027

value: Hypothalamus


title: Hypothalamus, day 39, A028

description: Library name: A028

value: High growth


title: X22_PD_M_RT_matched_rnaseq_PD_c_ma_RT_M_63

value: unknown


title: MEFs, P3, replicate 3, Input

description: C-Input


title: X23_PD_F_L_matched_rnaseq_PD_x_ma_L_F_85

value: JC


title: X21_PD_M_L_un_rnaseq_PD_c_u_L_M_63


title: Hypothalamus, day 39, A026

description: Library name: A026


title: MEFs, P3, replicate 2, Input

description: B-Input


title: YF336-1-H3K79me1

description: Library name: YF336-1-H3K79me1


title: Hypothalamus, day 39, A025

description: Library name: A025


title: YF534-2-H3K79me2

description: Library name: YF534-2-H3K79me2

value: Anti-Histone H3K79me2 (Abcam, ab3594)


title: YF534-1-H3K79me2

description: Library name: YF534-1-H3K79me2


title: MEFs, P3, replicate 2, MeRIP

description:
MeRIP-Seq
B-IP

value: Embryo


title: Hypothalamus, day 7, A011

description: Library name: A011


title: MEFs, P3, replicate 3, MeRIP

description:
MeRIP-Seq
C-IP

value: mouse embryonic fibroblasts


title: X19_PD_F_L_un_rnaseq_PD_q_u_L_F_80

value: prefrontal cortex, sorted for NEUN+


title: YF336-2-H3K79me2

description: Library name: YF336-2-H3K79me2


title: MEFs, P3, replicate 1, Input

description: A-Input


title: Hypothalamus, day 7, A010

description: Library name: A010


title: X17_PD_M_L_matched_rnaseq_PD_n_ma_L_M_77

value: Cardiopulmonary Arrest


title: X20_PD_F_RT_matched_rnaseq_PD_q_ma_RT_F_80

value: Parkinson's Disease

value: W


title: Hypothalamus, day 7, A009

description: Library name: A009


title: Rag2-/-SiteI.3Pr-/- pro-B cells, rep2 (Batch2)

city: Chicago

first: Hammad

last: Farooq

state: IL

address: 835 S Wolcot

department: Microbiology and Immunology

institute: University of Illinois Chicago, College of Medicine

data_processing:
Hi-C data was processed using the Juicer pipeline (v.1.5), CPU version. The pipeline was set up with BWA (0.7.15- r1140) to map each read end separately to the mm10 reference genome (GRCm38).
Duplicate and near-duplicate reads, as well as reads that map to the same fragment were removed. Among the remaining reads, those with mapping quality score (MAPQ) < 30 are retained. Arima-HiC-specific restriction sites (mm10_GATC_GANTC.txt) were obtained from ftp://ftp-arimagenomics.sdsc. edu/pub/JUICER CUTSITE FILES.
Both individual replicates and merged Hi-C reads of pro-B cells were processed using the Juicer pipeline. For individual replicates, raw reads from each sample were mapped separately to the reference genome, and then filtered by the MAPQ score. For merged replicates of each sample, valid read pairs from both replicates were merged, mapped to the reference genome, and then filtered by the MAPQ score.
Hi-C contact matrices were extracted from .hic files using the Dump command provided by a java-based program in the juicer tools. Hi-C maps were then normalized with the Knight and Ruiz (KR) matrix balancing method.
Assembly: mm10
Supplementary files format and content: hic files were generated

source_name: Rag2-/-SiteI.3Pr-/- pro-B cells

growth_protocol: In situ Hi-C was performed in mouse bone marrow pro-B cells using the Arima genome-wide Hi-C kit. CD19+ pro-B cells were isolated and grown in IL7 for 5 days.

extract_protocol:
After shearing DNA and biotin pull down adapters were added by ligation and Hi-C library was PCR amplified followed by paired-end sequencing. To increase the depth of sequencing the sequencing was performed again and the samples are mentioned as batch 1 and batch 2 for each iteration.
In situ Hi-C

treatment_protocol: The cells were then formaldyhyde crosslinked and digested with the Arima RE Cocktail.  The 5' overhangs were filled-in, tagged with biotin and ligated. DNA was sheared, pulled down and adapters were ligated for NGS.

value: bone marrow

value: pro-B cells


title: Hypothalamus, day 7, A012

description: Library name: A012


title: Hypothalamus, day 7, A008

description: Library name: A008


title: Rag2-/-SiteI.3Pr-/- pro-B cells, rep1 (Batch2)


title: X16dounce_PD_F_RT_Both_rnaseq_PD_v_nap_RT_F_82

value: Cerebrovascular Disease

value: Liz


title: X18_PD_M_RT_un_rnaseq_PD_n_u_RT_M_77


title: YF336YP-1-H3

description: Library name: YF336YP-1-H3

value: Anti-Histone H3 (Abcam, ab1791)

value: Wild type

value: 0.15x YP (Starvation, -N)


title: X16_PD_F_RT_Both_rnaseq_PD_v_nap_RT_F_82


title: Hypothalamus, day 7, A007

description: Library name: A007

value: Hypothalamus

value: Low growth


title: Rag2-/- pro-B cells, rep1 (Batch2)

source_name: Rag2-/- pro-B cells


title: Rag2-/- pro-B cells, rep2 (Batch2)


title: X15dounce_PD_F_L_Both_rnaseq_PD_v_nap_L_F_82


title: Hypothalamus, day 7, A006

description: Library name: A006

value: High growth


title: Hypothalamus, day 7, A005

description: Library name: A005


title: MEFs, P3, replicate 1, MeRIP

description:
MeRIP-Seq
A-IP


title: YF336YPD-1-H3

description: Library name: YF336YPD-1-H3

value: YPD (Nutrient-rich, +N)


title: Rag2-/-SiteI.3Pr-/- pro-B cells, rep2 (Batch 1)


title: YF336YP-2-H3K79me1

description: Library name: YF336YP-2-H3K79me1

value: Anti-Histone H3K79me1 (Active motif, 39145)


title: X14dounce_PD_M_RT_un_rnaseq_PD_aa_u_RT_M_88

value: Aspiration Pneumonia; Parkinson's Disease


title: YF336-1-H3K79me2

description: Library name: YF336-1-H3K79me2

value: Anti-Histone H3K79me2 (Abcam, ab3594)


title: Hypothalamus, day 7, A004

description: Library name: A004


title: YF336YPD-2-H3

description: Library name: YF336YPD-2-H3


title: Rag2-/-SiteI.3Pr-/- pro-B cells, rep1 (Batch 1)


title: X13dounce_PD_M_L_matched_rnaseq_PD_aa_ma_L_M_88

value: prefrontal cortex, sorted for NEUN+


title: YF336YP-2-H3

description: Library name: YF336YP-2-H3


title: YF336YP-1-H3K79me1

description: Library name: YF336YP-1-H3K79me1


title: Hypothalamus, day 7, A003

description: Library name: A003


title: YF336YPD-2-H3K79me1

description: Library name: YF336YPD-2-H3K79me1


title: YF336YPD-1-H3K79me1

description: Library name: YF336YPD-1-H3K79me1


title: Hypothalamus, day 7, A002

description: Library name: A002


title: X14_PD_M_RT_un_rnaseq_PD_aa_u_RT_M_88


title: YF336YP-2-H3K79me2

description: Library name: YF336YP-2-H3K79me2


title: YF336YP-1-H3K79me2

description: Library name: YF336YP-1-H3K79me2


title: Rag2-/- pro-B cells, rep2 (Batch 1)


title: X12_PD_M_RT_un_rnaseq_PD_b_u_RT_M_63

value: unknown

value: Parkinson's Disease; Ischemic Heart Disease


title: X10dounce_PD_F_RT_Both_rnaseq_PD_i_nap_RT_F_74

value: Respiratory Failure; Pneumonia

value: W


title: YTK251YP-2

description: Library name: YTK251YP-2

data_processing:
Resulting reads were then aligned to the S. cerevisiae S288C (sacCer3) reference genome  using the HISAT2 mapping tool.
Assembly: R64-1-1/sacCer3
Supplementary files format and content: Raw reads were mapped to the reference genome assembly sacCer3 using HISAT2. Differentially expressed genes in Excel file were analyzed using Cufflinks. For visualization in IGV genome browser, bigWig files were generated using makeBigWig tool (in HOMER suite).

extract_protocol:
RNA was extracted from cells harvested with hot phenol. Isolated RNA was resuspended in formamide for stability.
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) after ribosomal RNA was depleted with the Ribo-Zero yeast kit (Epicenter), following the manufacture’s instruction.


title: 20230620_Jen Niven _01_12, High Fat Diet Re

city: Birmingham

first: Adam

last: Croft

state: Please Select

address: Birmingham

country: United Kingdom

institute: University of Birmingham

description: Memory CD4 T cells isolated from spleens from mice on a 14 week diet reversal involving 8 weeks of high fat diet followed by 6 weeks of chow diet, with allogeneic immunisation at week 13. Total RNA isolated for mRNA-expression analysis using nCounter-based NanoString Technologies.

hyb_protocol: Nano String protocol

scan_protocol: Nano String protocol

data_processing: Data was normalized to house keeping genes using functions from nano R in R studio

label: Nano String nCounter Reporter Tags

source_name: T cells

label_protocol: Nano String protocol

extract_protocol: Memory CD4 T cells were isolated from spleens using the EasySep Mouse Memory CD4 T cell isolation kit (Stemcell Technologies) according to the manufacturer’s instructions.Total RNA isolated for mRNA-expression using  RNeasy micro kit (Qiagen) according to the manufacturer's instructions. RNA from each sample was run for mRNA-expression analysis using the nCounter® Mouse PanCancer Immune Profiling Panel (770 targets) (NanoString technologies).

treatment_protocol: Mice were received a 14 week chow diet (10% lipid,Test diet, USA, T-5755-1817109) or 14 week high-fat diet (60% lipid,Test diet, USA, T-58Y1-58126) or had a diet reversal (HFD-RE) with 8 weeks of high fat diet followed by 6 weeks of chow diet

value: T cells

value: High Fat Diet Re


title: YTK251YP-1

description: Library name: YTK251YP-1


title: X13_PD_M_L_matched_rnaseq_PD_aa_ma_L_M_88

value: JC


title: 20230620_Jen Niven _01_10, High Fat Diet Re


title: YF336YPD-2-H3K79me2

description: Library name: YF336YPD-2-H3K79me2

value: Wild type


title: 20230620_Jen Niven _01_11, High Fat Diet Re


title: X104_Un_Cont_M_RT_hcnt_rnaseq_W_j_hcnt_RT_M_90


title: Hypothalamus, day 7, A001

description: Library name: A001


title: YF336YPD-1-H3K79me2

description: Library name: YF336YPD-1-H3K79me2


title: YF336YP-2-H3K79me3

description: Library name: YF336YP-2-H3K79me3

value: Anti-Histone H3K79me3 (Abcam, ab2621)

value: 0.15x YP (Starvation, -N)


title: X103_Un_Cont_M_L_hcnt_rnaseq_W_j_hcnt_L_M_90

value: Prostate Cancer

value: Liz


title: YF336YP-1

description: Library name: YF336YP-1


title: X11_PD_M_L_matched_rnaseq_PD_b_ma_L_M_63


title: X102_Un_Cont_M_RT_hcnt_rnaseq_W_c_hcnt_RT_M_62


title: 20230620_Jen Niven _01_07, High Fat Diet

description: Memory CD4 T cells isolated from spleens from mice on a 14 week High fat diet with allogeneic immunisation at week 13. Total RNA isolated for mRNA-expression analysis using nCounter-based NanoString Technologies.

value: High Fat Diet


title: YF336YP-1-H3K79me3

description: Library name: YF336YP-1-H3K79me3


title: Rag2-/- pro-B cells, rep1 (Batch 1)

value: bone marrow

value: pro-B cells


title: 20230620_Jen Niven _01_08, High Fat Diet


title: YTK251YPD-2

description: Library name: YTK251YPD-2

value: YPD (Nutrient-rich, +N)


title: X101_Un_Cont_M_L_hcnt_rnaseq_W_c_hcnt_L_M_62

value: prefrontal cortex, sorted for NEUN+

value: Atherosclerotic Cardiovascular Disease


title: YF336YP-2

description: Library name: YF336YP-2


title: YTK251YPD-1

description: Library name: YTK251YPD-1


title: 20230620_Jen Niven _01_06, High Fat Diet


title: X100_Un_Cont_M_RT_hcnt_rnaseq_W_d_hcnt_RT_M_64

value: AA


title: YF336YPD-2-H3K79me3

description: Library name: YF336YPD-2-H3K79me3


title: YF336YPD-1-H3K79me3

description: Library name: YF336YPD-1-H3K79me3


title: R250CBm_RNA

status: Public on Mar 11 2026

city: New Haven

first: Yuting

last: Liu

state: CT

address: 333 Cedar Street

institute: YALE UNIVERSITY

description: Library name: R250CBm_GEX_MAH

library_source: transcriptomic single cell

data_processing:
Raw base call files were converted to FASTQ format and processed using Cell Ranger ARC (v2.0.1, 10x Genomics). Reads were aligned to species-specific reference genomes. Gene expression matrices and chromatin accessibility peak counts were generated using default Cell Ranger ARC parameters. Nuclei were filtered based on quality control thresholds including UMI counts, feature counts, mitochondrial gene percentage (>5%), total ATAC fragment counts (<1,000), and transcription start site enrichment score (<4). Downstream clustering and cell type annotation were performed using Seurat (v4.0.6).
Assembly: human, GRCh38; chimpanzees, panTro5;rhesus macaque, rheMac10; marmoset, calJac4
Supplementary files format and content: cellranger output: feature_bc_matrix.h5
Supplementary files format and content: cellranger output: atac_fragments.tsv.gz

molecule: nuclear RNA

organism: Macaca mulatta

source_name: cerebellum

extract_protocol:
Frozen cerebellar cortex tissue was homogenized and nuclei were isolated using detergent-based resuspension buffers containing NaCl, MgCl₂, Tris-HCl, NP-40, Tween-20, digitonin, protease inhibitors, DTT, BSA, and RNase inhibitor. Nuclei were filtered through 70 µm strainers, centrifuged at 500 × g at 4°C, and resuspended in nuclei buffer supplemented with DTT and RNase inhibitor. Nuclei concentration was adjusted to 4.5 × 10⁶ nuclei/mL prior to microfluidic capture.
Single-nucleus RNA and chromatin accessibility libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC and Gene Expression kit (10x Genomics, PN-1000283) according to the manufacturer’s instructions. Approximately 10,000 nuclei were targeted per sample using the Chromium microfluidic system with Multiome Gel Bead Kit A and Multiome GEM Kit A. RNA and ATAC libraries were generated in parallel from the same nuclei preparation.

value: cerebellum

tag: developmental stage

value: adult

tag: library type

value: mRNA


title: 20230620_Jen Niven _01_04, Control Diet

description: Memory CD4 T cells isolated from spleens from mice on a 14 week Chow diet with allogeneic immunisation at week 13. Total RNA isolated for mRNA-expression analysis using nCounter-based NanoString Technologies.

value: T cells

value: Control Diet


title: R218CBm_ATAC

description: Library name: R218CBm_ATAC_MAH

value: ATAC


title: R161CBm_ATAC

description: Library name: R161CBm_ATAC_MAH


title: YF336YPD-1

description: Library name: YF336YPD-1

value: Wild type


title: R218CBm_RNA

description: Library name: R218CBm_GEX_MAH


title: 20230620_Jen Niven _01_03, Control Diet


title: 20230620_Jen Niven _01_01, Control Diet


title: X10_PD_F_RT_Both_rnaseq_PD_i_nap_RT_F_74

value: Respiratory Failure; Pneumonia

value: W


title: R250CBm_ATAC

description: Library name: R250CBm_ATAC_MAH


title: R160CBm_RNA

description: Library name: R160CBm_GEX_MAH


title: CUT&RUN-RNAPolII_dsxmut_SH_male_brain_R3

city: Durham

first: Chengcheng

last: Du

state: North Carolina

address: French Family Science Center,, 124 Science Dr.

institute: Duke University

description:
Library name: RNAPolII_dsxmut_SH_male_brain_R3
RNAPolII_dsxmut_SH_male_brain_R3

data_processing:
Raw fastq files were processed using the standard nf-core/cutandrun pipeline (Ewels et al., 2020). Briefly, reads were trimmed by Trim Galore and aligned to the Drosophila melanogaster dmel-all-chromosome-r6.45 genome with Bowtie 2. Peak calling was performed by MACS2. The following analysis was performed in R (R Core Team, 2013; Wickham and Sievert, 2009). Counts of peaks were generated by csaw::regionCounts (Lun and Smyth, 2014, 2015). DEP analysis was performed with DESeq2 (Love et al., 2014). All control and mutant samples were incorporated into a single DESeqDataSet (dds) object for DEP analysis. Wald test was applied to the comparison between GH and SH of the same genotype, and the comparison between mutant and CS under the same housing conditions. ChIPseeker was used to annotate DNA peaks with genes. Gene ontology (GO), Reactome, and KEGG analyses were performed using the clusterProfiler library (Yu et al., 2012).
Assembly: Drosophila melanogaster dmel-all-chromosome-r6.45 genome
Supplementary files format and content: The "normalized_counts_H3K4me3.csv" and "normalized_counts_RNAPolII.csv" files include normalized counts (DESeq2) for peaks in each sample
Library strategy: CUT&Run

organism: Drosophila melanogaster

source_name: brain

extract_protocol:
Fly brains were dissected in dissection buffer (Schneider′s Insect Medium, Sigma-Aldrich S0146 with 1% BSA) and transferred into cold dissection buffer in 1.5 ml tubes on ice. Each genotype under the GH or SH conditions has three biological replicates. For H3K4me3 samples, fifteen male brains were used per sample, and for RNAPolII samples, thirty male brains were used per sample. After completing the dissection, the old dissection buffer was replaced with a fresh one. Collagenase Type I (Gibco, 17018029) stock solution was added directly into samples for a final 2mg/mL concentration. Samples were incubated at 37 °C for 20 minutes. During the incubation, samples were dissociated by gentle pipetting 20-30 times every 7 min with P200. The collagenase solution was removed after centrifugation at 300 xg for 5 min. Cells were washed with wash buffer supplied in CUTANA™ ChIC/CUT&RUN Kit (EpiCypher, 14-1048), and were centrifuged at 300 xg for 5 min. The old wash buffer was replaced with fresh wash buffer, and the cells were resuspended and processed according to the instructions in the user manual. 1 ul of antibody (anti-H3K4me3 antibodies supplied by the CUT&RUN Kit, and anti-RNAPolII antibody from MilliporeSigma 05-623) was added per sample.
CUTANA™ CUT&RUN Library Prep Kit (EpiCypher, 14-1001, 14-1002) was used to prepare libraries. The quality of libraries was examined by the D5000 ScreenTape station. Libraries were sequenced on the NextSeq 2000 sequencer, generating 75-bp paired-end reads.

value: brain


title: CUT&RUN-RNAPolII_frumut_SH_male_brain_R3

description:
Library name: RNAPolII_frumut_SH_male_brain_R3
RNAPolII_frumut_SH_male_brain_R3


title: R160CBm_ATAC

description: Library name: R160CBm_ATAC_MAH


title: CUT&RUN-RNAPolII_CS_GH_male_brain_R3

description:
Library name: RNAPolII_CS_GH_male_brain_R3
RNAPolII_CS_GH_male_brain_R5

value: Canton-S


title: CUT&RUN-RNAPolII_frumut_GH_male_brain_R3

description:
Library name: RNAPolII_frumut_GH_male_brain_R3
RNAPolII_frumut_GH_male_brain_R3


title: CUT&RUN-RNAPolII_Or67dmut_SH_male_brain_R3

description:
Library name: RNAPolII_Or67dmut_SH_male_brain_R3
RNAPolII_Or67dmut_SH_male_brain_R3


title: R161CBm_RNA

description: Library name: R161CBm_GEX_MAH


title: YF336YPD-2

description: Library name: YF336YPD-2


title: CUT&RUN-RNAPolII_Or47bmut_SH_male_brain_R3

description:
Library name: RNAPolII_Or47bmut_SH_male_brain_R3
RNAPolII_Or47bmut_SH_male_brain_R3


title: CUT&RUN-RNAPolII_Or47bmut_GH_male_brain_R3

description:
Library name: RNAPolII_Or47bmut_GH_male_brain_R3
RNAPolII_Or47bmut_GH_male_brain_R3


title: CUT&RUN-RNAPolII_Or67dmut_GH_male_brain_R3

description:
Library name: RNAPolII_Or67dmut_GH_male_brain_R3
RNAPolII_Or67dmut_GH_male_brain_R3


title: CUT&RUN-RNAPolII_dsxmut_SH_male_brain_R2

description:
Library name: RNAPolII_dsxmut_SH_male_brain_R2
RNAPolII_dsxmut_SH_male_brain_R2


title: CUT&RUN-RNAPolII_dsxmut_GH_male_brain_R2

description:
Library name: RNAPolII_dsxmut_GH_male_brain_R2
RNAPolII_dsxmut_GH_male_brain_R2


title: CUT&RUN-RNAPolII_CS_SH_male_brain_R3

description:
Library name: RNAPolII_CS_SH_male_brain_R3
RNAPolII_CS_SH_male_brain_R5


title: CUT&RUN-RNAPolII_Or47bmut_SH_male_brain_R2

description:
Library name: RNAPolII_Or47bmut_SH_male_brain_R2
RNAPolII_Or47bmut_SH_male_brain_R2


title: CUT&RUN-RNAPolII_dsxmut_GH_male_brain_R3

description:
Library name: RNAPolII_dsxmut_GH_male_brain_R3
RNAPolII_dsxmut_GH_male_brain_R3


title: CUT&RUN-RNAPolII_frumut_SH_male_brain_R1

description:
Library name: RNAPolII_frumut_SH_male_brain_R1
RNAPolII_frumut_SH_male_brain_R1


title: CUT&RUN-RNAPolII_Or47bmut_GH_male_brain_R2

description:
Library name: RNAPolII_Or47bmut_GH_male_brain_R2
RNAPolII_Or47bmut_GH_male_brain_R2


title: CUT&RUN-RNAPolII_frumut_GH_male_brain_R2

description:
Library name: RNAPolII_frumut_GH_male_brain_R2
RNAPolII_frumut_GH_male_brain_R2


title: CUT&RUN-RNAPolII_CS_SH_male_brain_R2

description:
Library name: RNAPolII_CS_SH_male_brain_R2
RNAPolII_CS_SH_male_brain_R4


title: CUT&RUN-RNAPolII_CS_GH_male_brain_R2

description:
Library name: RNAPolII_CS_GH_male_brain_R2
RNAPolII_CS_GH_male_brain_R4


title: CUT&RUN-RNAPolII_Or67dmut_SH_male_brain_R2

description:
Library name: RNAPolII_Or67dmut_SH_male_brain_R2
RNAPolII_Or67dmut_SH_male_brain_R2


title: CUT&RUN-RNAPolII_dsxmut_GH_male_brain_R1

description:
Library name: RNAPolII_dsxmut_GH_male_brain_R1
RNAPolII_dsxmut_GH_male_brain_R1


title: CUT&RUN-RNAPolII_Or67dmut_GH_male_brain_R1

description:
Library name: RNAPolII_Or67dmut_GH_male_brain_R1
RNAPolII_Or67dmut_GH_male_brain_R1


title: CUT&RUN-RNAPolII_Or47bmut_SH_male_brain_R1

description:
Library name: RNAPolII_Or47bmut_SH_male_brain_R1
RNAPolII_Or47bmut_SH_male_brain_R1


title: Mino parental bulk RNA-seq replicate 2

city: Charlottesville

first: Jing

last: Gao

state: VA

address: 21 HOSPITAL DR, OMS BLOG RM 4767

department: Pathology

institute: University of Virginia

description:
Library name: Mino_parental_rep2
Mino parental (untreated) biological replicate 2

data_processing:
Raw sequencing reads were aligned to the human reference genome (GRCh38/hg38) using Tophat2. Gene-level raw read counts were generated for downstream analysis.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Bulk_RNAseq_raw_counts.txt: tab-delimited gene-by-sample matrix containing raw gene-level read counts.

source_name: Mino

growth_protocol: HBL-2 and Mino mantle cell lymphoma cell lines were cultured under standard conditions. Cells were harvested at the indicated time points. Patient-derived PBMCs were treated as indicated prior to RNA extraction.

extract_protocol:
Total RNA was extracted from samples using the RNeasy Plus Mini Kit (Qiagen, Cat# 74134) following the manufacturer’s instructions. RNA quality was assessed using an Agilent Bioanalyzer, and only samples with RIN values greater than 8.0 were used for library preparation.
RNA-seq libraries were prepared from high-quality total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina, Cat# 20020594) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with MCL-1 inhibitor S63845 for 72 h (cell lines) or 12 h (patient PBMC) as indicated. Control samples were untreated (cell lines) or DMSO-treated (patient PBMC). MCL-1 inhibitor–resistant derivatives were maintained under selection and collected without acute drug treatment.

value: Mino

value: B cell lymphoma cell

tag: batch


title: CUT&RUN-RNAPolII_dsxmut_SH_male_brain_R1

description:
Library name: RNAPolII_dsxmut_SH_male_brain_R1
RNAPolII_dsxmut_SH_male_brain_R1


title: CUT&RUN-RNAPolII_Or67dmut_GH_male_brain_R2

description:
Library name: RNAPolII_Or67dmut_GH_male_brain_R2
RNAPolII_Or67dmut_GH_male_brain_R2


title: CUT&RUN-RNAPolII_Or67dmut_SH_male_brain_R1

description:
Library name: RNAPolII_Or67dmut_SH_male_brain_R1
RNAPolII_Or67dmut_SH_male_brain_R1


title: PBMC treated with S63845 bulk RNA-seq

description:
Library name: JT1_S63845_1uM_12h
Patient PBMC treated with MCL-1 inhibitor S63845 (1 µM) for 12 h

source_name: PBMC

value: PBMC


title: Mino treated with S63845 for 72h bulk RNA-seq replicate 1

description:
Library name: Mino_S63845_72h_rep1
Mino treated with MCL-1 inhibitor S63845 for 72 h, biological replicate 1


title: Mino MCL-1 inhibitor–resistant bulk RNA-seq replicate 1

description:
Library name: Mino_MCL1iRes_rep1
Mino MCL-1 inhibitor–resistant cells, biological replicate 1


title: Mino treated with S63845 for 72h bulk RNA-seq replicate 2

description:
Library name: Mino_S63845_72h_rep2
Mino treated with MCL-1 inhibitor S63845 for 72 h, biological replicate 2


title: Mino treated with S63845 for 72h bulk RNA-seq replicate 3

description:
Library name: Mino_S63845_72h_rep3
Mino treated with MCL-1 inhibitor S63845 for 72 h, biological replicate 3


title: CUT&RUN-RNAPolII_frumut_SH_male_brain_R2

description:
Library name: RNAPolII_frumut_SH_male_brain_R2
RNAPolII_frumut_SH_male_brain_R2


title: Arun_D6

city: barcelona

first: aintzane

last: rueda

state: Choose State

address: C/ del Dr. Trueta, 179, 08005 Barcelona

institute: Sequentia Biotech SL.

description: Library name: 1

data_processing:
Raw FASTQ files were processed using Cell Ranger (10x Genomics) with default parameters, following the manufacturer’s recommendations.
Assembly: GRCh38
Supplementary files format and content: Processed data consist of a sparse gene–cell UMI count matrix in Matrix Market format (matrix.mtx.gz), with corresponding cell barcodes (barcodes.tsv.gz) and gene annotations (features.tsv.gz).

extract_protocol:
Day 6 human preimplantation embryo models (blastoids) were collected and dissociated into single cell suspensions using TrypLE enzymatic treatment supplemented with DNase I to minimize cell aggregation. Dissociation was performed under gentle conditions to preserve cell viability and RNA integrity. Following enzymatic digestion, cells were passed through a cell strainer and washed in appropriate buffer. Single, viable cells were subsequently enriched by fluorescence-activated cell sorting (FACS) using a BD FACSAria Fusion instrument, based on forward and side scatter properties and viability gating. Sorted cells were immediately processed for downstream single cell RNA sequencing library preparation.
Following fluorescence-activated cell sorting, single viable cells were washed and resuspended in phosphate-buffered saline (PBS) supplemented with 0.04% bovine serum albumin (BSA). Cells were immediately loaded onto the 10x Genomics Chromium GEM-X platform for single cell encapsulation. Single cell barcoding, reverse transcription, cDNA amplification, and library construction were performed according to the manufacturer’s standard protocol for 10x Genomics Chromium single cell RNA sequencing. Final libraries were prepared for high-throughput sequencing following 10x Genomics guidelines.

value: Naive pluripotent stem cells

value: WT

value: DMSO


title: Mino MCL-1 inhibitor–resistant bulk RNA-seq replicate 3

description:
Library name: Mino_MCL1iRes_rep3
Mino MCL-1 inhibitor–resistant cells, biological replicate 3


title: CUT&RUN-RNAPolII_frumut_GH_male_brain_R1

description:
Library name: RNAPolII_frumut_GH_male_brain_R1
RNAPolII_frumut_GH_male_brain_R1


title: Mino parental bulk RNA-seq replicate 3

description:
Library name: Mino_parental_rep3
Mino parental (untreated) biological replicate 3


title: Mino parental bulk RNA-seq replicate 1

description:
Library name: Mino_parental_rep1
Mino parental (untreated) biological replicate 1


title: Mino MCL-1 inhibitor–resistant bulk RNA-seq replicate 2

description:
Library name: Mino_MCL1iRes_rep2
Mino MCL-1 inhibitor–resistant cells, biological replicate 2


title: PBMC treated with DMSO bulk RNA-seq

description:
Library name: JT1_DMSO_12h
Patient PBMC treated with DMSO control for 12 h


title: HBL-2 MCL-1 inhibitor–resistant bulk RNA-seq replicate 3

description:
Library name: HBL2_MCL1iRes_rep3
HBL-2 MCL-1 inhibitor–resistant cells, biological replicate 3


title: HBL-2 MCL-1 inhibitor–resistant bulk RNA-seq replicate 1

description:
Library name: HBL2_MCL1iRes_rep1
HBL-2 MCL-1 inhibitor–resistant cells, biological replicate 1


title: HBL-2 MCL-1 inhibitor–resistant bulk RNA-seq replicate 2

description:
Library name: HBL2_MCL1iRes_rep2
HBL-2 MCL-1 inhibitor–resistant cells, biological replicate 2


title: HBL-2 treated with S63845 for 72h bulk RNA-seq replicate 2

description:
Library name: HBL2_S63845_72h_rep2
HBL-2 treated with MCL-1 inhibitor S63845 for 72 h, biological replicate 2


title: HBL-2 parental bulk RNA-seq replicate 2

description:
Library name: HBL2_parental_rep2
HBL-2 parental (untreated) biological replicate 2


title: HBL-2 parental bulk RNA-seq replicate 1

description:
Library name: HBL2_parental_rep1
HBL-2 parental (untreated) biological replicate 1


title: HBL-2 treated with S63845 for 72h bulk RNA-seq replicate 1

description:
Library name: HBL2_S63845_72h_rep1
HBL-2 treated with MCL-1 inhibitor S63845 for 72 h, biological replicate 1


title: A549-sg

city: hangzhou

first: Bing

last: guo

state: zhejiang

address: cangqian street No.2318

department: school of Basic Medical Sciences

institute: HZNU

description: Library name: Sample6

data_processing:
The reduced genome was generated by extracting the sequences flanking the HindIII restriction sites (30 bp on each strand from the HindIII restriction sites to downstream) using the hg38 reference human genome, called 4C frag-ends. Non-unique frag-ends are discarded in subsequent analysis.
Subsequently, the highest covered frag-end was removed from the dataset in the normalization process and data are read-depth normalized to 1 million aligned intrachromosomal reads.
A Bioconductor package ‘r3Cseq’ with 2.5 kb sliding window was used to determine significant interactions and calculate interaction difference.
Assembly: hg38
Supplementary files format and content: bedgraph
Library strategy: 4C-Seq

growth_protocol: All cell lines were cultred in DMEM medium containg 10%FBS.

extract_protocol:
4C-seq was performed as previously described using Hind III for the first digestion, and Dpn II for the second digestion. In brief, cells were cross-linked in 2% formaldehyde for 10 min at room temperature and quenched with 0.2M glycine. Cells were then rinsed for 2 times with ice-cold PBS at room temperature and harvested and incubated in lysis buffer (50 mM Tris-Cl, 150 mM NaCl, 5 mM EDTA, 0.5% CA630, 0.5% Triton X-100 and protease inhibitor cocktail) while tumbling for 1 h at 4 °C. Cells were then pelleted, washed, and resuspended in Hind III buffer. SDS was added to a concentration of 0.3% for 1 h in a thermomixer at 37 °C and 400 rpm. Triton X-100 was then added to a concentration of 1.8% and cells were incubated in a thermomixer at 37 °C at 400 rpm for 3 h. 200 units of Hind III enzyme were added for a 4 h incubation in a thermomixer at 37 °C and 900 rpm; another 200 units of Hind III were added for overnight incubation. Cells were then incubated 20 min at 65 °C to heat inactivate enzyme, suspended in ligation buffer and 4,000 units of T4 ligase and incubated overnight at 16 °C. The next day, 300 μg Proteinase K was added for overnight incubation at 65 °C. Ligated DNA was purified and digested with 90 units Dpn II in Dpn II buffer overnight in a thermomixer at 37 °C and 500 rpm, followed by heat inactivation of enzyme (65 °C for 25 min). Samples were then diluted with ligation buffer and 100 units ligase were then added for overnight incubation at 16 °C. Circularized DNA was PCR-amplified using bait-specific inverse primers. Finally, PCR products were pooled and purified.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Samples Prep Kit. Briefly, DNA fragment end repair, add A base to 3'end, and connect sequencing adapter. PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on an Illumina sequencer following the manufacturer's protocols.

treatment_protocol: no treatment

value: human lung adenocarcinoma cell

value: sg


title: A549-CC

description: Library name: Sample4

value: CC


title: H1155-GG

description: Library name: Sample1

value: GG


title: HSV-1 RNaseH_DRIP-seq IP Rep1

city: Debrecen

first: Márton

last: Miskei

address: Egyetem tér1.

country: Hungary

institute: University of Debrecen

description: Library name: HSV-1 RNaseH_DRIP-seq IP

data_processing:
RNaseH treated DRIP-seq reads were aligned to the HSV-1 KOS reference sequence using bwa mem. Default settings were used for DRIP-seq samples.
PCR duplicates were filtered out.
RPKM (Reads Per Kilobase per Million mapped reads) normalized coverage (.bedgraph and .bigwig) files have been generated with 30 bp resolution using Deeptools bamCoverage v3.5.140.
Assembly: HSV-1 KOS reference sequence
Supplementary files format and content: bigwig file
Library strategy: DRIP-seq

organism: Human alphaherpesvirus 1

source_name: Jurkat human T lymphoblastoid

growth_protocol: The Jurkat human T lymphoblastoid cell line was cultured in RPMI-1640 medium (Sigma-Aldrich) supplemented with 10% fetal bovine serum albumin (BSA), L-glutamine and gentamicin at 37 °C, in a humidified / 5% CO2 chamber.

extract_protocol:
HSV-1 infected Jurkat cells were crosslinked with 1% paraformaldehyde (UP) for 10 minutes, followed by quenching with 2.5 M glycine (pH 6, final concentration 500 mM) for 5 minutes at room temperature. Lysis was performed using the lysis buffer from the NucleoSpin Tissue kit (Macherey-Nagel) at 65°C for 7 hours as per the kit protocol. Total nucleic acids were isolated using the NucleoSpin Tissue Kit and eluted in 100 µl of elution buffer (5 mM Tris-HCl, pH 8.5). The purified nucleic acid preparation was fragmented by sonication in 300 μl of Tris-HCl (pH 8.5, with 300 mM NaCl) for 2 cycles of 5 minutes (30 seconds ON, 30 seconds OFF, LOW setting, Bioruptor), yielding an average DNA fragment size of approximately 500 bp. Fragment analysis was performed using 1% agarose gel electrophoresis, with additional sonication applied if necessary. The sonicated DNA was purified using the NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel) and eluted in 100 μl of elution buffer (5 mM Tris-HCl, pH 8.5). Twelve micrograms of DNA was diluted to a total volume of 100 μl with 5 mM Tris-HCl (pH 8.5), and 2% of the sample was retained as input DNA. Half of the sample was treated with 8 μl of RNase H (5000 U/ml; NEB) in a total volume of 80 μl at 37°C overnight. Dynabeads Protein A magnetic beads (ThermoFisher Scientific) were pre-blocked with PBS/5 mM EDTA containing 0.5% BSA. For antibody immobilization, 50 µl of pre-blocked Dynabeads Protein A was incubated with 10 μg of S9.6 antibody in IP buffer (50 mM Hepes/KOH, pH 7.5; 0.14 M NaCl; 5 mM EDTA; 1% Triton X-100; 0.1% Na-Deoxycholate, ddH2O) at 4°C for 4 hours with rotation. Six micrograms of genomic DNA was added to the antibody-bead mixture and gently rotated at 4°C overnight. The beads were then recovered and washed successively with 1 ml of the following buffers at 4°C, twice for each step: Lysis Buffer 1 (low salt): 50 mM Hepes/KOH (pH 7.5), 0.14 M NaCl, 5 mM EDTA (pH 8), 1% Triton X-100, 0.1% Na-Deoxycholate. Lysis Buffer 2 (high salt): 50 mM Hepes/KOH (pH 7.5), 0.5 M NaCl, 5 mM EDTA (pH 8), 1% Triton X-100, 0.1% Na-Deoxycholate. Wash Buffer: 10 mM Tris-HCl (pH 8), 0.25 M LiCl, 0.5% NP-40, 0.5% Na-Deoxycholate, 1 mM EDTA (pH 8). TE Buffer: 10 mM Tris-HCl (pH 8), 1 mM EDTA (pH 8). Elution was performed in 100 μl of elution buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA; 1% SDS) for 15 minutes at 65°C. Following purification using the NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel), nucleic acids were eluted in 55 µl of elution buffer (5 mM Tris-HCl, pH 8.5).
Illumina TruSeq ChIP Sample Preparation protocol were used to DRIP-seq. Purified ligation products were then amplified by PCR. Amplified libraries were sequenced (at the EMBL Genomics Core Facility, Heidelberg) using an Illumina HiSeq 2500 instrument in the single-end sequencing mode.

treatment_protocol: Jurkat cells were incubated with a viral suspension at a multiplicity of infection (MOI) of 10. After the incubation period, the suspension was removed and replaced with fresh growth medium. Cells were then fixed with 1% formaldehyde at various time points post-infection.

value: Jurkat human T lymphoblastoid


title: A549-CG

description: Library name: Sample5

value: CG


title: HBL-2 treated with S63845 for 72h bulk RNA-seq replicate 3

description:
Library name: HBL2_S63845_72h_rep3
HBL-2 treated with MCL-1 inhibitor S63845 for 72 h, biological replicate 3


title: HSV-1 DRIP-seq IP Rep1

data_processing:
DRIP-seq reads were aligned to the HSV-1 KOS reference sequence using bwa mem. Default settings were used for DRIP-seq samples.
Alignments were filtered using samtools v1.10 keeping only primary alignments of properly paired reads that had >30 mapping quality score. PCR duplicates were also filtered out.
RPKM (Reads Per Kilobase per Million mapped reads) normalized coverage (.bedgraph and .bigwig) files have been generated with 30 bp resolution using Deeptools bamCoverage v3.5.140.
MACS2 was used to identify DRIP peaks in input normalized samples.
Assembly: HSV-1 KOS reference sequence
Supplementary files format and content: bigwig files from IP and input;
Supplementary files format and content: MACS2 was used to identify DRIP peaks in input normalized samples (bed files).
Library strategy: DRIP-seq

extract_protocol:
HSV-1 infected Jurkat cells were crosslinked with 1% paraformaldehyde (UP) for 10 minutes, followed by quenching with 2.5 M glycine (pH 6, final concentration 500 mM) for 5 minutes at room temperature. Lysis was performed using the lysis buffer from the NucleoSpin Tissue kit (Macherey-Nagel) at 65°C for 7 hours as per the kit protocol. Total nucleic acids were isolated using the NucleoSpin Tissue Kit and eluted in 100 µl of elution buffer (5 mM Tris-HCl, pH 8.5). The purified nucleic acid preparation was fragmented by sonication in 300 μl of Tris-HCl (pH 8.5, with 300 mM NaCl) for 2 cycles of 5 minutes (30 seconds ON, 30 seconds OFF, LOW setting, Bioruptor), yielding an average DNA fragment size of approximately 500 bp. Fragment analysis was performed using 1% agarose gel electrophoresis, with additional sonication applied if necessary. The sonicated DNA was purified using the NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel) and eluted in 100 μl of elution buffer (5 mM Tris-HCl, pH 8.5). Twelve micrograms of DNA was diluted to a total volume of 100 μl with 5 mM Tris-HCl (pH 8.5), and 2% of the sample was retained as input DNA. Half of the sample was treated with 8 μl of RNase H (5000 U/ml; NEB) in a total volume of 80 μl at 37°C overnight. Dynabeads Protein A magnetic beads (ThermoFisher Scientific) were pre-blocked with PBS/5 mM EDTA containing 0.5% BSA. For antibody immobilization, 50 µl of pre-blocked Dynabeads Protein A was incubated with 10 μg of S9.6 antibody in IP buffer (50 mM Hepes/KOH, pH 7.5; 0.14 M NaCl; 5 mM EDTA; 1% Triton X-100; 0.1% Na-Deoxycholate, ddH2O) at 4°C for 4 hours with rotation. Six micrograms of genomic DNA was added to the antibody-bead mixture and gently rotated at 4°C overnight. The beads were then recovered and washed successively with 1 ml of the following buffers at 4°C, twice for each step: Lysis Buffer 1 (low salt): 50 mM Hepes/KOH (pH 7.5), 0.14 M NaCl, 5 mM EDTA (pH 8), 1% Triton X-100, 0.1% Na-Deoxycholate. Lysis Buffer 2 (high salt): 50 mM Hepes/KOH (pH 7.5), 0.5 M NaCl, 5 mM EDTA (pH 8), 1% Triton X-100, 0.1% Na-Deoxycholate. Wash Buffer: 10 mM Tris-HCl (pH 8), 0.25 M LiCl, 0.5% NP-40, 0.5% Na-Deoxycholate, 1 mM EDTA (pH 8). TE Buffer: 10 mM Tris-HCl (pH 8), 1 mM EDTA (pH 8). Elution was performed in 100 μl of elution buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA; 1% SDS) for 15 minutes at 65°C. Following purification using the NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel), nucleic acids were eluted in 55 µl of elution buffer (5 mM Tris-HCl, pH 8.5).
Illumina TruSeq ChIP Sample Preparation protocol were used to DRIP-seq. DRIP DNA were end-repaired and indexed adapters were ligated to the inserts. Purified ligation products were then amplified by PCR. Amplified libraries were sequenced (at the EMBL Genomics Core Facility, Heidelberg) using an Illumina HiSeq 2500 instrument in the 2x125 paired-end sequencing mode.


title: HSV-1 Input DRIP-seq Rep1


title: HSV-1 DRIP-seq IP Rep2


title: HSV-1 Input DRIP-seq Rep2


title: APOBEC3G HSV-1 ChIP-seq Rep1

data_processing:
ChIP-seq reads were aligned to the HSV-1 KOS reference sequence using bwa mem.
For the A3A/A3G ChIP-seq samples, a mismatch penalty of -B 1 was applied. Alignments were filtered using samtools v1.10 keeping only primary alignments of properly paired reads that had >30 mapping quality score. PCR duplicates were also filtered out.
RPKM (Reads Per Kilobase per Million mapped reads) normalized coverage (.bedgraph and .bigwig) files have been generated with 30 bp resolution using Deeptools bamCoverage v3.5.140.
MACS2 was used with a cutoff of 1.3 (p=0.05) to identify ChIP peaks in input normalized samples.
Assembly: HSV-1 KOS reference sequence
Supplementary files format and content: bigwig files from IP and input;
Supplementary files format and content: MACS2 was used with a cutoff of 1.3 (p=0.05) to identify ChIP peaks in input normalized samples (bed files).

extract_protocol:
A total of 2 x 10^7 cells were fixed with 1% formaldehyde (20 ml volume) for 10 minutes at room temperature in T175 flasks, and quenched with 416 mM glycine for 5 minutes. Cells were washed three times in ice-cold PBS/T, pelleted by centrifugation at 1000xg for 5 minutes at 4°C, and stored at -80°C. Cell pellets were resuspended in 1.5 ml of ChIP Lysis Buffer (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA, pH 8; 1% Triton X-100; 0.1% Sodium Deoxycholate; 1% SDS; supplemented with protease inhibitors) and disrupted using a Fast Prep (speed: 6 m/s; time: 40 seconds; 2 cycles; pause time: 120 seconds). Chromatin lysates were sonicated in 1.5 ml LoBind tubes (600 μl per tube) using a Diagenode Bioruptor Plus (2 x 5 cycles, 30 seconds ON/OFF, LOW setting). Post-sonication, cell debris was pelleted by centrifugation at 16,000 g for 20 minutes at 4°C. The fragment length distribution of sonicated samples (50 μl) was assessed via 1% agarose gel electrophoresis following reverse crosslinking (at 65°C for 6 hours) and phenol-chloroform extraction. For immunoselection, 100 µl Dynabeads™ Protein G were precoated with 8 µg of rabbit polyclonal anti-APOBEC3A (D-23) (Sc-130688) and anti-APOBEC3G (H-63) (Sc-48820) rabbit polyclonal antibodies, respectively. Five percent of the sonicated chromatin was reserved as “input” while the remaining chromatin (“IP”) was diluted 1:10 with IP Dilution Buffer (1% Triton X-100; 2 mM EDTA, pH 8; 20 mM Tris-HCl, pH 8; 150 mM NaCl; supplemented with protease inhibitors) in 15 ml tubes and incubated with the antibody-coated magnetic beads at 4°C overnight with rotation. Beads were washed twice with each of the following buffers at 4°C for 1 minute using a MagnaRack: Low Salt Wash Buffer: 0.1% SDS; 1% Triton X-100; 2 mM EDTA, pH 8; 20 mM Tris-HCl, pH 8; 150 mM NaCl. High Salt Wash Buffer: 0.1% SDS; 1% Triton X-100; 2 mM EDTA, pH 8; 20 mM Tris-HCl, pH 8; 500 mM NaCl. LiCl Wash Buffer: 0.25 M LiCl; 1% NP-40; 1% Na-deoxycholate; 1 mM EDTA, pH 8; 10 mM Tris-HCl, pH 8. TE Buffer: 10 mM Tris-HCl, pH 8; 1 mM EDTA. Both IP and input samples were eluted in 100 μl of elution buffer (0.1 M NaHCO3; 1% SDS) for 15 minutes at 30°C with frequent vortexing. Supernatants were transferred to LoBind Eppendorf tubes and stored at -80°C.
Illumina TruSeq ChIP Sample Preparation protocol. ChIP DNA were end-repaired and indexed adapters were ligated to the inserts. Purified ligation products were then amplified by PCR. Amplified libraries were sequenced (at the EMBL Genomics Core Facility, Heidelberg) using an Illumina HiSeq 2500 instrument in the 2x125 paired-end sequencing mode.


title: HSV-1 Input ChIP-seq Rep1


title: HSV-1 Input ChIP-seq Rep2


title: APOBEC3A HSV-1 ChIP-seq Rep1


title: APOBEC3G HSV-1 ChIP-seq Rep2


title: APOBEC3A HSV-1 ChIP-seq Rep2


title: A549-GG

description: Library name: Sample3


title: scATACB4,zBrain,adult

city: Philadelphia

first: Bushra

last: Raj

state: PA

address: 421 Curie Boulevard

institute: University of Pennsylvania

description:
Library name: Sample14
10x Genomics

data_processing:
Raw sequencing data were processed using the Cell Ranger ATAC pipeline (v2.1.0, 10x Genomics). FASTQ files were aligned with the cellranger-atac count command to a zebrafish reference genome built from the zebrafish Dan_rerio.GRCz11.fa and danRer11.ensGene.gtf .
During processing of the adult data, we incorporated public scATAC-seq data from (Yang et al., 2020). Raw sequencing reads for adult zebrafish brain samples (GSM4662087 and GSM4662088) were retrieved from the NCBI Gene Expression Omnibus (GEO) under accession GSE134055. SRA files were converted to FASTQ format using the SRA Toolkit fasterq-dump utility.Individual sample matrices were generated using Cell Ranger ATAC. Samples from the same developmental timepoint were then aggregated using cellranger-atac aggr for downstream clustering and analysis.
Assembly: GRCz11
Supplementary files format and content: HDF5 format containing the filtered peak-by-barcode count matrix, including genomic coordinates for peaks and cell-associated barcodes.
Supplementary files format and content: Tabix-indexed, tab-delimited BED-like file containing Tn5 integration fragments, with columns: chromosome, start, end, cell barcode, and duplicate count.
Supplementary files format and content: R Signac objects containing processed data, including filtering, normalization, dimensionality reduction (UMAP/LSI), and metadata with cluster assignments and cell-type annotations

organism: Danio rerio

source_name: zebrafish whole brain

extract_protocol:
Nuclei were isolated from wild-type zebrafish at 3 dpf (pooled heads), 21 dpf (pooled brain/eyes), and adult 3 mpf (brain/eyes) stages. Tissues were dissected in cold Neurobasal/B27 media and mechanically dissociated via Dounce homogenization. For 3 dpf and 21 dpf samples, cells were pelleted at 500g and lysed in a 0.1x lysis buffer (containing 0.01% Digitonin and 0.1% NP-40) for 5 minutes on ice. For adult samples, homogenization was performed directly in 0.1x lysis buffer, followed by a 1.8M sucrose gradient centrifugation at 13,000g to remove cellular debris. All nuclei suspensions were filtered (ranging from 35µm to 10µm), washed, and resuspended in 10x Genomics Nuclei Buffer. Single-nucleus ATAC-seq libraries were prepared using the 10x Genomics Chromium platform according to the manufacturer’s instructions.
Single-nucleus ATAC-seq libraries were generated using the 10x Genomics Chromium platform with the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v2, targeting an initial capture of ~6,000 nuclei per channel. Following transposition and GEM generation, libraries were constructed according to the manufacturer’s instructions. Final pooled libraries were sequenced on an Illumina NovaSeq platform using SP 200-cycle kits (MedGenome)

value: zebrafish whole brain

tag: 5 mpf, Adult

value: WT/TLAB


title: scATACB3,zBrain,adult

description:
Library name: Sample13
10x Genomics


title: H1155-CC

description: Library name: Sample2


title: scATACB2,zEyes,adult

description:
Library name: Sample12
10x Genomics

source_name: zebrafish eyes

value: zebrafish eyes


title: HBL-2 parental bulk RNA-seq replicate 3

description:
Library name: HBL2_parental_rep3
HBL-2 parental (untreated) biological replicate 3


title: scATACA12,zBrain,21dpf

description:
Library name: Sample10
10x Genomics

tag: 21 dpf, Juvenile


title: scATACB1,zEyes,adult

description:
Library name: Sample11
10x Genomics


title: scATACA8,zEyes,21dpf

description:
Library name: Sample6
10x Genomics


title: scATACA9,zBrain,21dpf

description:
Library name: Sample7
10x Genomics


title: scATACA10,zHead,3dpf

description:
Library name: Sample8
10x Genomics

source_name: zebrafish whole head

value: zebrafish whole head

tag: 3 dpf, Larval


title: scATACA7,zHead,3dpf

description:
Library name: Sample5
10x Genomics

tag: tissue


title: scATACA6,zHead,3dpf

description:
Library name: Sample4
10x Genomics


title: scATACA2,zBrain,21dpf

description:
Library name: Sample1
10x Genomics


title: scATACA3,zBrain,21dpf

description:
Library name: Sample2
10x Genomics


title: adipose stromal cells, passage 3, donor A

city: København S

first: Tu

last: Hu

address: Oxford Have 73

country: Denmark

institute: True Signal

description: Library name: A_p3

data_processing:
Adapters, low-quality reads (>20% bases Q<15), and reads with N>0.1% were removed using SOAPnuke.
Clean reads were quantified with Salmon via nf-core/rnaseq v3.17.0 against Ensembl GRCh38 release 113 transcriptome.
Gene-level abundances were aggregated from transcript-level estimates using tximport defaults within the nf-core pipeline.
Assembly: Ensembl Homo sapiens GRCh38 (release 113).
Supplementary files format and content: Tab-delimited text file (salmon_gene_counts.tsv) containing Ensembl gene_id, gene_name, and gene-level Salmon TPM-like counts for 18 libraries.

source_name: adipose tissue

growth_protocol: Cryopreserved adipose stromal cells from five donors were thawed simultaneously, resuspended in αMEM (no nucleosides) supplemented with 5% heparin-free human platelet lysate plus penicillin 100 U/mL and streptomycin 100 µg/mL, and   seeded at 1×10³ cells/cm² in treated flasks. Cultures were maintained at 37 °C, 5% CO₂ with complete medium changes twice weekly and passaged weekly (p1–p3) and before confluence thereafter until senescence or passage 10.

extract_protocol:
Total RNA was extracted from cryopreserved ASC pellets using the TRIzol reagent workflow according to the manufacturer’s instructions.
Poly(A)+ RNA was captured with oligo(dT) magnetic beads, fragmented, and converted to double-stranded cDNA; libraries were end-repaired, A-tailed, adapter-ligated, PCR-enriched, denatured to single-stranded circular DNA, QC-verified, and sequenced on the MGI DNBSEQ platform (PE100).

value: adipose tissue

value: adipose stromal cells

tag: donor

value: Donor A

tag: passage


title: adipose stromal cells, passage 1, donor C

description: Library name: C_p1

value: Donor C


title: adipose stromal cells, passage 3, donor E

description: Library name: E_p3

value: Donor E


title: adipose stromal cells, passage 1, donor A

description: Library name: A_p1


title: adipose stromal cells, passage 10, donor E

description: Library name: E_p10


title: adipose stromal cells, passage 8, donor B

description: Library name: B_p8

value: Donor B


title: adipose stromal cells, passage 7, donor B

description: Library name: B_p7


title: adipose stromal cells, passage 6, donor E

description: Library name: E_p6


title: scATACA11,zHead,3dpf

description:
Library name: Sample9
10x Genomics


title: adipose stromal cells, passage 3, donor B

description: Library name: B_p3


title: adipose stromal cells, passage 9, donor C

description: Library name: C_p9


title: adipose stromal cells, passage 3, donor C

description: Library name: C_p3


title: adipose stromal cells, passage 7, donor A

description: Library name: A_p7


title: adipose stromal cells, passage 6, donor D

description: Library name: D_p6

value: Donor D


title: adipose stromal cells, passage 3, donor D

description: Library name: D_p3


title: adipose stromal cells, passage 1, donor D

description: Library name: D_p1


title: adipose stromal cells, passage 1, donor E

description: Library name: E_p1


title: adipose stromal cells, passage 10, donor D

description: Library name: D_p10


title: WT,  YPD medium ( 2% w/v glucose) ,6h, biological replicate 3

city: Tianjin

first: Feiyu

last: Fan

state: Tianjin

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

description:
Library name: Sample 9
Sample Designated as WT-Glu-rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to C. boidinii CICC#33029 genome using bowtie2 (2.5.4)
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated
Detailed parameters for reads mapping: bowtie2-build CB_Genome.fa CB && bowtie2 -x CB -1 LA-Glu-rep1_1.clean.fq.gz -2 LA-Glu-rep1_2.clean.fq.gz -p 8 -S LA-Glu-rep1.sam
Assembly: C. boidinii CICC#33029 genome (Genbank Accession numbers: CP149768-CP149778). Since the gene annotations were performed independently by our laboratory, we have included a CDS sequence file (CB_CDS.fa) on the series record. This file provides the correspondences between gene IDs and their coding sequences (CDS).
Supplementary files format and content: Tab-delimited text files include raw reads count and FPKM values for each Sample .

organism: [Candida] boidinii

extract_protocol:
Total RNA was isolated by the Trizol-Phenol-Chloroform method. An additional clean-up including the on-column DNase I treatment was performed by using the RNeasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Yeast cells

value: WT


title: WT,  YPM medium ( 2% w/v methanol) ,6h, biological replicate 1

description:
Library name: Sample 10
Sample Designated as WT-Met-rep1


title: WT,  YPM medium ( 2% w/v methanol) ,6h, biological replicate 2

description:
Library name: Sample 11
Sample Designated as WT-Met-rep2


title: WT,  YPM medium ( 2% w/v methanol) ,6h, biological replicate 3

description:
Library name: Sample 12
Sample Designated as WT-Met-rep3


title: adipose stromal cells, passage 1, donor B

description: Library name: B_p1


title: scATACA4,zBrain,21dpf

description:
Library name: Sample3
10x Genomics


title: LA001-14,  YPM medium ( 2% w/v methanol) ,6h, biological replicate 3

description:
Library name: Sample 6
Sample Designated as LA-Met-rep3

value: The LDH expression cassette (PENO1-BtL-LDH-TTEF2) and KanR expression cassette (PTDH3-KanR-TTEF2) were inserted into random chromosomal loci of WT


title: WT,  YPD medium ( 2% w/v glucose) ,6h, biological replicate 2

description:
Library name: Sample 8
Sample Designated as WT-Glu-rep2


title: LA001-14,  YPM medium ( 2% w/v methanol) ,6h, biological replicate 1

description:
Library name: Sample 4
Sample Designated as LA-Met-rep1


title: LA001-14,  YPM medium ( 2% w/v methanol) ,6h, biological replicate 2

description:
Library name: Sample 5
Sample Designated as LA-Met-rep2


title: LA001-14,  YPD medium ( 2% w/v glucose) ,6h, biological replicate 2

description:
Library name: Sample 2
Sample Designated as LA-Glu-rep2


title: LA001-14,  YPD medium ( 2% w/v glucose) ,6h, biological replicate 3

description:
Library name: Sample 3
Sample Designated as LA-Glu-rep3


title: LA001-14,  YPD medium ( 2% w/v glucose) ,6h, biological replicate 1

description:
Library name: Sample 1
Sample Designated as LA-Glu-rep1


title: CUT&RUN-RNAPolII_CS_SH_male_brain_R1

description:
Library name: RNAPolII_CS_SH_male_brain_R1
RNAPolII_CS_SH_male_brain_R3

value: brain

value: Canton-S


title: CUT&RUN-H3K4me3_dsxmut_GH_male_brain_R3

description:
Library name: H3K4me3_dsxmut_GH_male_brain_R3
H3K4me3_dsxmut_GH_male_brain_R3


title: WT,  YPD medium ( 2% w/v glucose) ,6h, biological replicate 1

description:
Library name: Sample 7
Sample Designated as WT-Glu-rep1


title: CUT&RUN-H3K4me3_Or67dmut_GH_male_brain_R3

description:
Library name: H3K4me3_Or67dmut_GH_male_brain_R3
H3K4me3_Or67dmut_GH_male_brain_R3


title: CUT&RUN-RNAPolII_CS_GH_male_brain_R1

description:
Library name: RNAPolII_CS_GH_male_brain_R1
RNAPolII_CS_GH_male_brain_R3


title: CUT&RUN-H3K4me3_dsxmut_SH_male_brain_R3

description:
Library name: H3K4me3_dsxmut_SH_male_brain_R3
H3K4me3_dsxmut_SH_male_brain_R3


title: CUT&RUN-H3K4me3_frumut_GH_male_brain_R3

description:
Library name: H3K4me3_frumut_GH_male_brain_R3
H3K4me3_frumut_GH_male_brain_R3


title: CUT&RUN-H3K4me3_frumut_SH_male_brain_R3

description:
Library name: H3K4me3_frumut_SH_male_brain_R3
H3K4me3_frumut_SH_male_brain_R3


title: CUT&RUN-H3K4me3_Or67dmut_SH_male_brain_R3

description:
Library name: H3K4me3_Or67dmut_SH_male_brain_R3
H3K4me3_Or67dmut_SH_male_brain_R3


title: CUT&RUN-RNAPolII_Or47bmut_GH_male_brain_R1

description:
Library name: RNAPolII_Or47bmut_GH_male_brain_R1
RNAPolII_Or47bmut_GH_male_brain_R1


title: CUT&RUN-H3K4me3_Or47bmut_GH_male_brain_R3

description:
Library name: H3K4me3_Or47bmut_GH_male_brain_R3
H3K4me3_Or47bmut_GH_male_brain_R3


title: CUT&RUN-H3K4me3_Or67dmut_GH_male_brain_R2

description:
Library name: H3K4me3_Or67dmut_GH_male_brain_R2
H3K4me3_Or67dmut_GH_male_brain_R2


title: CUT&RUN-H3K4me3_dsxmut_GH_male_brain_R2

description:
Library name: H3K4me3_dsxmut_GH_male_brain_R2
H3K4me3_dsxmut_GH_male_brain_R2


title: CUT&RUN-H3K4me3_dsxmut_SH_male_brain_R2

description:
Library name: H3K4me3_dsxmut_SH_male_brain_R2
H3K4me3_dsxmut_SH_male_brain_R2


title: CUT&RUN-H3K4me3_CS_GH_male_brain_R3

description:
Library name: H3K4me3_CS_GH_male_brain_R3
H3K4me3_CS_GH_male_brain_R5


title: CUT&RUN-H3K4me3_frumut_SH_male_brain_R2

description:
Library name: H3K4me3_frumut_SH_male_brain_R2
H3K4me3_frumut_SH_male_brain_R2


title: CUT&RUN-H3K4me3_CS_GH_male_brain_R2

description:
Library name: H3K4me3_CS_GH_male_brain_R2
H3K4me3_CS_GH_male_brain_R4


title: CUT&RUN-H3K4me3_Or67dmut_SH_male_brain_R2

description:
Library name: H3K4me3_Or67dmut_SH_male_brain_R2
H3K4me3_Or67dmut_SH_male_brain_R2


title: CUT&RUN-H3K4me3_frumut_GH_male_brain_R2

description:
Library name: H3K4me3_frumut_GH_male_brain_R2
H3K4me3_frumut_GH_male_brain_R2


title: CUT&RUN-H3K4me3_Or47bmut_GH_male_brain_R2

description:
Library name: H3K4me3_Or47bmut_GH_male_brain_R2
H3K4me3_Or47bmut_GH_male_brain_R2


title: CUT&RUN-H3K4me3_CS_SH_male_brain_R2

description:
Library name: H3K4me3_CS_SH_male_brain_R2
H3K4me3_CS_SH_male_brain_R4


title: CUT&RUN-H3K4me3_CS_SH_male_brain_R3

description:
Library name: H3K4me3_CS_SH_male_brain_R3
H3K4me3_CS_SH_male_brain_R5


title: CUT&RUN-H3K4me3_dsxmut_GH_male_brain_R1

description:
Library name: H3K4me3_dsxmut_GH_male_brain_R1
H3K4me3_dsxmut_GH_male_brain_R1


title: CUT&RUN-H3K4me3_frumut_SH_male_brain_R1

description:
Library name: H3K4me3_frumut_SH_male_brain_R1
H3K4me3_frumut_SH_male_brain_R1


title: CUT&RUN-H3K4me3_Or47bmut_SH_male_brain_R2

description:
Library name: H3K4me3_Or47bmut_SH_male_brain_R2
H3K4me3_Or47bmut_SH_male_brain_R2


title: CUT&RUN-H3K4me3_Or67dmut_GH_male_brain_R1

description:
Library name: H3K4me3_Or67dmut_GH_male_brain_R1
H3K4me3_Or67dmut_GH_male_brain_R1


title: CUT&RUN-H3K4me3_Or47bmut_SH_male_brain_R1

description:
Library name: H3K4me3_Or47bmut_SH_male_brain_R1
H3K4me3_Or47bmut_SH_male_brain_R1


title: CUT&RUN-H3K4me3_Or67dmut_SH_male_brain_R1

description:
Library name: H3K4me3_Or67dmut_SH_male_brain_R1
H3K4me3_Or67dmut_SH_male_brain_R1


title: CUT&RUN-H3K4me3_Or47bmut_GH_male_brain_R1

description:
Library name: H3K4me3_Or47bmut_GH_male_brain_R1
H3K4me3_Or47bmut_GH_male_brain_R1


title: Brain bulk RNA-seq (dsxmut_male_SH_Rep3)

description:
Library name: dsxmut_male_SH_Rep3
DSX_SH_R3

data_processing:
Raw fastq files were processed with the standard nf-core/rnaseq pipeline (Ewels et al., 2020). Briefly, reads were mapped to the Drosophila melanogaster BDGP6.46 genome with STAR, and read counts were generated using the Salmon method. The following analysis was performed in R (R Core Team, 2013; Wickham and Sievert, 2009). DEG analysis was performed with DESeq2 (Love et al., 2014). All control and mutant samples were incorporated into a single DESeqDataSet (dds) object for differential expression analysis. The Wald test was applied to the comparison between GH and SH of the same genotype, and the comparison between mutant and CS under the same housing conditions. Gene ontology (GO), Reactome, and KEGG analyses were performed using the clusterProfiler library (Yu et al., 2012).
Assembly: Drosophila melanogaster BDGP6.46 genome
Supplementary files format and content: The "raw_counts.tsv" file includes raw counts for each sample
Supplementary files format and content: The "normalized_counts.csv" file includes normalized counts (DESeq2) for each sample
Supplementary files format and content: Please refer to the information provided in the "rnaseq_batches.csv" file to remove batch effects caused by dissection (AC vs. notAC) using ComBat before performing DEG analysis.

extract_protocol:
Fly brains were dissected in cold RNase-free 1X PBS and transferred immediately to RNAlater (Sigma-Aldrich, R0901) on ice. Each genotype under the GH or SH conditions has three biological replicates, and each biological replicate contains 30 male fly brains. After the dissection, RNAlater with the sample was diluted 1:2 with 1X RNase-free PBS and centrifuged for 1 min at max speed, and the supernatant was removed. Brain samples were washed with 1 mL 1X RNase-free PBS and centrifuged for 1 min at max speed. The supernatant was removed and replaced with 300 μL of TRIzol reagent (Invitrogen, 15596026). To extract RNA, samples were ground sufficiently and processed with QIAGEN Shredder kit (QIAGEN, 79654), and RNeasy Mini Kit (QIAGEN, 74104). DNase I (TURBO DNA-free Kit, Invitrogen, Thermo Fisher Scientific AM1907) was applied to remove genomic DNA after the RNA extraction.
Around 500 ng total RNA in each sample was prepared for library preparation. KAPA Stranded mRNA-Seq Kit was used to generate mRNA libraries. Libraries were sequenced on the NextSeq 2000 sequencer, generating 75-bp or 100-bp paired-end reads.


title: CUT&RUN-H3K4me3_frumut_GH_male_brain_R1

description:
Library name: H3K4me3_frumut_GH_male_brain_R1
H3K4me3_frumut_GH_male_brain_R1


title: CUT&RUN-H3K4me3_CS_SH_male_brain_R1

description:
Library name: H3K4me3_CS_SH_male_brain_R1
H3K4me3_CS_SH_male_brain_R3


title: Brain bulk RNA-seq (dsxmut_male_SH_Rep2)

description:
Library name: dsxmut_male_SH_Rep2
DSX_SH_R2


title: CUT&RUN-H3K4me3_CS_GH_male_brain_R1

description:
Library name: H3K4me3_CS_GH_male_brain_R1
H3K4me3_CS_GH_male_brain_R3


title: Brain bulk RNA-seq (dsxmut_male_GH_Rep1)

description:
Library name: dsxmut_male_GH_Rep1
DSX_GH_R1


title: CUT&RUN-H3K4me3_dsxmut_SH_male_brain_R1

description:
Library name: H3K4me3_dsxmut_SH_male_brain_R1
H3K4me3_dsxmut_SH_male_brain_R1


title: CUT&RUN-H3K4me3_Or47bmut_SH_male_brain_R3

description:
Library name: H3K4me3_Or47bmut_SH_male_brain_R3
H3K4me3_Or47bmut_SH_male_brain_R3


title: Brain bulk RNA-seq (dsxmut_male_GH_Rep2)

description:
Library name: dsxmut_male_GH_Rep2
DSX_GH_R2


title: Brain bulk RNA-seq (dsxmut_male_SH_Rep1)

description:
Library name: dsxmut_male_SH_Rep1
DSX_SH_R1


title: Brain bulk RNA-seq (frumut_male_GH_Rep2)

description:
Library name: frumut_male_GH_Rep2
FRU_GH_R2


title: Brain bulk RNA-seq (frumut_male_SH_Rep1)

description:
Library name: frumut_male_SH_Rep1
FRU_SH_R1


title: Brain bulk RNA-seq (CS_male_SH_Rep1)

description:
Library name: CS_male_SH_Rep1
CS_SH_R1


title: Brain bulk RNA-seq (dsxmut_male_GH_Rep3)

description:
Library name: dsxmut_male_GH_Rep3
DSX_GH_R3


title: Brain bulk RNA-seq (frumut_male_GH_Rep3)

description:
Library name: frumut_male_GH_Rep3
FRU_GH_R3


title: Brain bulk RNA-seq (frumut_male_SH_Rep2)

description:
Library name: frumut_male_SH_Rep2
FRU_SH_R2


title: Brain bulk RNA-seq (CS_male_GH_Rep3)

description:
Library name: CS_male_GH_Rep3
CS_GH_R3


title: Brain bulk RNA-seq (CS_male_GH_Rep2)

description:
Library name: CS_male_GH_Rep2
CS_GH_R2


title: Brain bulk RNA-seq (CS_male_SH_Rep2)

description:
Library name: CS_male_SH_Rep2
CS_SH_R2


title: Brain bulk RNA-seq (CS_male_GH_Rep1)

description:
Library name: CS_male_GH_Rep1
CS_GH_R1


title: Brain bulk RNA-seq (frumut_male_SH_Rep3)

description:
Library name: frumut_male_SH_Rep3
FRU_SH_R3


title: Brain bulk RNA-seq (Or67dmut_male_SH_Rep2)

description:
Library name: Or67dmut_male_SH_Rep2
Or67d_SH_R2


title: Brain bulk RNA-seq (Or67dmut_male_GH_Rep2)

description:
Library name: Or67dmut_male_GH_Rep2
Or67d_GH_R2


title: Brain bulk RNA-seq (Or67dmut_male_GH_Rep3)

description:
Library name: Or67dmut_male_GH_Rep3
Or67d_GH_R3


title: Brain bulk RNA-seq (frumut_male_GH_Rep1)

description:
Library name: frumut_male_GH_Rep1
FRU_GH_R1


title: Brain bulk RNA-seq (Or67dmut_male_SH_Rep3)

description:
Library name: Or67dmut_male_SH_Rep3
Or67d_SH_R3


title: Brain bulk RNA-seq (Or67dmut_male_GH_Rep1)

description:
Library name: Or67dmut_male_GH_Rep1
Or67d_GH_R1


title: Brain bulk RNA-seq (CS_male_SH_Rep3)

description:
Library name: CS_male_SH_Rep3
CS_SH_R3


title: Brain bulk RNA-seq (Or47bmut_male_SH_Rep2)

description:
Library name: Or47bmut_male_SH_Rep2
Or47b_SH_R2


title: Brain bulk RNA-seq (Or47bmut_male_GH_Rep3)

description:
Library name: Or47bmut_male_GH_Rep3
Or47b_GH_R3


title: Brain bulk RNA-seq (Or47bmut_male_SH_Rep1)

description:
Library name: Or47bmut_male_SH_Rep1
Or47b_SH_R1


title: Brain bulk RNA-seq (Or67dmut_male_SH_Rep1)

description:
Library name: Or67dmut_male_SH_Rep1
Or67d_SH_R1


title: Brain bulk RNA-seq (Or47bmut_male_GH_Rep2)

description:
Library name: Or47bmut_male_GH_Rep2
Or47b_GH_R2


title: complex v GKD, replicate 2

city: New York

first: BiNGS

last: Core

address: 3 E 101st St

institute: Icahn School of Medicine at Mount Sinai

description: Library name: ComplexV_rep2

data_processing:
Quality control has been performed using FastQC (v0.11.8)
Trim Galore! (v0.6.6) has been used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using STAR aligner (v2.7.5b)
Gene level read counts are obtained by using Salmon (v1.2.1) for all libraries
Assembly: dm6
Supplementary files format and content: .csv, salmon raw gene counts

source_name: Ovary tissue

extract_protocol:
Ovaries were dissected in 1x PBS. RNA isolation was performed using Trizol. Samples were then lysed using a plastic pestle and electric pestle motor, and Trizol volume was brought up to 1ml. 200ul of chloroform was then added, and mixed. Samples were then incubated for 5 minutes at room temperature before centrifugation for 20 minutes at 13000g at 2-8C. The supernatant was transferred to a fresh tube, and sodium acetate (10% of collected supernatant volume), 1ul glyco blue, and 100% ethanol (maximum permissible volume) were added before vortexing. Samples were then incubated for 7 minutes before moving to -20C overnight. RNA pellets were generated from the sample by centrifugation for 15 minutes at 13000g at 4C. RNA pellets were washed with 75% ethanol, then eluted in 20-50ul RNAse free water. Integrity of the RNA was determined by running it on a 1% agarose gel and concentration of RNA was assessed using a Nanodrop. RNA samples were treated with Turbo DNase according to kit instructions (Life Technologies TURBO DNAfree Kit #AM1907). mRNA was enriched through poly(A) tail selection, and libraries were prepared using the Revvity NEXTFLEX Rapid Directional RNA-Seq Kit 2.0 (NOVA-5198-02). mRNA library quality was assessed using Qubit, before sequencing on an Illumina NextSeq2000 (single-end 100 base pair reads).
RNA libraries for RNA-seq were prepared using Revvity NEXTFLEX Rapid Directional RNA-seq library prep kit 2.0 following manufacturer's protocol.

value: Ovary tissue

value: Adult

value: rpS19b-GFP/complex V RNAi;nosGAL4


title: complex v GKD, replicate 1

description: Library name: ComplexV_rep1


title: Brain bulk RNA-seq (Or47bmut_male_GH_Rep1)

description:
Library name: Or47bmut_male_GH_Rep1
Or47b_GH_R1


title: afg3l2 GKD, replicate 1

description: Library name: Afg3l2_rep1

value: rpS19b-GFP/afg3l2 RNAi;nosGAL4


title: Wildtype, replicate 1

description: Library name: WT_rep1


title: Wildtype, replicate 2

description: Library name: WT_rep2


title: Control #5

description: Library name: WT_rep5

data_processing:
Quality control has been performed using FastQC (v0.11.8)
Trim Galore! (v0.6.6) has been used to trim the adapter sequences with a quality threshold of 20
The alignment was performed by using STAR aligner (v2.7.5b)
Gene level read counts are obtained by using Salmon (v1.2.1) for all libraries
Assembly: dm6
Supplementary files format and content: .csv, salmon raw gene counts and median-ratios normalized gene counts

extract_protocol:
Ovaries were dissected into PBS and transferred to RNase free microcentrifuge tubes. PBS was removed and 100ul of Trizol was added and ovaries were flash frozen and stored at -80 C. Ovaries were then lysed in the microcentrifuge tube using a plastic disposable pestle. Trizol was added to 1 mL total volume while vigorously shaking the tubes and incubated for 5 min at RT. The samples were centrifuged for 20 min at >13,000 g at 4 C, and the supernatant was transferred to a fresh microcentrifuge tube. 500 ul of chloroform was added, and the samples were vigorously shaken and incubated for 5 minutes at RT. Samples were spun at max speed for 10 minutes at 4 C. The supernatant was transferred to a fresh microcentrifuge tube and ethanol precipitated. Sodium acetate was added, equaling 10% of the volume transferred and 2-2.5 volumes of 100% ethanol were added. The samples were shaken thoroughly and left to precipitate at -20 C overnight. The samples were centrifuged at max speed at 4 C for 15 min to pellet the RNA. The supernatant was discarded and 500 ul of 75% ethanol was added to wash the pellet. The samples were vortexed to dislodge the pellet to ensure thorough washing. The samples were spun at 4 C for 5 min and the supernatant was discarded. The pellets were dried for 10-20 min and then resuspended in 20-50ul of RNAse-free water and the absorbance at 260 was measured on a nanodrop to measure the concentration of each sample.
RNA libraries for RNA-seq were prepared using Revvity NEXTFLEX Rapid Directional RNA-seq library prep kit 2.0 following manufacturer's protocol.

tag: dissection

value: dissected 1-3 days post-eclosion


title: ZFRP8 germline knockdown #2

description: Library name: ZFRP_rep2

value: nosGAL4; zfrp8 RNAi/TM6


title: Control #1

description: Library name: WT_rep1


title: Brain bulk RNA-seq (Or47bmut_male_SH_Rep3)

description:
Library name: Or47bmut_male_SH_Rep3
Or47b_SH_R3


title: Control #2

description: Library name: WT_rep2


title: ZFRP8 germline knockdown #1

description: Library name: ZFRP_rep1


title: Mio germline knockdown #2

description: Library name: Mio_rep2

value: mio RNAi/nosGAL4; MKRS/TM6


title: afg3l2 GKD, replicate 2

description: Library name: Afg3l2_rep2


title: Mio germline knockdown #1

description: Library name: Mio_rep1


title: Control #4

description: Library name: WT_rep4


title: Raptor germline knockdown #1

description: Library name: Raptor_rep1

value: nosGAL4; raptor RNAi/TM6


title: Raptor germline knockdown #2

description: Library name: Raptor_rep2


title: Control #3

description: Library name: WT_rep3


title: Nup44a germline knockdown #3

description: Library name: Nup44a_rep3

value: nosGAL4; Nup44a RNAi/TM6


title: Nup44a germline knockdown #2

description: Library name: Nup44a_rep2


title: microRNAs expression after 4-hour of flunarizine treatment SMA patient cells s4

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description: Library name: s4_FLU

data_processing:
star and bowtie2 align
Rsubread v1.4.6 featureCounts
Assembly: GRCh38
Supplementary files format and content: tabular raw count

source_name: Motor neuron

extract_protocol:
PureLink miR isolation kit (Ambion)
Ion Total RNA-Seq Kit v2

treatment_protocol: analyses of microRNAs expression after 4-hour of flunarizine treatment SMA patient cells (SF)compared to control vehicle

value: Motor neuron

value: fibroblaste

value: 4 hour of flunarizine treatment SMA patient cells


title: microRNAs expression after 4-hour of flunarizine treatment SMA patient cells s2

description: Library name: s2_FLU


title: microRNAs expression after 4-hour of flunarizine treatment SMA patient cells s3

description: Library name: s3_FLU


title: microRNAs expression control vehicle SMA patient cells s1

description: Library name: s1_DMSO

value: control vehicle SMA patient cells


title: 7337

city: Asheville

first: Melissa

middle: Marie

last: Heintz

state: NC

address: 31 College Place, Suite B118

institute: ToxStrategies

description: Library name: Sample 40

data_processing:
Sequencing reads are demultiplexed using the standard sequencing instrument software and sample-specific barcodes to give a FASTQ file for each sample
bcl2fastq2 v2.20 for demultiplexing
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
fastq files were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches
Assembly: templated oligo sequencing
Supplementary files format and content: comma-separated text file includes raw count values for each gene_probe

organism: Rattus norvegicus

source_name: liver

extract_protocol:
Mounted, unstained FFPE liver samples were scraped from the slides and processed according to the TempO-Seq® protocol by BioSpyder Technologies
TempO-Seq® protocol by BioSpyder Technologies

treatment_protocol: Pregnant (female) Sprague Dawley rats administered deionized water (vehicle control) or HFPO-DA in deionized water at 10, 100 or 1000 mg/kg by oral gavage once daily during gestation days (GD) 6 to 20, for a total of 15 days (developmental study), or non-pregnant female Sprague Dawley rats orally administered the same HFPO-DA doses daily for 90 days (subchronic study). Following the last treatment, rats were euthanized by CO2 anesthesia and exsanguination. Livers were fixed in 10% neutral-buffered formalin, embedded in paraffin (FFPE), and sections approximately 4 – 6 µm in thickness were mounted to glass slides.

value: liver

value: Sprague Dawley

tag: Sex

value: female

value: adult

tag: pregnancy status

value: non-pregnant

tag: exposure route

value: oral

tag: exposure duration

value: 90 days

value: 1000 mg/kg-d HFPO-DA


title: 7321

description: Library name: Sample 35

tag: strain

tag: treatment

value: 100 mg/kg-d HFPO-DA


title: 7304

description: Library name: Sample 31

tag: developmental stage

value: 10 mg/kg-d HFPO-DA


title: 7317

description: Library name: Sample 34


title: 7297

description: Library name: Sample 29


title: 7289

description: Library name: Sample 26


title: Nup44a germline knockdown #1

description: Library name: Nup44a_rep1

value: Ovary tissue

tag: genotype

value: dissected 1-3 days post-eclosion

value: Adult


title: 7283

description: Library name: Sample 25

value: 0 mg/kg-d HFPO-DA


title: 7293

description: Library name: Sample 28


title: 7299

description: Library name: Sample 30


title: 7282

description: Library name: Sample 24


title: 7292

description: Library name: Sample 27


title: 7325

description: Library name: Sample 36


title: 7274

description: Library name: Sample 22


title: 7310

description: Library name: Sample 32


title: 7314

description: Library name: Sample 33


title: 7335

description: Library name: Sample 39


title: 57393

description: Library name: Sample 18

value: pregnant

value: 15 days


title: 57368

description: Library name: Sample 17


title: 7272

description: Library name: Sample 21


title: 57394

description: Library name: Sample 19


title: 7329

description: Library name: Sample 38


title: 57398

description: Library name: Sample 20


title: 57356

description: Library name: Sample 13


title: 57357

description: Library name: Sample 14


title: 57363

description: Library name: Sample 16


title: 57362

description: Library name: Sample 15


title: 7277

description: Library name: Sample 23


title: 57326

description: Library name: Sample 9


title: 57316

description: Library name: Sample 5


title: 57324

description: Library name: Sample 8


title: 57321

description: Library name: Sample 6


title: 57330

description: Library name: Sample 10


title: 57337

description: Library name: Sample 11


title: 57352

description: Library name: Sample 12


title: 57307

description: Library name: Sample 1


title: 57308

description: Library name: Sample 2


title: 57314

description: Library name: Sample 4


title: TAC-BacNav mouse 2

first: Nenad

last: Bursac

address: 101 Science Drive

description: Library name: Sample 10

data_processing:
Quality control and adaptor trimming were performed using FastP software. The reads were aligned to M. musculus genome using HiSAT2 and aligned reads were counted using featureCounts.
Assembly: GRCh38
Supplementary files format and content: comma-delimited csv file includes raw counts for each Sample

source_name: Heart

extract_protocol:
Total RNA from snap-frozen mouse ventricles was extracted using TRIzol Reagent (Invitrogen) and RNeasy Mini Kit (Qiagen).
RNA sequencing libraries were prepared at Genewiz and sequencing was performed using Illumina HiSeq, 2 × 150–base pair with 20 million paired-end reads per sample.

value: Heart

value: WT


title: TAC-mScarlet mouse 2

description: Library name: Sample 6


title: 57323

description: Library name: Sample 7

value: liver

value: Sprague Dawley


title: TAC-BacNav mouse 3

description: Library name: Sample 11


title: Sham-NT mouse 1

description: Library name: Sample 1

value: PBS


title: TAC-BacNav mouse 1

description: Library name: Sample 9


title: Sham-NT mouse 4

description: Library name: Sample 4


title: TAC-mScarlet mouse 4

description: Library name: Sample 8


title: TAC-mScarlet mouse 1

description: Library name: Sample 5


title: TAC-mScarlet mouse 3

description: Library name: Sample 7


title: TAC-BacNav mouse 4

description: Library name: Sample 12


title: 57312

description: Library name: Sample 3

value: female

value: adult


title: C3

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

country: Italy

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

description: Library name: Sample 5

data_processing:
The final libraries for single-read sequencing of 101 base pairs was carried out on an Illumina HiSeq2000. Reads quality was evaluated using FastQC (version 0.11.2, Babraham Institute Cambridge, UK) tool and will be trimmed using FastqToolkit with the following parameter: --adapters-3 "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC" --adapter-trimming-stringency "0.90" --min-length "50" --min-quality-mean "30" --trim-5 "12" --trim-qual-5 "30" --trim-qual-3 "30" --filter-non-pf".
Then reads will be mapped to the human Ensembl GRCm39 build reference genome using STAR version 2.7.11a (Dobin et al., 2013) using Gene annotations corresponding to the Ensembl annotation release 109 which will be used to build a transcriptome index and provided to STAR during the alignment.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file with raw counts for each Sample

source_name: pancreatic neoplastic lesion

extract_protocol:
Total RNA was extracted from flash frozen mouse pancreata using Qiagen RNeasy Plus.
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen, Vienna, Austria) according to manufacturer's instructions.

value: pancreatic neoplastic lesion

tag: time

value: M

tag: dietary regimen

value: HFD


title: C4

description: Library name: Sample 6


title: 7326

description: Library name: Sample 37

value: non-pregnant

value: oral

value: 90 days

value: 10 mg/kg-d HFPO-DA


title: Sham-NT mouse 3

description: Library name: Sample 3


title: C2

description: Library name: Sample 4


title: A2

description: Library name: Sample 1

value: LFD


title: A4

description: Library name: Sample 3


title: 24-month doxycycline treated tTAxAPP, ID80

city: Bonn

first: Kan

last: Xie

address: Venusberg-Campus 1/99

department: Translational Gerontology

country: Germany

institute: German Center for Neurodegenerative Diseases

data_processing:
align with mm10 using STAR 2.4.0
Assembly: mm10
Supplementary files format and content: Tab-delimited text file contains normalized counts for individual biological replicates.

source_name: Brain

extract_protocol:
RNA was isolated in a two-stepped protocol using peqGold TriFast and RNeasy Mini Kit.
Library preparation was completed using the TruSeq RNA Library Prep Kit following the manufacturer´s instructions.

treatment_protocol: Doxycycline was administered by adding 200 mg/kg doxycycline to chow.

value: Brain

tag: age

value: male

value: Camk2a-tTA x tetO-APPSwInd

value: Doxycycline


title: Whole heart tissue, mG4H-OFF, rep 1 [Bisulfite-Seq]

first: Sayan

last: Bakshi

state: Alabama

department: Department of Pathology

institute: University of Alabama at Birmingham

data_processing:
Fastq files generated from RRBS were checked for quality using FastQC (v0.11.9). In this step, Con-ON sample failed to meet the quality needed for downstream analysis, hence, excluded from rest of the analysis.
Prior to alignment to the reference mouse genome, each sequence in the raw FASTQ files was trimmed on base call quality and sequencing adapter contamination using the Trim Galore! wrapper tool. Reads shorter than 20 base pairs were removed from the FASTQ files.
Trimmed reads were aligned to the reference genome using the Bismark, which then generated methylation coverage files.
From these coverage files, differentially methylated CpG (DMC) sites were detected via methylKit (v1.16.1)
Assembly: mm39
Supplementary files format and content: excel file include beta values for all samples

source_name: Whole heart tissue

extract_protocol:
Whole hearts were excised and were snap frozen in liquid nitrogen and stored at - 80 °C until subjected to further analysis.
DNA was isolated using Qiagen DNeasy DNA isolation and purification kit following the manufacturer’s guidelines. DNA was subsequently sent to Zymo Research for bisulfite conversion, library preparation, and reduced representation bisulfite sequencing (RRBS).
RRBS was performed via Zymo’s Methyl-MidiSeq protocol.

value: Whole heart tissue

value: 2 weeks DOX to induce glucose delivery, followed by 2 weeks of no DOX treatment (OFF)


title: 24-month doxycycline treated tTAxAPP, ID3


title: Sham-NT mouse 2

description: Library name: Sample 2

value: Heart

value: WT

value: PBS


title: 24-month placebo treated tTAxAPP, ID27

value: female

value: Placebo


title: 24-month placebo treated tTAxAPP, ID1590


title: 24-month placebo treated tTAxAPP, ID1547


title: 18-month doxycycline treated tTAxAPP, ID205


title: 18-month doxycycline treated tTAxAPP, ID199


title: A3

description: Library name: Sample 2

value: pancreatic neoplastic lesion

value: M


title: 18-month placebo treated tTAxAPP, ID204


title: 18-month doxycycline treated tTAxAPP, ID176


title: Whole heart tissue, Con-OFF, rep 1 [Bisulfite-Seq]

value: Control


title: C799CBm_ATAC

description: Library name: C799CBm_ATAC_MAH

data_processing:
Raw base call files were converted to FASTQ format and processed using Cell Ranger ARC (v2.0.1, 10x Genomics). Reads were aligned to species-specific reference genomes. Gene expression matrices and chromatin accessibility peak counts were generated using default Cell Ranger ARC parameters. Nuclei were filtered based on quality control thresholds including UMI counts, feature counts, mitochondrial gene percentage (>5%), total ATAC fragment counts (<1,000), and transcription start site enrichment score (<4). Downstream clustering and cell type annotation were performed using Seurat (v4.0.6).
Assembly: human, GRCh38; chimpanzees, panTro5;rhesus macaque, rheMac10; marmoset, calJac4
Supplementary files format and content: cellranger output: feature_bc_matrix.h5
Supplementary files format and content: cellranger output: atac_fragments.tsv.gz

organism: Callithrix jacchus

extract_protocol:
Frozen cerebellar cortex tissue was homogenized and nuclei were isolated using detergent-based resuspension buffers containing NaCl, MgCl₂, Tris-HCl, NP-40, Tween-20, digitonin, protease inhibitors, DTT, BSA, and RNase inhibitor. Nuclei were filtered through 70 µm strainers, centrifuged at 500 × g at 4°C, and resuspended in nuclei buffer supplemented with DTT and RNase inhibitor. Nuclei concentration was adjusted to 4.5 × 10⁶ nuclei/mL prior to microfluidic capture.
Single-nucleus RNA and chromatin accessibility libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC and Gene Expression kit (10x Genomics, PN-1000283) according to the manufacturer’s instructions. Approximately 10,000 nuclei were targeted per sample using the Chromium microfluidic system with Multiome Gel Bead Kit A and Multiome GEM Kit A. RNA and ATAC libraries were generated in parallel from the same nuclei preparation.

value: cerebellum

value: adult

tag: library type

value: ATAC


title: C799CBm_RNA

description: Library name: C799CBm_GEX_MAH

tag: tissue

value: mRNA


title: 18-month placebo treated tTAxAPP, ID172

value: Brain

value: male


title: C798CBm_RNA

description: Library name: C798CBm_GEX_MAH


title: 18-month placebo treated tTAxAPP, ID167

value: Camk2a-tTA x tetO-APPSwInd