title: Sample 42

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

data_processing:
RNA preparation, library construction and sequencing on BGISEQ-500 was performed at Beijing Genomics Institute.
Reads were aligned to the mouse genome (GRCm38) using STAR  (-runThreadN 2 --genomeDir ../../../star/genome --readFilesIn *.fq.gz *.fq.gz --readFilesCommand gunzip -c --outFileNamePrefix ../STAR/*_ --outSAMtype BAM SortedByCoordinate --outSAMunmapped None --outSAMattrIHstart 0 --outFilterType BySJout --sjdbGTFfile Mus_musculus.GRCm38.101.gtf --sjdbOverhang 100 --quantMode TranscriptomeSAM
Reads were quantified using Htseq
Genome_build: Mus_musculus.GRCm38 - mm10
Supplementary_files_format_and_content: Raw counts using HTSeq

source_name: C2C12, muscle cells

growth_protocol: The following culture media were used; C2C12 differentiation medium (DM-C2C12; DMEM (GlutaMAX with pyruvate) + 2% horse serum heat inactivated (30 minutes 56°C) + 1% Penicillin/Streptavidin (P/S, Penicillin (10,000 IU) and Streptomycin (10,000 g/mL))), growth medium (GM; DMEM + 10% fetal calf serum (FCS) + 1% P/S) and GM-low glucose medium (GM-LG; DMEM (low glucose GlutaMAX™ with pyruvate) + 10% FCS + 1% P/S). C26 (kindly obtained from Donna McCarthy, Ohio State University, USA), LLC (kindly obtained from Josep Argiles, University of Barcelona, Spain) and C2C12 (kindly obtained from Francina Dijk, Nutricia, the Netherlands) cells were maintained in GM. KPC and the genetic variation KPC-4662 (4662) (kindly obtained from Elizabeth Jaffee and Daniel Marks, Oregon Health and Science University, USA) were maintained in GM-LG. To make conditioned medium (CM), cells were taken from 90% confluent flasks and seeded 1:5 (C26 and LLC) and 1:3 (KPC and 4662) in a T75 flask. Cells were allowed to adhere to the flask for two hours in their maintenance medium (GM or GM-LG), thereafter cells were washed twice with phosphate buffered saline (PBS) and 12 mL of DM-C2C12 was added. All cells were incubated at 37°C and 5% CO2 for 96 hours to create CM. After 96 hours, CM was harvested and pooled per cell line, centrifuged (5 minutes at 500 g), aliquoted and stored at -20°C.

extract_protocol:
Cells were washed once with PBS before harvesting. For the RNA samples, cells were collected with TRIzol Reagent (Invitrogen, 15596018) or RLT buffer (Qiagen, 74004) + B-mercaptoethanol. Lysates were homogenized and stored at -20°C. Samples were thawed and 0.2 mL chloroform per 1 mL of TRIzol was added and incubated for 2–3 minutes. Samples were centrifuged for 15 minutes at 12000 g at 4°C and the aqueous phase was transferred to a new tube. From this aqueous phase the RNA was isolated using RNeasy Micro Kit (Qiagen, 74004) following the manufacturer’s instructions. RNA was eluted in 14uL RNase-free water and RNA yield was determined by nanodrop. RNA quality was determined using the Bioanalyzer (Agilent) and the RNA 6000 Nano Kit (Agilent, 5067-1511). Technical triplicates were pooled, resulting in a total of three biological replicates per conditions. All samples were diluted to a concentration of 40 ng/uL and shipped in dry ice to BGI tech solutions (Hongkong).
RNA preparation, library construction and sequencing on BGISEQ-500 was performed at Beijing Genomics Institute. At BGI tech solutions, DNBseq eukaryotic transcriptome re-sequencing (strand specific) was done applying at least 20M clean reads per sample. Filtered sequencing reads were collected (6-9 GB data per sample).

treatment_protocol: C2C12 were maintained sub-confluent in GM. For the differentiation experiments, cells were seeded in a 24 wells plate at 1.14x105 cells/mL and 1 mL per well. After 24 hours, medium was changed to DM (fresh medium control (FM)) or DM with 33% CM. At day 3 of the differentiation, medium of all conditions were refreshed. Additionally, on day 3 and 5 samples were harvested for RNA isolation (duplicate or triplicate per day). Experiments were repeated (N) 3 or 4 times.

value: CTRL

tag: differentiation day


title: poolA-93

status: Public on Dec 05 2025

type: SRA

city: Essen

first: Florian

last: Rambow

department: IKIM

country: Germany

institute: University Hospital Essen

library_source: transcriptomic single cell

data_processing:
BAM files were converted to merged, demultiplexed FASTQ files, cleaned using fastq-mcf (ea-utils r819), and QC checked with FastQC (0.11.4). Reads were then mapped to the mouse genome (mm10) using STAR (2.4.1b) and quantified with Subread (1.4.6-p2).
The merged gene expression matrix (raw counts) containing all samples was analyzed with the Seurat3 package in R. Cells were filtered by nFeature_RNA (genes detected) >3000 and <7000, percent.mt (percentage of mitochondria genes) < 10. This resulted in n=306 valid cells for downstream analysis. After filtering cells, log-normalization was performed using the default NormalizeData function in Seurat. The scaled data was regressed for cell cycle phases (S.Score and G2M.Score) and number of genes per cell (nFeature_RNA) before performing UMAP based dimension reduction (dims=1:20, resolution =0.4).
Assembly: mm10
Supplementary files format and content: csv

molecule: polyA RNA

organism: Mus musculus

source_name: tumor

extract_protocol:
Single cells were sorted (BD FACSAriaIII) in 96 well plates (VWR) containing 2μL of PBS including 0.2% Triton X-100 and 4U of RNase inhibitor (Takara) per well. Plates were properly sealed and spun down at 2000g for 1min before storing at −80°C. Whole transcriptome amplification was performed with a modified SMART-seq2 protocol as described previously, using 20 instead of 18 cycles of cDNA amplification. PCR purification was realized with a 0.8:1 ratio (ampureXP beads:DNA). Amplified cDNA quality was monitored with a high sensitivity DNA chip (Agilent) using the Bioanalyzer (Agilent)
SMART-seq2 based scRNA-seq; Sequencing libraries were performed using the Nextera XT kit (Illumina) as described previously, using 1/4th of the recommended reagent volumes and 1/5th of input DNA with a tagmentation time of 9min. Library quality was monitored with a high sensitivity DNA chip (Agilent) using the Bioanalyzer (Agilent). Indexing was performed with the Nextera XT index Kit V2 (A-D).

tag: tissue

value: tumor

tag: cell type

tag: treatment


title: meRIP seq Input of MOLM13:RBM15B-knockdown rep1

city: Guangzhou

first: Wen-Tao

last: Wang

state: Guangdong

address: No. 135, Xingang Xi Road

department: School of Life Sciences

country: China

institute: sun yat sen university

description: B-1 input

library_source: transcriptomic

data_processing:
Trim-galore (v0.6.10) was used to trim adapters and filter for sequences, remaining reads were then aligned to the Hg19  using Bowtie2 (v2.5.0) Hisat2 aligner (v2.1.0)
m6A peaks were identified using exomePeak2 R package (v1.6.1) under parameters: “FRAGMENT_LENGTH=140,p_cutoff = 1e-05,paired_end = TRUE” ; for epz_meRIP data , called peaks under parameters:"FRAGMENT_LENGTH=140, log2FC_cutoff = 1,p_cutoff = 1e-05,paired_end = TRUE" for shRBM15B_meRIP data.
CUT&Tag peaks were  identified using MACS2 (v2.2.7.1) under parameters:"-f BAMPE -g hs --keep-dup all -B -q 0.05 -m 5 50"
Assembly: Hg19
Supplementary files format and content: bed, narrowPeak (except for lnput sample)
Library strategy: m6A-RIP-seq

molecule: total RNA

organism: Homo sapiens

source_name: Bone Marrow

extract_protocol:
For Cut&Tag, 5 × 104 MOLM13 cells were sorted and washed once in 0.5 mL wash buffer (20 mM Hepes (pH 7.5); 150 mM NaCl; 0.5 mM spermidine; and 1 × protease inhibitors) and were incubated with 10 μL pre-washed concanavalin A–coated magnetic beads in a 1.5 mL microtube at 25 °C for 10 min. Cells were resuspended in 80 μL ice-cold antibody incubation buffer with 1 μg RBM15B antibody per sample (22249-1-AP, proteintech) and then rotated end-over-end at 4 °C overnight. The cells were resuspended in 100 μL of dig-wash buffer [20 mM Hepes (pH 7.5); 150 mM NaCl; 0.5 mM spermidine; 1 × protease inhibitors; 0.025% digitonin) with rabbit anti-mouse IgG (1:100 dilution, Ab6709; ThermoFisher) and rotated end-over-end at 25 °C for 1 h. After washing, home-made pA-Tn5 adapter complexes in dig-300 buffer (20 mM Hepes pH 7.5; 300 mM NaCl; 0.5 mM spermidine; 1 × protease inhibitors; 0.01% digitonin) were added to the samples at a final concentration of 1:100 and then rotated end-over-end at 25 °C for 1 h. After washing, the cells were resuspended in 300 μL fragmentation buffer (dig-300 buffer with 10 mM MgCl2) and incubated at 37 °C for 1 h. After extraction with phenol–chloroform and ethanol precipitation, the libraries were amplified by PCR.  For m6A-RIP, Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018). The concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). 10μg total RNA was fragmented into 100-200 nt RNA fragments using 10X RNA Fragmentation Buffer (100 mM Tris-HCl, 100 mM ZnCl2 in nuclease-free H2O). The fragmented RNA was incubated with anti-m6A monoclonal antibody (abcam,ab208577) for 3 h at 4℃ and then with protein A/G magnetic beads (Invitrogen, 8880210002D/10004D) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The m6A-enriched RNA was purified using TRIzol™ Reagent (Invitrogen, 15596018).
For Cut&Tag sequencing, the barcoded libraries were pooled and sequenced on the Illumina HiSeq X™ Ten platform to generate 150 bp paired-end reads. For m6A-RIP sequencing, the library was prepared by smart-seq method. Both the input samples without IP and the m6A IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.

treatment_protocol: For Cut&Tag sequencing, the MOLM-13 cells treated by 1uM epz5676 or DMSO(negative control)  for 72 hours.

value: Bone Marrow

tag: cell line

tag: genotype

value: acute myeloid leukemia cells

value: Negative control


title: Sample 41

tag: batch

value: LPS


title: Sample 40

value: OLD


title: poolA-92


title: DOX-3

city: Chongqing

first: Chen

last: yan

address: 30 Gaotanyan Main Street

institute: Third Military Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of pval below 0.05 and absolute fold change ≥ 1.5 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Mus_musculus.GRCm38 v101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Heart

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: strain

value: Heart

tag: age

value: 8–12 weeks old

value: Wildtype

value: DOX


title: no-behavior_female_dls_cort_rep3

city: Philadelphia

first: Keegan

middle: Scott

last: Krick

state: PA

address: 3400 Civic Center Blvd

country: USA

institute: University of Pennsylvania

description: Library name: no-behavior_female_dls_cort_rep3

data_processing:
Raw reads had adapters trimmed using BBDuk and were then aligned to the mm39 genome and quantified using kallisto.
Assembly: mm39
Supplementary files format and content: Matrix of TPM abundances for each sample

source_name: brain

growth_protocol: 8-week-old male and female C57BL/6J mice housed under a 12-hour light-dark cycle at 23 ºC.

extract_protocol:
Bilateral 2mm-diameter biopsy punches of dorsal medial striatum (DMS) and dorsal lateral striatum (DLS) were taken from two coronal slices (4 total punches per region per animal). Tissue samples were processed for RNA and chromatin using single sample sequencing (S3EQ) as described in Xu and Heller 2018 (PMID: 30031009)
Libraries were prepared from polyA-selected RNA for Illumina sequencing by Azenta Life Sciences (Plainfield, NJ).

treatment_protocol: Vehicle-treated groups received 1% ethanol in their drinking water. Mice had ad libitum access to water, which was weighed and replaced with fresh solutions every two days. A CORT concentration of 50µg/mL was used for mice undergoing operant behavior. Water bottle weights and mouse body weights per cage were used to calculate the average CORT dose per cage of ~7mg/kg/day. Mice underwent two weeks of water administration before beginning behavior, and water administration continued throughout the duration of behavior.

value: brain

tag: brain region

value: dls

tag: behavior paradigm

value: no-behavior

tag: Sex

value: female

value: cort


title: meRIP seq of MOLM13:RBM15B-knockdown rep1

value: epz5676, 1uM for 72 hours


title: meRIP seq Input of MOLM13:RBM15B-knockdown rep2

description: B-2 input


title: limited_female_dms_vehicle_rep1

description: Library name: limited_female_dms_vehicle_rep1

value: dms

value: limited

value: vehicle


title: meRIP seq of MOLM13:EPZ5676-treated rep3

value: Bone Marrow

value: acute myeloid leukemia cells


title: meRIP seq Input of MOLM13:EPZ5676-treated rep3

description: 3rd_1 input


title: Sample 38


title: poolA-91

value: tumor


title: Sample 37


title: meRIP seq of MOLM13:DMSO-treated rep3

value: Negative control


title: no-behavior_male_dms_cort_rep2

description: Library name: no-behavior_male_dms_cort_rep2

value: male


title: meRIP seq Input of MOLM13:DMSO-treated rep3

description: 3rd_0 input


title: Sample 39

value: KPC


title: poolA-89


title: Sample 36

value: LLC


title: poolA-88


title: no-behavior_female_dms_cort_rep3

description: Library name: no-behavior_female_dms_cort_rep3


title: no-behavior_female_dls_cort_rep2

description: Library name: no-behavior_female_dls_cort_rep2


title: meRIP seq Input of MOLM13:DMSO-treated rep2

description: 2nd_0 input


title: poolA-87


title: Sample 35

value: CTRL


title: Sample 34

value: LPS


title: no-behavior_male_dls_cort_rep2

description: Library name: no-behavior_male_dls_cort_rep2

value: brain

value: dls


title: Sample 33

value: OLD


title: no-behavior_male_dls_cort_rep1

description: Library name: no-behavior_male_dls_cort_rep1

value: no-behavior

value: cort


title: no-behavior_female_dms_cort_rep2

description: Library name: no-behavior_female_dms_cort_rep2

value: dms

value: female


title: meRIP seq Input of MOLM13:EPZ5676-treated rep2

description: 2nd_1 input

value: epz5676, 1uM for 72 hours


title: poolA-90


title: Sample 32


title: poolA-84


title: no-behavior_male_dms_cort_rep1

description: Library name: no-behavior_male_dms_cort_rep1


title: poolA-85


title: poolA-83


title: meRIP seq of MOLM13:DMSO-treated rep2

value: Bone Marrow


title: meRIP seq Input of MOLM13:EPZ5676-treated rep1

description: 1st_1 input

value: acute myeloid leukemia cells


title: no-behavior_female_dls_cort_rep1

description: Library name: no-behavior_female_dls_cort_rep1


title: Sample 31


title: no-behavior_female_dms_cort_rep1

description: Library name: no-behavior_female_dms_cort_rep1


title: meRIP seq of MOLM13:RBM15B-NC rep1


title: Sample 30


title: meRIP seq of MOLM13:EPZ5676-treated rep1


title: meRIP seq Input of MOLM13:DMSO-treated rep1

description: 1st_0 input


title: Sample 29


title: meRIP seq of MOLM13:DMSO-treated rep1


title: poolA-82

value: tumor


title: poolA-86


title: poolA-81


title: poolA-79


title: meRIP seq of MOLM13:EPZ5676-treated rep2


title: no-behavior_female_dms_vehicle_rep3

description: Library name: no-behavior_female_dms_vehicle_rep3

value: vehicle


title: no-behavior_male_dls_vehicle_rep3

description: Library name: no-behavior_male_dls_vehicle_rep3

value: male


title: no-behavior_male_dms_vehicle_rep3

description: Library name: no-behavior_male_dms_vehicle_rep3


title: Sample 28


title: Sample 27


title: poolA-78


title: poolA-80


title: 1352

type: genomic

city: Ann Arbor

first: Lana

last: Garmire

state: Michigan

address: 1600 Huron Parkway

institute: University of Michigan

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Preprocessed, normalized, and batch removed with ChAMP (version  2.16.2) in R

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Cord Blood

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from prepared cord blood samples using AllPrep DNA/RNA/Protein Mini Kit (Qiagen, USA) according to the manufacturer’s instructions by HiBR. We obtained pre-extracted genomic DNA of whole cord blood samples from the HiBR and conducted DNA Illumina EPIC Beadchip assays through the University of Hawaii Cancer Center Genomics Core.

value: Cord Blood

value: Disease


title: poolA-77


title: no-behavior_male_dls_vehicle_rep2

description: Library name: no-behavior_male_dls_vehicle_rep2


title: 1227


title: 519

value: Controls


title: 1173


title: Sample 25

value: KPC


title: no-behavior_male_dms_vehicle_rep2

description: Library name: no-behavior_male_dms_vehicle_rep2

value: brain


title: 1108


title: Sample 24


title: poolA-76


title: no-behavior_female_dls_vehicle_rep2

description: Library name: no-behavior_female_dls_vehicle_rep2

value: dls


title: poolA-75


title: poolA-74


title: Sample 22

value: LLC


title: no-behavior_female_dms_vehicle_rep2

description: Library name: no-behavior_female_dms_vehicle_rep2

value: no-behavior


title: Sample 26

value: OLD


title: 7146


title: poolA-73


title: 8866


title: 7012


title: no-behavior_female_dls_vehicle_rep3

description: Library name: no-behavior_female_dls_vehicle_rep3


title: Sample 21

value: CTRL


title: no-behavior_male_dls_vehicle_rep1

description: Library name: no-behavior_male_dls_vehicle_rep1


title: no-behavior_male_dms_vehicle_rep1

description: Library name: no-behavior_male_dms_vehicle_rep1

value: dms


title: Sample 20

value: LPS


title: poolA-72


title: 7064


title: 6350


title: poolA-70


title: Sample 19


title: poolA-71


title: no-behavior_female_dms_vehicle_rep1

description: Library name: no-behavior_female_dms_vehicle_rep1

value: female


title: no-behavior_female_dls_vehicle_rep1

description: Library name: no-behavior_female_dls_vehicle_rep1


title: Sample 18


title: 2065


title: extended_male_dls_cort_rep3

description: Library name: extended_male_dls_cort_rep3

value: extended

value: cort


title: Sample 23


title: 6716


title: extended_male_dms_cort_rep3

description: Library name: extended_male_dms_cort_rep3


title: 7200


title: poolA-69

value: tumor


title: Sample 17


title: Sample 16


title: poolA-67


title: poolA-68


title: poolA-66


title: extended_female_dms_cort_rep3

description: Library name: extended_female_dms_cort_rep3


title: 1950


title: Sample 14


title: extended_male_dls_cort_rep2

description: Library name: extended_male_dls_cort_rep2

value: male


title: poolA-65


title: Sample 15


title: 3677

value: Cord Blood


title: extended_male_dms_cort_rep2

description: Library name: extended_male_dms_cort_rep2


title: 4456


title: extended_female_dls_cort_rep2

description: Library name: extended_female_dls_cort_rep2


title: Sample 12


title: Sample 11


title: poolA-64


title: extended_female_dms_cort_rep2

description: Library name: extended_female_dms_cort_rep2


title: 1355


title: 7168


title: extended_female_dls_cort_rep3

description: Library name: extended_female_dls_cort_rep3


title: 4527


title: poolA-62


title: Sample 10


title: extended_male_dms_cort_rep1

description: Library name: extended_male_dms_cort_rep1


title: extended_male_dls_cort_rep1

description: Library name: extended_male_dls_cort_rep1


title: Sample 9


title: poolA-61


title: Sample 13


title: 2282


title: Sample 8


title: poolA-60


title: 683


title: extended_female_dls_cort_rep1

description: Library name: extended_female_dls_cort_rep1


title: poolA-59


title: Sample 6


title: poolA-58


title: Sample 7


title: extended_female_dms_cort_rep1

description: Library name: extended_female_dms_cort_rep1


title: 4217


title: Sample 5


title: 8870


title: poolA-57


title: Brain, sleep deprived, ZT6, rep3, IgG

first: Shintaro

last: Yamazaki

address: 10-179/180 Smilow Center, 3400 Civic Center Boulevard, Building 421

department: Department of Systems Pharmacology & Therapeutics

description:
Library name: Sample 17
Rabbit IgG Negative Control Antibody (EpiCypher, 130042)

library_source: genomic

data_processing:
Sequencing using a NovaSeq X Plus 10B flow cell platform with paired-end 300-500bp reads and subsequent quality filtering of reads was performed according to the manufacturer’s instructions (Illumina).
FASTQ files containing sequence reads were processed with CUT&RUNTools2.0. Peak calling for ant-HSF1 antibody was performed using control, corresponding aligned data for IgG negative control antibody in each replicate, with MACS2 (version 2.2.9.1) using standard threshold setting (q<0.05).
The peak calling results were annotated with transcription starting sites (: TSS. Within ± 3,000bp from gene) using ChIPseeker (R package version 3.38.0) along with BSgenome.Mmusculus.UCSCmm39 (R package version1.4.3), and the TSS-associated genes were listed in each replicate. Genes associated with HSF1-binding loci increased by sleep deprivation (increased-genes in SD) were determined by subtracting the genes found in all replicates of NS group from the genes found in one or more replicates in SD group.
Assembly: GRCm39
Supplementary files format and content: bigwig files contains signal data for visualization. The bam files from CUT&RUNTools2.0 process were converted to bedgraph files by the following steps: sorted using samtools (version 1.13), converted to bedgraph usng bedtools (version 2.26.0), and sorted (-k1, -k2,2n). The bedgraph files were converted to bigwig files using bedGraphToBigWig (version 4).
Supplementary files format and content: narrow.Peak files contain peak calling results for ant-HSF1 antibody using control, corresponding aligned data for IgG negative control antibody in each replicate, with MACS2 (version 2.2.9.1) using standard threshold setting (q<0.05).
Library strategy: CUT&RUN

source_name: cerebral cortex

growth_protocol: singly housed in chambers for habituation with ad libitum access to food and water under standard humidity and temperature (21 ± 1 °C) on a 12h:12h light-dark cycle

extract_protocol:
For the brain sample collection, 6 hours sleep deprivations during ZT0 – ZT6 was performed by a gentle handling after 2 weeks of acclimatization. The samples were flash-frozen in liquid nitrogen and stored at -80°C until use. Intact nuclei were extracted used for CUT&RUN. Minced cerebral cortex tissues were incubated in the Nuclear Extraction Buffer: 20mM HEPES (Gibco, 15630080), 10mM Potassium chloride (Sigma-Aldrich, P9541), 20% (v/v) Glycerol (Sigma-Aldrich, G5516), 0.1% NP-40 (Thermo Scientific, 85124), 0.5mM Spermidine (Sigma-Aldrich, S0266), 1X Halt Protease Inhibitor Cocktail (Fisher Scientific, 78425) and 2% Bovine Serum Albumin (Sigma-Aldrich, B6917), for 10min on ice and filtered through 40µm CellPro Premium Cell Strainer (DOT SCIENTIFIC INC., CS4040). These steps were repeated three times before proceeding the following workflows. CUT&RUN wes performed according to the manufacture’s instruction. In brief, activated Concanavalin A Conjugated Paramagnetic Beads (: ConA beads, EpiCypher, 211401) were incubated with the extracted nuclei to bind for 10min at room temperature. The ConA beads-nuclei mixture was resuspended in cold Antibody Buffer: 20mM HEPES (Gibco), 150mM Sodium chloride (Sigma-Aldrich, S5150), 0.5mM Spermidine (Sigma-Aldrich), 1X Halt Protease Inhibitor Cocktail (Fisher Scientific), 0.05% Digitonin (Millipore Sigma, 300410), 2mM EDTA (Invitrogen, 15575020) and 2% Bovine Serum Albumin (Sigma-Aldrich), and incubated with 0.5µg of anti-HSF1 antibody (Cell Signaling, 4356S), SNAP-ChIP Certified H3K4me3 Positive Control Antibody (Thermo Fisher, MA511198) or Rabbit IgG Negative Control Antibody (EpiCypher, 130042) per 5x105 nuclei at 4°C overnight on nutator. After washing twice in cold Digitonin Buffer: 20mM HEPES (Gibco), 150mM Sodium chloride (Sigma-Aldrich, S5150), 0.5mM Spermidine (Sigma-Aldrich), 1X Halt Protease Inhibitor Cocktail (Fisher Scientific), 0.05% Digitonin (Millipore Sigma, 300410) and 2% Bovine Serum Albumin (Sigma-Aldrich), the ConA beads-nuclei-antibody mixtures were resuspended in Digitonin Buffer and incubated with 2.5µL of CUTANA pAG-MNase (EpiCypher,151116) per 5x105 nuclei for 1 hour at 4°C on nutator for binding. The mixtures were washed twice, resuspended in Digitonin Buffer with 2mM Calcium chloride (Sigma-Aldrich, 21115) and incubated at 4°C for 2 hours for chromatin digestion. After the incubation, Stop Buffer: 340mM Sodium chloride (Sigma-Aldrich), 20mM EDTA (Invitrogen), 4mM EGTA (Sigma-Aldrich, E8145), 50µg/mL RNase A (Thermo Scientific, EN0531), 50µg/mL Glycogen (Roche, 10901393001), 0.5mM Spermidine (Sigma-Aldrich), 1X Halt Protease Inhibitor Cocktail (Fisher Scientific), 0.02% Digitonin (Millipore Sigma, 300410) and 2% Bovine Serum Albumin (Sigma-Aldrich), was added and incubated for 10min at 37°C to stop the digestion. The cleaved chromatins were collected from the supernatant and purified using Monarch PCR&DNA Cleanup Kit (BioLabs, T1030L) according to the manufacture’s instruction.
Sequencing libraries for each condition were prepared using 10ng of CUT&RUN enriched DNA fragments in total made by pooling equal amount DNAs of three replicates. End repair was performed using NEBNext Ultra II End Repair/dA-Tailing Module (New England BioLabs, E7546L) according to the manufacture’s instructions. Then, the samples were ligated to the NEBNext Adaptors (New England BioLabs, E6440L) and cleaned up using 1.75X (v/v) SPRIselect beads (Beckman Coulter, B23318). Adaptor-ligated DNA fragments were amplified using NEBNext Unique Dual Index Primer Pairs (New England BioLabs, E6441A) with NEBNext Ultra II Q5 Master Mix (New England BioLabs, M0544S). PCR was performed using the following parameters: initial denaturation at 98°C for 30sec, 14 cycles of denaturation at 98°C for 10sec and annealing/extension at 65°C for 75sec, final extension at 65°C for 5min. Size selections for 150-500bp were performed on the PCR products by applying 0.6X and 1.2X SPRIselect beads successively.

treatment_protocol: 6 hours sleep deprivation (ZT0-6) by gentle handling

value: cerebral cortex

value: WT

value: sleep deprivation


title: 1657

value: Controls


title: Brain, sleep deprived, ZT6, rep3, H3K4me3

description:
Library name: Sample 18
H3K4me3 Positive Control Antibody (Thermo Fisher, MA511198)


title: Brain, sleep deprived, ZT6, rep3, HSF1

description:
Library name: Sample 16
anti-HSF1 antibody (Cell Signaling, 4356S)


title: poolA-55


title: 6680


title: 5258


title: poolA-63


title: Brain, sleep deprived, ZT6, rep2, IgG

description:
Library name: Sample 14
Rabbit IgG Negative Control Antibody (EpiCypher, 130042)


title: Sample 1


title: Brain, sleep deprived, ZT6, rep2, H3K4me3

description:
Library name: Sample 15
H3K4me3 Positive Control Antibody (Thermo Fisher, MA511198)


title: 5323


title: 6598


title: poolA-54


title: poolA-53


title: poolA-51


title: Brain, sleep deprived, ZT6, rep1, H3K4me3

description:
Library name: Sample 12
H3K4me3 Positive Control Antibody (Thermo Fisher, MA511198)


title: poolA-52


title: Huh7 cells, miR-361-3p mimics, Day2 rep3

city: wuhan china

first: haisu

last: tao

address: jiefang street 1095

institute: Wuhan Tongji Hospital.

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.clean data were mapped to the reference genome of Homo_sapiens from ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/ using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1)
A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a pvalue cutoff of 0.05 to judge statistically significant enrichment.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cell lines

growth_protocol: Huh7 cell line were purchased from China Center for Type Culture Collection (CCTCC, China). Huh7 cells were cultured in high-glucose DMEM (HyClone,USA) supplemented with 10% FBS at 37°C in an atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted from tissues or cell lines using TRIzol reagent (Invitrogen, USA).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for MGI® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

treatment_protocol: miR-361-3p mimics and mimics-NC were designed by RiboBio (Guangzhou, China). When cells reach 70% density, the cell transfections were carried out using Lipo 3000 Transfection Reagent (Invitrogen).

value: cell lines

value: HCC cell lines

value: miR-361-3p mimics

value: Huh7 cells with miR-361-3p mimic


title: Brain, sleep deprived, ZT6, rep2, HSF1

description:
Library name: Sample 13
anti-HSF1 antibody (Cell Signaling, 4356S)


title: 4696


title: 702


title: Huh7 cells, miR-361-3p mimics, Day2 rep2


title: poolA-56


title: poolA-50


title: Sample 3


title: poolA-49


title: 7354

value: Disease


title: Brain, sleep deprived, ZT6, rep1, IgG

description:
Library name: Sample 11
Rabbit IgG Negative Control Antibody (EpiCypher, 130042)


title: Sample 4

value: KPC


title: Huh7 cells, miR-361-3p mimics, Day2 rep1


title: Brain, normal sleep, ZT6, rep3, H3K4me3

description:
Library name: Sample 9
H3K4me3 Positive Control Antibody (Thermo Fisher, MA511198)

value: normal sleep


title: Brain, sleep deprived, ZT6, rep1, HSF1

description:
Library name: Sample 10
anti-HSF1 antibody (Cell Signaling, 4356S)


title: 7453


title: poolA-48


title: Brain, normal sleep, ZT6, rep3, HSF1

description:
Library name: Sample 7
anti-HSF1 antibody (Cell Signaling, 4356S)


title: 5525


title: 7081


title: 5346


title: poolA-47


title: poolA-45


title: F2_WT

city: Bethesda

first: Tom

last: Hill

state: Maryland

address: NIHBC 10 - CLINICAL CENTER BG RM 11N244A, 10 CENTER DR

institute: NIAID

description:
Library name: F2_WT
10X Genomics

data_processing:
Data processed to fastq using cellranger mkfastq
Data aligned to mm10 using cellranger count
Data processed and filtered using Seurat
Assembly: mm10
Supplementary files format and content: matrix generated using cellranger count
Supplementary files format and content: barcodes generated using cellranger count
Supplementary files format and content: features generated using cellranger count

source_name: Thymic T cells

growth_protocol: Mice grown under standard lab conditions

extract_protocol:
Cells extracted and sorted at facility for sc-RNA seq to study the transcriptomic differences between the wild type and Ikzf4 cKO Tregs.
Followed standard scRNA library processing steps

treatment_protocol: mice treated during experiment using standard procedures

value: Thymic T cells


title: Sample 2


title: F2_Ikzf4_cKO

description:
Library name: F2_Ikzf4_cKO
10X Genomics


title: Brain, normal sleep, ZT6, rep3, IgG

description:
Library name: Sample 8
Rabbit IgG Negative Control Antibody (EpiCypher, 130042)


title: Huh7 cells, mimics-NC, Day2 rep3

value: Wild type Huh7 cells


title: Huh7 cells, mimics-NC, Day2 rep2


title: 9043


title: 4906


title: poolA-44


title: F1_Ikzf4_cKO

description:
Library name: F1_Ikzf4_cKO
10X Genomics


title: Brain, normal sleep, ZT6, rep2, IgG

description:
Library name: Sample 5
Rabbit IgG Negative Control Antibody (EpiCypher, 130042)


title: Brain, normal sleep, ZT6, rep2, HSF1

description:
Library name: Sample 4
anti-HSF1 antibody (Cell Signaling, 4356S)


title: Brain, normal sleep, ZT6, rep1, H3K4me3

description:
Library name: Sample 3
H3K4me3 Positive Control Antibody (Thermo Fisher, MA511198)


title: 6052


title: 618


title: Huh7 cells, mimics-NC, Day2 rep1


title: poolA-42


title: F1_WT

description:
Library name: F1_WT
10X Genomics


title: Brain, normal sleep, ZT6, rep1, IgG

description:
Library name: Sample 2
Rabbit IgG Negative Control Antibody (EpiCypher, 130042)


title: 4039


title: poolA-46


title: SVZ Single cell, NDUFS4 KO, rep1

city: Blacksburg

first: Alicia

middle: Mae

last: Pickrell

state: Virginia

address: 970 Washington St SW

department: School of Neuroscience

institute: Virginia Polytechnic Institute and State University

description:
Library name: NDUFS4KO1_061724
PIPseeker™ Software

data_processing:
Barcodes identifying individual PIPs/cells were assigned to sequenced cDNA constructs using PIPseeker™ v3.3. PIPseeker first identified barcode combinations and molecular identifiers (MI) for each read before mapping with STAR. After gathering molecule information, reads were assigned to genes by aligning coordinates against the STAR reference, with duplicate reads sharing the same MI collapsed into single counts.
The resulting counts were organized into a sparse matrix, where each entry corresponded to a cell barcode and gene. Barcodes were categorized as either cell-containing PIPs or background PIPs using a barcode rank plot ("knee plot"), which orders barcodes by transcript count. Following cell calling, directories were created for each sensitivity level, containing text files with selected cell barcodes, knee plot images, and filtered count matrices for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lateral wall of SVZ

extract_protocol:
Single-cell suspensions were prepared and diluted to 5,000 cells/µL in Cell Suspension Buffer (Fluent Biosciences, FB0002440), with a total of 40,000 cells per reaction. Each suspension was supplemented with 40U of RNase inhibitor (MilliporeSigma #3335399001). T20 PIPs (FB0003914) were thawed, briefly centrifuged, and placed on ice. Each T20 PIPs (FB003914) tube received 8 µL of the cell suspension, 40U of RNase inhibitor, and 1 mL of Partitioning Reagent (FB0003123). After mixing and vortexing, the excess Partitioning Reagent was removed, leaving the PIPs+cells. Chemical Lysis Buffer 3 (CLB3, FB0003910) was added to the PIP tubes and the samples were incubated in preheated PIPseq™ Dry bath (FBS-SCR-PDB, 25°C for 15 mins- 37°C for 45 mins- 25°C for 10 mins), to complete lysis.
Purified cDNA was processed through fragmentation, end-repair, adapter ligation, and indexed PCR using reagents from the PIPseq T20 3’ RNA Kit. Cleanup was performed after each step, with a double-sided size selection following indexing PCR. Libraries were assessed for concentration and quality using Qubit and fragment analysis prior to sequencing. This workflow provided sequencing-ready libraries within two days, suitable for downstream gene expression analysis and single-cell clustering. Premade libraries were sent to MedGenome for sequencing on the NovaSeq X+ platform. Libraries were sequenced using 10B lanes with a target of 400 million paired end reads per library and a sequencing depth of 20,000 reads per input cell.

value: Lateral wall of SVZ

value: Female

value: NDUFS4 KO


title: 1142

value: Cord Blood


title: poolA-40

value: tumor


title: Brain, sleep deprivation, ZT6, rep3

description: Library name: Sample 6

data_processing:
NovaSeq X Plus 10B flow cell platform with paired-end 300-500bp reads
FASTQ files were trimmed using TrimGalore (version 0.5.0) with parameters: clip first 40 bases of both forward and reverse readas, then aligned to the STAR index built on GRCm39 using STAR (version 2.7.11b). Counts, FPKM and TPM were computed using Stringtie (version 2.2.1) with options: -e -B -G. The read count information was extracted and compiled to a table by running prepDE.py3 script with default setting.
Assembly: GRCm39
Supplementary files format and content: csv file includes read counts for each Sample

extract_protocol:
For the brain sample collection, 6 hours sleep deprivations during ZT0 – ZT6 was performed by a gentle handling after 2 weeks of acclimatization. The samples were flash-frozen in liquid nitrogen and stored at -80°C until use. Total RNA was extracted using Direst-zol RNA miniprep (ZYMO RESEARCH, R2052) from the minced cerebral cortex tissues. messenger RNA (mRNA) was isolated using NEBNext Poly(A) Magnetic Isolation Module (NEB, E7490L) according to the manufacture’s instruction.
RNA-seq libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770). End repair was performed using NEBNext Ultra II End Repair/dA-Tailing Module (New England BioLabs, E7546L) according to the manufacture’s instructions. Then, the samples were ligated to the NEBNext Adaptors (New England BioLabs, E6440L) and cleaned up using 1.8X (v/v) SPRIselect beads (Beckman Coulter, B23318). Adaptor-ligated DNA fragments were amplified using NEBNext Unique Dual Index Primer Pairs (New England BioLabs, E6441A) with NEBNext Ultra II Q5 Master Mix (New England BioLabs, M0544S). PCR was performed using the following parameters: initial denaturation at 98°C for 30sec, 7 cycles of denaturation at 98°C for 10sec and annealing/extension at 65°C for 75sec, final extension at 65°C for 5min. Size selections for 150-500bp were performed on the PCR products by applying 0.9X and 1.2X SPRIselect beads successively. The libraries were quantified by qPCR using NEBNext Library Quant Kit for Illumina (NEB, E7642S) according to the manufacture’s instruction, and mixed in equal weight proportion to form the sequence library.

value: cerebral cortex

value: WT


title: SVZ Single cell, Wildtype, rep2

description:
Library name: WT2_061724
PIPseeker™ Software


title: Brain, normal sleep, ZT6, rep1, HSF1

description:
Library name: Sample 1
anti-HSF1 antibody (Cell Signaling, 4356S)


title: 5567

value: Controls


title: SVZ Single cell, Wildtype, rep1

description:
Library name: WT1_060524
PIPseeker™ Software

value: pooled male and female


title: Brain, sleep deprivation, ZT6, rep1

description: Library name: Sample 4

value: sleep deprivation


title: poolA-43


title: 5579


title: supT1, HIV 20h, rep2, FTO

city: Gif sur Yvette

first: Delphine

last: Naquin

address: avenue de la terrasse

country: France

institute: CNRS

description: Library name: SupT1_20h_pi_rep2_FTO

data_processing:
dorado for 6mA basecalling
Reads are mapped using minimap2 on HIV-pNL4-3 XCS  (parameters: --x splice and –secondary=no)
modkit for modification detection
Assembly: HIV-pNL4-3 XCS
Supplementary files format and content: bam file with modification tags

organism: Human immunodeficiency virus

growth_protocol: Cells were cultured with RPMI GlutaMax 1640 (Gibco) complemented with 10% FBS (Dutscher) and 1% penicillin/streptomycin

extract_protocol:
The total RNA was extracted using RNeasy Mini Kit (Qiagen) and polyA RNA was isolated using oligo(dT)25 Dynabeads (Thermo Fisher Scientific)
The polyA RNA was used for ONT direct RNA sequencing using the RNA004 kit.

treatment_protocol:
SupT1 cells were infected with 800 ng of VSV-G-HIVNL4-3 XCS HIV-Gagp24 for 3h in IMDM plus 10mM HEPES (Gibco/ThermoFisher Scientific) supplemented with 2 µg/ml of DEAE-dextran (Sigma)
Biological polyA RNA was treated with demethylases ALKBH5 or FTO (New England Biolabs).

value: 20h infection with HIV NL4-3 XCS + FTO treatment


title: Brain, sleep deprivation, ZT6, rep2

description: Library name: Sample 5


title: supT1, HIV 20h, rep2, ALKBH5

description: Library name: SupT1_20h_pi_rep2_ALKBH5

value: 20h infection with HIV NL4-3 XCS + ALKBH5 treatment


title: poolA-38


title: poolA-37


title: Brain, snRNAseq

description: Library name: Sample1

data_processing:
Sequencing was performed using an Illumina NovaSeq X Plus instrument with a 25B flow cell (1 lane) with 150 base paired-end reads.
snRNA-seq data were preprocessed using the EasySci pipeline (https://github.com/JunyueCaoLab/EasySci). Sample names listed in SampleID.txt were reformatted to ensure a uniform file naming convention. Barcoding of reads was performed using ligation and reverse transcription (RT) barcode matching files (ligation_barcodes.pickle2, RT_barcodes.pickle2, RT_barcode_matching.txt) along with random RT barcodes (RT_randomN_barcodes.txt). Raw Illumina binary base call (BCL) files generated from sequencing were demultiplexed and converted to FASTQ format according to PCR barcodes (PCR_batch) from the final amplification step of the EasySci protocol, using Illumina’s bcl2fastq Conversion Software (version 2.20.0.422). Demultiplexing allowed a barcode mismatch of one and processed dual-indexed paired-end reads. FASTQ files were generated for index reads, and lane splitting was disabled to ensure all reads were treated as a single set. The sequencing structure was used to define base usage, and trimming options ensured retention of all sequencing data for downstream analysis. Custom sample sheets were used to assign barcodes to their corresponding samples. The resulting barcoded FASTQ files were prepared for subsequent analyses. Barcoded reads underwent adapter trimming using TrimGalore (version 0.6.7). Adapters were removed from both paired-end reads using a custom adapter sequence (-a2 AAAAAAAA) with a stringency level of 3 to reduce false-positive trimming. Trimmed reads were aligned to the GRCm39 mouse reference genome (GENCODE vM27) using STAR (version 2.7.10a). Gene annotations were provided using a comprehensive GTF file containing all genomic features, as well as an exon-only GTF file. After duplicate removal, gene expression levels and exon-level read quantifications were performed using HTSeq (Python package version 2.0.3). The resulting expression matrices were outputted in Matrix Market format.
Single-nucleus RNA sequencing data underwent quality control filtering using Scanpy (v1.9.5). Initial criteria removed nuclei with fewer than 200 detected genes and genes detected in fewer than 3 cells, followed by exclusion of cells with mitochondrial gene content exceeding 5% or ribosomal gene content above 1%. Gene expression matrices were further refined by excluding cells exceeding the 98th percentile for both gene counts (>1,852 genes) and total counts (>5,470). Doublets were identified and removed using SOLO (scvi-tools v0.20.3). The SOLO model was trained on the 2,000 most highly variable genes determined using Scanpy (flavor="seurat_v3"). An scVI model on these data was trained on raw count data with 30 latent dimensions, 1024 hidden features, and 2 layers. Technical variation from well-to-well differences in initial RT barcoding (experimental group identity) was corrected using scVI, with subsequent analyses utilizing scVI-normalized expression data. Cell clustering and differential expression analyses were conducted separately for three experimental comparisons: Hsf1 knockout versus control (Hsf1 floxed) mice, sleep-deprived versus normal sleep in control (Hsf1 floxed) mice, and sleep-deprived versus normal sleep in Hsf1 knockout mice. For each comparison, clustering was performed using the Leiden algorithm (resolution=2.0) based on the 2,000 most highly variable genes (flavor="seurat_v3"), with neighborhood graphs computed using 30 nearest neighbors.  Major cell types were manually annotated using canonical marker gene panels, revealing distinct populations of glutamatergic neurons (subtypes: Sv2b+, Cux1+Cux2+, Foxp2+, Satb2+, and Slc17a7+), GABAergic neurons, oligodendrocytes/OPCs, astrocytes, and microglia. Classification relied on established lineage markers: glutamatergic neurons were identified through expression of vesicular glutamate transporters (Slc17a7), synaptic proteins (Sv2b), and layer-specific transcription factors (Cux1/2, Foxp2, Satb2); GABAergic neurons through Gad1 and interneuron subtype markers (e.g. Pvalb, Sst, Vip); oligodendrocytes through myelin-associated genes (e.g. Mbp, Plp1, Mog) and their precursors (OPCs) through Pdgfra and Sox10; astrocytes through transporters and structural proteins (e.g. Gfap, Aldh1l1, Slc1a2/3); and microglia through immune-related markers (e.g. Cx3cr1, P2ry12, Tmem119). UMAP visualizations were systematically examined to confirm proper mixing of experimental conditions (genotype and sleep groups) within each identified cell cluster.
Cell type-specific differential expression was computed using Scanpy's rank_genes_groups function on scVI-normalized data, implementing the Wilcoxon rank-sum test, with significance threshold set at adjusted p-value < 0.05. A threshold of adjusted p-value <0.05 and log2(fold change) >1.7 was applied to select significant differentially-expressed genes (DEGs). Clusters within a cell type (five sub-types for glutamatergic neurons) were merged, and duplicate DEGs were filtered by retaining the highest absolute log2(fold change) per gene. To link HSF1-regulated genes to snRNA-seq results, a subset of DEGs overlapping with genes bound by HSF1 in CUT&RUN analysis was extracted for each cell type. These genes were further divided into upregulated and downregulated groups based on their direction of expression change. GO analysis was conducted using the enrichGO function from clusterProfiler (R package version 3.0.4) with adjusted p value <0.05 and q value <0.05 as thresholds. Background gene sets for GO analysis were defined as the union of genes detected in all snRNA-seq conditions. Venn diagrams were created to visualize the overlap between HSF1-regulated genes and DEGs in each cell type. GO enrichment results were visualized as dot plots using enrichplot (R package version 1.24.0). Volcano plots were generated for each cell type to illustrate the distribution of DEGs, highlighting upregulated and downregulated genes using ggplot function from ggplot2 (R package version 3.5.1). Heatmaps summarizing the top 12 GO terms for each cell type were generated using the Heatmap function from ComplexHeatmap (R package version 2.20.0) to display enriched biological processes across cell types.
Assembly: GRCm39
Supplementary files format and content: exon_annotation.csv (csv file) : Exon annotation file including exon id, gene type and gene short name. exon_expression_matrix.mtx (matrix market file) : A sparse matrix file: each row corresponds to exon id (with exon information in the exon_annotation.csv); each column corresponds to each cell (with cell source information in the cell_annotation.csv); each value in the matrix corresponds to the expression of the corresponding exon in the corresponding cell. gene_annotation.csv (csv file) : Gene annotation file including gene id, gene type and gene short name. gene_expression_matrix.mtx (matrix market file) : A sparse matrix file: each row corresponds to gene id (with gene information in the gene_annotation.csv); each column corresponds to each cell (with cell source information in the cell_annotation.csv); each value in the matrix corresponds to UMI count. wt_vs_ko_differential_expression_results_scanpy.csv (csv file) : Differential expression analysis results comparing Hsf1 knockout to control mice in normal sleep condition. Including gene short name, significance score, log2 (fold change), raw p-value, adjusted p-value, and associated cell cluster. wt_ctl_vs_sd_differential_expression_results_scanpy.csv (csv file) : Differential expression analysis results comparing sleep deprived condition to normal sleep condition in control mice. Including gene short name, significance score, log2 (fold change), raw p-value, adjusted p-value, and associated cell cluster. ko_ctl_vs_sd_differential_expression_results_scanpy.csv (csv file) : Differential expression analysis results comparing sleep deprived condition to normal sleep condition in Hsf1 knockout mice. Including gene short name, significance score, log2 (fold change), raw p-value, adjusted p-value, and associated cell cluster. cell_annotation_ko_ctl_vs_sd.csv (csv file) : Annotation for cells analyzed under sleep deprivation and normal sleep conditions in Hsf1 knockout mice. Includes cell-level information such as UMI count, gene count, batch identifiers, barcodes, number of genes detected (n_genes), experimental sample, genotype, sleep condition (e.g., normal sleep or sleep deprivation), replicate number, treatment group, doublet status, clustering information (leiden cluster), annotated cell type, and UMAP coordinates (umap1, umap2). cell_annotation_wt_ctl_vs_sd.csv (csv file) : Annotation for cells analyzed under sleep deprivation and normal sleep conditions in control mice. Includes cell-level information such as UMI count, gene count, batch identifiers, barcodes, number of genes detected (n_genes), experimental sample, genotype, sleep condition (e.g., normal sleep or sleep deprivation), replicate number, treatment group, doublet status, clustering information (leiden cluster), annotated cell type, and UMAP coordinates (umap1, umap2). cell_annotation_wt_vs_ko.csv (csv file) : Annotation for cells analyzed in control and Hsf1 knockout mice under normal sleep condition. Includes cell-level information such as UMI count, gene count, batch identifiers, barcodes, number of genes detected (n_genes), experimental sample, genotype, sleep condition (e.g., normal sleep or sleep deprivation), replicate number, treatment group, doublet status, clustering information (leiden cluster), annotated cell type, and UMAP coordinates (umap1, umap2).

molecule: nuclear RNA

extract_protocol:
Intact nuclei were extracted using a protocol optimized for single-nucleus RNA sequencing (snRNA-seq) using the EasySci protocol adapted for mouse cortex tissue. The tissue was kept on dry ice, minced into fine pieces, and immediately placed in pre-chilled PBS (AM9624, Thermo Fisher Scientific) treated with 1% diethyl pyrocarbonate (DEPC, D5758-25ML, Sigma Aldrich). After several washes with ice-cold EZ Lysis Buffer (78425, Thermo Fisher Scientific) supplemented with RNase inhibitors (SUPERase In RNase Inhibitor, AM2694, Invitrogen), the tissue was mechanically disrupted using a syringe plunger and filtered through 40 µm cell strainers (CS4040, dot scientific inc.) to isolate nuclei. Nuclei were then resuspended in EZ Lysis Buffer supplemented with RNase inhibitors to ensure RNA integrity during processing. Formaldehyde was added at a final concentration of 0.1% (16% Formaldehyde Solution, 28906, Thermo Scientific) for 10 minutes to crosslink the nuclei. Following crosslinking, the nuclei were pelleted, washed, and stored at -80°C in a cryoprotective medium containing 10% dimethyl sulfoxide (DMSO, D8418, Sigma-Aldrich) for long-term storage until further processing.
For library preparation, we followed the EasySci protocol. Nuclei were thawed and washed in Nuclei Storage Buffer (NSB) (Nuclease-free water, 10977-015, Invitrogen) supplemented with 0.1% Triton X-100 (93443-100ML, Sigma-Aldrich). The nuclei were counted and distributed into multi-well plates at a density of 20,000 nuclei per well. Reverse transcription was initiated using short-dT and randomN primers followed by the addition of reverse transcription reaction mix (Maxima Reverse Transcriptase, EP0741, Thermo Fisher Scientific). The reaction was carried out using a thermocycler with a multi-step temperature protocol for optimal reverse transcription. Afterwards, tagmentation was performed using a 1:100 dilution of Tagmentase and 2X Tagmentation Buffer (NEBNext Ultra II Q5 Master Mix, E7649AA, New England BioLabs). Following the addition of indexed P7 primers (E7335, New England BioLabs) and NEBNext Ultra II Q5 Master Mix (E7649AA, New England BioLabs), the samples were amplified through PCR to generate the final cDNA libraries. Libraries were purified using AMPure XP beads (A63882, Beckman Coulter) and checked for quality before sequencing. The libraries were quantified by qPCR using NEBNext Library Quant Kit for Illumina (E7642S, New England BioLabs) according to the manufacturer’s instructions.

treatment_protocol: Hsf1 knockout by tamoxifen-induced Cre/LoxP system. 6 hours sleep deprivation by gentle handling

value: tamoxifen, sleep deprivation


title: Brain, normal sleep, ZT6, rep3

description: Library name: Sample 3


title: 9064

value: Disease


title: 6780


title: poolA-41


title: Brain, normal sleep, ZT6, rep2, H3K4me3

description:
Library name: Sample 6
H3K4me3 Positive Control Antibody (Thermo Fisher, MA511198)

value: normal sleep


title: poolA-35


title: SVZ Single cell, NDUFS4 KO, rep2

description:
Library name: NDUFS4KO2_062424
PIPseeker™ Software


title: 6461


title: IVT2, HIV

description: Library name: IVT2

source_name: IVT

treatment_protocol:
SupT1 CD4+ T cells were infected with 800 ng of VSV-G-HIVNL4-3 XCS HIV-Gagp24 for 3h in IMDM plus 10mM HEPES (Gibco/ThermoFisher Scientific) supplemented with 2 µg/ml of DEAE-dextran (Sigma)
CD4+ T cells from donors were infected at a multiplicity of infection (moi) 0,01 with VSV-G-HIVNL4-3 XCS (representing around 1000 ng of HIVGagp24 / 107 cells) for 3h in IMDM plus 10mM HEPES supplemented with 2 µg/ml of DEAE-dextran

value: IVT


title: poolA-34


title: supT1, HIV 20h, rep1, ALKBH5

description: Library name: SupT1_20h_pi_rep1_ALKBH5

value: 20h infection with HIV NL4-3 XCS + ALBH5 treatment


title: poolA-39


title: Brain, normal sleep, ZT6, rep1

description: Library name: Sample 1


title: 6770


title: poolA-36


title: 6449


title: poolA-33


title: supT1, HIV 30h, rep2

description: Library name: SupT1_30h_pi_rep2

value: 30h infection with HIV NL4-3 XCS


title: GMI1000, lov, Dark, rep2

city: Madison

first: Jose

middle: Alberto

last: Sanchez

state: WI

address: 1630 Linden Drive

institute: University of Wisconsin-Madison

description:
Library name: Sample 25
L2_D

data_processing:
Raw reads were processed as follows (Novogene's pipeline): first adapters were removed, raw reads containing N >10% were removed, and reads with Qcore of 50% bases of the read is <=5.
Bowtie2 was used for mapping the sequences to the reference genome. Mismatch parameter was set to 2.
Assembly: Ralstonia pseudosolanacearum GMI1000 ASM912v1
Supplementary files format and content: No processed data files included
Supplementary files format and content: file contains FPKM values for each sample

organism: Ralstonia pseudosolanacearum

source_name: In vitro grown cultures of GMI1000 lov

growth_protocol: Tomato plants (wilt-susceptible cv. Bonny Best and wilt-resistant Hawaii 7996) were grown in a growth chamber at 28C with a 12-hr photoperiod. Plants were transplanted at 14-days old into 4-inch pots and inoculated with Ralstonia pseudosolanacearum wild-type and ∆lov.

extract_protocol:
Samples were extracted using a Phenol/Chloroform extraction.
Novogene's pipeline

treatment_protocol: Three-days post inoculation, a 100mg portion of the stem was collected (above the inoculation site) and flash frozen in liquid nitrogen prior to RNA extraction.

value: In vitro grown cultures of GMI1000 lov

value: Ralstonia pseudosolanacearum GMI1000

value: GMI1000 lov

value: Dark

value: In vitro


title: GMI1000, lov, Dark, rep3

description:
Library name: Sample 26
L3_D


title: poolA-32

value: tumor


title: poolA-31


title: supT1, HIV 30h, rep1

description: Library name: SupT1_30h_pi_rep1


title: 1604

value: Cord Blood

value: Controls


title: Brain, normal sleep, ZT6, rep2

description: Library name: Sample 2

value: cerebral cortex

value: WT


title: supT1, HIV 20h, rep2

description: Library name: SupT1_20h_pi_rep2

value: 20h infection with HIV NL4-3 XCS


title: IVT1, HIV

description: Library name: IVT1


title: GMI1000, lov, Blue light, rep3

description:
Library name: Sample 23
L3_B

value: Blue light


title: GMI1000, lov, Blue light, rep2

description:
Library name: Sample 22
L2_B


title: 927


title: supT1, HIV 20h, rep1

description: Library name: SupT1_20h_pi_rep1


title: 3728

value: Disease


title: poolA-30


title: GMI1000, lov, Dark, rep1

description:
Library name: Sample 24
L1_D


title: poolA-29


title: 4690


title: GMI1000, WT, Dark, rep 2

description:
Library name: Sample 19
W2_D

source_name: In vitro grown cultures of GMI1000 wild-type

value: GMI1000 WT


title: GMI1000, lov, Blue light, rep1

description:
Library name: Sample 21
L1_B


title: Culex pallen, siILP1 (ILP1 knockdown mosquitoes) bio rep 3

city: Arua

first: John Roberts

last: Padde

address: Independence Road

country: Uganda

institute: Muni University

data_processing:
Illumina HiSeq 1000 reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Read quality was checked for each sample using FastQC v0.10.1.
TopHat2 HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software was used to align the filtered Reads to the reference genome
HTSeq to statistically compare the Read Count value of each gene as the original expression level of the gene.
To make the gene expression levels of different genes and different samples comparable, we used FPKM to normalize the expression (Normalization), FPKM (Fragments Per Kilo bases per Million fragments).
Relative transcript abundance was defined as the sum of FPKM values of the siILP1 and NC mosquitoes, sorted from highest to lowest.
DESeq was used to perform differential analysis of gene expression, and the conditions for screening differentially expressed genes were: expression difference fold |log2FoldChange| > 1, and significance P-value<0.05 were regarded to be differentially expressed.
Assembly: Culex_quinquefasciatus.CpipJ2.dna.toplevel.fa
Supplementary files format and content: Tab-delimited text files containing raw counts for each sample
Supplementary files format and content: Tab-delimited text files containing RPKM values counts for each sample

organism: Culex pipiens pallens

source_name: Whole mosquito

growth_protocol: Culex pallens mosquitoes were maintained at 27°C-28°C, 75% relative humidity and 14hr light and 10hrs dark photoperiod. Larvae were reared in water with complete larval diet (a mixture of rat chow, yeast and lactalbumin, 1:1:1 ratio), and adult mosquitoes were reared in cages with access to water and 10% (wt/vol) glucose solution. Female mosquito adults were blood fed on mice. The treatment of vertebrate animals was approved by Nanjing Medical University Institutional Animal Care and Use Committee.

extract_protocol:
Total RNA was extracted using the Trizol method following the manufucturers instructions
1 μg of total RNA was subjected to library synthesis using the TruSeq RNA Library Preparation Kit (Illumina). Three independent biological replicates of each group were performed, giving three RNA-seq libraries per group. 1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR.

treatment_protocol: Cx. pallens ILP1 was depleted using small interfering RNA (siRNA) primers by microinjection as previously described [31, 32] using Needles with fine tips prepared by pulling capillary tubes using the SUTTER P-97 laser needle pulling instrument, with the following parameters set. H=570, P=80, V=90, T=100. Mosquitoes were injected with 100nL of siRNA targeting ILP1 (referred herein as siILP1) or control RNA (NC) using Nanoject Ⅲ Auto-Nanoliter Injecto microinjector. The mosquitoes were transferred to 27℃ and 75% humidity to recover. 3 days post injection, RNA was extracted and successful ILP1 knockdown was confirmed by qRT-PCR.

value: Whole mosquito

tag: developmental stage

value: Adult

value: Female

value: ILP1 knockdown


title: CD4, HIV 72h

description: Library name: CD4_72h_pi

value: 72h infection with HIV NL4-3 XCS


title: 3974


title: GMI1000, WT, Dark, rep 1

description:
Library name: Sample 18
W1_D

value: In vitro grown cultures of GMI1000 wild-type

value: Ralstonia pseudosolanacearum GMI1000


title: 1423


title: 6127


title: GMI1000, WT, Dark, rep 3

description:
Library name: Sample 20
W3_D

value: Dark

value: In vitro


title: 3791

value: Cord Blood


title: GMI1000, WT, Blue light, rep 3

description:
Library name: Sample 17
W3_B


title: poolA-24

value: tumor


title: CD4, HIV 48h

description: Library name: CD4_48h_pi

value: 48h infection with HIV NL4-3 XCS


title: poolA-27


title: GMI1000, WT, Blue light, rep 2

description:
Library name: Sample 16
W2_B


title: 6077


title: poolA-25


title: poolA-22


title: Culex pallen, siILP1 (ILP1 knockdown mosquitoes) bio rep 2


title: poolA-26


title: Culex pallen, NC (Control) bio rep 3

value: Negative control RNA


title: Culex pallen, siILP1 (ILP1 knockdown mosquitoes) bio rep 1


title: GMI1000, WT, Blue light, rep 1

description:
Library name: Sample 15
W1_B


title: 5764


title: poolA-23


title: poolA-28


title: Culex pallen, NC (Control) bio rep 2


title: GMI1000, lov, Hawaii 7996, rep1

description:
Library name: Sample 12
HL1

source_name: Stem tissue of Hawaii 7996 tomatoes infected with lov

value: GMI1000 lov

value: Hawaii 7996

value: In planta


title: Culex pallen, NC (Control) bio rep 1


title: poolA-20


title: 7462

value: Controls


title: 4416


title: Tk>brp RNAi replicate 3

city: Boston

first: Paula

last: Watnick

state: MA

address: 300 Longwood Avenue

institute: Boston Childrens Hospital

description: Library name: 20230214_Tk-brpRNAi3_DB10717_S189

data_processing:
Salmon and DESeq2
The final library pool was sequenced on an Illumina Novaseq X Plus targeting 40 million 150bp read pairs per library at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.
Sequenced reads were aligned to the UCSC hg38 reference genome assembly and gene counts were quantified using Salmon
Differential gene expression testing was performed by DESeq2 (v1.22.1)
RNAseq analysis was performed using the VIPER snakemake pipeline
Assembly: hg38
Supplementary files format and content: CSV file contains raw counts for each sample

organism: Drosophila melanogaster

source_name: Intestine

extract_protocol:
Total RNA was isolated from 10-15 fly intestines using TRIzol reagent (Thermo Fisher Scientific 15596026) and the Direct-zol RNA Miniprep plus kit (Zymo Research R2070)
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200ng of purified total RNA according to the manufacturer's protocol on a Beckman Coulter Biomek i7. The finished dsDNA libraries were quantified by Qubit fluorometer and Agilent TapeStation 4200. Uniquely dual indexed libraries were pooled in an equimolar ratio and shallowly sequenced on an Illumina MiSeq to further evaluate library quality and pool balance.

treatment_protocol: Tk> (Tk-Gal4) flies were crossed to TRiP control, Tk RNAi, GulpR (GPRx) RNAi, and brp RNAi flies. Progeny was collected and raised at 26°C for 4-7 days in standard fly food.

value: Intestine

value: Tk>brp RNAi


title: poolA-21


title: 5094

value: Disease


title: poolA-19


title: GMI1000, lov, Hawaii 7996, rep3

description:
Library name: Sample 14
HL3

value: Stem tissue of Hawaii 7996 tomatoes infected with lov


title: 6519


title: GMI1000, WT, Hawaii 7996, rep4

description:
Library name: Sample 11
HW4

source_name: Stem tissue of Hawaii 7996 tomatoes infected with GMI1000

value: GMI1000 WT


title: GMI1000, WT, Hawaii 7996, rep3

description:
Library name: Sample 10
HW3

value: Stem tissue of Hawaii 7996 tomatoes infected with GMI1000


title: poolA-17


title: Tk>GulpR RNAi replicate 3

description: Library name: 20230214_Tk-GPRxRNAi3_DB10717_S183

value: Tk>GulpR RNAi


title: poolA-18


title: poolA-16


title: Gestational weeks 13 telencephalon 2

city: San Francisco

first: Tianzhi

last: Wu

state: CA

address: 500 Parnassus Ave

institute: University of California, San Francisco

description: Library name: sample5_2

data_processing:
The Cell Ranger multi pipeline V8.0.1 was implemented for cell barcode calling, read alignment and quality assessment according to the protocols described by 10x Genomics.
Assembly: GRCh38
Supplementary files format and content: A feature-barcode matrix where each element of the matrix is the number of unique molecular identifiers (UMIs) associated with a feature (row) and a barcode (column).

source_name: Brain

extract_protocol:
tissue samples were dissociated using the Papain Dissociation System (Worthington, LK003150), dissociated cells were centrifuged, the supernatant removed, and the pellet resuspended in ice-cold PBS supplemented with 0.04% BSA. After a second centrifugation and supernatant removal, the cell pellet was resuspended in 1 mL of Fix & Perm Buffer (room temperature) and incubated for 17.5 h at 4 °C without agitation. Cells were then centrifuged at 850 × g for 5 min at room temperature, the supernatant removed, and 1 mL of chilled Quenching Buffer added and mixed by pipetting (5×). Next, 100 μL of pre-warmed Enhancer was added, followed by glycerol to a final concentration of 10%. Cells were subsequently fixed with the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics).
Single-cell gene expression libraries were prepared with the 10x Genomics Chromium Single Cell Gene Expression Flex Kit (PN-1000414) following the manufacturer’s protocol (CG000527 Rev E). Approximately 40,000 cells per sample were loaded onto a Chromium Next GEM Chip and processed on the Chromium Controller to generate Gel Bead-in-Emulsions (GEMs) for probe-based capture, reverse transcription, and barcoding of mRNA with unique molecular identifiers (UMIs) and cell barcodes. After cDNA amplification, libraries were constructed by fragmentation, end repair, A-tailing, adapter ligation, and final PCR enrichment. Library quality and concentration were assessed on an Agilent 2100 Bioanalyzer and a Thermo Fisher Qubit 4 Fluorometer. Pooled libraries were sequenced on an Illumina NovaSeq X, targeting ~20,000 reads per cell.

value: Brain


title: Tk>GulpR RNAi replicate 2

description: Library name: 20230214_Tk-GPRxRNAi2_DB10717_S182


title: poolA-15

source_name: tumor


title: GMI1000, WT, Hawaii 7996, rep2

description:
Library name: Sample 9
HW2

value: Ralstonia pseudosolanacearum GMI1000


title: Gestational weeks 13 telencephalon 1

description: Library name: sample5_1


title: Tk>GulpR RNAi replicate 1

description: Library name: 20230214_Tk-GPRxRNAi1_DB10717_S181


title: GMI1000, lov, BonnyBest, rep4

description:
Library name: Sample 7
BL4

source_name: Stem tissue of BonnyBest tomatoes infected with lov

value: BonnyBest


title: Tk>brp RNAi replicate 2

description: Library name: 20230214_Tk-brpRNAi2_DB10717_S188


title: GMI1000, WT, Hawaii 7996, rep1

description:
Library name: Sample 8
HW1


title: Gestational weeks 15 cortical plate regions

description: Library name: sample4


title: Gestational weeks 19 cortical plate regions

description: Library name: sample2


title: poolA-14

value: tumor


title: GMI1000, lov, Hawaii 7996, rep2

description:
Library name: Sample 13
HL2


title: Gestational weeks 15 germinal zone region

description: Library name: sample3


title: poolA-13


title: Tk>Tk RNAi replicate 2

description: Library name: 20230214_Tk-TkRNAi2_DB10717_S185

value: Tk>Tk RNAi


title: poolA-12


title: GMI1000, lov, BonnyBest, rep1

description:
Library name: Sample 4
BL1

value: Stem tissue of BonnyBest tomatoes infected with lov


title: Tk>TRiP replicate 3

description: Library name: 20230214_Tk-TRiP3_DB10717_S177

value: Tk>TRiP


title: Oligo_library_OSC_STARRseq_dev_rep3

city: Vienna

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

description:
Library name: Sample 8
150bp

data_processing:
A custom index containing the corresponding sequences was generated using the buildindex function from the Rsubread R package (Liao et al 2019 version 2.10.0). STARR-seq paired-end reads were then aligned using the align function from the same package, with the following parameters: type = “dna”, unique = TRUE, maxMismatches = 2. Then, UMI sequences were retrieved and collapsed as previously described described (DOI: https://doi.org/10.1038/s41588-022-01048-5).
Assembly: dm3 (custom oligo library)
Supplementary files format and content: For each replicate per condition, "counts.txt" file contains the umi-collapsed counts ("umi_counts" column) for each sequence ID (column "ref_ID").

source_name: OSC

growth_protocol: Schneider 2 cells were grown in Schneider’s Medium supplemented with 10% heat inactivated FBS at 27ºC. OSC cells were cultured in Shields and Sang M3 Insect Medium supplemented with 0.6 mg mL-1 glutathione, 10% FBS, 10 mU mL-1 insulin and 10% fly extract. Cells were passaged every 2-3 days.

extract_protocol:
UMI-STARR-Seq was performed as previously described (DOI: https://doi.org/10.1002/cpmb.105)
UMI-STARR-Seq libraries were UMI-tagged and constructed as previously described (DOI: https://doi.org/10.1002/cpmb.105)

value: OSC

value: screen


title: Tk>Tk RNAi replicate 1

description: Library name: 20230214_Tk-TkRNAi1_DB10717_S184


title: GMI1000, WT, BonnyBest, rep2

description:
Library name: Sample 2
BW2

source_name: Stem tissue of BonnyBest tomatoes infected with GMI1000

value: In planta


title: poolA-11

data_processing:
BAM files were converted to merged, demultiplexed FASTQ files, cleaned using fastq-mcf (ea-utils r819), and QC checked with FastQC (0.11.4). Reads were then mapped to the mouse genome (mm10) using STAR (2.4.1b) and quantified with Subread (1.4.6-p2).
The merged gene expression matrix (raw counts) containing all samples was analyzed with the Seurat3 package in R. Cells were filtered by nFeature_RNA (genes detected) >3000 and <7000, percent.mt (percentage of mitochondria genes) < 10. This resulted in n=306 valid cells for downstream analysis. After filtering cells, log-normalization was performed using the default NormalizeData function in Seurat. The scaled data was regressed for cell cycle phases (S.Score and G2M.Score) and number of genes per cell (nFeature_RNA) before performing UMAP based dimension reduction (dims=1:20, resolution =0.4).
Assembly: mm10
Supplementary files format and content: csv

extract_protocol:
Single cells were sorted (BD FACSAriaIII) in 96 well plates (VWR) containing 2μL of PBS including 0.2% Triton X-100 and 4U of RNase inhibitor (Takara) per well. Plates were properly sealed and spun down at 2000g for 1min before storing at −80°C. Whole transcriptome amplification was performed with a modified SMART-seq2 protocol as described previously, using 20 instead of 18 cycles of cDNA amplification. PCR purification was realized with a 0.8:1 ratio (ampureXP beads:DNA). Amplified cDNA quality was monitored with a high sensitivity DNA chip (Agilent) using the Bioanalyzer (Agilent)
SMART-seq2 based scRNA-seq; Sequencing libraries were performed using the Nextera XT kit (Illumina) as described previously, using 1/4th of the recommended reagent volumes and 1/5th of input DNA with a tagmentation time of 9min. Library quality was monitored with a high sensitivity DNA chip (Agilent) using the Bioanalyzer (Agilent). Indexing was performed with the Nextera XT index Kit V2 (A-D).


title: Oligo_library_OSC_STARRseq_dev_rep1

description:
Library name: Sample 6
150bp


title: GMI1000, WT, BonnyBest, rep3

description:
Library name: Sample 3
BW3

value: Stem tissue of BonnyBest tomatoes infected with GMI1000


title: poolA-09


title: poolA-10


title: Tk>TRiP replicate 2

description: Library name: 20230214_Tk-TRiP2_DB10717_S176

value: Intestine


title: GMI1000, lov, BonnyBest, rep3

description:
Library name: Sample 6
BL3

value: GMI1000 lov


title: acinar_cell, ATAC-Seq, rep2

city: BeiJing

first: li

last: yong

address: Hai Dian

department: biomedical

institute: tsinghua university

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Trimmed reads were aligned to the mm10 genome with the following parameters: --very-sensitive -k 10 by Bowtie2 (v.2.3.5.1)
Aligned reads stored in SAM format were manipulated to generate BAM files and PCR duplicates were removed using SAMtools (v.1.10)
ATAC-seq peaks were called by Genrich (v.0.6) using the parameters: -j -y -r -e chrM -v.
All peaks from all samples were merged and raw counts of merged peaks in each sample were counted by featureCounts (v.2.0.1). Size factor for each sample were calculated using DESeq2 (v.1.24.0). Normalized bigwig files were generated with 1/(size factor) using bamCoverage from deepTools (v.3.4.3).
Assembly: mm10
Supplementary files format and content: bigwig

source_name: pancreas

extract_protocol:
Mouse pancreases were digested into single-cell suspensions as previously described(Reichert, M. et al. Isolation, culture and genetic manipulation of mouse pancreatic ductal cells. Nat. Protoc. 8, 1354–1365 (2013).)
ATAC-seq was performed using 3000 cells isolated from each mouse as previous described（Mutant Kras co-opts a proto-oncogenic enhancer network in inflammation-induced metaplastic progenitor cells to initiate pancreatic cancer. Nat Cancer 2, 49-65, doi:10.1038/s43018-020-00134-z (2021).）

value: pancreas

value: acinar

value: Pdx1-Cre; Klf5-mCherry-CreERT2


title: GMI1000, WT, BonnyBest, rep1

description:
Library name: Sample 1
BW1

value: GMI1000 WT


title: poolA-08


title: Oligo_library_S2_STARRseq_dev_rep2

description:
Library name: Sample 4
150bp

source_name: S2 cells

value: S2 cells


title: acinar_cell, ATAC-Seq, rep1


title: Oligo_library_S2_STARRseq_dev_rep1

description:
Library name: Sample 3
150bp


title: Gestational weeks 19 germinal zone region

description: Library name: sample1

value: Brain


title: 47.PAC2_PP_Run4

city: Duebendorf

first: Ksenia

middle: J

last: Groh

address: Ueberlandstrasse 133

department: Environmental Toxicology (Utox)

country: Switzerland

institute: Eawag - Swiss Federal Institute of Aquatic Science and Technology

description:
Library name: Sample7
Column name in raw_counts.txt: 47.PAC2_PP_Run4

data_processing:
The final sequencing was performed on an Illumina NovaSeq X system using a 300-cycle 10B flow cell and yielded an average of approximately 20 million paired-end reads (2 × 150 bp) per sample. Raw data (sample reads provided by the sequencing facility (FGCZ)) were pre-processed by the GDC, including the pseudo-alignment which was performed using Kallisto (version v0.50.1) (Bray et al., 2016) and the reference transcriptome from Ensembl (Danio rerio, GRCz11/GCA_000002035.4). Transcripts remapping was on average above 83%, with most samples yielding between 12-33 million aligned reads. The fragment length ranged between 168-209 bp.
Downstream data analysis: Transcript-level abundance estimates from Kallisto (in HDF5 format) were imported into RStudio (version 4.4.2) and summarized to the gene level counts based on the reference transcriptome. Raw counts per million (CPM) values were extracted and normalized using transcript length and effective library size, thus accounting for the sequencing depth and gene length bias. The normalized dataset was log-transformed. Differentially Expressed Genes (DEGs) analysis was performed using the edgeR package (version 4.6.2) (ADD REF: Chen et al., 2025). A design matrix accounting for the two experimental conditions of interest (exponential vs. stationary growth phases) was generated. Genes with low expression were filtered using the filterByExpr function. The filtering step removed approximately 13’000 genes, going from 30’628 to 17’570 genes. The glmQLFit function, which applies a negative binomial model and robust estimation to reduce the impact of outliers, was used to model the variation in gene expression across samples. Differential expressions were tested applying a quasi-likelihood F-Test (glmQLFTest function) and corrected by false discovery rate obtained using the Benjamini-Hochberg (BH) adjustment. Thresholds for comparison were established at FDR<0.05. Following statistical testing, DEGs were z-score normalized and hierarchically clustered using Euclidean distance and complete linkage. Heatmaps of clustered DEGs were generated in RStudio using the pheatmap package for visualization. To visualize the data, transcripts were filtered according to the transcript per million (TPM) value, where each transcript`s geometric mean was calculated across samples and within each cell population growth phase. Normalized data with TPM>1 was selected for PCA, performed using the prcomp function with default parameters. The first two components were visualized using ggplot2 (v3.5.2). Samples were grouped by day, with convex hulls (chull) to illustrate group boundaries. Variance explained by each component was indicated on the axes. To identify the top regulated DEGs, a volcano plot was generated using visualization tools from Perseus.
Assembly: Danio rerio, GRCz11/GCA_000002035.4
Supplementary files format and content: csv file including normalized counts

organism: Danio rerio

growth_protocol: The permanent zebrafish embryonic cell line PAC2 (Cellosaurus accession number: CVCL_5853) was routinely cultured at 26°C ± 1°C in T-75 flasks (Thermo Fisher Scientific) with 10 mL of Lebovitz`s cell culture medium (L-15; PAN-Biotech), supplemented with 5% fetal calf serum (FCS; Eurobio Scientific). Sub-culturing was performed after reaching full confluence and involved washing with Versene (Gibco™), detachment with 0.25% trypsin (ADD SOURCE) in Dulbecco's phosphate buffered saline (PAN-Biotech), cell counting by Casy cell counter (OLS OMNI Life Science, Bremen, Germany) and seeding at one to two million into a new T-75 flask in fresh culture medium.

extract_protocol:
To collect the samples for transcriptomics analysis, cells were washed with ice cold 1x PBS before adding RNeasy Plus lysis buffer (QIAGEN, Ref. 1053393). Cellular lysis was facilitated using scrapers with swiveling 13mm blades. Lysed cells were harvested from multiple wells in 1.5 mL DNase/RNase-free Eppendorf Collection Tubes (QIAGEN) placed on ice, vortexed at maximal speed for 1 min and immediately stored at –70°C until further processing. RNA extraction was performed according to manufacturer’s instructions using the RNeasy Plus Mini Kit (QIAGEN, Ref. 172034266), including a gDNA removal step. RNA quality was analyzed with the RNA ScreenTape Assay for TapeStation 4200 System (Agilent), following the assay instructions and using the electronic ladder. For all samples, the measured RNA Integrity Number (RIN) was equal to 10. After this quality control, the samples were transported in dry ice to the Genomic Diversity Centre (GDC), ETH Zürich, which provides access to managed instruments and expertise in genetic techniques and genomic data. Here, samples were treated with DNase using the DNase I Amplification Grade Kit (Invitrogen, Ref. 18068015) to eliminate any residual gDNA, using 1 µg of RNA for each sample and following the kit instructions. After DNAse treatment, three random samples were tested again with the TapeStation to ensure the quality of RNA was not changed. All tested samples showed RINs equaling 10.
To prepare the mRNA library, DNAse-treated RNA samples were first quantified using the Qubit RNA Broad Range (BR) Assay Kit (Invitrogen, Ref. Q10211) following kit instruction. Measurements were performed in a 384-well black plate (Faust, Ref. 4000246) using a plate reader Spark M10 (Tecan). mRNA library was prepared with starting amount of 0.5 µg for each sample, using the TruSeq Stranded mRNA Library Preparation Kit from Illumina (96 Samples, Ref. 2002055), which includes poly-A mRNA enrichment through oligo(dT) magnetic beads. For increased demultiplexing accuracy and reduced sample misassignment during sequencing, IDT for Illumina – TruSeq RNA Unique Dual (UD) Indexes v2 (96 Indexes, 96 Samples, Ref. 20040871) were used. The whole procedure was performed following manufacturer’s instructions but using half-volumes of all reagents. This modification of the protocol was previously tested and validated (internal trial; data not shown). Following the preparation, the concentration of each mRNA library was measured using a Qubit dsDNA BR Assay Kit (Invitrogen, Ref. Q32853) following the kit instructions. One sample (day 14, biological replicate 3) appeared to be lost during library preparation and was therefore not included in downstream analyses. The remaining mRNA libraries were normalized and pooled following the specifications required by the sequencing platform.

treatment_protocol: Cells were not treated but raised under normal conditions and collected for transcriptomics analysis at day 8 and day 14 after seeding, corresponding to exponential and stationary cell population growth phases. Cell culturing for omics analyses was performed in 6-well plates seeded at a density of 90,000 cells in 4 mL/well culture medium. Plates were sealed and incubated in the dark at 26°C ± 1°C. Culture medium was exchanged after 7 days post-seeding. On days 8 and 14, corresponding to exponential and stationary growth phases, two sets of samples, one for global proteomics and one for transcriptomics, were collected from the same plate (top row was used to collect cells for the transcriptomics samples and bottom row for the proteomics samples), thus ensuring direct pairing of multiomics samples. These experiments were performed in four biological replicates with different cell passage numbers (P85-88), and experiments started on different days.

value: Embryo

value: WT


title: Tk>brp RNAi replicate 1

description: Library name: 20230214_Tk-brpRNAi1_DB10717_S187

value: Tk>brp RNAi


title: acinar, RNA-Seq, rep6

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Adaptor-trimmed reads were aligned to the mm10 genome with the following parameters: --readFilesCommand zcat --outFilterMismatchNoverLmax 0.2 by STAR (v.2.7.9a)
Aligned reads stored in SAM format were converted to BAM files using SAMtools with parameter: samtools view -bS -h -F 4 -f 2 -q 7.
FeatureCounts counted reads stored in BAM format to exon sites of genes included in GTF files from Ensembl
Assembly: mm10
Supplementary files format and content: raw counts

extract_protocol:
300 GFP-positive cells were sorted by FACS for small scale RNA-seq. Small scale RNA-seq library was constructed using Smart-seq2 method with modifications allowing higher quality library generation from pancreatic cells. Briefly, mouse pancreatic cells were directly sorted into 8 μl of denaturing lysis buffer (6 M guanidine HCl, 0.2% (vol/vol) Triton X-100 and 1% (vol/vol) β-mercaptoethanol). RNA SPRI beads (RNA Clean XP beads, Beckman A63987) were added (2.2X) to the lysis buffer and RNA was purified, followed by library preparation by the standard Smart-seq2 protocol, except with a 12-cycle PCR pre-amplification step.
Smart-seq2 protocol.


title: poolA-07

first: Florian

last: Rambow

value: tumor


title: poolA-06


title: Oligo_library_S2_STARRseq_dev_rep3

description:
Library name: Sample 5
150bp


title: Tk>TRiP replicate 1

description: Library name: 20230214_Tk-TRiP1_DB10717_S175

value: Tk>TRiP


title: poolA-05


title: 44.PAC2_SP_Run2

description:
Library name: Sample4
Column name in raw_counts.txt: 44.PAC2_SP_Run2


title: Oligo_library_input_dev_rep1

description:
Library name: Sample 1
150bp

source_name: oligo library (in STARR-seq vector)

value: oligo library (in STARR-seq vector)

value: input


title: 48.PAC2_SP_Run4

description:
Library name: Sample8
Column name in raw_counts.txt: 48.PAC2_SP_Run4


title: poolA-04


title: Tk>Tk RNAi replicate 3

description: Library name: 20230214_Tk-TkRNAi3_DB10717_S186

value: Tk>Tk RNAi


title: GMI1000, lov, BonnyBest, rep2

description:
Library name: Sample 5
BL2

value: Stem tissue of BonnyBest tomatoes infected with lov

value: Ralstonia pseudosolanacearum GMI1000

value: BonnyBest

value: In planta


title: OSC_screen_rep2

description:
Library name: Sample 3
100bp

data_processing:
After initial quality checks using fastqc, STARR-Seq reads were trimmed using trim_galore (version 0.6.0) with default parameters and aligned to the dm3 version of the Drosophila genome using bowtie2 (version 2.3.5.1) with default parameters. Aligned reads with a mapping quality >= 20 were then UMI-collapsed (tolerating for one mismatch) and peaks were called using MACS2 (version 2.2.5) with the following parameters: -g dm --keep-dup all -f BED --nomodel --extsize 200 --SPMR -B.
Assembly: dm3
Supplementary files format and content: BigWig files contain normalized genome-wide coverage
Supplementary files format and content: narrowPeak files contain enhancer peaks called with MACS2

value: OSC

value: screen


title: acinar, RNA-Seq, rep3

value: pancreas

value: acinar

value: Pdx1-Cre; Klf5-mCherry-CreERT2


title: Oligo_library_OSC_STARRseq_dev_rep2

description:
Library name: Sample 7
150bp


title: poolA-03


title: 43.PAC2_PP_Run2

description:
Library name: Sample3
Column name in raw_counts.txt: 43.PAC2_PP_Run2

value: Embryo


title: poolA-02


title: acinar, RNA-Seq, rep2


title: OSC_screen_rep1

description:
Library name: Sample 2
100bp


title: 42.PAC2_SP_Run1

description:
Library name: Sample2
Column name in raw_counts.txt: 42.PAC2_SP_Run1

value: WT


title: 41.PAC2_PP_Run1

description:
Library name: Sample1
Column name in raw_counts.txt: 41.PAC2_PP_Run1


title: poolA-01


title: acinar, RNA-Seq, rep5


title: 45.PAC2_PP_Run3

description:
Library name: Sample5
Column name in raw_counts.txt: 45.PAC2_PP_Run3


title: acinar, RNA-Seq, rep1


title: AAA 178

status: Public on Dec 04 2025

city: Düsseldorf

first: Patrick

last: Petzsch

state: NRW

address: Universitätsstrasse 1

department: BMFZ

institute: UKD

description:
Library name: 453-8
453-8_RPKM

data_processing:
The Illumina bcl2fastq tool (v2.20.0.422) was used to convert the bcl files to fastq files as well for adapter trimming and demultiplexing.
Sequenced reads were adapter trimmed and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2). Mapping was done against the Mus musculus (GRCm39.112; July 17, 2024) genome sequence using CLC Genomics Workbench v24.0.1 with standard parameters.
Reads Per Kilobase and per Megabase (RPKM) were calculated using CLC Genomics Workbench v24.0.1 with standard parameters. Multi-group comparisons were calculated using the CLC Differential Expression for RNA-Seq tool (version 2.8, Qiagen, Venlo, Netherlands). The resulting p values were corrected for multiple testing by FDR and Bonferroni-correction. A p value of ≤ 0.05 was considered significant. Cut-off for differential gene expression was set to 1.5 fold.
Assembly: GRCm39.112
Supplementary files format and content: The excel file includes RPKM values for each sample

source_name: aorta

extract_protocol:
Total RNA was isolated from the aortic tissue specimen using the RNeasy® Plus Universal Kit Mini 50 (Qiagen GmbH, Hilden, Germany).
The library preparation was performed according to the manufacturer’s protocol using the ‘VAHTS™ Stranded mRNA-Seq Library Prep Kit V6’ for Illumina®. Briefly, 500 ng total RNA were used as input for mRNA capturing, fragmentation, the synthesis of cDNA, adapter ligation and library amplification. Bead purified libraries were normalized and finally sequenced on the HiSeq 3000/4000 system (Illumina Inc. San Diego, CA, USA) with a read setup of SR 1x150 bp.

treatment_protocol: AAA formation was induced by implantation of osmotic minipumps releasing 1000ng/kg/min of Angiotension II. 3 days post-operation mice were sacrificed and the aorta isolated. A total of 9 aortic tissue specimen (n = 5 for Apoe/Has3-DKO and n= 4 for Apoe-KO) were prepared for transcriptome analysis.

value: aorta

value: Apoe-/-

value: Angiotensin II

value: 3d post OP


title: AAA 176

description:
Library name: 453-6
453-6_RPKM


title: AAA 177

description:
Library name: 453-7
453-7_RPKM


title: Oligo_library_input_dev_rep2

description:
Library name: Sample 2
150bp

value: oligo library (in STARR-seq vector)

value: input


title: acinar, RNA-Seq, rep4


title: AAA 173

description:
Library name: 453-3
453-3_RPKM

value: Apoe-/- Has3-/-


title: AAA 171

description:
Library name: 453-1
453-1_RPKM


title: AAA 172

description:
Library name: 453-2
453-2_RPKM


title: ALL survivor 140

city: Toronto

first: Sarah

middle: J.

last: Goodman

state: ON

address: PGCRL, 686 Bay St.

department: Genetics and Genome Biology

country: Canada

institute: Hospital for Sick Children

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC V1.0 Beadchip using standard Illumina protocol

scan_protocol: standard  protocol for Illumina HiScan

data_processing:
The raw IDAT files were processed into β-values, which quantify DNA methylation levels on a scale from 0 to 1, using the minfi package from Bioconductor in R v4.1.1. The data was then normalized using the preprocessIllumina function in minfi to correct for technical variation. The preprocessing pipeline included several filtering steps: removal of non-specific probes; exclusion of probes with detection p-values greater than 0.05 in more than 25% of samples; elimination of probes located near SNPs (within 10 bp of the CpG site or single base extension) or associated with SNPs having a minor allele frequency above 1%; removal of xyz probes with β-values of 0 or 1 in more than 0.25% of samples; exclusion of non-CpG probes; and filtering out probes located on sex chromosomes. Quality control was performed using standard minfi metrics such as median intensity plots, density distributions, and control probe assessments, with all samples passing QC and included in the final analysis.  The raw IDAT files were processed into β-values, which quantify DNA methylation levels on a scale from 0 to 1, using the minfi package from Bioconductor in R v4.1.1. The data was then normalized using the preprocessIllumina function in minfi to correct for technical variation. The preprocessing pipeline included several filtering steps: removal of non-specific probes; exclusion of probes with detection p-values greater than 0.05 in more than 25% of samples; elimination of probes located near SNPs (within 10 bp of the CpG site or single base extension) or associated with SNPs having a minor allele frequency above 1%; removal of probes with β-values of 0 or 1 in more than 0.25% of samples; exclusion of non-CpG probes; and filtering out probes located on sex chromosomes. Quality control was performed using standard minfi metrics such as median intensity plots, density distributions, and control probe assessments, with all samples passing QC and included in the final analysis.
processed value definition: normalized betas

source_name: primary

extract_protocol: Genomic DNA was extracted from blood samples using DNEasy (Qiagen) chemistry and columns. No modification was made to the manufacturer's specifications.

value: primary

value: Whole blood

value: M

tag: age at sample collection


title: ALL survivor 138

value: F


title: ALL survivor 139


title: AAA 174

description:
Library name: 453-4
453-4_RPKM


title: ALL survivor 132


title: ALL survivor 136


title: ALL survivor 129


title: ALL survivor 133


title: ALL survivor 128


title: ALL survivor 130


title: ALL survivor 127


title: ALL survivor 134


title: ALL survivor 126


title: ALL survivor 125


title: OSC_input

description:
Library name: Sample 1
100bp

value: whole genome library (in STARR-seq vector)


title: ALL survivor 122


title: ALL survivor 120


title: ALL survivor 123


title: ALL survivor 119


title: ALL survivor 118


title: ALL survivor 124


title: ALL survivor 137


title: ALL survivor 117


title: ALL survivor 114


title: ALL survivor 116


title: ALL survivor 121


title: ALL survivor 115


title: ALL survivor 111


title: ALL survivor 112


title: ALL survivor 135


title: ALL survivor 131


title: ALL survivor 108


title: ALL survivor 113


title: ALL survivor 109


title: ALL survivor 105


title: ALL survivor 106


title: ALL survivor 104


title: ALL survivor 107


title: ALL survivor 110


title: AAA 175

description:
Library name: 453-5
453-5_RPKM


title: ALL survivor 101


title: ALL survivor 99


title: ALL survivor 98


title: ALL survivor 97


title: ALL survivor 94


title: ALL survivor 96


title: ALL survivor 93


title: ALL survivor 95


title: ALL survivor 91


title: ALL survivor 89


title: ALL survivor 84


title: ALL survivor 86


title: ALL survivor 88


title: ALL survivor 100


title: ALL survivor 83


title: ALL survivor 85


title: ALL survivor 80


title: ALL survivor 81


title: ALL survivor 90


title: ALL survivor 82


title: ALL survivor 79


title: ALL survivor 87


title: ALL survivor 77


title: ALL survivor 78


title: ALL survivor 76


title: ALL survivor 102


title: AAA 179

description:
Library name: 453-9
453-9_RPKM


title: ALL survivor 103


title: ALL survivor 92


title: ALL survivor 73


title: ALL survivor 74


title: ALL survivor 75


title: ALL survivor 71


title: ALL survivor 69


title: ALL survivor 68


title: ALL survivor 72


title: ALL survivor 65


title: ALL survivor 63


title: ALL survivor 67


title: ALL survivor 61


title: ALL survivor 59


title: ALL survivor 62


title: ALL survivor 64


title: ALL survivor 52


title: ALL survivor 55


title: ALL survivor 60


title: ALL survivor 56


title: ALL survivor 58


title: ALL survivor 53


title: ALL survivor 51


title: ALL survivor 47


title: ALL survivor 49


title: ALL survivor 50


title: ALL survivor 48


title: ALL survivor 46


title: ALL survivor 44


title: ALL survivor 66


title: ALL survivor 42


title: ALL survivor 43


title: ALL survivor 45


title: ALL survivor 40


title: ALL survivor 70


title: ALL survivor 38


title: ALL survivor 41


title: ALL survivor 57


title: ALL survivor 39


title: ALL survivor 36


title: ALL survivor 37


title: ALL survivor 54


title: ALL survivor 34


title: ALL survivor 33


title: ALL survivor 32


title: ALL survivor 27


title: ALL survivor 30


title: ALL survivor 31


title: ALL survivor 29


title: ALL survivor 26


title: ALL survivor 25


title: ALL survivor 22


title: ALL survivor 20


title: ALL survivor 24


title: ALL survivor 21


title: ALL survivor 23


title: ALL survivor 19


title: ALL survivor 18


title: ALL survivor 14


title: ALL survivor 13


title: ALL survivor 17


title: ALL survivor 15


title: ALL survivor 35


title: ALL survivor 16


title: ALL survivor 8


title: ALL survivor 7


title: ALL survivor 9


title: ALL survivor 28


title: ALL survivor 10


title: ALL survivor 11


title: ALL survivor 12


title: ALL survivor 6


title: ALL survivor 1


title: ALL survivor 5


title: ALL survivor 3