title: BJ, WT, 9Months Cerebral organoid hBG_s56

city: Evry

first: Marco Antonio

last: MENDOZA-PARRA

address: 2 rue Gaston Crémieux

country: France

institute: CNRS UMR8030

description:
BJ, WT, 9Months Cerebral organoid
Spatial transcriptomics

data_processing:
Primary analysis has been performed with our in-house developed tool SysISTD (SysFate Illumina Spatial transcriptomics Demultiplexer: https://github.com/SysFate/SysISTD).  SysISTD takes as entry paired-end sequenced reads (fastq or fastq.gz format), and two TSV files, the first one containing the sequence of the molecular barcodes associated to the rows or column in the printed arrays and the second file presenting the physical position architecture of the spatial barcodes. SysISTD search for the Gibson sequence (regex query), then for two neighboring barcodes. Paired-reads presenting these features were aligned to the human genome (hg19) with Bowtie2, and known transcripts were annotated with featureCounts.
As outcome, SysISTD generated a matrix presenting read counts associated to physical coordinates in the array in columns and known transcripts ID in rows. To focus the downstream analysis to the physical positions corresponding to the analyzed tissue, we used an in-house R script taking as entry an image of the DNA array scanned with the TRICT filter after the reverse transcription step. Indeed, this image reveals the presence of the fiducial borders and the cDNA within the tissue. Specifically, we upload to R a croped image within the fiducials (imager package) and we use the “px.flood” function to retrieve the pixels associated to the tissue. Finally we applied a pixel to gexel coordinates conversion prior to cross this information with the outcome of SysISTD.
The “tissue-focused” matrix presenting read counts associated to spatial coordinates in columns, known transcripts in rows was processed with our previously described tool MULTILAYER. For human brain organoids processed in Figure 1, tissue partitioning has been performed with ≥ 4 contiguous gexels per pattern; Tanimoto Similarity threshold: 25%; while for the 3-dimensional tissue reconstruction in Figure 2, tissue partitioning has been performed with ≥ 3 contiguous gexels per pattern; Tanimoto Similarity threshold: 10%.  To compare contiguous sections, the “batch option” of MULTILAYER has been used, allowing to compute spatial classes in addition to spatial communities. Spatial classes, Spatial communities and tissue relationships were visualized within Cytoscape.
3-dimensional view of upregulated genes across sections were generated with an in-house R script (library “rgl”). Prior visualization, spatial gexels across sections were aligned relative to the center of the left human brain organoid (L-hBG) and the angle between the horizontal axis and a vector between the centers of the L-hBG and the R-hBG. Pseudo coordinates were computed by rotating tissues by the aforementioned angle and by centering the zero coordinate to the center of the L-hBG.  Cell/tissue type enrichment analysis has been performed with EnrichR (12) with the ARCHS4, CellMarkerAugmented and Panglao databases. These databases are incorporated within MULTILAYER, allowing to perform the aforementioned enrichment analysis directly within this tool.
Assembly: hg19
Supplementary files format and content: Matrices presenting spatial coordinates in columns and known transcripts in rows. This matrices can be uploaded in MULTILAYER for visualization (Moehlin et al; Cell Systems 2021; STAR Protocols 2021: https://star-protocols.cell.com/protocols/998).

source_name: BJ

growth_protocol: Human induced Pluripotent Stem Cells were cultured in mTeSR Plus Medium (100-0276 Stem Cell) + Penicillin/Streptomycin (P/S) 1% (15140122 Thermo Fisher Scientific) on Matrigel coating (354277 Corning).

extract_protocol:
Tissue samples were cryosectionned (20 µm sections collected at -20°C) and deposited on the double-barcoded DNA-arrays defined regions. During this process, slides were kept inside the cryostat chamber in order to conserve the integrity of the RNA and at -80°C for long storage.  Tissue sections were fixed with 4% Para-formaldheyde (PFA) (Life technologies 28908) in 1X PBS (Life technologies 70011-036) at room temperature during 10 minutes, then washed twice with 1X PBS, followed by a wash with double-distilled water (ddH2O). Tissues deposited on DNA arrays were covered with ddH2O and heat at 65°C during 5 minutes, followed by a fast chilling procedure (-20°C; 2 minutes). Remaining water was replaced by hybridization mix (10 U RNAse Inhibitor(New England Biolads M0314) in 6X SSC), and incubated at room temperature for 30 minutes. DNA arrays were washed by dipping them into a 50 mL falcon of 0.1X SSC then into a 50 mL falcon of ddH2O. Finally, tissue sections were air dried during 10 minutes. To avoid evaporation, reverse transcription (RT) is realised within sealed chambers (Thermoscientific small size; AB-0576). DNA arrays presenting tissue sections were incubated with RT mix (1 U/µL of SuperScript IV at (18090200 Life Technologies), 1X SSIV buffer (18090200 Life Technologies), 5 mM DTT (18090200 Life Technologies), 20 µg/mL actinomycin D (A1410-2MG Sigma), 0.2 mg/mL Bovine Serum Albumine (BSA) (Sigma Merk A9418-10G), a mix of dATP/dTTP/dGTP (130 µM each), 125 µM of dCTP and 5 µM dCTP-Cy3, 1 U/µL of RNAse Inhibitors) at 42°C overnight with a heated lid at 70°C. Next day, slides were washed by dipping them into a 50 mL falcon of 0.1X SSC, then into a 50 mL falcon of ddH2O and spin-dried. Finally, DNA arrays were scanned with the TRICT filter to reveal the presence of the fiducial borders as well as the physical position of tissue sections on top of the printed DNA arrays and revealed by the newly synthesized cDNA. After imaging, tissue sections were digested during 1 hour at 37°C and at 300rpm (20 mg/mL proteinase K (Invitrogen 4333793) at 7.5 mg/mL in PKD buffer (Quiagen 1034963)). Slides were washed in containers containing large volumes and under agitation (400 rpm) as following:  100 mL of preheated buffer 1 (2X SSC and 0.1X SDS (Sigma 71736); 50°C) during 10 minutes, 5 minutes with buffer 2 (0.2X SSC; room temperature), 5 minutres with buffer 3 (0.1X SSC; room temperature). Finally the slides were washed by dipping them in a 50 mL falcon containing ddH2O and spin-dried. DNA arrays were inspected at this stage to make sure that tissues was completely removed. DNA arrays were incubated with a freshly prepared 0.1 N NaOH solution during 10 minutes at room temperature, washed with the same solution, then neutralized for 2 minutes (for 100µL of 0.1 N NaOH, add 11.8 µL of 10X TE and, 6.5 µL of 1.25 M acetic acid). Finally, slides were washed by dipping them into a 50 mL falcon of 0.1X SSC, then into a 50 mL falcon of ddH2O and spin-dried.
DNA arrays were incubated with a poly-C tailing mix ( 0.6 U/µL TDT (New England Biolads M0315), 1X terminal transferase buffer (New England Biolads BO315), 0.3X CoCl2 (New England Biolads B0252), 0.2 mM dCTP) during 35 minutes at 37°C, then 20 minutes at 70°C to deactivate the enzyme and cooled at 12°C. Under these conditions, the length of the poly-C tail should be of ~20 nts  in average (4). Then, slides were washed in a 50 mL falcon containing 0.1X SSC , then in a falcon containing ddH2O prior to be spin-dried.  To generate a complementary DNA strand, DNA arrays were incubated with a 2nd strand sythesis mix (0.1 U/µL  klenow exo- (Biolads M0212), 0.2 mg/mL BSA, 1X NEB2 buffer (New Englad Biolads B7002), 0.5 mM dNTPs) in presence of an oligonucleotide presenting a complementary sequence for the poly-C tailed sequence, as well as a 5’-extremity providing an adapter sequence (1µM conc: “GTTCAGACGTGTGCTCTTCCGATCTGGGGGGGGGH”). Second strand synthesis was performed within sealed chambers at 47°C during 5 minutes (primer anhealing), 37°C during 1 hour (extension),   10 minutes at 70°C (enzyme deactivation) and cooled et 12°C. Slides were washed in a 50 mL falcon containing 0.1X SSC and a second falcon containing ddH2O.  Newly synthesized complementary DNA strands were recovered by incubating DNA arrays with 100 µL of 0.1N NaOH solution. After 10 minutes of incubation, NaOH solution has been collected in a 1.5 mL eppendorf, DNA arrays were washed with other 100 µL of 0.1N NaOH solution and collected within the same eppendorf. The 200 µL collected NaOH solution has been neutralized with 23.6 µL of 10X TE and 13 µL of 1.25 mM acetic acid. DNA arrays were also neutralized with 100µL 0.1N NaOH solution mixed with 11.8µL 10X TE and 6.5µL 1.25mM acetic acid, then washed with 0.1X SCC and ddH2O for potential reuse if required.  Collected solution has been ethanol precipitated (2X EtOH volume,  200 mM NaCl, 1µL of 35 mg/mL glycogen; 1 hour at -20°C; centrifuged at 12000 rpm, washed with 70% EtOH) and resuspended in  23 µL of ddH2O for 15 minutes at room temperature.  The 23 µL of cDNA’s complementary-probe strand solution in ddH2O has been mixed with 25 µL of Q5 hot start high fidelity 2X master mix(M0464L) , 1 µL adapter seq1 primer (GTTCAGACGTGTGCTCTTCCGATCT; 0.02 µM final conc.) and 1 µL adapter seq2 primer containing a part of the T7-promoter sequence (TACACTCTTTCCCTACACGACGCTCTTCCGATCTGACTCGTAATAC; 0.02 µM final conc.).   This mix has been PCR amplifyied (98°C, 30 sec; 15 cycles: 98°C 10 sec; 65°C 75 sec; then 65°C 5 minutes; 12°C hold), cleanned at 0.9X ratio with SPRIselect beads (Beckman Coulter B23318) and resuspended in 24µL of ddH2O.  A second round of PCR amplification has been performed by mixing the 24 µL of adaptors linked cDNA’s complementary-probe strand with 25 µL 2X Q5 high fidelity ot start master mix, 0.5 µL of universal primer and 0.5 µL of index primer (each at 0.5µM concentration; NEBNext multiplex oligos for Illumina  index primers set 1 E7335). This mix has been amplified for 15 cycles (same amplification conditions as before), then cleanned at an 0.8X ratio with SPRISelect Beads (this ratio is used to get rid off fragments < 200nt because the DNA-array probes added to the illumina sequencing adaptors and barcodes is 223nt long without capturing any RNA). Final elution has been done in 25 µL of ddH2O.  5 µL of this library are used for quantitative PCR evaluation, targeting known transcript sequences (poly-A proximal regions), and the remaining 20 µL of this library is used for Illumina sequencing (150 nts paired-ends sequencing; NovaSeq).
poly-T captured mRNA-seq performed with double-barcoded DNA arrays.

treatment_protocol: Cerebral organoids were cultured by forming embryoid bodies (EBs) using hanging drops (20,000 cells per drop of 22 µL) in EB Formation Medium (for 50 mL: 40 mL DMEM/F12 (11330-032 Thermo Fisher Scientific), 10 mL KOSR (10828-028 Thermo Fisher Scientific), 500 µL GlutaMAX (35050-038 Thermo Fisher Scientific), 500 µL MEM-NEAA (11140-050 Thermo Fisher Scientific), 500 µL P/S supplemented just before use with bFGF (PHG0264 Thermo Fisher Scientific) at 4 ng/mL, Y-27632 dihydrochloride (ROCK Inhibitor, 72304 Stem Cell Technologies) at 50 µM, SB-431542 (72232 Stem Cell Technologies) at 10 µM and LDN-193189 (72147 Stem Cell Technologies) at 100 nM). After 2-3 days as hanging drops, EBs were transferred in 24 well Ultra Low Attachment plates (Thermo Fisher Scientific P24; ref. 144530 “ untreated Nunc”) with EB Formation Medium (same as above except that ROCK Inhibitor is used at 20 µM), to refresh 2 days after transfer. After 1 week in EB Formation Medium,  EBs were transferred in Neural Induction Medium (for 50 mL: 48.5mL DMEM/F12, 500 µL N2 Supplement (17505-048 Thermo Fisher Scientific), 500 µL GlutaMAX, 500 µL P/S, 500 µL MEM-NEAA) until embedding in Matrigel® Matrix (354230 Corning) using an Organoid Embedding Sheet (08579 Stem Cell Technologies). After embedding, droplets were put in 6-well Ultra Low Attachment Plates (Thermo Fisher Scientific P6 : REF 150239 “untreated Nunc”) in Expansion Medium without vitamin A (for 50 mL: 24 mL DMEM/F12, 24 mL Neurobasal Medium (21103-049 Thermo Fisher Scientific), 500 µL GlutaMAX, 500 µL P/S, 500 µL B27 without Vitamin A Supplement (12587-010 Thermo Fisher Scientific), 250 µL N2 Supplement, 250 µL MEM-NEAA, 12.5 µL Insulin solution, 0.5 µL 2-Mercaptoethanol). After 4 days in Expansion Medium, Organoids were transfered to Maturation Medium with Vitamin A (same as Expansion Medium, except B27 without Vitamin A is replaced by B27 Supplement (17504-044 Thermo Fisher Scientific)) and cultured under shaking at 60 rpm (Infors Celltron Orbital Shaker) with refresh of medium once a week. Human brain organoids used in this study were collected either at 4 or 9 months of culture by snap-freezing in isopentane and embedded in OCT prior cryosectioning.

value: BJ

value: human induced pluripotent stem cell

value: Cerebral organoid differentiation

value: 9 months


title: HFF, H3K27me3, HSV-1 12 hpi, Rep2

status: Public on Jul 01 2023

type: SRA

city: Seattle

first: Daphne

last: Avgousti

state: WA

address: 1100 Fairview Avenue North C1-201

department: Human Biology

country: USA

institute: Fred Hutchinson Cancer Research Center

library_source: genomic

data_processing:
CUT&Tag raw sequencing data were aligned to a custom genome made by concatenating human (hg38), HSV (JN555585.1), and E. coli (U00096.3 Escherichia coli str. K-12 substr. MG1655, complete genome). We performed alignments using bowtie2.
Coverage at 100 bp windows of the human hg38 reference genome was calculated as number of reads of given length (120-1000 bp for the analyses presented here) that mapped at that window normalized by the factor N:   N= 10,000/(Total number of reads that mapped to E. coli genome)   Here 10,000 is an arbitrarily chosen number. The normalized coverage at each base-pair from each replicate was averaged when combining multiple replicates.
The normalized read density in 100 bp bins were then smoothed with a running average over the bins spanning +/- 1000 bp around each bin.
Assembly: hg38
Assembly: HSV-1 strain 17 JN555585.1
Library strategy: CUT&Tag

molecule: genomic DNA

organism:
Homo sapiens
Human alphaherpesvirus 1

source_name: Skin

extract_protocol:
Cells were harvested using trypsin, washed three times with ice-cold phosphate-buffered saline (PBS) via centrifugation at 600 xg for 3 minutes and counted using a hemocytometer. Nuclei from six hundred thousand cells were isolated by hypotonic lysis in 1 mL buffer NE1 (20 mM HEPES-KOH pH 7.9; 10 mM KCl; 0.5 mM spermidine; 0.1% Triton X-100; 20% Glycerol; Roche EDTA-free protease inhibitor) for 10 minutes on ice followed by centrifugation at 1300 xg for 4 minutes. Nuclei were resuspended in Wash buffer (20 mM HEPES-NaOH pH 7.5; 150 mM NaCl; 0.5 mM spermidine; Roche EDTA-free protease inhibitor) and counted using a hemocytometer. BioMag Plus Concanavalin A coated beads (Polysciences 86057-3) were equilibrated with Binding buffer (20 mM HEPES-KOH pH 7.9; 10 mM KCL; 1mM CaCl2; 1 mM MnCl2). The beads (5 µL) were mixed with aliquots of seventy-five thousand nuclei and incubated at room temperature (RT) for 10 minutes, then were placed on a magnet stand to clear (1 min) and be decanted through removal of liquid with a pipettor. The beads were resuspended in 50 µL primary antibody (anti-mH2A1, anti-H3K27me3, anti-mouse IgG 1:100) in Wash buffer supplemented with 2 mM EDTA and 0.1% bovine serum albumin (BSA) and incubated on a nutator at 4 °C for 5 days. The beads were decanted on a magnet stand then resuspended in 50 µL secondary antibody (Guinea pig anti-rabbit IgG 1:100) in Wash buffer supplemented with 2 mM EDTA and 0.1% BSA and incubated on a nutator at room temperature for 1 hr. The beads were decanted on a magnet stand and washed with 200 µL Wash buffer, then were resuspended in 50 µL pA-Tn5 (1:200) in 300-Wash buffer (Wash buffer containing 300 mM NaCl) and incubated on a nutator at room temperature for 1 hr. The beads were decanted on a magnet stand and washed twice with 200 µL 300-Wash buffer, then resuspended in 50 µL Tagmentation buffer (300-Wash buffer supplemented with 10 mM MgCl2) and incubated at 37 °C for 1 hr. Following tagmentation, the beads were decanted on a magnet stand and washed with 50 µL TAPS wash buffer (10 mM TAPS pH 8.5, 0.2 mM EDTA), then resuspended in 5 µL TAPS wash buffer supplemented with 0.1% SDS and incubated at 58 °C C for 1 hr. Tubes were placed on ice and SDS was neutralized with 15 µL 0.67% Triton-X100
2 µL of 10 mM indexed P5 and P7 primer solutions and 25 µL NEBnext High-Fidelity 2X Master Mix were added. Gap-filling and 15 cycles of PCR were performed using an MJ PTC-200 Thermocycler. Library clean-up was performed by incubating beads with 65 µL SPRI bead slurry for 5-10 minutes, then magnetization and two washes with 200 µL 80% ethanol. Libraries were eluted with 22 µL Tris-HCl pH 8.0 and 2 µL was used for Agilent 4200 Tapestation analysis. The barcoded libraries were mixed to achieve equimolar representation as desired aiming for a final concentration as recommended by the manufacturer for sequencing on an Illumina HiSeq 2500 2-lane Turbo flow cell.

tag: tissue

value: Skin

tag: cell line

value: HFF

tag: cell type

value: Primary human foreskin fibroblast

tag: cut&tag antibody

tag: treatment

value: HSV-1 infection

tag: time

value: 12 hours post-infection


title: BJ, WT, 9Months Cerebral organoid hBG_s50

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: genotype

value: WT


title: HFF, IgG, HSV-1 12 hpi, Rep3

value: IgG


title: HFF, H3K27me3, Mock, Rep2

value: Mock (no infection)


title: HFF, macroH2A1, HSV-1 4 hpi, Rep2

value: 4 hours post-infection


title: HFF, IgG, HSV-1 8 hpi, Rep3

value: 8 hours post-infection


title: siAHR-CLB6

city: Madrid

first: Angel

middle: L

last: Corbí

state: Madrid

address: Ramiro de Maeztu 9

department: Molecular Microbiology and Infection Biology

country: Spain

institute: Consejo Superior de Investigaciones Científicas

data_processing:
BGISEQ-500 platform
Low quality reads were filtered using filtering software SOAPnuke (developed by BGI, Version v1.5.2, with parameters -l 15 -q 0.2 -n 0.05) to remove the reads containing the adaptor(adaptor pollution), the reads whose N content is greater than 5%, and low-quality reads (defined as those with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" were saved in FASTQ format. Sequences were mapped to GRCh38 genome (version GCF_000001405.38_GRCh38.p12) using Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

source_name: RNA from  monocyte-derived macrophages 48 hours after transfection with a AhR-specific siRNA and exposure to CL264 for 4 hours #6

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 1000 U/ml M-CSF to generate M-CSF-polarized macrophages.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Monocyte-derived macrophages (at day 5 along the differentiation protocol) were transfected with AhR-specific siRNA or control siRNA, kept in culture for 48 hours, and then stimulated (or not) with CL264 (1 microgram/ml). After 4 hours, cells were lysed and RNA isolated for transcriptional analysis.

value: Monocyte-derived M-CSF macrophages

value: AhR-specific siRNA; Exposed to CL264


title: siAHR-CLB4

source_name: RNA from  monocyte-derived macrophages 48 hours after transfection with a AhR-specific siRNA and exposure to CL264 for 4 hours #4


title: HFF, H3K27me3, HSV-1 4 hpi, Rep2


title: HFF, IgG, HSV-1 4 hpi, Rep3


title: BJ, WT, 9Months Cerebral organoid hBG_9M_WT

description:
BJ, WT, 9Months Cerebral organoid
Visium Spatial transcriptomics


title: BJ, WT, 9Months Cerebral organoid hBG_s47


title: siAHRB5

source_name: RNA from monocyte-derived macrophages 48 hours after transfection with a AhR-specific siRNA #5

value: AhR-specific siRNA; untreated


title: siAHRB6

source_name: RNA from monocyte-derived macrophages 48 hours after transfection with a AhR-specific siRNA #6


title: HFF, IgG, HSV-1 12 hpi, Rep2


title: siAHRB4

source_name: RNA from monocyte-derived macrophages 48 hours after transfection with a AhR-specific siRNA #4


title: HFF, IgG, Mock, Rep3


title: HFF, H3K27me3, HSV-1 8 hpi, Rep2


title: siAHR-CLB5

source_name: RNA from  monocyte-derived macrophages 48 hours after transfection with a AhR-specific siRNA and exposure to CL264 for 4 hours #5


title: HFF, IgG, HSV-1 8 hpi, Rep2


title: HFF, IgG, HSV-1 4 hpi, Rep2


title: HFF, IgG, Mock, Rep2


title: female Poecilia latipinna 19, whole brain, Ff treatment

city: Austin

first: Rebecca

last: Young

state: TX

address: 2415 Speedway

department: Integrative Biology

institute: University of Texas at Austin

data_processing:
Libraries were demultiplexed using a custom python script. Raw 101 bp reads were trimmed to remove low quality base pairs (Phred quality score < 20), reads with few contiguous high-quality base pairs (fewer than 30 bp) using a python script.
python script (http://genomics-pubs.princeton.edu/prv/resources/scripts/TQSfastq.py)
Adapter sequences were trimmed using the program cutadapt (https://cutadapt.readthedocs.io/en/stable/).
To evaluate the quality of the trimmed reads, we ran FastQC (Andrew, 2010) using TACC (Texas Advanced Computing, The University of Texas at Austin).
Reads were pseudoaligned to the Sailfin molly Poecilia latipinna (assembly GCA_001443285.1, retrieved from Ensembl January 2019) with Kallisto (version 0.43.0) using the single-end reads option with a length of 100bp (-l 100), standard deviation of 20 (-s 20).
Assembly: GCA_001443285.1
Supplementary files format and content: tab-delimited Kalisto abundance text files include estimated counts and transcripts per million

organism: Poecilia latipinna

source_name: whole brain

growth_protocol: Fish were maintained in semi-natural on-campus outdoor ponds at the Brakenridgen Field Laboratory at the University of Texas, Austin

extract_protocol:
Immediately following the 30-minute behavioral trial, focal females were immediately decapitated, whole brains were removed and individually immersed in RNAlater solution (Applied Biosystems, Carlsbad, CA, USA) at 4˚ Celsius with gentle shaking for 24 hours, then stored at -80 C (without RNAlater) for subsequent RNA profiling. 1-4 μg of total RNA were used as input for RNA library preparation and sequencing.
RNA libraries for RNA-seq were prepared using Illumina’s TruSeq mRNA Sample Prep Kit.

treatment_protocol: Sexually experienced P. latipinna females were collected from a semi-natural environment and socially isolated for two weeks to ensure sexual receptivity. Each female was subjected to short-term (30min) non-contact dichotomous choice assays. Females were randomly assigned to one of two social choice treatment groups (mate preference with male stimuli to female shoaling partner with female stimuli) without a non-social control. Focal females made preference decisions based on stimuli size differences in both treatments.Each focal female was acclimatized in an opaque cylinder for 5 minutes in the central neutral zone before being released. Following release from habituation, focal females were observed for 15 minutes and position and behavior in tank recorded.  After the first 15 minutes of observations, focal females were brought back to the neutral area and placed in the opaque habituation cylinder while the stimulus fish were switched to opposite sides to ensure that our preference measures were directed at a specific fish rather than a location preference in our experimental tank. Following the stimulus switch, focal females were observed for an additional 15 minutes.

value: whole brain

tag: preference behavior

value: Ff social context


title: HFF, H3K27me3, HSV-1 4 hpi, Rep3


title: siCNT-CLB6

source_name: RNA from  monocyte-derived macrophages 48 hours after transfection with a control siRNA and exposure to CL264 for 4 hours #6

value: Control siRNA; Exposed to CL264


title: female Poecilia latipinna 17, whole brain, Ff treatment


title: BJ, WT, 9Months Cerebral organoid hBG_s44

value: BJ

value: human induced pluripotent stem cell

value: Cerebral organoid differentiation

value: 9 months


title: female Poecilia latipinna 13, whole brain, Mm treatment

value: Mm mate choice context


title: siCNT-CLB5

source_name: RNA from  monocyte-derived macrophages 48 hours after transfection with a control siRNA and exposure to CL264 for 4 hours #5


title: BJ, WT, 9Months Cerebral organoid hBG_s40


title: siCNT-CLB4

source_name: RNA from  monocyte-derived macrophages 48 hours after transfection with a control siRNA and exposure to CL264 for 4 hours #4


title: siCNTB6

source_name: RNA from  monocyte-derived macrophages 48 hours after transfection with a control siRNA #6

value: Control siRNA; untreated


title: female Poecilia latipinna 9, whole brain, Ff treatment


title: female Poecilia latipinna 10, whole brain, Mm treatment


title: BJ, WT, 9Months Cerebral organoid hBG_s31

value: WT


title: BJ, WT, 9Months Cerebral organoid hBG_s27


title: female Poecilia latipinna 11, whole brain, Mm treatment


title: siCNTB5

source_name: RNA from  monocyte-derived macrophages 48 hours after transfection with a control siRNA #4


title: BJ, WT, 9Months Cerebral organoid hBG_s34


title: female Poecilia latipinna 7, whole brain, Ff treatment


title: female Poecilia latipinna 6, whole brain, Mm treatment


title: female Poecilia latipinna 8, whole brain, Ff treatment


title: siCNTB4

source_name: RNA from monocyte-derived macrophages 48 hours after transfection with a control siRNA #4


title: female Poecilia latipinna 5, whole brain, Mm treatment


title: TAC+pimobendan biological replicate 3

city: Changchun

first: Yi

last: Gao

state: Jilin

address: 126th Xiantai Street, Changchun, Jilin, China.

department: Cardiovascular

country: China

institute: China-Japan Union Hospital of Jilin University

description: The 3rd mouse has been operated on  transverse aortic constriction surgery at the age of 8 weeks, administered oral pimobendan (1mg/kg/ day) for four weeks, and was sampled at the age of 12 weeks.

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterward clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) . Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then the expression level of the gene was calculated by RSEM (v1.2.12). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. The differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take an insight into the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed genes was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni.
Genome_build: GRCm38
Supplementary_files_format_and_content: include gene TPM and FPKM values for each Sample

organism: Mus musculus

source_name: left ventricle

extract_protocol:
Under anesthesia with an anesthesia machine (R580, RWD Life Science, China), the mice were weighed and sacrificed by cervical dislocation. We Started below the xiphoid, made a V-shaped thoracotomy, opened the thorax, and exposed the heart. The heart was arrested in diastole with 1% KCl in 0.01M PBS, quickly removed, rinsed with cold PBS, and blotted dried.
1. mRNA Isolation mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. 2. mRNA Fragment mRNA molecules were fragmented into small pieces using fragmentation reagent after reaction a certain period in proper temperture. 3. cDNA Synthesis First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. 4. End Repair, Add A and Adaptor Ligation The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments. 5. PCR This process was to amplify the cDNA fragments with adapters from previous step. PCR products were purified with Ampure XP Beads (AGENCOURT), and dissolved in EB solution. 6. Library Quality Control Library was validated on the Agilent Technologies 2100 bioanalyzer. 7. Circularization The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. 8. Sequencing The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and single end 50 (pair end 100/150) bases reads were generated in the way of combinatorial Probe-Anchor Synthesis (cPAS).

treatment_protocol: Mice were anesthetized via the inhalation of oxygen containing 3% isoflurane, followed by sham or TAC surgery to induce hypertrophy. The skin of the thoracic region of the mice was removed using the depilation cream and disinfected with alcohol. The skin of the neck was cut open to expose the trachea, which was separated into the mediastinum along the upper part of the trachea. After the thymus was stripped, the aortic arch was exposed, and the perivascular tissue was separated. Between the first and second branches on the left side of the aortic arch, the ligating clip were used for ligation by clamping the vascular clamp, which was recalibrated before using the 27G needle. This ligation was not performed in the sham operation group.

tag: strain

value: left ventricle

tag: age

value: 12 week

value: TAC+pimobendan


title: female Poecilia latipinna 4, whole brain, Mm treatment


title: female Poecilia latipinna 2, whole brain, Ff treatment


title: female Poecilia latipinna 3, whole brain, Mm treatment


title: BJ, WT, 9Months Cerebral organoid hBG_s37


title: female Poecilia latipinna 1, whole brain, Ff treatment


title: TAC+pimobendan biological replicate 2

description: The 2nd mouse has been operated on  transverse aortic constriction surgery at the age of 8 weeks, administered oral pimobendan (1mg/kg/ day) for four weeks, and was sampled at the age of 12 weeks.


title: BJ, WT, 4Months Cerebral organoid BT

description:
BJ, WT, 4Months Cerebral organoid
Spatial transcriptomics

value: 4 months


title: female Poecilia latipinna 12, whole brain, Mm treatment


title: BJ, WT, 4Months Cerebral organoid BW


title: TAC+control biological replicate 3

description: The 3rd mouse has been operated on  transverse aortic constriction surgery at the age of 8 weeks, and was sampled at the age of 12 weeks.

value: TAC+control


title: TAC+pimobendan biological replicate 1

description: The 1st mouse has been operated on  transverse aortic constriction surgery at the age of 8 weeks, administered oral pimobendan (1mg/kg/ day) for four weeks, and was sampled at the age of 12 weeks.


title: BJ, WT, 4Months Cerebral organoid Fig1_BX


title: Sample D-3

city: suzhou

first: zhang

middle: shu

last: yu

address: No. 199, Ren'ai Road

department: soochow university

institute: Soochow University

data_processing:
Illumina bcf2fastq v2.20 software used for basecalling.
fastp version 0.20.1 software was first used for adpter removing, then low-quality   bases and N-bases or low-quality reads were filtered out.Then sequencing reads were mapped to the Rat genome （Hg38.p13) using HISAT2 version 2.2.1.0 with parameters --rna-strandness rf --fr
Counts and Fragments Per Kilobase of exon model per Million mapped fragments(FPKM) of each gene was calculated using htseq-count version 0.11.2
Assembly: Hg38.p13
Supplementary files format and content: Matrix table with raw counts for every gene and every sample.

extract_protocol:
Total RNA from heart samples was extracted using the mirVana™ miRNA Isolation Kit (Ambion, AM1561) following the manufacturer’s protocol.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

value: human fibroblast

value: UVB exposure with TAT-UIFSP 6 pretreatment


title: Sample D-4


title: TAC+control biological replicate 2

description: The 2nd mouse has been operated on  transverse aortic constriction surgery at the age of 8 weeks, and was sampled at the age of 12 weeks.


title: TAC+control biological replicate 1

description: The 1st mouse has been operated on  transverse aortic constriction surgery at the age of 8 weeks, and was sampled at the age of 12 weeks.


title: Sample D-2


title: Sample D-1


title: BJ, WT, 4Months Cerebral organoid BR


title: BJ, WT, 4Months Cerebral organoid BQ


title: Sham+pimobendan biological replicate 3

description: The 3rd mouse has been operated on sham surgery at the age of 8 weeks, administered oral pimobendan (1mg/kg/ day) for four weeks, and was sampled at the age of 12 weeks.

value: Sham+pimobendan


title: Sham+pimobendan biological replicate 1

description: The 1st mouse has been operated on sham surgery at the age of 8 weeks, administered oral pimobendan (1mg/kg/ day) for four weeks, and was sampled at the age of 12 weeks.


title: Sample C-3

value: UVB exposure with TAT-UIFSP 5 pretreatment


title: Sample C-4


title: Sample C-2


title: Sham+control biological replicate 2

description: The 2nd mouse has been operated on sham surgery at the age of 8 weeks, and was sampled at the age of 12 weeks.

value: Sham+control


title: Sample C-1


title: WT2

city: Paris

first: Olivia

last: Lenoir

address: 56 rue Leblanc

institute: Inserm

data_processing:
STAR v.2.7.1a + RSEM
--genomeDir [/path/to/reference/index] --sjdbGTFfile [/path/to/reference/gtf] --runThreadN [number of threads] 15 --readFilesIn [all fastq.gz archives] --outFileNamePrefix [prefix for this sample] --twopassMode Basic --outReadsUnmapped None --sjdbOverhang [read size minus 1] 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
rsem-calculate-expression -p 20 --paired-end --bam --no-bam-output $alignedToTransciptomFile $reference_name $sample_name
R version 3.6.1,  DESeq2_1.24.0, tidyverse_1.2.1
Assembly: Mus musculus GRCm38 from Ensembl release 96
Supplementary files format and content: NGS19-076_GRCm38r96_deseq2_NormalizedMatrix.tsv
Supplementary files format and content: Normalized count

source_name: endothelial cells

growth_protocol: HUVEC were grown in ECGM growth medium

extract_protocol: mRNA were extracted using Qiagen mini kit

value: endothelial cells

value: HUVEC

value: endothelial


title: Sham+control biological replicate 1

description: The 1st mouse has been operated on sham surgery at the age of 8 weeks, and was sampled at the age of 12 weeks.


title: Sample B-4

value: UVB exposure


title: Sham+pimobendan biological replicate 2

description: The 2nd mouse has been operated on sham surgery at the age of 8 weeks, administered oral pimobendan (1mg/kg/ day) for four weeks, and was sampled at the age of 12 weeks.


title: WT3


title: WT1


title: vecATG5-2

value: ATG5 KD


title: vecATG5-3


title: vecATG5-1


title: SAMPLE 6_M1_rep3

type: RNA

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

country: Germany

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed following the Agilent protocol at 65°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 µm/pixel resolution and analyzed with Mapix 6.5.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

organism: Mus

source_name: isolated macrophages

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

growth_protocol: C57BL/6 and B6.SJL-Ptprca mice expressing the CD45.1 alloantigen (Ly5.1 PTP) on circulating leukocytes with C57BL/6 genetic background were purchased from Charles River Laboratories. Ccr2-/- (B6.129P2-Ccr2tm1Mae) mice were generated as described previously and backcrossed to the C57BL/6 background (Kuziel WA et al., 1997). All mice together with their respective littermate controls were bred under specific pathogen-free conditions and were used between 10 and 14 weeks of age

extract_protocol: The sorted macrophages were re-suspended in 300uL RLT buffer and stored at -80°C until RNA isolation with QIAgen RNeasy following the kit instructions.

treatment_protocol: Mice were anaesthetized and oro-tracheally inoculated with 2.5-5x102 plaque-forming units (pfu) of influenza A virus PR8 (A/PR/8/1934(H1N1)) diluted in 70μl sterile PBS-/-.

tag: strain background

value: day 7 p.i.

value: isolated macrophages


title: Sample B-3

value: WT


title: SAMPLE 8_M2_rep4

value: day 21 p.i.


title: SAMPLE 3_M1_rep2


title: WZ28

city: Beijing

first: Wei

last: Zhang

address: No. 168 Litang Road, Changping District

institute: Department of Neurosurgery, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University

description: tumors of the central nervous system

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control: Raw data (raw reads) was firstly processed through Fastq-Mcf tool with defaults parameters (https://github.com/ExpressionAnalysis/ea-utils/blob/wiki/FastqMcf.md). Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reads mapping: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.1.0 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12
Quantification of gene expression level: Cufflinks version 2.2.1 was used to count the reads numbers mapped to each gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: glioblastoma

extract_protocol:
Total cellular RNA was extracted using TRIzol (TaKaRa, Tokyo, JPN). RNA degradation and contamination were monitored on 1% agarose gels. RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: glioblastoma stem cell

value: glioblastoma


title: SAMPLE 5_M2_rep3


title: WZ31

description: tumors of the central nervous system


title: WZ29

description: tumors of the central nervous system


title: SAMPLE 4_M2_rep2


title: SAMPLE 7_M1_rep4


title: NMN_Mus_Oocyte_3

city: Nanjing

first: Miao

last: Yilong

address: Tongwei Road

institute: Nanjing Agricultural University

description:
N3
instrument model: MGISEQ-2000

data_processing:
uses the filtering software SOAPnuke V1.5.2 developed by BGI independently for filtering
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Bowtie2 V2.2.5 with -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Reads Per Kilobase of exon per Megabase of library size (RSEM) were calculated using a protocol from Li, B et al., BMC Bioinformatics, 2011. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RESM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: oocyte

extract_protocol:
Single cell sequencing uses the smart-seq2 method to reverse transcribe mRNA directly through oligo dT, and uses the reverse transcriptase MMLVRT to obtain a full-length single-stranded cDNA template containing fixed sequences at both ends, and then uses this cDNA as a template for extensive amplification
RNA libraries were prepared for sequencing using standard DNBseq protocols

tag: development stage

value: Metaphase II

value: ICR

tag: group

value: NMN supplementation


title: SAMPLE 1_M2_rep1


title: WZ27

description: tumors of the central nervous system


title: Sham+control biological replicate 3

description: The 3rd mouse has been operated on sham surgery at the age of 8 weeks, and was sampled at the age of 12 weeks.

value: left ventricle

value: 12 week


title: Sample B-2

value: human fibroblast


title: WZ05

description: tumors of the central nervous system


title: SAMPLE 2_M1_rep1


title: Sample A-4

value: white space handling


title: CC6

city: Boston

first: Peter

middle: A

last: Nigrovic

state: Massachusetts

address: 1 Blackfan Cir Bldg 10004C, Karp Research

department: Immunology

institute: Boston Children's Hospital

description: CD4+ T cells, CC genotype

data_processing:
Raw data was processed using release 3.9 of the nextflow nf-core “rnaseq” pipeline
adapter and quality trimming using Trim Galore (version 0.6.7)
aligned reads to the GRCh38 reference genome using STAR (version 2.7.10)
quantified transcript expression with Salmon (version 1.5.2)
aggregated transcript abundances to gene level measurements with bioconductor-tximeta (version 1.8.0)
Assembly: GRCh38
Supplementary files format and content: Excel file includes log2(TPM+1) counts for all the samples
Supplementary files format and content: Excel file includes statistics for cis eQTL analysis for all the samples

source_name: Primary CD4+ T cell

extract_protocol:
RNA was isolated from human CD4+ T cells using RNeasy Micro kit. 10 ng sample of RNA was used for the construction of sequencing libraries
RNA-seq libraries were prepared using the Illumina SmartSeq2 platform
Low-input RNA-seq

value: Primary CD4+ T cell

value: CC for the SNP rs117701653


title: CC4

description: CD4+ T cells, CC genotype


title: Age_Mus_Oocyte_2

description:
A2
instrument model: MGISEQ-2000

value: aged


title: CC8

description: CD4+ T cells, CC genotype


title: NMN_Mus_Oocyte_2

description:
N2
instrument model: MGISEQ-2000


title: Sample A-3


title: CC2

description: CD4+ T cells, CC genotype


title: Age_Mus_Oocyte_1

description:
A1
instrument model: MGISEQ-2000


title: Sample A-2


title: WZ12

description: tumors of the central nervous system


title: AC7

description: CD4+ T cells, AC genotype

value: AC for the SNP rs117701653


title: Sample A-1


title: Young_Mus_Oocyte_2

description:
C2
instrument model: MGISEQ-2000

value: young


title: AC8

description: CD4+ T cells, AC genotype


title: CC3

description: CD4+ T cells, CC genotype


title: Age_Mus_Oocyte_3

description:
A3
instrument model: MGISEQ-2000


title: Young_Mus_Oocyte_1

description:
C1
instrument model: MGISEQ-2000


title: AC5

description: CD4+ T cells, AC genotype


title: CC1

description: CD4+ T cells, CC genotype


title: NMN_Mus_Oocyte_1

description:
N1
instrument model: MGISEQ-2000


title: CC7

description: CD4+ T cells, CC genotype


title: Sample B-1

value: UVB exposure


title: DAOY-siPRKAA1-2

first: Cai

last: Jing

state: Jiangsu

address: dongshan street

department: Department of Medical Genetics

institute: Nanjing Medical University

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

source_name: Cerebellum

growth_protocol: DAOY cells (ATCC Cat# HTB-186, RRID:CVCL_1155) were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS, Gibco), 1× glutamine (Gibco), and 1 mM sodium pyruvate (Gibco).

extract_protocol: A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer’s instructions.

treatment_protocol: siRNAs specific for the human PRKAA1 were purchased from GenePharma (Shanghai, China).Total RNA was extracted at 48 hours of siRNA processing

value: Cerebellum

value: DAOY

value: SHH

value: WT


title: AC4

description: CD4+ T cells, AC genotype


title: DAOY-siPRKAA1-3


title: CC5

description: CD4+ T cells, CC genotype


title: AC1

description: CD4+ T cells, AC genotype


title: A.baumannii colistin+sulbactam rep3

city: Shanghai

first: Xingchen

last: Bian

state: Shanghai

address: Fudan university, Huashan hospital

institute: Huashan hospital, Fudan University

data_processing:
Data Filtering criteria: 1) Use Cutadapt to remove the sequence of 3' end band connectors; 2) Reads with average quality scores lower than Q20 were removed.
Alignment software: Bowtie2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Acinetobacter baumannii

source_name: bacteria

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: bacteria

value: A. baumannii

value: colistin+sulbactam


title: Young_Mus_Oocyte_3

description:
C3
instrument model: MGISEQ-2000

value: Metaphase II

value: ICR


title: AA8

description: CD4+ T cells, AA genotype

value: AA for the SNP rs117701653


title: AA7

description: CD4+ T cells, AA genotype


title: AC3

description: CD4+ T cells, AC genotype


title: AC2

description: CD4+ T cells, AC genotype


title: DAOY-siNC-3

value: siNC


title: DAOY-siNC-2


title: A.baumannii colistin+sulbactam rep2


title: A.baumannii sulbactam rep3

value: sulbactam


title: AC6

description: CD4+ T cells, AC genotype

value: Primary CD4+ T cell


title: A.baumannii colistin+sulbactam rep1


title: AA6

description: CD4+ T cells, AA genotype


title: DAOY-siNC-1


title: AA4

description: CD4+ T cells, AA genotype


title: A.baumannii sulbactam rep2


title: AA3

description: CD4+ T cells, AA genotype


title: AA2

description: CD4+ T cells, AA genotype


title: A.baumannii sulbactam rep1


title: Sample 12_HCCLM3 CCDC137-APOBEC1 +doxycycline

city: Guang zhou

first: Shuang

last: Tao

address: 2693 Kaichuang Avenue

institute: Sun Yat-sen University

data_processing:
Raw data was filtered using Cutadapt(https://cutadapt.readthedocs.io/en/stable/, v1.16) and a self-made program for removing adaptor contamination and low quality reads, respectively. rRNA contamination was filtered by Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml, version: bowtie2, v2.3.3.1)
Clean reads were mapped to the genome  using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml，v2.1.1)
The expression level of mRNA were calculte using RSEM (RNA-Seq by Expectation Maximization) (v1.3.1) by normalized to FPKM (Fragments Per Kilobase Per Million reads)
The differentially expressed mRNAs were screened using edgeR package (https://bioconductor.org/packages/release/bioc/html/edgeR.html)in R. |log2Foldchange| ≥ 1and Pvalue < 0.05 was considered siginificant.
Assembly: hg18
Supplementary files format and content: xls files include comparative gene expression profiling analysis of mRNA-seq data from GFP/CCDC137-APOBEC1 overexpressing HCCLM3 cells with or without doxycycline treatment.

extract_protocol:
Total RNA was isolated and purified using TRIzol(Life, cat.265709, CA, USA) following the manufacturer's procedure.
VAHTS® Universal V6 RNA-seq Library Prep Kit (Vazyme, cat.NR604, Nanjing, China

value: Human Hepatocellular Carcinoma Cells

value: CCDC137-APOBEC1 overexpressing

value: doxycycline


title: Sample 11_HCCLM3 CCDC137-APOBEC1

value: CCDC137-APOBEC1 transfected


title: AA1

description: CD4+ T cells, AA genotype


title: Sample 10_HCCLM3 GFP-APOBEC1 +doxycycline

value: GFP-APOBEC1 overexpressing


title: DAOY-siPRKAA1-1

value: Cerebellum

value: DAOY


title: 48 hr SPEDOX 5 uM UF DOX equivalent, hiPSC-cardiac spheroid, replicate 2

city: Los Angeles

first: Arun

last: Sharma

state: CA

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

data_processing:
Demultiplexing and conversion of raw sequencing data to FASTQ was performed with Illumina bcl2fastq software.
Assembly: FastQC was used to assess sequence quality and reads were aligned to the GRCh38 genome assembly (GENCODE 28) using Salmon version 0.11.3.
Supplementary files format and content: Gene-level read counts were quantified with Salmon, and differential gene expression and normalization was subsequently performed using DESeq2.

source_name: hiPSC-derived cardiac spheroid

extract_protocol:
Total RNA was isolated from hiPSC-CSs treated with DMSO, UF DOX (5 µM), and SPEDOX-6 (5 µM UF DOX equivalent) using a RNeasy Mini Kit (QIAGEN) with on-column DNase digestion. Nine spheroids were treated per condition for 48 hours at 40,000 cells per spheroid, following previously published ratios of hiPSC-CMs, hiPSC-ECs, and hiPSC-CFs (Arzt et al., 2023). Each spheroid was washed with 200 μL PBS and then followed by a wash with 350 μL Buffer RLT containing B-mercaptoethanol and DTT to lyse the cells. Still in Buffer RLT, 3 spheroids from 1 condition were then transferred to an Eppendorf tube to generate 3 replicates of 3 spheroids per condition, or 120,000 cells per replicate. The contents of each tube were pipetted up and down and centrifuged at 8000 x g for 3 minutes. After discarding each supernatant, another 350 μL 70% ethanol was added per tube and the contents were transferred to RNeasy MinElute spin columns inside 2 mL collection tubes which were centrifuged for 15 seconds at 8000 x g. Buffer RW1 was then added to each column at 350 μL and spun for 15 seconds at 8000 x g. A mixture of Buffer RDD and DNase 1 was then added to each column at 80 μL and incubated at room temperature for 15 minutes. An additional 350 μL Buffer RW1 was added to each collection tube and centrifuged at 8000 x g for 15 seconds. A final addition of 500 μL 80% ethanol was added to each column and centrifuged at 8000 x g for 2 minutes. After transferring the spin column to a new collection tube, each column was spun at 5 minutes at full speed. The columns were transferred to a 1.5 mL tube and 14 μL RNase free water was added to the center of each column followed by centrifugation at full speed for 1 minute to elute the RNA.
After a verification of the RNA yield of each tube via a NanoDrop 2000 Spectrophotometer (ThermoFisher), the samples were submitted to the Cedars-Sinai Genomics Core. RNA integrity was checked with an Agilent 2100 Bioanalyzer and only samples with an RNA integrity (RIN) score >9 were selected for cDNA library construction.
Libraries were prepared with SMART-Seq v4 Ultra Low Input RNA Kit (Takara) and sequenced on a NextSeq 500 (Illumina) using single-end 75 bp reads at the Cedars-Sinai Genomics Core.

value: hiPSC-derived cardiac spheroid

value: human induced pluripotent stem cell derived cardiac spheroids, comprised of cardiomyocytes, endothelial cells, and fibroblasts

value: WT

value: 48 hr SPEDOX-6 treatment at 5uM DOX equivalent dose


title: 48 hr DOX 5 uM, hiPSC-cardiac spheroid, replicate 3

value: 48 hr doxorubicin treatment at 5uM


title: 48 hr SPEDOX 5 uM UF DOX equivalent, hiPSC-cardiac spheroid, replicate 1


title: A.baumannii polymyxin B rep2

value: bacteria

value: A. baumannii

value: polymyxin B


title: A.baumannii polymyxin B rep1


title: Sample 9_HCCLM3 GFP-APOBEC1

value: GFP-APOBEC1 transfected


title: AA5

description: CD4+ T cells, AA genotype

value: Primary CD4+ T cell

value: AA for the SNP rs117701653


title: 48 hr DMSO, hiPSC-cardiac spheroid, replicate 3

value: 48 hr DMSO


title: 48 hr DOX 5 uM, hiPSC-cardiac spheroid, replicate 2


title: 48 hr DMSO, hiPSC-cardiac spheroid, replicate 2


title: 48 hr DOX 5 uM, hiPSC-cardiac spheroid, replicate 1


title: A.baumannii colistin B rep3

value: colistin B


title: sample 3_PLC/PRF/5 control cells

data_processing:
to get high quality clean reads, reads were further  filtered by Cutadapt
we aligned reads of all samples to the reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
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.
Assembly: ftp://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/
Supplementary files format and content: xlsx files include RPKM values for each Sample and the fold changes in each group

extract_protocol:
RNA was harvested using Trizol reagent (thermofisher, 15596018). Approximately 1 ug of total RNA was used for the construction of sequencing libraries.
Following purification, the mRNA was fragmented  into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module  (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create  the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA)

value: Human Hepatocellular Carcinoma Cells

value: control vector


title: A.baumannii colistin B rep2


title: 48 hr DMSO, hiPSC-cardiac spheroid, replicate 1


title: MDA-MB-231_mtAsn-1-LNA_2

city: New York

first: Christopher

last: Rouya

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Fastq file quality was assessed using FastQC, and reads were aligned to the hg38 human genome with bowtie2 using default parameters. For CUT&RUN, peaks were called using MACS2, and bam to bigwig conversion (normalizing by reads per bin) was carried out using deeptools. Differentially bound regions were identified using the Diffbind package.
Assembly: hg38
Supplementary files format and content: narrowPeak and bed files

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
For GRO-seq, BrU-labelled nascent transcripts were immunopurified and isolated using phenol-chloroform extraction.  For CUT&RUN, samples were prepared using standard manufacturer's protocol (Epicypher).
GRO-seq libraries were prepared as described in Zhu et al., (2018).  CUT&RUN libraries were prepared according to manufacturer's protocol (Epicypher).
GRO-seq and CUT&RUN

treatment_protocol: Cells were transfected with 20 nM of respective LNA using Lipofectamine 2000, and harvested two days post transfection


title: MDA-MB-231_ControlLNA_3


title: A.baumannii colistin rep3

value: colistin


title: MDA-MB-231_ControlLNA_2


title: sample 1_Huh-7 empty cells

value: empty vector


title: MDA-MB-231_ControlLNA_1


title: A.baumannii polymyxin B rep3


title: MDA-MB-231_mtAsn-1-LNA_3


title: sample 4_PLC/PRF/5 CCDC137-knockdown cells

value: CCDC137 knockdown


title: CRC, CD14 sorted, replicate 3, scRNAseq

city: Wuhan

first: Fu

last: Haoyu

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Gastrointestinal Surgery

institute: Union Hospital, Tongji Medical College,Huazhong University of Science and Technology

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw data was processed using Cell Ranger toolkit. With cellranger count function, raw data was mapped to the reference genome GRCh38 and generated the gene-cell UMI matrix for downstream analyses
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colorectal cancer

extract_protocol:
Tumor tissues were immediately cut into small pieces in RPMI medium after collected from CRC patients. Then each sample was enzymatically digested using Collagenase IV (1 mg/mL), DNase I (100 μg/mL) and hyaluronidase (100 μg/mL) on a 37 °C shaker for 1 h. Subsequently, suspensionwere sorted using magnetic bead sorting according to the manufacturer’s protocol.
scRNA-seq was performed according to the manufacturer’s protocol. Single-cell suspensions were mixed with Chromium Single cell 3′ Reagent v3 kits and then were loaded on Chromium Controller to generate single-cell gel beads in emulsions (GEMs). Cell lysis and reverse transcription reactions were performed in GEMs to generate barcoded full-length cDNA. Then GEMs were disrupted and cDNA was amplificated. The amplificated cDNA was fragmented, end-repaired, A-tailed, and ligated to an index adaptor to generate barcoded scRNA-seq libraries.

value: Colorectal cancer


title: A.baumannii colistin rep2

value: WT


title: CRC, CD14 sorted, replicate 2, scRNAseq

description: 10x Genomics


title: MDA-MB-231_mtAsn-1-LNA_1


title: A.baumannii colistin B rep1


title: A.baumannii colistin rep1


title: sample 2_Huh-7 CCDC137-overexpressing cells

value: CCDC137 overexpressing


title: CRC, CD14 sorted,replicate 1, scRNAseq

description: 10x Genomics


title: A.baumannii control rep3

value: control


title: hiPSC differentiated for 0h, repl 2

city: Leiden

first: Susana

last: Chuva de Sousa Lopes

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: Leiden University Medical Center

description:
10x Genomics
Sample0H_B

data_processing:
For all samples Cell Ranger Single Cell Software Suite 6.1.1 was used to perform sample demultiplexing, barcode processing,  (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38 (refdata-cellranger-GRCh38-2020-A)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: hiPSC

extract_protocol:
Cells were dissociated using Accutase for 15min at 37C, filtered through a 35um strainer, ressuspended in 0.5% BSA/DPBS and FACS-sorted for live cells (7AAD-negative cells).
Sequencing libraries were prepared according to the user guide of the 10x Genomics Chromium Single Cell 3' Library and Gel Bead Kit v3, Product Code PN-1000348.

value: hiPSC

tag: time of_differentiation


title: A.baumannii control rep2

value: bacteria

value: A. baumannii


title: hiPSC differentiated for 0h, repl 1

description:
10x Genomics
Sample0H_A


title: TEX3

city: Innsbruck

first: Alexander

last: Kirchmair

address: Innrain 80-82

country: Austria

institute: Medical University of Innsbruck

data_processing:
The nf-core rnaseq pipeline 3.6 was used to align reads to the GRCh38 reference genome and to quantify gene expression with salmon 1.5.2.
Assembly: GRCh38
Supplementary files format and content: raw counts table

source_name: CD8+ T cells

extract_protocol:
Total RNA isolation with the RNeasy Plus Mini Kit (Qiagen)
Lexogen QuantSeq 3’mRNA protocol with multiplexing (Lexogen GmbH, Vienna, Austria)

value: CD8+ T cells

tag: donor

tag: batch

value: B

value: 4x stimulation with NY-ESO-1-peptide-loaded HLA-A2+ T2 tumor cells (1:3) and IL-2 (50 U/mL)


title: A.baumannii control rep1


title: TEX1b


title: hiPSC differentiated for 120h

description:
10x Genomics
Sample120H


title: TEX1a

value: A


title: TAC-dantrolene biological replicate 3

description:
The 3rd mouse has been operated on  transverse aortic constriction surgery at the age of 8 weeks, administered oral dantrolene (30mg/kg/ day) for four weeks, and was sampled at the age of 12 weeks.
Y_Med_3

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue < =0.05
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

extract_protocol:
Under anesthesia with an anesthesia machine (R580, RWD Life Science, China), the mice were weighed and sacrificed by cervical dislocation. We Started below the xiphoid, made a V-shaped thoracotomy, opened the thorax, and exposed the heart. The heart was arrested in diastole with 1% KCl in 0.01M PBS, quickly removed, rinsed with cold PBS, and blotted dried.
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agarose gel electrophoresis. For each sample, 1µg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (Invitrogen) before being used for directional RNA-seq library preparation. Purified mRNAs were fragmented at 95℃ in fragmentation buffer followed by end repair and 5' adaptor ligation. Then reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80℃ before sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illunima HiSeq X Ten system for 150 nt paired-end sequencing

tag: Sex

value: male

value: left ventricle

value: 12 week

tag: surgical treatment

value: TAC

tag: drug treatment

value: dantrolene


title: hiPSC differentiated for 48h

description:
10x Genomics
Sample48H

tag: cell type


title: TEFF2

value: 1x stimulation with NY-ESO-1-peptide-loaded HLA-A2+ T2 tumor cells (1:3) and IL-2 (50 U/mL)


title: TAC-dantrolene biological replicate 2

description:
The 2nd mouse has been operated on  transverse aortic constriction surgery at the age of 8 weeks, administered oral dantrolene (30mg/kg/ day) for four weeks, and was sampled at the age of 12 weeks.
Y_Med_2

tag: tissue


title: TEFF3

tag: treatment


title: TEFF1b


title: RNA-Seq MDA-MB-231_mtLysLNA_3

data_processing:
Fastq file quality was assessed using FastQC, and reads were aligned to the hg38 human genome with STAR v.2.6.0a using default parameters. Read counts were obtained from mapped bam files using featureCounts .v.1.5.3, and DESeq2 was used to identify differentially expressed genes (DEGs).
Assembly: hg38
Supplementary files format and content: tab-delimited text files contain normalized read counts as generated by DESeq2

extract_protocol:
Total RNA was extracted using the Norgen Total RNA purification kit
RNA sequencing libraries were prepared using the TruSeq RNA Library Kit v2.

tag: cell line


title: TEFF1a


title: T98G GBM cell line

type: genomic

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

description: status quo genomic copy number characterisation

hyb_protocol: Hybridisation and washing of slides was carried out according to Agilent's protocol for array CGH.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Foreground and background intensities were imported into R followed by normalisation and correction for spatial artefacts using the MANOR Bioconductor package. Normalised log2-ratios were corrected for GC waving patterns using the CGHwave package (Mark van de Wiel) prior circular binary segmentation and copy number calling using functions of the Bioconductor CGHcall package.

source_name: Human glioblastoma cell line

label_protocol: 125 ng of DNA were labelled with Cy3 and Cy5, respectively using the CYTAG kit (Enzo).

growth_protocol: The human GBM cell lines A172, LN18, LN229, T98G, U87-MG, U138-MG and U251-MG were analyzed in this study. A172, LN18, LN229, U87-MG and T98G were obtained from the American type culture collection (ATCC, Manassas, Virginia, USA), U138-MG and U251-MG from the cell line repository CLS (Eppelheim, Germany). The cells were cultivated at 37°C and 7,5% CO2 in DMEM Glutamax (ThermoFisher, Waltham, MA, USA) supplemented with 10% FCS and 1% penicillin/streptomycin and kept at low passage numbers (<10).

extract_protocol: Genomic DNA was extracted from cell line pellets using the Qiagen Allprep kit.

source_name: Promega female genomic DNA

tag: sample type

value: Reference DNA


title: A172 GBM cell line


title: LN229 GBM cell line

source_name: Promega male genomic DNA


title: U138-MG GBM cell line


title: TEM3

value: 2x stimulated with anti-CD3/CD28 beads (1:1) and IL-2 (30 U/mL)

tag: day


title: RNA-Seq MDA-MB-231_mtLysLNA_2


title: U87-MG GBM cell line


title: TAC-dantrolene biological replicate 1

description:
The 1st mouse has been operated on  transverse aortic constriction surgery at the age of 8 weeks, administered oral dantrolene (30mg/kg/ day) for four weeks, and was sampled at the age of 12 weeks.
Y_Med_1

tag: strain


title: U251-MG GBM cell line


title: LN18 GBM cell line


title: TEM2


title: TEM1


title: RNA-Seq MDA-MB-231_mtLysLNA_1


title: TEX2


title: TAC-control biological replicate 3

description:
The 3rd mouse has been operated on  transverse aortic constriction surgery at the age of 8 weeks, and was sampled at the age of 12 weeks.
Y_NC_3

tag: age


title: TCM3

value: 1x stimulated with anti-CD3/CD28 beads (1:1) and IL-2 (30 U/mL)


title: TAC-control biological replicate 2

description:
The 2nd mouse has been operated on  transverse aortic constriction surgery at the age of 8 weeks, and was sampled at the age of 12 weeks.
Y_NC_2

value: control


title: RNA-Seq MDA-MB-231_mtAsn-2-LNA_3


title: TCM2


title: TCM1


title: RNA-Seq MDA-MB-231_mtAsn-2-LNA_2


title: TSCM2


title: TAC-control biological replicate 1

description:
The 1st mouse has been operated on  transverse aortic constriction surgery at the age of 8 weeks, and was sampled at the age of 12 weeks.
Y_NC_1


title: Sham-dantrolene biological replicate 3

description:
The 3rd mouse has been operated on sham surgery at the age of 8 weeks, administered oral dantrolene (30mg/kg/ day) for four weeks, and was sampled at the age of 12 weeks.
N_Med_3

value: sham


title: TSCM1


title: TN3

value: unstimulated


title: Sham-dantrolene biological replicate 2

description:
The 2nd mouse has been operated on sham surgery at the age of 8 weeks, administered oral dantrolene (30mg/kg/ day) for four weeks, and was sampled at the age of 12 weeks.
N_Med_2


title: RNA-Seq MDA-MB-231_mtAsn-2-LNA_1


title: TN2


title: RNA-Seq MDA-MB-231_mtAsn-1-LNA_3


title: TN1


title: DSCs_high

city: Guangzhou

first: Kaitao

last: Li

state: Guangdong Province

address: 1838 North Guangzhou AV

institute: Nanfang Hospital of Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Hair follicle dermal sheath cells

growth_protocol: DPCs and DSCs were routinely generated by re-plating  (typically 5 × 10^5 cells into a T25 flask) in DMEM medium (Gibico, Grand Island, USA)

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols

value: Hair follicle dermal sheath cells

tag: genotype

value: WT

value: 9th passage

tag: passage


title: RNA-Seq MDA-MB-231_mtAsn-1-LNA_2


title: Sham-control biological replicate 3

first: Yi

last: Gao

address: 126th Xiantai Street, Changchun, Jilin, China.

institute: China-Japan Union Hospital of Jilin University

description:
The 3rd mouse has been operated on sham surgery at the age of 8 weeks, and was sampled at the age of 12 weeks.
N_NC_3


title: DSCs_low

value: 3rd passage


title: RNA-Seq MDA-MB-231_mtAsn-1-LNA_1


title: Sham-control biological replicate 2

description:
The 2nd mouse has been operated on sham surgery at the age of 8 weeks, and was sampled at the age of 12 weeks.
N_NC_2


title: RNA-Seq MDA-MB-231_ControlLNA_3


title: Sham-dantrolene biological replicate 1

description:
The 1st mouse has been operated on sham surgery at the age of 8 weeks, administered oral dantrolene (30mg/kg/ day) for four weeks, and was sampled at the age of 12 weeks.
N_Med_1


title: OtC0397_GF_Morphine_5

city: Winston-Salem

first: Jonathon

middle: P

last: Sens

state: NC

address: 115 S Chestnut St

department: Physiology/Pharmacology

institute: Wake Forest Baptist Health

data_processing:
Raw FASTQ files were quality checked using  FASTQC (Babraham Institute, Cambridge, UK).
The raw FASTQ file for each sample was aligned to the Mus musculus 10 reference genome (NCBI) with the STAR package v2.4.0 (Dobin et al., 2013).
For pairwise comparisons aligned non-normalized read counts were analyzed for differential gene expression using the Biojupies analysis package with default settings (Torre et al., 2018). Statistical significance was set at a threshold of FDR-corrected p value of less than 0.05. Lists of significantly differentially expressed genes were analyzed for gene ontology pathways using G:Profiler (Raudvere et al., 2019)
Assembly: Mus musculus 10 reference genome
Supplementary files format and content: comma seperated-values (.csv)
Supplementary files format and content: Normalized read counts of genes. Normalization was performed using Trimmed Mean of the M-values (TMM; edgeR R package)

molecule: polyA RNA

source_name: Nucleus accumbens (brain)

extract_protocol:
RNA was extracted using TRIzol reagent (Thermo Fisher #15596026) according to manufacturer’s instructions.
cDNA was generated using the SMARTer cDNA kit (Clonetech Laboratories # 634925) from total RNA. cDNA was fragmented using Bioruptor (Diagenode) and illumina-ready, indexed sequencing libraries were made using SPRIworks HT Reagent Kit (Beckamn Coulter, Inc. # B06938).

treatment_protocol: Conventionally raised mice were the ones described in the published manuscript by Hofford et al. in 2021, thus all methods for conventional mice are identical to that manuscript (Hofford et al., 2021). The conventionally raised C57BL/6J mice (7-9 weeks old, Jackson Laboratories) were group-housed in a humidity, temperature-controlled, and specific pathogen-free colony facility on a 24 hour light/dark cycle (lights on at 7AM and lights off at 7PM). All studies were performed in accordance with the National Institutes of Health Guide for the Care and Use of Laboratory Animals under an approved protocol from the Mt. Sinai Icahn School of Medicine Institutional Animal Care and Use Committee. Germ-free (GF) C57BL/6J mice were bred in-house at the Mount Sinai Microbiome Translational Center and were maintained in flexible vinyl isolators throughout the experiment. Germ-free status was confirmed throughout the procedure via culturing and PCR per facility protocols. Germ-free mice were age-matched to the conventionally raised mice. Both conventionally raised mice and GF mice were provided food and water, ad libitum. All mice received the same standardized mouse chow and water from the same source, but food and water for germ-free mice were sterilized prior to administration. Cages (4-5 mice/cage) were randomly assigned to H2O or Abx. The Abx drink solution was comprised of vancomycin (0.5 mg/mL; Chem-Impex International #00315), bacitracin (0.5 mg/mL; Research Products International #B3200025), pimaricin (1.2 µg/mL; Infodine Chemical #7681-93-8), and neomycin (2 mg/mL; Fisher Scientific #BP266925). Mice were administered their respective drink solution (ABX or H2O) for two weeks prior to beginning experimental procedures and remained on their respective solution for the duration of the experiment. Morphine sulfate was kindly provided by the NIDA drug supply program from the National Institute on Drug Abuse. Morphine sulfate was diluted in saline and injected at a dose of 20 mg/kg. For GF mice, the morphine solution was 0.2 um filtered to sterilize prior to administration.

value: Nucleus accumbens (brain)

value: Bulk

value: No Microbiome

value: Morphine (20mg/kg/day/7 days)


title: DPCs_low

source_name: Hair follicle dermal papilla cells

value: Hair follicle dermal papilla cells


title: TSCM3

value: CD8+ T cells


title: OtC0398_GF_Morphine_6


title: RNA-Seq MDA-MB-231_ControlLNA_2


title: DPCs_high


title: OtC0392_GF_Saline_6

value: Saline


title: OtC0393_GF_Morphine_1


title: VMRC-LCD cells, siASCL1_#1

city: Durham

first: Naoya

last: Miyashita

state: NORTH CAROLINA

address: 307 Research Drive Nanaline Duke Building Room 353

institute: Duke university

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 18 hr at 48℃ on GeneChip™ Hybridization Oven 645.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip Scanner 3000 7G.

data_processing: The data were digitized with Affymetrix® Expression Console™ Software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: VMRC-LCD

label_protocol: Biotin-labeled samples were prepared using the FlashTag™ Biotin HSR RNA Labeling Kit.

growth_protocol: VMRC-LCD cells were cultured in EMEM with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: Total RNA was extracted from VMRC-LCD cells 48 h after siRNA transfection using the RNeasy Mini Kit (Qiagen).

treatment_protocol: VMRC-LCD cells were transfected with 20 nM siRNA using Lipofectamine RNAiMAX.

value: VMRC-LCD

value: ASCL1-positive lung adenocarcinoma

value: transfected with ASCL1 siRNAs


title: OtC0391_GF_Saline_5


title: RNA-Seq MDA-MB-231_ControlLNA_1


title: VMRC-LCD cells, siASCL1_#2


title: MDA-MB-231_HDAC2C&R_mtAsnLNA_3

tag: applicable cut&run_antibody


title: Sham-control biological replicate 1

city: Changchun

description:
The 1st mouse has been operated on sham surgery at the age of 8 weeks, and was sampled at the age of 12 weeks.
N_NC_1

source_name: left ventricle

value: male

value: left ventricle

value: 12 week

value: control


title: VMRC-LCD cells, siControl

value: transfected with control siRNAs


title: MDA-MB-231_HDAC2C&R_mtAsnLNA_2


title: OtC0388_GF_Saline_2


title: OtC0390_GF_Saline_4


title: OtC0389_GF_Saline_3


title: OtC0387_GF_Saline_1


title: OtC0395_GF_Morphine_3


title: OtC0385_Abx_Morphine_5

value: Depleted Microbiome


title: MDA-MB-231_HDAC2C&R_ControlLNA_2


title: iDKO2, scRNAseq

city: Omaha

first: Hamid

last: Band

state: Nebraska

address: 42nd and Emile

department: Eppley

institute: University of Nebraska Medical Center

description: 10x Genomics

data_processing:
Demultiplexing, alignment to the transcriptome and UMI were performed through 10X genomics recommended cell ranger standard pipeline (Cell Ranger toolkit, version 3.0.1)
Assembly: mm10
Supplementary files format and content: Tab seperated values files and matrix files

source_name: Intestinal crypt

extract_protocol:
Organoids were dissociated into single cells. The single cells were checked for viability and processed through the GemCode Single Cell Platform. An input of 7,000 cells was added to each channel of a chip with a recovery rate of 1,200 cells on average.
The cells were then partitioned into Gel Beads in Emulsion (GEMs) in the GemCode instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, shearing and 5′ adaptor and sample index attachment.

value: Intestinal crypt

value: Cbl and Cblb KO


title: MDA-MB-231_HDAC2C&R_mtAsnLNA_1


title: OtC0384_Abx_Morphine_4

value: Nucleus accumbens (brain)

value: Bulk


title: OtC0394_GF_Morphine_2

value: No Microbiome

value: Morphine (20mg/kg/day/7 days)


title: OtC0382_Abx_Morphine_2


title: iDKO1, scRNAseq

description: 10x Genomics


title: OtC0383_Abx_Morphine_3


title: Control 1, scRNAseq

description: 10x Genomics


title: Control 2, scRNAseq

description: 10x Genomics


title: MDA-MB-231_HDAC2C&R_ControlLNA_1


title: OtC0381_Abx_Morphine_1


title: OtC0378_H2O_Morphine_4

value: Normal Microbiome


title: OtC0379_H2O_Morphine_5


title: KO, 8 hpi, Rep3

city: Seattle

first: Daphne

last: Avgousti

address: 1100 Fairview Avenue North C1-201

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis software v3.4.4, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v2.20.
Sequencing reads were mapped using 2-pass mapping in STAR v2.7.1 to a combined reference of human genome assembly hg38 and HSV1 genome JN555585.1 in conjunction with GENCODE human gene annotation V31 and GCA_000859985.2_ViralProj15217. HSV1 annotated genes were collapsed into non-overlapping transcription units for alignment and expression quantification.
QC was performed using FastQC v0.11.8 and RSeQC v4.0.0 to examine read quality, insert fragment size, read duplication rates, gene body coverage and read distribution in different genomic regions.
Gene-level expression was quantified by counting unstranded paired-end reads using FeatureCounts in Subread v1.6.5.
Differential gene expression were analyzed between genotype groups using Bioconductor package edgeR v3.26.8. Protein-coding and lncRNA genes with low expression were excluded by requiring at least one count per million in at least N samples (N is equal to the number of samples in the smallest group). The filtered expression matrix was normalized by TMM method and subject to significance testing using quasi-likelihood pipeline. Genes were deemed differentially expressed if BH-corrected p-values are less than 0.05.
Assembly: hg38, HSV1 genome JN555585.1
Supplementary files format and content: Both files are in text format containing raw read counts of annotated human or HSV1 genes across samples.

source_name: Skin

extract_protocol:
Three biological replicates per time point were obtained by independent infections. Cells were harvested at the indicated times post-infection by trypsinization, washed with PBS and centrifuged at 5000 xg for 2 minutes. The resulting pellets were lysed with TRIzol (Thermo Fisher 15-596-026) and total RNA was harvested according to manufacturer’s instructions. RNAs were then treated with DNase (Qiagen 79254) on RNeasy columns (Qiagen 74104) per manufacturer’s instructions. To improve RNA quality, RNAs were precipitated with 3 volumes ice-cold 96% ethanol (Fisher BP8202500), 1 volume 3 M sodium acetate pH 5.5 (Fisher BP333-500) and 1 µL glycogen (Thermo Fischer R055) overnight at -80 °C. Precipitated RNAs were pelleted at 15,000 xg and 4 °C for 30 min, washed with ice-cold 75% ethanol and spun as above for 10 min. Ethanol was removed and RNAs were resuspended in nuclease-free water in Lo-Bind microcentrifuge tubes (Eppendorf 022-43-102-1).
RNA concentrations were quantified by Nanodrop and their integrity confirmed using the 4200 Tapestation Bioanalyzer system (Agilent). 500 ng of total RNA with an RNA Integrity Number (RIN) greater than 9.5 were used to prepare sequencing libraries with the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina). Library concentrations were measured with Invitrogen Qubit dsDNA HS Assay Kit then analyzed with Agilent High Sensitivity D5000 ScreenTape System and pooled. Libraries were sequenced with 100-bp paired-end reads on an Illumina NovaSeq 6000 SP sequencer at the Fred Hutch Genomics Core Facility.

value: Skin

value: mH2A1 KO HFF-T

value: macroH2A1 knockout tert-immortalized human foreskin fibroblast

value: mH2A1 KO

tag: infection

tag: time

value: 8 hours post-infection


title: OtC0377_H2O_Morphine_3


title: OtC0376_H2O_Morphine_2


title: KO, 4 hpi, Rep3

value: 4 hours post-infection


title: OtC0374_Abx_Saline_6

value: Saline


title: Eightweek-old male C57Bl/6J mouse [H8]

city: nanjing

first: Kaiqiang

last: Ye

state: jiangsu

address: NO.2 SiPaiLou, Xuanwu district, Nanjing, Jiangsu Province, China

institute: Southeast University

data_processing:
Clean data were processed by FastQC software (v0.11.4) for quality control (QC) and mapped to the mouse reference genome mm10 using Hisat2 software with default parameters
Reads uniquely mapped to reference were conducted by HTSeq, while counts ˃ 0 or ＞1 were used to calculate the number of genes detected.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Eightweek-old male C57Bl/6J mouse

extract_protocol:
We use LIFT-based isolation method to collect small tissues from section.
Based on Smart-seq2 protocols and standard illumina protocols

value: brain

value: male

value: 8 weeks

tag: group

value: isolated from the hippocampus region of mouse brain


title: Eightweek-old male C57Bl/6J mouse [H7]

tag: Sex


title: KO, Mock, Rep3

value: mock

value: Mock (no infection)


title: WT, 12 hpi, Rep3

value: HFF-T

value: Tert-immortalized human foreskin fibroblast

value: wild-type

value: 12 hours post-infection


title: Eightweek-old male C57Bl/6J mouse [H6]


title: OtC0371_Abx_Saline_3

value: Nucleus accumbens (brain)

value: Bulk

value: Depleted Microbiome


title: OtC0372_Abx_Saline_4


title: Eightweek-old male C57Bl/6J mouse [H5]


title: WT, 8 hpi, Rep3

value: Skin


title: OtC0373_Abx_Saline_5


title: OtC0370_Abx_Saline_2


title: Eightweek-old male C57Bl/6J mouse [H4]


title: OtC0368_H2O_Saline_9

value: Normal Microbiome


title: WT, 4 hpi, Rep3

value: 4 hours post-infection


title: OtC0369_Abx_Saline_1

value: Saline


title: Eightweek-old male C57Bl/6J mouse [H3]

value: brain


title: OtC0380_H2O_Morphine_6

value: Morphine (20mg/kg/day/7 days)


title: KO, 12 hpi, Rep3

value: mH2A1 KO HFF-T

value: macroH2A1 knockout tert-immortalized human foreskin fibroblast

value: mH2A1 KO


title: OtC0367_H2O_Saline_8


title: Eightweek-old male C57Bl/6J mouse [H9]

value: male

value: 8 weeks

value: isolated from the hippocampus region of mouse brain


title: OtC0366_H2O_Saline_6


title: Otc0363_H2O_Saline_3


title: OtC0365_H2O_Saline_5


title: WT, Mock, Rep3

value: HFF-T

value: Tert-immortalized human foreskin fibroblast

value: wild-type

value: mock

value: Mock (no infection)


title: Microglia depletion #4

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

data_processing:
Bulk RNAseq analysis: On average we received 30 million paired ends for each of the replicates. RNAseq libraries were checked for their quality using the fastqc program http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. The results from fastqc were aggregated using multiqc software1. Reads were mapped with the “splice aware” aligner ‘STAR’,2 to the transcriptome and genome of mm10 genome build. The HTseq3 software will be used to count aligned reads that map onto each gene. The count table was imported to R to perform differential gene expression analysis using the DESeq2 package4. Low expressed genes (genes expressed only in a few replicates and had low counts) was excluded from the analysis before identifying differentially expressed genes. Data normalization, dispersion estimates, and model fitting (negative binomial) was carried out with the DESeq function. The log-transformed, normalized gene expression of 500 most variable genes will be used to perform an unsupervised principal component analysis. The differentially expressed genes was ranked based on the log2fold change and FDR corrected p-values. The ranked file was used to perform pathway analysis using GSEA software5.  The enriched pathways were selected based on enrichment scores as well as normalized enrichment scores. The Enrichment Analysis for Gene Ontology was performed by topGO. The heatmaps were generated using pheatmap function in R.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Whole forebrain

growth_protocol: C57BL/6J male mice were purchased from Jax lab. Male mice at 10 to 20 weeks of age were used for experiments unless stated otherwise. All experiments were approved by the Institutional Animal Care and Use Committee of the University of Virginia.

extract_protocol:
Whole forebrain were extracted for bulk RNA sequencing.
Library was constructed at UVA Genome Analysis and Technology Core.

treatment_protocol: Eight mice were used for RNA-Seq experiments. Four mice were treated with PLX food and four mice were treated with control food. Treatment duration is 9 days.

value: Whole forebrain


title: KO, 12 hpi, Rep2

value: Skin

value: 12 hours post-infection


title: Eightweek-old male C57Bl/6J mouse [H2]


title: Eightweek-old male C57Bl/6J mouse [H1]


title: Microglia depletion #3


title: Microglia depletion mouse #2


title: KO, 8 hpi, Rep2

value: 8 hours post-infection


title: Microglia depletion mouse #1


title: Eightweek-old male C57Bl/6J mouse [C9]

value: brain

value: isolated from the cortex region of mouse brain


title: KO, 4 hpi, Rep2

value: mH2A1 KO HFF-T

value: 4 hours post-infection


title: Control mouse #3


title: Control mouse #4


title: KO, Mock, Rep2

value: macroH2A1 knockout tert-immortalized human foreskin fibroblast

value: mH2A1 KO


title: Control mouse #2


title: Eightweek-old male C57Bl/6J mouse [C8]

value: male

value: 8 weeks


title: Eightweek-old male C57Bl/6J mouse [C7]


title: Control mouse #1


title: skin, 1d depilation

first: Yang

last: Sun

address: Nanfang Hospital

institute: Nanfang Hospital, Southern Medical University

description: Dorsal skin 1d after depilation

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.Matrix table with raw gene counts for every gene and every sample.

source_name: skin

value: skin

value: NOD/SCID

value: Depilation


title: Eightweek-old male C57Bl/6J mouse [C5]


title: WT, 12 hpi, Rep2

value: HFF-T

value: Tert-immortalized human foreskin fibroblast

value: wild-type


title: skin, 6d depilation

description: Dorsal skin 6d after depilation


title: skin, 2d depilation

description: Dorsal skin 2d after depilation


title: OtC0364_H2O_Saline_4

value: Nucleus accumbens (brain)

value: Bulk

value: Normal Microbiome

value: Saline


title: skin, 4d depilation

description: Dorsal skin 4d after depilation


title: WT, 8 hpi, Rep2

value: Skin

value: 8 hours post-infection


title: WT, 4 hpi, Rep2

value: 4 hours post-infection


title: Eightweek-old male C57Bl/6J mouse [C4]

value: brain

value: isolated from the cortex region of mouse brain


title: skin, 4h depilation

description: Dorsal skin 4h after depilation


title: skin, 12h depilation

description: Dorsal skin 12h after depilation


title: Eightweek-old male C57Bl/6J mouse [C3]

value: male


title: WT8

city: Tampa

first: Feng

last: Cheng

state: FL

address: 12901 Bruce B Downs Blvd MDC 30

department: Department of Pharmaceutical Science

institute: University of South Florida

description: WT8 mouse Gastrocnemius muscle was excised from the euthanized mice and immediately processed in RNA later and later stored at -80 degree Celsius without RNA later for further processing

data_processing:
RNA-seq data was analyzed by using two open source software programs: TopHat and Cufflinks
Raw reads was mapped to mice GRCm38 genome by using Tophat
Cufflinks quantified genes across WT and KO groups to find differentially expressed genes (q-value <0.05)
Assembly: GRCm38
Supplementary files format and content: FPKMs_allsamples.csv
Supplementary files format and content: Ensembl_gene_id, Gene_Symbol, and FPKM

source_name: Gastrocnemius

extract_protocol:
Total RNA was extracted using RNeasy Mini Plus kit (Qiagen). 1.0-1.5µl of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared by TruSeq Stranded mRNA library prep Kit (Cat#20020595)

value: Gastrocnemius

value: muscle

value: tissue

value: WT

value: No treatment


title: WT7

description: WT7 mouse Gastrocnemius muscle was excised from the euthanized mice and immediately processed in RNA later and later stored at -80 degree Celsius without RNA later for further processing


title: KO, 12 hpi, Rep1

state: WA

value: mH2A1 KO HFF-T

value: macroH2A1 knockout tert-immortalized human foreskin fibroblast

value: mH2A1 KO

value: 12 hours post-infection


title: WT, Mock, Rep2

value: HFF-T

value: Tert-immortalized human foreskin fibroblast

value: wild-type

value: mock

value: Mock (no infection)


title: WT1

description: WT1 mouse Gastrocnemius muscle was excised from the euthanized mice and immediately processed in RNA later and later stored at -80 degree Celsius without RNA later for further processing


title: Eightweek-old male C57Bl/6J mouse [C2]

value: brain

value: 8 weeks


title: KO, 8 hpi, Rep1

value: Skin

value: 8 hours post-infection


title: Eightweek-old male C57Bl/6J mouse [C1]

value: male

value: isolated from the cortex region of mouse brain


title: Eightweek-old male C57Bl/6J mouse [C6]


title: KO7

description: KO7 mouse Gastrocnemius muscle was excised from the euthanized mice and immediately processed in RNA later and later stored at -80 degree Celsius without RNA later for further processing

value: Gastrocnemius

value: muscle

value: tissue

value: KO


title: KO, 4 hpi, Rep1

value: mH2A1 KO HFF-T

value: macroH2A1 knockout tert-immortalized human foreskin fibroblast

value: mH2A1 KO

value: 4 hours post-infection


title: KO, Mock, Rep1


title: skin, 0h depilation

description: Dorsal skin 0h after depilation

value: skin

value: NOD/SCID

value: Depilation


title: Eightweek-old male C57Bl/6J mouse [1.4A-4]

value: brain

value: isolated by a laser device with a current intensity of 1.4A


title: Exon2KO （biol rep 3）

city: Beijing

first: Gu

last: Qianchong

address: No. 3, yard 1, Beichen West Road

institute: Institute of Microbiology, Chinese Academy of Sicences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl script
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1)
Assembly: mm10
Supplementary files format and content: tab-delimited Excel files include RPKM values for each Sample

source_name: Tregs

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparation.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

value: Tregs


title: KO1

description: KO1 mouse Gastrocnemius muscle was excised from the euthanized mice and immediately processed in RNA later and later stored at -80 degree Celsius without RNA later for further processing

value: No treatment


title: Eightweek-old male C57Bl/6J mouse [1.4A-2]

value: male

value: 8 weeks


title: WT, 12 hpi, Rep1

value: Skin

value: HFF-T

value: Tert-immortalized human foreskin fibroblast

value: wild-type

value: 12 hours post-infection


title: WT, 8 hpi, Rep1

value: 8 hours post-infection


title: Exon2KO （biol rep 2）


title: Eightweek-old male C57Bl/6J mouse [1.4A-3]


title: WT（biol rep 3）

value: WT


title: WT, 4 hpi, Rep1

value: 4 hours post-infection