title: WD, Hi-C, regeneration, rep2

first: Carlos

last: Camilleri-Robles

address: Av. Diagonal

institute: UB

description: Library name: Sample 4

data_processing:
Hi-C data production, from raw FASTQ files through to interaction matrices, was conducted using the TADbit pipeline. The workflow began with quality control checks on the raw FASTQ data. Sequencing reads were then mapped using the GEM mapper to the Drosophila melanogaster reference genome (dm6). Mapping was done using an iterative alignment strategy. Following mapping, reads were subjected to a series of filters to eliminate artifacts, such as non-specific ligations, sequencing errors, and other experimental anomalies. Specifically, TADbit’s default filtering applied nine distinct criteria: self-circles, dangling ends, errors, extra dangling ends, over-represented fragments, overly short or long fragments, duplicates, and random breaks. Next, the data were normalized using the ICE (Iterative Correction and Eigenvector decomposition) balancing method. The resulting valid read pairs were binned at multiple resolutions (2kb, 4kb, 5kb, 8kb, 10kb, 20kb, 25kb, 50kb, 100kb, 500kb, 1Mb), with normalization biases and decay corrections incorporated to construct interaction matrices. Replicate datasets were compared and merged using TADbit’s merging function, which incorporates the HiCRep similarity score.
Assembly: dm6
Supplementary files format and content: Multiple resolution (2kb, 4kb, 5kb, 8kb, 10kb, 20kb, 25kb, 50kb, 100kb, 500kb, 1Mb) mcool files, replicates per each condition were pooled.

organism: Drosophila melanogaster

source_name: Wing imaginal discs

extract_protocol:
200 wing discs for each replicate were quickly dissected (<1 hour) from wandering larvae at room temperature (RT) in Schneider’s insect medium before being directly processed. Wing discs were washed twice in PBS and resuspended in A1 Buffer (60 mM KCl, 15 mM NaCl, 4 mM MgCl2, 15 mM HEPES, 0.5% Triton-X-100, 0.5 mM DTT, 1x Protease Inhibitor Cocktail (Sigma-Aldrich), H2O). Then, formaldehyde was added to reach a 1.8% final concentration and transferred on a rotating wheel for 10 minutes at RT. Formaldehyde was quenched with 1.25 M glycine and samples were washed twice with ice-cold A1 Buffer. Supernatant was discarded and fixed wing discs were air dried and then snapped frozen in liquid nitrogen to process all samples in parallel. For all samples, wing discs were thawed on ice and resuspended in ice-cold A1 Buffer. The samples were homogenized on ice using a tight Tenbroeck, centrifuged and resuspended in 0.5% SDS for 10 min at 62°C to permeabilize nuclei. SDS was quenched by adding Triton-X-100 and incubated for 15 min at 37°C with rotation. Next, samples were resuspended in lysis buffer for a 30 min incubation on ice and nuclei were subjected to Mbo I treatment O/N at 37°C in NEB2.1 buffer. The next day, restriction sites were end-repaired and biotinylated using Klenow [New England BioLabs (NEB), catalog no. M0210] and biotin-14-dATP (Life Technologies, catalog no. 19524-016) before being re-ligated using T4 DNA ligase (NEB, catalog no. M0202) O/N at 16 ºC. Next day, samples were treated with RNAse A for 15 min at 37ºC and then incubated with proteinase K and reverse crosslinked for 6 h at 65°C. Subsequently, DNA was purified using AMPure XP beads (Beckman CoulterTM, catalog no. A63880) and then sheared to obtain fragments of an average size of 300–400 bp using the Bioruptor Pico (Diagenode; 1µg of DNA in 100µl; 6 cycles; 20’’ ON, 60’’ OFF).
For library preparation, biotinylated DNA was pulled down by adding an equal volume of Dynabeads MyOne Streptavidin T1 beads (Life Technologies, catalog no. 65602). Biotin was removed from unligated ends, and pulled-down DNA fragments were end-repaired and A-tailed with NEBNext A-tailing module (E6053L). Illumina adaptors were ligated, and libraries were amplified by eight cycles of PCR using NEBNext High-Fidelity 2X PCR Master Mix (catalog no. M0541S). DNA was size selected using AMPure XP beads (Beckman CoulterTM, catalog no. A63880) at a ratio of beads to library of 0.9:1 to isolate 300- to 800-bp fragments. Lastly, the quality of the libraries was visualized with the Agilent Bioanalyzer High Sensitivity DNA Assay (Agilent Technologies, Savage, DE) and checked by low sequencing depth on a NextSeq 500 prior to higher sequencing depth on NovaSeq6000 platform at the Centre for Genomic Regulation (CRG) sequencing facility in Barcelona, Spain. A minimum of 500 million paired-end 150-bp-long reads were obtained per sample.

treatment_protocol: Cell death was induced by activating the expression of the gene rpr for 16 hours using the Gal4/UAS system.

value: Wing imaginal discs

value: Epithelial cells

value: Cell death induction

tag: batch


title: MDCK cells IAV infection 24h-1

status: Public on Dec 28 2025

type: SRA

city: Tianjin

first: Shu-Lin

last: Liu

address: No.94 of Weijin Road

country: China

institute: Nankai University

description: Library name: 24h-1

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Assembly: canFam4
Supplementary files format and content: CSV(.list) files include FPKM value for each sample

molecule: polyA RNA

organism: Canis lupus familiaris

source_name: MDCK cells

extract_protocol:
RNA was purified using the Takara RNA Extraction Kit. 1 μg of total RNA was used for library construction.
The extracted and purified mRNA is subjected to quality control. Samples that pass the quality control are then used for library construction with a kit.

tag: tissue

value: MDCK cells

tag: cell line

tag: cell type

value: Epithelial cell


title: Setdb1 2c matKO single embryo replicate 16

city: Grand Rapids

first: Piroska

last: Szabó

state: MI

address: 333 Bostwick Ave NE

department: Department of Epigenetics

country: USA

institute: Van Andel Insitute

data_processing:
Base calling was done by Illumina RTA3, and the output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0. We obtained an average of 25 M reads/library.
Adaptor sequences and low-quality reads of RNA-seq reads were trimmed using Trim Galore. Trimmed reads were aligned to mm10 reference genome using STAR with parameter “--quantMode GeneCounts”.
Bigwig tracks of alignment was generated using bamCoverage from deepTools with normalization method “CPM” (counts per million); reverse and forward strand aligment were separated
Assembly: mm10
Supplementary files format and content: bigwig files of each samples, with alignment to top and bottom strands of genome separated.

molecule: total RNA

organism: Mus musculus

source_name: C57Bl/6N X JF1Ms F1

growth_protocol: The Setdb1 conditional knockout mouse line (Setdb1f/f) was derived from the line Setdb1tm1a(EUCOMM)Wtsi (European Mouse Mutant Archive). We removed the Pgk-neo positive selection cassette by crossing with an Flpe recombinase expressing transgenic mouse B6.Cg-Tg(Pgk1-flpo)10Sykr/J from the Jackson Laboratory (JAX#011065). Zp3-cre transgenic mice C57BL/6-Tg(Zp3-cre)93Knw/J, from the Jackson Laboratory (JAX#003651), were used to excise the SET-domain–encoding exons from Setdb1 in growing oocytes. Setdb1f/f; Zp3-CreTg+ female mice were used as the experimental group. Setdb1f/f female mice without the Zp3-Cre transgene were used as the control group. Setdb1f/f and Zp3-Cre mice were maintained on a C57BL/6N and C57BL/6J genetic background, respectively.

extract_protocol:
Total RNA was isolated from single 2c and 8c embryos using RNA-Bee extraction followed by ethanol precipitation according to the manufacturer's instructions. Briefly, the tubes containing single embryos in 100 µL RNA-Bee were thawed and vortexed and 20 µL of chloroform was added. After vortexing rigorously for 15-30 seconds, the tubes were placed on ice for 5 min and then centrifuged at 12,000 g for 15 min at 4°C. The aqueous phase was transferred into a new 1.5 mL tube containing 3 µL of 0.25% linear polyacrylamide which was used as a carrier. 50 µL of isopropanol was added and vortexed for 15 sec, and the samples were kept on ice for 30 minutes to precipitate the RNA. After centrifugation at 10,000g for 15 min at 4°C the pellet of RNA was washed with 0.4 mL of cold 75% ethanol. After re-spinning and brief air drying, the total RNA was dissolved in 22.3 µL of 10 mM Tris-HCl buffer pH 8.5 containing 0.2 U/µL RNasin® ribonuclease inhibitor (Promega, Cat. N2515). Potential genomic DNA contamination was removed from the total RNA using 0.2 µL of rDNase I from the DNA-free Kit (Ambion, Cat. AM1906). After the DNase Inactivation Reagent (0.1 volume) was added and centrifuged, the RNA was transferred into a new tube containing 3 µL of 0.25% linear polyacrylamide and recovered by ethanol precipitation.  The single embryo total RNA samples were eluted in 7 µL of 10 mM Tris-HCl buffer pH 8.5 containing 0.2 U/µL RNasin® ribonuclease inhibitor.
Libraries were prepared by the Van Andel Genomics Core (RRID: SCR_022913) using the Takara SMART-Seq Stranded Kit (Cat. No. 634444, Takara Biosciences USA, Mountain View CA) with the following specifics. Samples were randomized before beginning processing to avoid batch effects. Fragmentation for embryo RNA and Takara control RNA was performed for 10 min or 6 min, respectively, at 85°C to obtain an average insert size of 250 bp. 10 cycles were used for PCR1, during which unique dual indexes were added to each sample, then 8 samples were pooled for subsequent steps. PCR2 used 12 cycles. Library pools were assessed for quality using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems).

treatment_protocol: To collect WT and Setdb1mat-/+ embryos at 2c stage, female mice at 6~8 weeks of age were superovulated by intraperitoneally injecting 5 IU of human chorionic gonadotropin (hCG) 46~48 hours after injecting 5 IU of pregnant mare serum gonadotropin (PMSG) and then mated with wild-type male mice. To collect WT and Setdb1mat-/+ embryos at 8c stage, we used CARD HyperOva (Cosmo Bio, Catalog No: KYD-010-EX) on 26~30 days old female mice.  2-cell and 8-cell embryos were harvested from the oviduct in M2 medium at 1.5 dpc and 2.5 dpc, respectively. The embryos were washed three times in PBS. Individual embryo was manually picked into 1.5 mL tubes, added 100 µL RNA-Bee (Tel-Test or Amsbio, Cat. CS-105B), snap frozen on dry ice and kept at -80 °C until RNA isolation.

tag: age days_post_coitum

tag: collection time

tag: embryo stage

value: 2 cell

tag: genotype

tag: strain

value: C57Bl/6N X JF1Ms F1


title: Setdb1 2c matKO single embryo replicate 14


title: WD, Hi-C, regeneration, rep1

city: Barcelona

country: Spain

description: Library name: Sample 3

library_source: genomic

molecule: genomic DNA

tag: treatment


title: RNA_s-microg_24h_laminin

city: Wako city

first: Taisei

last: Wakigawa

state: Saitama prefecture

address: 2-1, Hirosawa

country: Japan

institute: RIKEN

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: human, hg38; mouse, mm10; C. elegans, WBcel235
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

organism: Homo sapiens

extract_protocol:
Spaceflight samples, HEK293: Cells in a disposable cultivation chamber were thawed, washed with ice-cold PBS, lysed with 500 µl of lysis buffer and triturated ten times in a syringe with a 30-gauge needle. Spaceflight samples, C. elegans: Frozen nematode culture (1.5-4.5 ml) was thawed in 10 ml of wash buffer. The adult worms were filtrated through a 30-µm ÜberStrainer (pluriSelect Life Science) and washed three times with wash buffer. Then, the nematodes were pelleted by centrifugation at 1,600 × g for 1 min at 4°C, resuspended in 600 µl of lysis buffer, dripped into liquid nitrogen, and pulverized using the Multi-beads Shocker at 2800 rpm for 10 sec. Simulated microgravity samples: Cells in DCC were washed with PBS and lysed with 500 µl of lysis buffer. Mouse soleus muscles: Frozen soleus muscles were pulverized with 600 µl of frozen lysis buffer containing cOmplete, EDTA-free Protease Inhibitor Cocktail (Roche) and 1000 U/ml RNase inhibitor, Murine (New England Biolabs [NEB]), using the Multi-beads Shocker at 3000 rpm for 30 sec for 2 cycles.
For standard ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification. For Thor-Ribo-Seq, preadenylated linkers with the antisense sequence of T7 promoter were ligated and footprints were amplified by in vitro transcription. For RNA-Seq, the libraries were prepared by SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input (TaKaRa) or TruSeq Stranded mRNA Library Prep kit (Illumina).

value: simulated microgravity with laminin-coating

tag: time


title: Setdb1 2c matKO single embryo replicate 13


title: Sample 135, baseline (t0)

first: Anna

last: Ramos-Triguero

address: C/ del Rosselló, 149

institute: FRCB-IDIBAPS

description: Library name: Sample_135_t0

data_processing:
RNA was analyzed at Microomics Systems S.L. using an Illumina TruSeq Stranded mRNA, yielding 2x125bp sequences. Quality-control was evaluated using FastQC.
Pre-processing with Trimmomatic, alignment to GRCh38 with STAR, and alignment quality-control with FastQC and MultiQC.
Reads were counted with featureCounts.
Assembly: GRCh38
Supplementary files format and content: tab-delimeted csv file includes counts for each sample

source_name: Blood

extract_protocol:
Two 5 mL tubes of blood were collected in BD Vacutainer® K3E 15% Aprotinin 250KIU (SGSH;BD361017). Peripheral blood mononuclear cells were isolated by centrifugation in Blood Collection tube BD Vacutainer®, BD CPT™ (Avantor, BDAM362781). RNA was isolated using QIAshredder (Qiagen,79654) and RNAsy Mini-Kit (Qiagen, 74104) protocols.
RNA libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit following the manufacturer’s instructions. Poly-A mRNA was purified using poly-T oligo-attached magnetic beads, fragmented, and converted to cDNA with random primers. Libraries were size-selected and sequenced on an Illumina HiSeq 2500 platform to generate 2×125 bp paired-end reads.

treatment_protocol: Participants received 9 mg/kg/day of EGCG via FontUp, a cocoa-flavored nutritional powder dissolved in 200 mL of semi-skimmed milk. FontUp was purchased from Grand Fontaine Laboratories (Barcelona, Spain).

value: Blood

value: PBMCs

value: baseline


title: Setdb1 2c matKO single embryo replicate 15


title: WD, Hi-C, control, rep2

description: Library name: Sample 2

value: Control


title: Setdb1 2c matKO single embryo replicate 12


title: Setdb1 2c matKO single embryo replicate 9


title: Setdb1 2c matKO single embryo replicate 11


title: RNA_s-microg_1h_laminin

value: 1 h


title: MitoIP-Ribo_laminin_retapamulin_120s_2

description:
MitoIP-Thor-Ribo-Seq
L84

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: The human  nuclear genomes (hg38) and custom-made mitochondrial transcript sequences
Supplementary files format and content: Fpcount text files contain three columns:  1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts. Fpframing text files contain nine columns:  1. the length of mitoribosome footprint; 2. the fraction of mitoribosome footprint; 3~5. the number of mitoribosome footprint at each frames;  6~8,the fraction of mitoribosome footprint at each frames; 9. the relative entropy of mitoribosome footprint.
Library strategy: MItoIP-Thor-Ribo-Seq

extract_protocol:
MitoIP-Thor-Ribo-Seq: Cells were cultured in 15-cm dishes, washed with ice-cold PBS, and lysed with 1200 µl of hypotonic buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 1.5 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol). The lysate was incubated with anti-TOM22 antibody-conjugated beads from Mitochondria Isolation Kit, Human (Miltenyi Biotec) for 60 min at 4°C. The subsequent wash and elution steps were performed with wash buffer (10 mM HEPES-KOH pH 7.5, 10 mM KCl, 15 mM MgCl2, 1 mM DTT, 100 µg/ml cycloheximide, and 100 µg/ml chloramphenicol), according to the manufacturer’s instructions. The eluted mitochondrial fraction was pelleted by centrifugation at 7,000 × g for 10 min at 4°C and resuspended in modified lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 15 mM MgCl2, 1 mM DTT, 1% Triton X-100, 100 µg/ml cycloheximide, 100 µg/ml chloramphenicol, and 2.5 U/ml TURBO DNase). After clarification by centrifugation at 20,000 × g for 10 min at 4°C, the supernatant was used for library preparation. For the mitoribosome run-off assay, HEK293 cells were pre-treated with 100 µg/ml retapamulin for 30, 60, 90, 120 s, or 30 min and then incubated with 100 µg/ml chloramphenicol and 100 µg/ml cycloheximide to arrest translation elongation. Subsequently, cell lysis and mitochondrial purification were performed as described above, adding 100 µg/ml retapamulin to all the solutions.
MitoIP-Thor-Ribo-Seq: preadenylated linkers with the antisense sequence of T7 promoter were ligated and footprints were amplified by in vitro transcription.

value: Laminin-coating


title: RNA_1g_laminin_2

value: 1 g with laminin-coating


title: Setdb1 2c matKO single embryo replicate 10


title: Setdb1 2c matKO single embryo replicate 8


title: RNA_1g_laminin_1


title: MitoIP-Ribo_laminin_retapamulin_90s_2

description:
MitoIP-Thor-Ribo-Seq
L83


title: RNA_s-microg_24h

value: simulated microgravity


title: Setdb1 2c matKO single embryo replicate 6


title: Setdb1 2c matKO single embryo replicate 7


title: MitoIP-Ribo_laminin_retapamulin_60s_2

description:
MitoIP-Thor-Ribo-Seq
L82


title: Setdb1 2c matKO single embryo replicate 5


title: RNA_s-microg_1h


title: Setdb1 2c matKO single embryo replicate 4


title: Setdb1 2c matKO single embryo replicate 3


title: MitoIP-Ribo_laminin_retapamulin_30s_2

description:
MitoIP-Thor-Ribo-Seq
L81


title: RNA_1g_2

value: 1 g


title: Setdb1 2c matKO single embryo replicate 2


title: db/db 2 Gy-3

city: Seoul

first: Yeonghoon

last: Son

address: 75, Nowon-ro

country: South Korea

institute: Korea Institute of Radiological & Medical Sciences (KIRAMS)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: hippocampus

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: hippocampus

value: db/db

tag: Sex

value: male

value: 14 weeks after radiation

value: radiation


title: WD, Hi-C, control, rep1

description: Library name: Sample 1

value: Wing imaginal discs

value: Epithelial cells


title: db/db 2 Gy-2


title: MitoIP-Ribo_laminin_retapamulin_0s_2

description:
MitoIP-Thor-Ribo-Seq
L80


title: MitoIP-Ribo_laminin_retapamulin_120s_1

description:
MitoIP-Thor-Ribo-Seq
L79


title: db/db 2 Gy-1


title: db/db 0.1 Gy-3


title: Ribo_s-microg_24h_laminin

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: human, hg38; mouse, mm10; C. elegans, WBcel235
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribosome profiling

value: simulated microgravity with laminin-coating


title: MitoIP-Ribo_laminin_retapamulin_90s_1

description:
MitoIP-Thor-Ribo-Seq
L78


title: MitoIP-Ribo_laminin_retapamulin_60s_1

description:
MitoIP-Thor-Ribo-Seq
L77


title: Ribo_s-microg_1h_laminin


title: db/db 0.1 Gy-1


title: db/db 0 Gy-2

value: sham


title: Ribo_1g_laminin_2


title: MitoIP-Ribo_laminin_retapamulin_30s_1

description:
MitoIP-Thor-Ribo-Seq
L76


title: B6 0 Gy-3


title: db/db 0 Gy-3


title: db/db 0 Gy-1


title: Ribo_1g_laminin_1


title: B6 0 Gy-2


title: B6 0 Gy-1


title: MitoIP-Ribo_laminin_retapamulin_0s_1

description:
MitoIP-Thor-Ribo-Seq
L75


title: Ribo_s-microg_24h


title: RNA_MMS_14d_2

source_name: Soleus

value: Soleus

value: minimized mechanical stress


title: RNA_MMS_14d_1


title: MitoIP-Ribo_C75_laminin_2

description:
MitoIP-Thor-Ribo-Seq
L74

value: C75 with laminin-coating


title: RNA_control_10w_1

value: control


title: Ribo_s-microg_1h

value: 1 h


title: RNA_1g_1


title: RNA_control_10w_2


title: Ribo_1g_2


title: MitoIP-Ribo_C75_2

description:
MitoIP-Thor-Ribo-Seq
L73


title: Ribo_1g_1


title: db/db 0.1 Gy-2


title: RNA_MMS_3d_2

value: 3 d


title: RNA_microg_4d_ISS_2

organism: Caenorhabditis elegans

source_name: Whole body

value: Whole body

value: microgravity

value: 4 d


title: MitoIP-Ribo_C75_laminin_1

description:
MitoIP-Thor-Ribo-Seq
L70


title: WD, L3-crispr, regeneration, rep1

description: Library name: Sample 19

data_processing:
Reads were aligned to the Drosophila melanogaster dm6 genome using STAR v2.7.10b, with up to 4 mismatches per alignment, using the FlyBase genome annotation version r6.62. Reads mapping to more than 10 loci were discarded. Gene expression was quantified in the number of counts using the featureCounts function from the Rsubread package v2.22.1 in R. Genes whose sum of counts in all replicates was lower than 10 were discarded.
Assembly: dm6
Supplementary files format and content: Processed files contain raw count matrixes for each replicate. Number of counts was quantified using featureCounts from the Rsubread package v2.22.1 in R.

extract_protocol:
40 wing discs per sample were dissected in cold Schneider’s medium. The Quick-RNA Microprep kit (Zymo Research) was used following manufacturer’s instructions, including a 15-minute DNase incubation, to isolate the RNA. The purity and concentration of the resulting RNA were assessed using Nanodrop (Thermo Fisher Scientific) and Bioanalyzer (Agilent Technologies).
500 ng of total RNA were used for reverse transcription. Ribosomal RNA (rRNA) was depleted by using poly-A selection. All libraries were sequenced on an Illumina NextSeq2000 sequencer, using 50-bp paired-end reads. Library preparation and sequencing were performed at the Genomics Unit of the Center for Genomic Regulation (CRG).

value: Cell death induction


title: MitoIP-Ribo_C75_1

description:
MitoIP-Thor-Ribo-Seq
L69


title: WD, L3-crispr, regeneration, rep2

description: Library name: Sample 20


title: WD, L3-crispr, regeneration, rep3

description: Library name: Sample 21


title: RNA_MMS_3d_3


title: MitoIP-Ribo_DMSO_2

description:
MitoIP-Thor-Ribo-Seq
L71

value: DMSO


title: RNA_1g_4d_ISS_2

value: centrifuge 1 g


title: RNA_MMS_1d_2

value: 1 d


title: WD, L2-crispr, regeneration, rep2

description: Library name: Sample 17

value: Wing imaginal discs


title: MitoIP-Ribo_DMSO_1

description:
MitoIP-Thor-Ribo-Seq
L67


title: MitoIP-Ribo_DMSO_laminin_2

description:
MitoIP-Thor-Ribo-Seq
L72

value: DMSO with laminin-coating


title: MitoIP-Ribo_DMSO_laminin_1

description:
MitoIP-Thor-Ribo-Seq
L68


title: RNA_control_8w_3


title: Ribo_microg_4d_ISS_2


title: RNA_MMS_3d_1


title: RNA_control_8w_2


title: RNA_MMS_1d_3


title: RNA_microg_4d_ISS_1


title: RNA_1g_4d_ISS_1


title: WD, L2-crispr, regeneration, rep1

description: Library name: Sample 16

value: Epithelial cells


title: RNA_microg_48h_ISS_2


title: Ribo_1g_4d_ISS_2


title: RNA_control_8w_1


title: Ribo_1g_4d_ISS_1


title: WD, control-crispr, regeneration, rep2

description: Library name: Sample 14

value: w-; +; salE/Pv-LHG:tub-Gal80TS/lexO-rpr


title: Lung, Young, Day61

city: Charlottesville

first: Jie

last: Sun

state: VA

address: 345 Crispell Dr

department: Beirne B. Carter Center for Immunology Research

institute: University of Virginia

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Annotation and alignment was performed using Cell Ranger.
With Seurat, the i.v. labeling information was added to the object, and saved as rds
Assembly: mm10
Supplementary files format and content: h5
Supplementary files format and content: rds

source_name: Lung

extract_protocol:
To distinguish tissue resident and circulating/vasculature-associated immune population, 2μg/ms anti-mouse biotin conjugated CD45 antibody (Biolegend, Clone: 30-F11) was injected intravascularly 5min before humanely euthanizing the animal. Lungs were perfused with 20 ml PBS through pulmonary circulation starting from right ventricle. For Lung single cell suspension preparation, lung tissue was mined into fine pieces and put in digestion buffer (IMDM with 183 U/ml type 2 collagenase (Worthington)). After incubation at 37 C° for 30min, the homogenate was put through the “m_lung_02” program on a gentleMACS tissue disrupter (Miltenyi). The suspension was then filtered through 70 μm mesh (Falcon). The flow through was palleted and washed with MACS buffer (PBS with 2% FBS and 2mM/L Na2EDTA), followed by lysis of red blood cells with ACK buffer. After 2 washes with MACS buffer, single cell suspension from lung homogenate was stained with DNA-oligo conjugated streptavidin. Single Cell 5’ Library & Gel Bead Kit with Feature Barcoding was then utilized for scRNAseq library construction.
Library construction was performed according to the manufacture's instructions.

value: Lung

tag: age

value: Young


title: WD, L2-crispr, regeneration, rep3

description: Library name: Sample 18


title: RNA_microg_48h_ISS_1


title: Ribo_microg_4d_ISS_1


title: WD, control-crispr, regeneration, rep3

description: Library name: Sample 15


title: RNA_1g_48h_ISS_2


title: RNA_microg_24h_ISS_2


title: Ribo_MMS_14d_2

value: Soleus

value: minimized mechanical stress


title: Lung, Young, Day30

description: 10X Genomics


title: WD, control-crispr, regeneration, rep1

description: Library name: Sample 13


title: Ribo_MMS_3d_3


title: Lung, Aged, Day30

description: 10X Genomics

value: Aged


title: WD, Df(A)Df(B), regeneration, rep3

description: Library name: Sample 12


title: RNA_1g_24h_ISS_1


title: Ribo_MMS_14d_1


title: Ribo_MMS_3d_2

value: 3 d


title: Ribo_control_10w_2

value: control


title: Lung, Young, Day14

description: 10X Genomics


title: RNA_MMS_1d_1


title: Lung, Aged, Day61

description: 10X Genomics


title: Lung, Aged, Day14

description: 10X Genomics


title: Ribo_microg_48h_ISS_2

value: microgravity


title: RNA_1g_24h_ISS_2


title: Ribo_microg_48h_ISS_1


title: Ribo_control_10w_1


title: WD, Df(A)Df(B), regeneration, rep1

description: Library name: Sample 10


title: WD, Df(A), regeneration, rep3

description: Library name: Sample 7


title: WD, Df(B), regeneration, rep2

description: Library name: Sample 9


title: WD, Df(A), regeneration, rep2

description: Library name: Sample 6


title: Ribo_MMS_1d_2


title: WD, Df(B), regeneration, rep1

description: Library name: Sample 8


title: Ribo_MMS_3d_1


title: WD, Df(A), regeneration, rep1

description: Library name: Sample 5


title: Ribo_MMS_1d_3


title: Lung, Young, Day9

description: 10X Genomics


title: Ribo_microg_24h_ISS_1


title: Lung, Aged, Day9

description: 10X Genomics


title: WD, control-Df, regeneration, rep4

description: Library name: Sample 4


title: Lung, Young, Day2

description: 10X Genomics


title: Ribo_microg_24h_ISS_2


title: Ribo_1g_48h_ISS_2


title: Ribo_control_8w_3


title: Ribo_MMS_1d_1


title: WD, control-Df, regeneration, rep3

description: Library name: Sample 3


title: Lung, Young, Day0

description: 10X Genomics


title: Lung, Aged, Day2

description: 10X Genomics


title: WD, control-Df, regeneration, rep1

description: Library name: Sample 1


title: WD, Df(A)Df(B), regeneration, rep2

description: Library name: Sample 11


title: Ribo_control_8w_2


title: WD, control-Df, regeneration, rep2

description: Library name: Sample 2


title: Ribo_1g_48h_ISS_1


title: Ribo_control_8w_1


title: RNA_1g_48h_ISS_1


title: Ribo_1g_24h_ISS_1


title: Lung, Aged, Day0

description: 10X Genomics


title: Adult_Chow3

status: Public on Dec 27 2025

city: Saint Louis

first: Marion

middle: Isabelle

last: Stunault

state: MISSOURI

address: 660 S Euclid Ave

institute: Washington University School of Medicine

description: Library name: Adult_Chow3

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a77.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.378. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.279.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.080. All gene counts were then imported into the R/Bioconductor package EdgeR81 and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one sample greater than one count-per-million were excluded from further analysis.
Gene‑level raw count matrices were provided separately for young and adult cohorts (10 samples per cohort; 5 control and 5 ketogenic diet). Duplicate Ensembl gene IDs were aggregated by summing counts across duplicates. The two cohorts were aligned to the identical set of 55,487 genes prior to filtering, and low-abundance genes were filtered prior to statistical testing: a gene was retained if it had ≥10 raw counts in ≥3 samples in either age group, yielding 22,934 tested genes used as the background “universe” for enrichment analyses.
Differential expression testing was performed within each age using DESeq2 (v1.42.1) comparing ketogenic diet (keto) versus control. Size‑factor normalization and dispersion estimation followed DESeq2 defaults; Wald tests were used for inference. P values were adjusted for multiple testing using Benjamini–Hochberg; genes with FDR (padj) < 0.05 were considered differentially expressed.
Over‑representation analysis of Gene Ontology (GO) terms was performed using clusterProfiler (v4.10.1, `enrichGO`) with Mus musculus annotations from org.Mm.eg.db. Prior to enrichment, significant genes (padj < 0.05) were split by direction (up vs. down) and by age. Gene symbols were mapped to Entrez IDs via org.Mm.eg.db. The tested gene set after filtering (22,934 genes) served as the universe for all GO analyses, with enrichment parameters pAdjustMethod = "BH", pvalueCutoff = 0.05, and qvalueCutoff = 0.1.
Assembly: org.Mm.eg.db
Supplementary files format and content: tab-delimited text file includes raw count for each sample

source_name: Hippocampus

extract_protocol:
Frozen hippocampi were thawed on ice and 25-30mg of tissue was used for RNA extraction. Hippocampi were dissociated mechanically using a motor tissue grinder (Fisherbrand®, #12-1413-61) and 1.5mL pestles- RNase-free (KIMBLE, #749521-1590) in lysis buffer (QIAGEN, #1015762) and β-mercaptoethanol. RNA extraction was performed using the RNeasy mini-kit (QIAGEN, #74104) according to manufacturer’s instructions.
RNA libraries were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000.

treatment_protocol: 4 week-old C57BL6/NJ mice were placed on a 3-week ketogenic diet or chow diet / 12 week-old C57BL6/NJ mice were placed on a 4-week ketogenic diet or chow diet and fasted for 4h prior euthanasia

value: Hippocampus

tag: diet

value: Chow


title: Adult_Chow2

description: Library name: Adult_Chow2


title: Adult_KD4

description: Library name: Adult_KD4

value: Keto


title: Adult_KD2

description: Library name: Adult_KD2


title: Adult_KD3

description: Library name: Adult_KD3


title: Adult_KD1

description: Library name: Adult_KD1


title: Adult_Chow4

description: Library name: Adult_Chow4


title: Young_KD2

description: Library name: Young_KD2


title: Young_KD4

description: Library name: Young_KD4


title: Young_KD1

description: Library name: Young_KD1


title: Young_KD5

description: Library name: Young_KD5


title: Adult_Chow1

description: Library name: Adult_Chow1


title: Young_KD3

description: Library name: Young_KD3


title: Young_Chow5

description: Library name: Young_Chow5


title: Young_Chow4

description: Library name: Young_Chow4


title: Adult_KD5

description: Library name: Adult_KD5


title: Young_Chow3

description: Library name: Young_Chow3


title: Young_Chow1

description: Library name: Young_Chow1


title: Young_Chow2

description: Library name: Young_Chow2


title: Dox3

city: Honolulu

first: Xue

last: Wang

state: HI

address: 701 Ilalo Street

department: Cancer Biology Program

institute: University of Hawaii Cancer Center

description:
Library name: Dox3
Column name in Processed data_fpkm.txt: Dox3

data_processing:
Poor quality reads were trimmed using the fastq-mcf (v1.05). Reads quality was checked using the fastqc (v0.11.7).
Gene read counts were in Ensembl Gene ID and converted to Entrez Gene ID.
Corresponding Symbol annotations and full gene names were added using the “org.Hs.eg.db” library. NA (Not Annotated), duplicate Entrez IDs and genes without symbols were removed.
After removing the duplicated genes, the fragments per kilobase of transcript per million mapped reads (FPKM) were calculated.
Assembly: GRCh38
Supplementary files format and content: The tab-delimited text file includes FPKM values for each sample

source_name: SNU449 liver cancer cells

growth_protocol: pInducer20-FOXO1AAA SNU449 cells were cultured in RPMI 1640 medium (DMEM) (Cat# 11875093, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in an atmosphere of humidified air containing 5% CO2. Cell viability was more than 90% according to trypan blue exclusion analysis.

extract_protocol:
Total RNA was extracted from Cont (n=3) and Dox (n=3) groups using RNAiso Plus according to the manufacturer’s protocol.
RNA-seq libraries were prepared by poly(A) capture, followed by reverse transcription into cDNA.

treatment_protocol: pInducer20-FOXO1AAA SNU449 cells were treated with or without 2 μM doxycycline hydrochloride (Dox) for 48 hours.

value: SNU449 liver cancer cells

value: total RNA

value: WT


title: Ribo_1g_24h_ISS_2

value: centrifuge 1 g


title: Adult_Chow5

description: Library name: Adult_Chow5


title: Dox2

description:
Library name: Dox2
Column name in Processed data_fpkm.txt: Dox2


title: Dox1

description:
Library name: Dox1
Column name in Processed data_fpkm.txt: Dox1


title: NMCMs,HO + β-SITO (T4)

city: Xiamen

first: Zhonggui

last: Shan

state: Fujian

address: No. 55, Zhenhai Road

department: School of Medicine

institute: Xiamen University

description: Library name: A4C

data_processing:
Raw sequencing reads were quality-checked using FastQC. Reads were aligned to the mouse reference genome using HISAT2. Gene expression levels were quantified using featureCounts and normalized as TPM.
Assembly: Mus musculus GRCm39 release-109
Supplementary files format and content: tsv file includes raw counts for each sample

source_name: NMCMs

extract_protocol:
Total RNA was extracted from NMCMs using standard extraction methods.
Library construction was performed using the Illumina TruseqTM RNA sample prep Kit method

value: NMCMs

value: Primary neonatal mouse cardiomyocytes


title: NMCMs,HO + Vehicle (V1)

description: Library name: A1


title: NMCMs,HO + Vehicle (V3)

description: Library name: A3


title: NMCMs,HO + β-SITO (T6)

description: Library name: A6C


title: NMCMs,HO + β-SITO (T5)

description: Library name: A5C


title: NMCMs,HO + Vehicle (V2)

description: Library name: A2


title: RNA_microg_24h_ISS_1


title: Cont3

description:
Library name: Cont3
Column name in Processed data_fpkm.txt: Cont3


title: scRNA, scxa+, head, 14dpf

city: Los Angeles

first: Gage

last: Crump

state: CA

address: 1425 San Pablo St.

department: Stem Cell

institute: USC

description:
Library name: scxa_mCh_head_14dpf_scRNA
3' mRNA (10x Genomics): read1 file contains cell barcode and UMI; read2 file contains transcripts

data_processing:
The accessible peaks of ATAC libraries were called and refined by Snaptools and SnapATAC as described in (Fabian et al., 2022) to account for peaks contributed from cell clusters with smaller numbers. To calculate the cell-by-gene-activity matrices of snATAC data, we used the gmat generated by SnapATAC as anchors to impute scRNA expression from corresponding libraries of the same developmental time point through anchoring functions in Seurat v5.1.0. All single-cell datasets were integrated based on the cell-by-gene matrices of scRNA and snMultiome datasets, as well as the cell-by-gene-activity matrices of snATAC datasets, through the integration functions in the Seurat package. The integrated datasets were used for further dimensional reduction by PCA and visualization by UMAP. For motif enrichment, CallPeaks from Signac package v1.14 was used to extract accessible peaks from tendon and ligament clusters.
Assembly: Zebrafish GRCz11
Supplementary files format and content: CellRanger-Arc output files: multiome-matrix.h5, ATAC-fragments.tsv.gz
Supplementary files format and content: CellRanger output files: cell-by-gene-matrix.h5
Supplementary files format and content: CellRanger-ATAC output files: cell-by-peak-matrix.h5, ATAC-fragments.tsv.gz

organism: Danio rerio

source_name: 14dpf head

extract_protocol:
From scxa:mCherry zebrafish, we dissected and pooled 120 heads each for the 5 dpf scRNA-seq and multiome, 110 heads for the 5 dpf snATAC-seq, and 80 heads for the 14 dpf scRNA-seq experiment. Heads were partitioned into Eppendorf tubes on ice (12 heads per tube for 5 dpf and 8 heads per tube for 14 dpf) and washed twice in Ringer's solution, followed by enzymatic dissociation in pre-warmed 20 mg/mL Collagenase D (from stock of 400 mg/mL Collagenase D in HBSS), and 0.25% trypsin, 1 mM EDTA (pH 8.0) in PBS at 28.5°C for 1 to 1.5 h with vigorous pipetting every 10 min. The reaction was stopped with 6 mM CaCl2 and 30% fetal bovine serum (FBS) in PBS solution, and cells were collected by centrifugation at 2000 rpm for 5 min at 4°C. Cells from each stage were pooled into one tube after being resuspended and rinsed twice with 1% FBS, 0.8 mM CaCl2, 50 U/ml Penicillin, and 0.05 mg/ml Streptomycin in Leibovitz Medium solution and passed through a cell strainer. Cells were incubated with DAPI and subjected to fluorescence activated cell sorting (FACS). We collected approximately ~100,000 scxa:mCherry+ live cells (based on exclusion of DAPI) into a PBS solution with 0.04% BSA. Cells from each experiment were processed for nuclei isolation following 10X Genomics low cell count protocol (protocol CG000169) for snATAC-seq and Multiome, or used directly for scRNA-seq. Nuclei were imaged on a confocal microscope for absence of blebbing or abnormal morphology prior to proceeding.
Cell and nucleus partitioning, barcoding, and library synthesis were performed following protocols of 10X Genomics for snMultiome (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, protocol CG000338), scRNA-seq (Single Cell 3 ’ Reagent Kits v2, protocol CG00052), and snATAC-seq (Chromium Next GEM Single Cell ATAC Reagent, protocol CG000209). Libraries were sequenced on the Illumina NextSeq/HiSeq platform to reach a depth of 60,000 and 45,800 reads per cell for 5 and 14 dpf RNA libraries, and 10,600 reads per nuclei for the 5 dpf ATAC library. The 5 dpf multiome had a depth of 9,000 reads per nuclei for the ATAC library and 736 genes per nuclei for the GEX library. Libraries were aligned against the reference genome built with the genomic sequence of GRCz11, the gene annotation of GRCz11.104, and the motif matrix of JASPAR2020; the mCherry sequence is built in as an extra chromosome.

value: 14dpf head

value: scxa+ sorted cells


title: Cont2

description:
Library name: Cont2
Column name in Processed data_fpkm.txt: Cont2


title: 11 rep2

city: Guangzhou

first: 雷名

last: 吴

address: sun-yat san university

institute: 中山大学药学院

description:
Library name: sample5
fpkm_11 rep2

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: Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver

extract_protocol:
Cells were harvested, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 mg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: human hepatic stellate cells


title: Model rep3

description:
Library name: sample3
fpkm_Model rep3

value: TGF-β1 + DMSO


title: PR5

city: Dalian, Liaoning

first: Ye

last: Gao

address: No.467, Zhong Shan Street

institute: Second Affiliated Hospital of Dalian Medical University

description:
Library name: sample 19
Cecal ligation and puncture (CLP)-induced ARDS model.

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes gene counts and rna conut for each sample

organism: Rattus norvegicus

source_name: lung

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: lung

value: CLP


title: Sting-knockout, mice endometrium, LPS-stimulated, 24 h, rep2

city: Yantai

first: Min

last: Chu

state: Shandong

address: No. 20 Yuhuangding Estern Road

institute: Yantai Yuhuangding Hospital

description:
Library name: Sample 5
STKO-2-FPKM

data_processing:
Raw reads of fastq were firstly processed through in-house perl script with FASTQ (0.23.1)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FASTQ(parameter- Qphred≤15)
Trimmed sequence reads were mapped to GRCm39/mm39 using HISAT2 (2.2.1)
Read count extraction and normalization were performed using the software subRead package
Differential expression analysis of two groups was performed using the DESeq2 R package (1.16.1)
Assembly: GRCm39
Supplementary files format and content: processed data.xls files include FPKM values and raw counts for each Sample

source_name: endometrium LPS stimulated

extract_protocol:
RNA was harvested using RNeasy Plus Mini Kit (Qiagen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit  for Illumina® following maunfacturer's protocols.

value: endometrium LPS stimulated

value: Sting knockout

value: LPS stimulated


title: Model rep2

description:
Library name: sample2
fpkm_Model rep2


title: PR6

description:
Library name: sample 20
Cecal ligation and puncture (CLP)-induced ARDS model.


title: 11 rep1

description:
Library name: sample4
fpkm_11 rep1


title: Multiome, scxa+, head, 5dpf, GEX

description:
Library name: scxa_mCh_head_5dpf_multiome_GEX
3' mRNA (10x Genomics): read1 file contains cell barcode and UMI; read2 file contains transcripts

source_name: 5dpf head

value: 5dpf head


title: PR3

description:
Library name: sample 17
Cecal ligation and puncture (CLP)-induced ARDS model.


title: PR1

description:
Library name: sample 16
Cecal ligation and puncture (CLP)-induced ARDS model.


title: Sting-knockout, mice endometrium, LPS-stimulated, 24 h, rep3

description:
Library name: Sample 6
STKO-3-FPKM


title: PR4

description:
Library name: sample 18
Cecal ligation and puncture (CLP)-induced ARDS model.


title: wild-type, mice, endometrium, LPS-stimulated, 24 h, rep2

description:
Library name: Sample 2
WT-2-FPKM


title: Sting-knockout, mice endometrium, LPS-stimulated, 24 h, rep1

description:
Library name: Sample 4
STKO-1-FPKM


title: wild-type, mice, endometrium, LPS-stimulated, 24 h, rep3

description:
Library name: Sample 3
WT-3-FPKM


title: 11 rep3

description:
Library name: sample6
fpkm_11 rep3


title: PM1

description:
Library name: sample 11
CLP-induced ARDS rats receiving right cervical vagus nerve stimulation.

value: CLP + VNS


title: PM11

description:
Library name: sample 15
CLP-induced ARDS rats receiving right cervical vagus nerve stimulation.


title: PM3

description:
Library name: sample 12
CLP-induced ARDS rats receiving right cervical vagus nerve stimulation.


title: Bd21-3 shoots,  Week 4, Replicate 1  (Shoot4_1)

city: Berkeley

first: Yezhang

last: Ding

address: 1 Cyclotron Road

institute: Berkeley Lab

description: Library name: Sample 10

data_processing:
Clustering of the index-coded samples was carried out according to the manufacturer’s instructions. Once cluster generation was complete, the libraries were sequenced on an Illumina platform, producing paired-end reads. The raw reads in fastq format were initially processed using Perl scripts. During this step, clean reads were obtained by removing reads containing adapters, reads with poly-N sequences, and low-quality reads from the raw data. Simultaneously, Q20, Q30, and GC content of the clean data were calculated. Paired-end clean reads were then aligned to the reference genome (B. distachyon B21-3 v1.1) using Hisat2 (v2.0.5) (Kim et al., 2015). FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene (Liao et al., 2014). The FPKM (Fragments Per Kilobase of transcript sequence per Million base pairs) for each gene was then calculated based on the gene’s length and the number of reads mapped to it using HTSeq (v0.6.1) (Anders et al., 2015).
Assembly: Bd21-3
Supplementary files format and content: tab delimited text, including raw counts for each sample

organism: Brachypodium distachyon

source_name: shoots

growth_protocol: The culture vessels (PTL-100™, PhytoTech Labs) were rinsed five times with MilliQ water and autoclaved. Two seedlings of each B. distachyon line were placed onto a floating plastic holder and then transferred to each vessel with 40 mL of 0.5 × MS. Plants were grown in a 16 h light/8 h dark regime at 22 °C and 50% relative humidity with 150 μmol m-2s-1 illumination for four weeks. The culture vessels without plants, filled with the growth medium, were incubated in the same conditions as the controls. At week two and four, root and shoot tissues were harvested and stored at -80°C for further analysis.

extract_protocol:
Root and shoot tissues were harvested from hydroponically grown B. distachyon Bd21-3 plants at weeks 2 and 4. Total RNA was isolated with a NucleoSpin® RNA Plant Kit (Takara Bio USA) according to the manufacturer’s protocol. Three biological replicates were performed using different plants. RNA quality was assessed based on RNA integrity number using an Agilent Bioanalyzer.
RNA-seq library construction and sequencing were performed by Novogene. Messenger RNA (mRNA) was isolated from total RNA using poly-T oligo-attached magnetic beads. Following fragmentation, the first strand of cDNA was synthesized using random hexamer primers, and the second strand of cDNA was then synthesized using either dUTP for directional library preparation or dTTP for non-directional library preparation. The libraries were assessed for quantification using Qubit and real-time PCR, and the size distribution was analyzed with a Bioanalyzer. The quantified libraries were pooled and sequenced on Illumina platforms, based on the effective library concentration and desired data yield.

value: shoots

value: whole shoots

value: week 4


title: Cont1

description:
Library name: Cont1
Column name in Processed data_fpkm.txt: Cont2

value: SNU449 liver cancer cells

value: total RNA

value: WT


title: M5

description:
Library name: sample 10
Sham-operated rats receiving right cervical vagus nerve stimulation.

value: Sham + VNS


title: PM5

description:
Library name: sample 13
CLP-induced ARDS rats receiving right cervical vagus nerve stimulation.


title: Bd21-3 shoots , Week 4, Replicate 2  (Shoot4_1)

description: Library name: Sample 11


title: Bd21-3 shoots,  Week 2, Replicate 3  (Shoot2_3)

description: Library name: Sample 9

value: week 2


title: M3

description:
Library name: sample 8
Sham-operated rats receiving right cervical vagus nerve stimulation.


title: Model rep1

description:
Library name: sample1
fpkm_Model rep1

value: liver

value: human hepatic stellate cells


title: Bd21-3 shoots,  Week 2, Replicate 1  (Shoot2_1)

description: Library name: Sample 7


title: M2

description:
Library name: sample 7
Sham-operated rats receiving right cervical vagus nerve stimulation.

value: lung


title: TDP-43Q331K cortex replicate 3

city: Columbia

first: Jose

last: Viteri

state: MO

address: 1030 Hitt St

institute: University of Missouri - Columbia

description:
Library name: 954
Bulk RNA-seq of 4-month cortex from TDP-43Q331K mouse

data_processing:
Raw paired-end FASTQ files were aligned to the Mus musculus reference genome (GRCm39) using STAR (v2.7.6a) in sorted BAM output mode with Ensembl gene annotation. Lowly expressed genes (CPM ≤ 1 in fewer than two samples) were filtered out. Library size normalization was performed using the Trimmed Mean of M-values (TMM) method in edgeR (v4.4.2). Differential gene expression was assessed using quasi-likelihood F-tests (QLF). Additional analyses, including GO/KEGG enrichment (clusterProfiler, fgsea, msigdbr), PCA, and heatmaps (pheatmap), were conducted in R (v4.3.1). Processed data files contain normalized counts, log₂ fold-changes, FDR-adjusted p-values, and DEG tables for each sample.
Assembly: GRCm39
Supplementary files format and content: Processed data files include a TMM-normalized gene expression matrix, in which each row corresponds to a Mus musculus Ensembl gene ID (Ensembl gene_id), and each column corresponds to an individual RNA-seq sample (e.g., X330_S25_L003, X337_S26_L003, etc.). Values represent TMM-normalized log₂ CPM expression estimates generated using edgeR after low-expression filtering. These processed files are provided as tab-delimited text (.txt) or comma-separated values (.csv) and allow users to reproduce differential expression analyses without re-aligning raw FASTQ files.

source_name: Brain Cortex

extract_protocol:
Cortical tissue was dissected, wrapped in aluminum foil, flash-frozen in liquid nitrogen, and stored at −80 °C until processing. Total RNA was isolated by homogenizing tissue in 400 µL TRIzol (Thermo Fisher Scientific) with 80 µL chloroform and homogenizing beads, followed by centrifugation at 12,000 × g. The aqueous phase was transferred to a silica-column purification system (Quick-RNA MicroPrep Kit, Zymo Research) and processed according to the manufacturer’s instructions. RNA was eluted and adjusted to a final concentration of 50 ng/µL for library construction.
RNA sequencing libraries were generated at the University of Missouri Genomics Technology Core using the Illumina Stranded RNA Prep, Ligation Kit (Illumina, Cat. #20040534). mRNA was captured with oligo(dT) magnetic beads, fragmented, and used as template for first- and second-strand cDNA synthesis. Dual-indexed adapters were ligated, and libraries were PCR-amplified and purified using Axyprep Mag PCR Clean-up beads (Fisher Scientific). Library size distribution was assessed using the Fragment Analyzer, quantified with the Qubit HS dsDNA assay, and sequenced on an Illumina NovaSeq X.

value: Brain Cortex

value: Bulk tissue


title: M4

description:
Library name: sample 9
Sham-operated rats receiving right cervical vagus nerve stimulation.


title: M1

description:
Library name: sample 6
Sham-operated rats receiving right cervical vagus nerve stimulation.


title: TDP-43Q331K cortex replicate 4

description:
Library name: 956
Bulk RNA-seq of 4-month cortex from TDP-43Q331K mouse


title: Bd21-3 roots , Week 4, Replicate 2  (Root4_2)

description: Library name: Sample 5

source_name: roots

value: roots

value: whole roots


title: CR5

description:
Library name: sample 5
Sham-operated control rats; midline laparotomy with gentle cecum manipulation but without ligation or puncture.

value: Sham


title: PM8

description:
Library name: sample 14
CLP-induced ARDS rats receiving right cervical vagus nerve stimulation.

value: CLP + VNS


title: WT cortex replicate 4

description:
Library name: 953
Bulk RNA-seq of 4-month cortex from WT mouse


title: Bd21-3 roots,  Week 4, Replicate 3  (Root4_3)

description: Library name: Sample 6


title: TDP-43Q331K cortex replicate 2

description:
Library name: 398
Bulk RNA-seq of 4-month cortex from TDP-43Q331K mouse


title: Bd21-3 shoots,  Week 4, Replicate 3  (Shoot4_1)

description: Library name: Sample 12

value: shoots


title: Bd21-3 roots,  Week 4, Replicate 1  (Root4_1)

description: Library name: Sample 4


title: WT cortex replicate 3

description:
Library name: 342
Bulk RNA-seq of 4-month cortex from WT mouse


title: wild-type, mice, endometrium, LPS-stimulated, 24 h, rep1

description:
Library name: Sample 1
WT-1-FPKM

value: endometrium LPS stimulated

value: LPS stimulated


title: TDP-43Q331K cortex replicate 1

description:
Library name: 341
Bulk RNA-seq of 4-month cortex from TDP-43Q331K mouse


title: Bd21-3 roots,  Week 2, Replicate 3  (Root2_3)

description: Library name: Sample 3


title: CR3

description:
Library name: sample 3
Sham-operated control rats; midline laparotomy with gentle cecum manipulation but without ligation or puncture.


title: CR4

description:
Library name: sample 4
Sham-operated control rats; midline laparotomy with gentle cecum manipulation but without ligation or puncture.


title: snATAC, scxa+, head, 5dpf

description:
Library name: scxa_mCh_head_5dpf_snATAC
ATAC: read1 files contain cell barcode and UMI; read2 files contain ATAC sequences

library_source: genomic single cell

value: 5dpf head

value: scxa+ sorted cells


title: Bd21-3 roots , Week 2, Replicate 2  (Root2_2)

description: Library name: Sample 2

value: WT


title: CR2

description:
Library name: sample 2
Sham-operated control rats; midline laparotomy with gentle cecum manipulation but without ligation or puncture.


title: WT cortex replicate 2

description:
Library name: 337
Bulk RNA-seq of 4-month cortex from WT mouse


title: WT cortex replicate 1

description:
Library name: 330
Bulk RNA-seq of 4-month cortex from WT mouse


title: Bd21-3 shoots , Week 2, Replicate 2  (Shoot2_2)

description: Library name: Sample 8

value: whole shoots


title: CR1

description:
Library name: sample 1
Sham-operated control rats; midline laparotomy with gentle cecum manipulation but without ligation or puncture.


title: Multiome, scxa+, head, 5dpf, ATAC

description:
Library name: scxa_mCh_head_5dpf_multiome_ATAC
ATAC: read1 files contain cell barcode and UMI; read2 files contain ATAC sequences


title: cac-1_suz12_input

status: Public on Dec 26 2025

city: Athens

first: Zachary

middle: A

last: Lewis

state: GA

address: 120 E. Green St.

department: Microbiology

institute: University of Georiga

description: Library name: 152-88

data_processing:
Trim_Galore v0.6.10
BWA v0.7.18 (mem, option -M)
SAMtools v1.21 (sort, index)
deepTools v3.5.5 (bamCoverage)
Assembly: BioProject PRJNA13841 Genbank accession: GCA_000182925.2
Supplementary files format and content: bigwig files; read counts in 25 base pair bins

organism: Neurospora crassa

source_name: mycelicum

growth_protocol: Overnight growth in Vogel's Minimal Medium + 1.5% sucrose

extract_protocol:
sonication
end repair, adaptor ligation, PCR amplification

treatment_protocol: formaldahyde fixation (1%)

value: mycelicum


title: WT_H3K36me3

description: Library name: 152-111


title: cac-2_comp_Kac_Rep1

description: Library name: 152-121


title: cac-2_input

description: Library name: 6147_136-89


title: cac-2_comp_FLAG_Rep1

description: Library name: 152-93


title: cac-2_comp_FLAG_Rep2

description: Library name: 152-94


title: WT_H3K27me3

description: Library name: 152-110


title: cac-1_input

description: Library name: 6147_136-85


title: cac-1_comp_FLAG_Rep2

description: Library name: 152-92


title: Bd21-3 roots,  Week 2, Replicate 1 (Root2_1)

description: Library name: Sample 1

value: week 2


title: cac-2_comp_input_Rep1

description: Library name: 149-130


title: cac-3_input_Rep1

description: Library name: 6147_136-14


title: cac-2_comp_Kac_Rep2

description: Library name: 152-122


title: cac-3_input

description: Library name: 129-46


title: cac-2_input_Rep2

description: Library name: 138-74


title: cac-2_comp_input_Rep2

description: Library name: 149-131


title: cac-2_input_Rep1

description: Library name: 6147_136-13


title: WT_input

description: Library name: 129-43


title: cac-1_input_Rep2

description: Library name: 138-73


title: scRNA, scxa+, head, 5dpf

description:
Library name: scxa_mCh_head_5dpf_scRNA
3' mRNA (10x Genomics): read1 file contains cell barcode and UMI; read2 file contains transcripts


title: cac-1_comp_FLAG_Rep1

description: Library name: 152-91


title: cac-1_comp_H3K4me2_Rep1

description: Library name: 152-89


title: cac-1_comp_input_Rep2

description: Library name: 152-96


title: suz-12_input_Rep1

description: Library name: 152-86


title: cac-1_comp_input_Rep1

description: Library name: 152-95


title: cac-1suz-12_input_Rep1

description: Library name: 152-112


title: suz-12_input_Rep2

description: Library name: 152-114


title: set-7_input_Rep2

description: Library name: 149-138


title: cac-2_comp_H3K27me3_Rep2

description: Library name: 149-123


title: cac-1_comp_H3K36me3_Rep1

description: Library name: 152-117


title: cac-3_input_Rep2

description: Library name: 138-75


title: cac-1_comp_H3K27me3_Rep2

description: Library name: 152-116


title: cac-1_comp_H3K27me3_Rep1

description: Library name: 152-115


title: cac-1_input_Rep1

description: Library name: 6147_136-12


title: set-7_H4K20me3_Rep2

description: Library name: 138-71


title: cac-2_H4K20me3_Rep2

description: Library name: 138-69


title: WT_input_Rep1

description: Library name: 6147_136-11


title: WT_input_Rep2

description: Library name: 138-72


title: cac-2_comp_H3K4me2_Rep2

description: Library name: 149-129


title: cac-2_comp_H3K4me2_Rep1

description: Library name: 149-128


title: cac-2_H4K20me3_Rep1

description: Library name: 133-21


title: cac-2_comp_H3K36me3_Rep2

description: Library name: 152-120


title: cac-1_comp_H3K36me3_Rep2

description: Library name: 152-118


title: cac-1_comp_H3K4me2_Rep2

description: Library name: 152-90


title: set-7_H3K9me3_Rep1

description: Library name: 133-26


title: WT_H4K20me3_Rep1

description: Library name: 133-19


title: set-7_input_Rep1

description: Library name: 138-76


title: cac-2_comp_H3K27me3_Rep1

description: Library name: 149-122


title: cac-2_H3K9me3_Rep2

description: Library name: 149-106


title: set-7_H4K20me3_Rep1

description: Library name: 133-22


title: cac-1_H3K9me3_Rep1

description: Library name: 133-24


title: WT_H3K9me3_Rep2

description: Library name: 149-104


title: cac-2_comp_H3K36me3_Rep1

description: Library name: 152-119


title: cac-1_H4K20me3_Rep1

description: Library name: 133-20


title: WT_H4K20me3_Rep2

description: Library name: 138-67


title: suz-12_HKac_Rep1

description: Library name: 152-74


title: set-7_H3K9me3_Rep2

description: Library name: 149-108


title: suz-12_Hkac_Rep2

description: Library name: 152-80


title: cac-1_H3K9me3_Rep2

description: Library name: 149-105


title: set-7_HKac_Rep2

description: Library name: 151-115


title: cac-1_H4K20me3_Rep2

description: Library name: 138-68


title: cac-3_HKac_Rep1

description: Library name: 150-138


title: cac-2_HKac_Rep2

description: Library name: 151-113


title: WT_H3K9me3_Rep1

description: Library name: 133-23


title: cac-3_HKac_Rep2

description: Library name: 151-114


title: cac-2_H3K9me3_Rep1

description: Library name: 133-25


title: cac-2_HKac_Rep1

description: Library name: 150-137


title: cac-1suz-12_HKac_Rep2

description: Library name: 152-82


title: WT_HKac_Rep2

description: Library name: 151-111


title: WT_HKac_Rep1

description: Library name: 150-135


title: cac-1suz-12_HKac_Rep1

description: Library name: 152-76


title: set-7_HKac_Rep1

description: Library name: 150-139


title: cac-1_HKac_Rep2

description: Library name: 151-112


title: cac-1suz-12_H3K36me3_Rep1

description: Library name: 152-101


title: cac-1suz-12_H3K36me3_Rep3

description: Library name: 152-79


title: suz-12_H3K36me3_Rep2

description: Library name: 152-97


title: cac-1suz-12_H3K36me3_Rep2

description: Library name: 152-98


title: set-7_H3K36me3_Rep3

description: Library name: 138-66


title: set-7_H3K36me3_Rep2

description: Library name: 150-134


title: suz-12_H3K36me3_Rep3

description: Library name: 152-77


title: cac-3_H3K36me3_Rep2

description: Library name: 150-131


title: suz-12_H3K36me3_Rep1

description: Library name: 152-100


title: cac-1_H3K36me3_Rep3

description: Library name: 138-63


title: cac-3_H3K36me3_Rep3

description: Library name: 138-65


title: set-7_H3K36me3_Rep1

description: Library name: 149-103


title: WT_H3K36me3_Rep3

description: Library name: 138-62


title: cac-3_H3K36me3_Rep1

description: Library name: 149-102


title: cac-1_H3K36me3_Rep1

description: Library name: 149-100


title: cac-2_H3K36me3_Rep2

description: Library name: 150-116


title: cac-1suz-12_H3K4me2_Rep3

description: Library name: 152-85


title: cac-2_H3K36me3_Rep1

description: Library name: 149-101


title: WT_H3K36me3_Rep1

description: Library name: 149-99


title: cac-1suz-12_H3K4me2_Rep2

description: Library name: 152-104


title: set-7_H3K4me2_Rep1

description: Library name: 146-23


title: suz-12_H3K4me2_Rep1

description: Library name: 152-106


title: cac-2_H3K36me3_Rep3

description: Library name: 138-64


title: WT_H3K36me3_Rep2

description: Library name: 150-93


title: cac-2_H3K4me2_Rep2

description: Library name: 146-31


title: cac-3_H3K4me2_Rep1

description: Library name: 146-22


title: cac-1_H3K4me2_Rep1

description: Library name: 146-20


title: cac-2_H3K4me2_Rep1

description: Library name: 146-21


title: cac-1suz-12_H3K4me2_Rep1

description: Library name: 152-107


title: WT_H3K4me2_Rep1

description: Library name: 146-19


title: cac-1_H3K36me3_Rep2

description: Library name: 150-94


title: cac-1_HKac_Rep1

description: Library name: 150-136


title: cac-3_H3K4me2_Rep2

description: Library name: 146-32


title: set-7_H3K27me3_abcam_Rep3

description: Library name: 6147_136-77


title: set-7_H3K4me2_Rep2

description: Library name: 146-33


title: suz-12_H3K4me2_Rep2

description: Library name: 152-103


title: cac-1_H3K4me2_Rep2

description: Library name: 146-30


title: cac-3_H3K27me3_AbC_Rep1

description: Library name: 129-41


title: WT_H3K4me2_Rep2

description: Library name: 146-29


title: cac-3_H3K27me3_abcam_Rep2

description: Library name: 6147_136-4


title: cac-2_H3K27me3_AbC_Rep1

description: Library name: 129-40


title: cac-1_H3K27me3_AbC_Rep1

description: Library name: 129-39


title: cac-2_H3K27me3_abcam_Rep2

description: Library name: 6147_136-3


title: suz-12_H3K4me2_Rep3

description: Library name: 152-83


title: WT_H3K27me3_abcam_Rep2

description: Library name: 6147_136-1


title: WT_H3K27me3_AbC_Rep1

description: Library name: 129-38


title: cac-1suz-12_H3K27me3_CS

description: Library name: 152-109


title: set-7_H3K27me3_CS_Rep3

description: Library name: 138-61


title: set-7_H3K27me3_CS_Rep1

description: Library name: 126-58


title: set-7_H3K27me3_CS_Rep2

description: Library name: 6147_136-83


title: cac-3_H3K27me3_Rep3

description: Library name: 138-60


title: cac-3_H3K27me3_CS_Rep2

description: Library name: 6147_136-81


title: cac-3_H3K27me3_CS_Rep1

description: Library name: 6147_136-9


title: cac-2_H3K27me3_CS_Rep2

description: Library name: 6147_136-80


title: cac-1_H3K27me3_Rep3

description: Library name: 138-58


title: cac-1_H3K27me3_CS_Rep2

description: Library name: 6147_136-79


title: set-7_H3K27me3_AbC_Rep1

description: Library name: 129-42


title: WT_H3K27me3_CS_Rep2

description: Library name: 6147_136-78


title: cac-1_H3K27me3_CS_Rep1

description: Library name: 6147_136-7


title: RNA_cac-1_suz-12_Rep3

description: Library name: 149-98

data_processing:
Trim_Galore v0.6.10
STAR v2.7.11 (alignReads)
SAMtools v1.21 (index)
Subread v2.0.6 (featureCounts)
deepTools v3.5.5 (bamCoverage)
Assembly: BioProject PRJNA13841 Genbank accession: GCA_000182925.2
Supplementary files format and content: bigwig files; read counts in 50 base pair bins

extract_protocol:
Mycelium ground in liquid N2, TRIzol extraction
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer protocols

value: cac-1, suz-12 knockout


title: WT_H3K27me3_Rep3

description: Library name: 138-57


title: WT_H3K27me3_CS_Rep1

description: Library name: 6147_136-6


title: RNA_cac-1_suz-12_Rep1

description: Library name: 149-96


title: RNA_cac-1_suz-12_Rep2

description: Library name: 149-97


title: RNA_cac-1_Rep3

description: Library name: 149-117

value: cac-1 knockout


title: cac-2_H3K27me3_Rep3

description: Library name: 138-59


title: cac-1_H3K27me3_abcam_Rep2

description: Library name: 6147_136-2


title: RNA_cac-1_Rep2

description: Library name: 149-116


title: RNA_cac-1_Rep1

description: Library name: 149-115


title: E_hCD4_cMaf CUT&RUN

first: Jing

last: Chen

address: 600 S Euclid Ave

institute: Washington University in St. Louis

description: Library name: E_hCD4_cMaf

data_processing:
The adaptor sequences were removed by Trimmomatic program. The trimmed reads were aligned and mapped to the mouse reference genome (GRCm38/mm10) by Bowtie2 software version 2.2.5. Duplicated reads are discarded using 'make tag directory' of Homer software package (version 4.9). Data were visualized with the 'makeUCSCfile' of Homer. Peaking calling was performed with Homer software package.
Assembly: Genome_build: mm10
Supplementary files format and content: bedGraph files were generated with Homer software package using the "makeUCSCfile" command.
Library strategy: CUT&Run

source_name: cultured BM cells

extract_protocol:
0.25 million fresh cells were adsorbed to activated Concanavalin A (ConA) beads, permeabilized with 0.01% digitonin, and incubated with 0.5 mg indicated antibodies overnight at 4 °C. After antibody binding, the targete-DNA complex is cleaved by the Protein A/Protein G-Micrococcal Nuclease (pAG-MNase) for 2 hours at 4 °C. 0.05ng E. coli Spike-in DNA was added before releasing CUT&RUN fragments at 37°C for 10 min. The CUT&RUN enriched DNA is purified from the supernatant.
Libraries were prepared with a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) and cleaned-up with AMPureXP.

value: cultured BM cells

value: Zeb2 -165kb mice

value: empty vector

tag: antibody

value: Maf (abcam BLR045F)


title: MJ_Thy1_1_cJun CUT&RUN

description: Library name: MJ_Thy1_1_cJun

value: Jun OE

value: Jun (epicypher)


title: MJ_DP_cJun CUT&RUN

description: Library name: MJ_DP_cJun

value: Jun-Maf double OE


title: WT_ATAC

description: Library name: WT_ATAC

data_processing:
We used the Cell Ranger ARC v2.0.2 pipeline to demultiplex Illumina sequencer files and generate count matrices for gene expression and ATAC data. Nuclei with barcodes in both RNA and ATAC were retained, and peak sets for WT and KO libraries were loaded into Signac to generate a unified peak set. RNA data were normalized using SCTransform, followed by dimensional reduction, Harmony batch integration, and UMAP embedding. ATAC data were normalized using term frequency inverse document frequency (TF-IDF), and differential gene expression identified myeloid cell states. Motif enrichment analysis was performed using JASPAR2020 and chromVar, and peaks were linked to genes using Signac's LinkPeaks function for target gene annotation.
Assembly: mm10
Supplementary files format and content: RNA (feature, barcode and matrix files), ATAC (fragments, annotation)

source_name: E12.5 fetal liver

extract_protocol:
Nuclei were isolated according to 10X multiome low cell input nuclei isolation protocol. Briefly, nuclei from 50,000 cells by centrifuging the cell suspension at 300 rcf for 5 minutes at 4°C, followed by resuspension in PBS + 0.04% BSA. After incubating the cells in chilled Lysis Buffer for 4 minutes on ice, Wash Buffer was added without mixing. The sample was centrifuged at 500 rcf for 5 minutes at 4°C, and the supernatant was carefully removed, leaving the nuclei pellet. The pellet was then resuspended in chilled Diluted Nuclei Buffer, and a final centrifugation step was performed. The resulting nuclei were counted, with an expected recovery of about 25% of the initial cell input for sequencing.
10X single nuclei multiome ATAC + 3' RNAseq

value: E12.5 fetal liver

value: wildtype


title: WT_RNA

description: Library name: WT_RNA

molecule: nuclear RNA


title: WT 2

description: Library name: WT 2

data_processing:
Basecalls and demultiplexing were performed with Illumina’s DRAGEN and BCLconvert version 4.2.4 software. RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04. All gene counts were then imported into the R/Bioconductor package EdgeR5 and TMM normalization size factors were calculated to adjust for samples for differences in library size.
Assembly: mm10
Supplementary files format and content: tsv table

source_name: E15.5 Fetal Liver

extract_protocol:
RNA was isolated from 50k monocytes from indicated tissue using NucleoSpin RNA XS Kit (Macherey-Nagel).
Samples were prepared according to library kit manufacteruer's protocol (Takara-Clontech SMARTer Ultra Low RNA kit for Illumina), indexed, pooled and sequenced on Illumina NovaSeq X Plus.

value: E15.5 Fetal Liver

value: Ly6C+ monocyte


title: WT 1

description: Library name: WT 1

source_name: E13.5 Fetal Liver

value: E13.5 Fetal Liver

value: WT


title: MJ_hCD4_cMaf CUT&RUN

description: Library name: MJ_hCD4_cMaf

value: Maf OE


title: MJ_DP_cMaf H3K27ac CUT&RUN

description: Library name: MJ_DP_cMaf


title: Mixed 2

description: Library name: Mixed 2


title: KO 3

description: Library name: KO 3

value: KO


title: cac-2_H3K27me3_CS_Rep1

description: Library name: 6147_136-8

value: mycelicum


title: Mixed 3

description: Library name: Mixed 3


title: BM 3

description: Library name: BM 3

source_name: bone marrow

value: bone marrow


title: KO 1

description: Library name: KO 1


title: BM 2

description: Library name: BM 2


title: RPM_WT3

description: Library name: RPM_WT3

source_name: spleen

extract_protocol:
RNA was isolated from 100,000 macrophages sorted from digested tissue using NucleoSpin RNA XS Kit (Macherey-Nagel).
Samples were prepared according to library kit manufacteruer's protocol (Takara-Clontech SMARTer Ultra Low RNA kit for Illumina), indexed, pooled and sequenced on Illumina NovaSeq X Plus.

value: spleen

value: splenic macrophage


title: BM 1

description: Library name: BM 1


title: RPM_WT2

description: Library name: RPM_WT2


title: M_WT2

description: Library name: M_WT2

source_name: brain

value: brain

value: microglia


title: RPM_KO1

description: Library name: RPM_KO1


title: RPM_WT1

description: Library name: RPM_WT1


title: RPM_KO3

description: Library name: RPM_KO3


title: M_WT3

description: Library name: M_WT3


title: M_WT1

description: Library name: M_WT1


title: M_KO3

description: Library name: M_KO3


title: M_KO2

description: Library name: M_KO2


title: M_KO1

description: Library name: M_KO1


title: WT 3

description: Library name: WT 3


title: Mixed 1

description: Library name: Mixed 1


title: KC_WT2

description: Library name: KC_WT2

value: liver

value: kupffer cells


title: KC_WT3

description: Library name: KC_WT3


title: KC_KO2

description: Library name: KC_KO2


title: KO 2

description: Library name: KO 2


title: KC_WT1

description: Library name: KC_WT1


title: KC_KO1

description: Library name: KC_KO1


title: AM_KO3

description: Library name: AM_KO3

value: lung

value: alveolar macrophage


title: AM_WT1

description: Library name: AM_WT1


title: AM_WT3

description: Library name: AM_WT3


title: AM_WT2

description: Library name: AM_WT2


title: AM_KO2

description: Library name: AM_KO2


title: AM_KO1

description: Library name: AM_KO1


title: KO_ATAC

description: Library name: KO_ATAC

value: E12.5 fetal liver

value: knockout


title: RPM_KO2

description: Library name: RPM_KO2


title: KO_RNA

description: Library name: KO_RNA


title: KC_KO3

description: Library name: KC_KO3


title: CAF2_CON2

city: Wuhan

first: Hui

last: Zhao

address: Luoyu Road

institute: Wuhan university

description: Library name: CAF2_CON2

data_processing:
The raw data was filtered with SOAPnuke (v1.6.5) by 1) Removing reads containing adapters (adapter contamination); 2) Removing reads whose unknown base ('N' base) ratio is more than 1%; 3) Removing reads whose low-quality base ratio (Base quality less than or equal to 15) is more than 40%, afterwards clean reads were obtained and stored in FASTQ format.
The clean data were mapped to the assembled unique gene by Bowtie2 (v2.4.5).
The expression level of genes was calculated by RSEM (v1.3.1).
Assembly: GRCh38.p14
Supplementary files format and content: Comma-separated values file (.csv) containing the tpm-normalized gene expression matrix for all samples.

source_name: OSCC tissue

growth_protocol: Cancer-associated fibroblasts (CAFs) isolated from tissues of OSCC patients were cultured in high-glucose medium supplemented with 10% fetal bovine serum (FBS) and antibiotics, and maintained in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from all samples using TRIzol reagent (Thermo Fisher Scientific, USA) following the manufacturer’s instructions. RNA concentration and purity were measured using a NanoDrop spectrophotometer (Thermo Fisher Scientific, USA), and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China).

treatment_protocol: we performed RNA sequencing on two CD36-high CAF lines treated with or without 50μM PA for 24h.

value: OSCC tissue

value: Cancer-associated fibroblast

value: Fibroblast

value: Untreated cells served as the control group.

value: single batch


title: CAF2_PA1

description: Library name: CAF2_PA1

value: WT

value: The cell lines were then treated with 50 μM PA for 24 hours.


title: CAF1_CON2

description: Library name: CAF1_CON2


title: CAF1_CON3

description: Library name: CAF1_CON3


title: CAF1_CON1

description: Library name: CAF1_CON1


title: CAF2_CON1

description: Library name: CAF2_CON1


title: CAF1_PA2

description: Library name: CAF1_PA2


title: Testis, High-VCR, rep 3

city: Fuzhou

first: Meng

last: Fu

address: 310 Yangqiao Middle Road

institute: Fujian Children's Hospital

description:
Library name: A-109
High-VCR_3

data_processing:
Raw sequencing reads were quality-trimmed and adapter-trimmed using Trimmomatic v0.39 with parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36.
Cleaned reads were aligned to the mouse reference genome (GRCm39/mm39) using STAR aligner v2.7.10b with default parameters.
Gene-level read counts were generated using featureCounts (Subread package v2.0.3) with the Ensembl gene annotation (release 107).
Count normalization and differential expression analysis were performed using DESeq2 v1.36.0 in R.
Assembly: GRCm39/mm39 (Ensembl release 107)
Supplementary files format and content: Tab-delimited text file containing gene symbols and raw read counts for each sample. File:count_matrix_clean_Symbol.csv

source_name: testis

growth_protocol: Six-week-old male NSG mice were housed under specific pathogen-free (SPF) conditions at 22 ± 2°C, 50 ± 5% humidity with a 12/12-hour light/dark cycle. A B-ALL patient-derived xenograft (PDX) model was established via tail vein injection of 4×10⁵ PDX-derived B-ALL cells. Mice were grouped based on leukemia infiltration index.

extract_protocol:
Total RNA was extracted from snap-frozen mouse testis tissues using TRIzol reagent (Beyotime). RNA integrity was assessed via Agilent Bioanalyzer (RIN > 7.0), and RNA purity was verified by A260/A280 ratio (1.8–2.0).
RNA sequencing libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB, USA) according to the manufacturer's protocol. Briefly, mRNA was enriched using oligo-dT beads, fragmented, and reverse transcribed into cDNA. After end repair, adapter ligation, and PCR amplification, libraries were size-selected and quantified using Qubit and Agilent Bioanalyzer.

treatment_protocol: Vincristine sulfate (0.5 mg/kg) was administered intraperitoneally once weekly for three weeks, starting on day 69 post-modeling. Control groups received equivalent volumes of sterile saline.

value: testis

value: mixed testicular cells

value: NOD scid gamma (NSG)

value: vincristine + high B-ALL infiltration


title: Testis, High-VCR, rep 4

description:
Library name: A-113
High-VCR_4


title: CAF2_PA3

description: Library name: CAF2_PA3


title: CAF1_PA1

description: Library name: CAF1_PA1


title: CAF2_CON3

description: Library name: CAF2_CON3


title: CAF2_PA2

description: Library name: CAF2_PA2


title: Testis, Low-VCR, rep 4

description:
Library name: A-105
Low-VCR_4

value: vincristine + low B-ALL infiltration


title: Testis, High-VCR, rep 2

description:
Library name: A-29
High-VCR_2


title: Testis, High-VCR, rep 1

description:
Library name: A-26
High-VCR_1


title: Testis, VCR-treated, rep 1

description:
Library name: A-5
VCR_1

value: vincristine


title: Testis, Low-VCR, rep 3

description:
Library name: A-103
Low-VCR_3


title: Testis, B-ALL PDX model, rep 3

description:
Library name: A-102
ALL_3

value: B-ALL engraftment


title: Testis, Low-VCR, rep 1

description:
Library name: A-27
Low-VCR_1


title: Testis, B-ALL PDX model, rep 4

description:
Library name: A-116
ALL_4


title: CAF1_PA3

description: Library name: CAF1_PA3


title: Testis, VCR-treated, rep 4

description:
Library name: A-8
VCR_4


title: Testis, normal control, rep 4

description:
Library name: A-4
NC_4

value: normal control


title: Testis, B-ALL PDX model, rep 2

description:
Library name: A-33
ALL_2


title: Testis, B-ALL PDX model, rep 1

description:
Library name: A-28
ALL_1


title: Testis, VCR-treated, rep 2

description:
Library name: A-6
VCR_2


title: Testis, normal control, rep 2

description:
Library name: A-2
NC_2


title: Testis, normal control, rep 1

description:
Library name: A-1
NC_1


title: Model-1

city: Nanjing

first: po

last: hu

state: jiangsu

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

institute: 南京中医药大学

description:
Library name: sample5
Model-1_FPKM

data_processing:
Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
Use HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Assembly: Ensembl
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: xls file includes FPKM values for each Sample

source_name: ear

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies. Three micrograms of RNA were used as input material for the RNA sample preparations.
Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare forhybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA).DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

value: ear


title: Model-4

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample8
Model-4_FPKM


title: IsoL-4

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample12
IsoL-4_FPKM

value: Isoliensinine


title: Testis, normal control, rep 3

description:
Library name: A-3
NC_3


title: Model-3

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample7
Model-3_FPKM


title: Model-2

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample6
Model-2_FPKM


title: IsoL-3

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample11
IsoL-3_FPKM


title: 11-23-21_nonTh9_2-3_S8

city: Pittsburgh

first: Daniella

last: Schwartz

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

description:
Library name: Sample 8
FPKM.INFER_mice_Tcells.txt

data_processing:
Fastq files were processed with bcl2fastq v.2.20.0.422. Reads of 50 bases were processed using the nextflow-core pipeline [9] (https://nf-co.re/rnaseq/2.0). Adaptor sequences were trimmed (Trim Galore) and mapped to mouse transcriptome mm10 or human transcriptome GRCh38 (STAR). Gene expression values (fragments per kilobase exon per million mapped reads; tags per million mapped reads; counts) were generated using RSEM.
Assembly: mm10 (murine Th9 cells)
Assembly: GRCh38 (IL-9-treated endothelial cells)
Supplementary files format and content: tab delimited text (.txt) file (FPKM.*cells.txt) contains Fragments Per Kilobase of transcript per Million mapped reads

source_name: Splenic IL-9-negative CD4+ T cells

growth_protocol:
For murine Th9 cells: N/A
Primary human aortic endothelial cells (HAoEC) from >9 donors (PromoCell) were cultured in endothelial growth media (Promocell) and passaged up to 9 times

extract_protocol:
Sorted cells were lysed in Trizol, and RNA was extracted per the manufacturer's protocol
Libraries for mRNA-sequencing were prepared using the NEBNext Ultra II Directional RNA-seq Library kit. Samples were sequenced on a NovaSeq 6000, paired end (PE), for 50 cycles .
HAoEC were lysed in Trizol, and RNA was extracted per the manufacturer's protocol
Libraries for mRNA-sequencing were prepared using the NEBNext Ultra II Directional RNA-seq Library kit. Samples were sequenced on a NovaSeq 6000, paired end (PE), for 50 cycles .

treatment_protocol:
INFER (IL-9 reporter) mice received daily topical 5% Imiquimod (IMQ, Glenmark 60 mg) or Vanicream on shaved dorsal skin for three 5-day cycles with 13-day recovery periods (6 weeks total).
Spleens were extracted from IL-9 reporter mice (INFER) and homogenized in RPMI with DNAse. After RBC lysis (ACK buffer), organ suspensions were transferred to 96-well plates and stained with DAPI and cell surface antibodies. Live, doublet-excluded cells were sorted for CD45.2+/TCR-beta+/CD4+/CD8-/CD44+ cells, then for GFP+ (Th9) and GFP- (non-Th9) cells.
HAoEC were treated for 14 hours with human recombinant IL-9 100ng/mL vs. vehicle control.

value: Splenic IL-9-negative CD4+ T cells

value: INFER (IL-9 reporter) het

value: Imiquimod (in vivo)


title: S2_Th9_S11

description:
Library name: Sample 5
FPKM.INFER_mice_Tcells.txt

source_name: Splenic IL-9+ CD4+ T cells

value: Splenic IL-9+ CD4+ T cells


title: Testis, VCR-treated, rep 3

description:
Library name: A-7
VCR_3


title: Blank-4

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample4
Blank-4_FPKM


title: IsoL-2

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample10
IsoL-2_FPKM


title: IsoL-1

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample9
IsoL-1_FPKM


title: Testis, Low-VCR, rep 2

description:
Library name: A-31
Low-VCR_2


title: S1_nonTh9_S10

description:
Library name: Sample 9
FPKM.INFER_mice_Tcells.txt


title: Blank-3

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample3
Blank-3_FPKM


title: 11-09-21_nonTh9_2_S4

description:
Library name: Sample 7
FPKM.INFER_mice_Tcells.txt


title: S2_nonTh9_S12

description:
Library name: Sample 10
FPKM.INFER_mice_Tcells.txt


title: Blank-2

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample2
Blank-2_FPKM


title: Blank-1

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample1
Blank-1_FPKM


title: 11-23-21_Th9_2-3_S7

description:
Library name: Sample 3
FPKM.INFER_mice_Tcells.txt


title: 11-09-21_nonTh9_1_S2

description:
Library name: Sample 6
FPKM.INFER_mice_Tcells.txt


title: S1_Th9_S9

description:
Library name: Sample 4
FPKM.INFER_mice_Tcells.txt


title: 11-09-21_Th9_1_S1

description:
Library name: Sample 1
FPKM.INFER_mice_Tcells.txt


title: 11-09-21_Th9_2_S3

description:
Library name: Sample 2
FPKM.INFER_mice_Tcells.txt


title: db/db_4_zone3_3

city: Hangzhou

first: Rongfang

last: Guo

address: 866 Yuhangtang Road, Xihu District

institute: Zhejiang university

description:
Library name: sample171
DSP-1001660015391-D-G05

data_processing:
FASTQ files were converted to .DCC files and extracted as a matrix using the Nanostring NGS pipeline and GeoMxTools R package
Assembly: Mouse Whole Transcriptome Atlas RNA v1.0
Supplementary files format and content: .dcc: processed counts (used for input in GeoMxTools R package)
Library strategy: Spatial Transcriptomics

source_name: liver

extract_protocol:
Liver tissues were fixed in 10% neutral formalin for 24 hours and sectioned into 4-µm-thick slices after paraffin embedding. Following deparaffinization, rehydration, and antigen retrieval, sections were incubated overnight with a Mouse Whole Transcriptome Atlas oligonucleotide probe mix at 37 °C. The next day, after washing and blocking, fluorescently labeled antibodies were applied to all slides for morphological staining. After washing, the prepared slides were loaded into GeoMx Digital Spatial Profiler and scanned. Regions of interest (ROIs) were selected and segmented into areas of illumination (AOIs) based on the morphological staining.
Oligonucleotide barcodes were released upon exposure to ultraviolet light, then collected, amplified, and purified. Libraries were constructed and sequenced on the NovaSeq 6000 platform.

value: liver

tag: group

value: model


title: db/db_4_zone2_3

description:
Library name: sample170
DSP-1001660015391-D-G04


title: db/db_4_zone1_3

description:
Library name: sample169
DSP-1001660015391-D-G03


title: db/db_4_zone3_2

description:
Library name: sample168
DSP-1001660015391-D-G02


title: db/db_4_zone2_2

description:
Library name: sample167
DSP-1001660015391-D-G01


title: db/db_4_zone1_1

description:
Library name: sample163
DSP-1001660015391-D-F09


title: Met_3_zone3_3

description:
Library name: sample162
DSP-1001660015391-D-F08

value: Met

value: Metformin


title: db/db_4_zone2_1

description:
Library name: sample164
DSP-1001660015391-D-F10


title: db/db_4_zone3_1

description:
Library name: sample165
DSP-1001660015391-D-F11


title: Met_3_zone2_3

description:
Library name: sample161
DSP-1001660015391-D-F07


title: Met_3_zone1_3

description:
Library name: sample160
DSP-1001660015391-D-F06


title: Met_3_zone2_1

description:
Library name: sample155
DSP-1001660015391-D-F01


title: Met_2_zone3_3

description:
Library name: sample153
DSP-1001660015391-D-E11


title: Met_3_zone3_1

description:
Library name: sample156
DSP-1001660015391-D-F02


title: db/db_4_zone1_2

description:
Library name: sample166
DSP-1001660015391-D-F12


title: Met_2_zone1_2

description:
Library name: sample148
DSP-1001660015391-D-E06


title: Met_2_zone2_2

description:
Library name: sample149
DSP-1001660015391-D-E07


title: Met_2_zone3_1

description:
Library name: sample147
DSP-1001660015391-D-E05


title: Met_3_zone2_2

description:
Library name: sample158
DSP-1001660015391-D-F04


title: Met_3_zone3_2

description:
Library name: sample159
DSP-1001660015391-D-F05


title: Met_2_zone1_3

description:
Library name: sample151
DSP-1001660015391-D-E09


title: Met_2_zone1_1

description:
Library name: sample145
DSP-1001660015391-D-E03


title: Met_2_zone2_1

description:
Library name: sample146
DSP-1001660015391-D-E04


title: Met_1_zone3_3

description:
Library name: sample144
DSP-1001660015391-D-E02


title: Met_3_zone1_2

description:
Library name: sample157
DSP-1001660015391-D-F03


title: Met_1_zone1_3

description:
Library name: sample142
DSP-1001660015391-D-D12


title: Met_1_zone2_3

description:
Library name: sample143
DSP-1001660015391-D-E01


title: Met_1_zone2_2

description:
Library name: sample140
DSP-1001660015391-D-D10


title: Met_2_zone3_2

description:
Library name: sample150
DSP-1001660015391-D-E08


title: Met_1_zone3_2

description:
Library name: sample141
DSP-1001660015391-D-D11


title: D9P7_IL-9_14hr_S12

description:
Library name: Sample 18
FPKM.Endothelial_cells.txt

source_name: primay human aortic endothelial cells (HAoEC)


title: Met_1_zone1_2

description:
Library name: sample139
DSP-1001660015391-D-D09


title: Met_1_zone2_1

description:
Library name: sample137
DSP-1001660015391-D-D07


title: Met_1_zone3_1

description:
Library name: sample138
DSP-1001660015391-D-D08


title: D9P6_IL-9_14hr_S6

description:
Library name: Sample 17
FPKM.Endothelial_cells.txt

value: primay human aortic endothelial cells (HAoEC)


title: Met_2_zone2_3

description:
Library name: sample152
DSP-1001660015391-D-E10


title: Met_3_zone1_1

description:
Library name: sample154
DSP-1001660015391-D-E12


title: D4P6_IL-9_14hr_S3

description:
Library name: Sample 15
FPKM.Endothelial_cells.txt


title: Met_1_zone1_1

description:
Library name: sample136
DSP-1001660015391-D-D06


title: D9P7_control_S10

description:
Library name: Sample 14
FPKM.Endothelial_cells.txt

value: vehicle


title: D4P7_IL-9_14hr_S9

description:
Library name: Sample 16
FPKM.Endothelial_cells.txt


title: D9P6_control_S4

description:
Library name: Sample 12
FPKM.Endothelial_cells.txt


title: BBR_3_zone1_3

description:
Library name: sample133
DSP-1001660015391-D-D03

value: BBR

value: Berberine


title: Tau441 overexpression neuron, biol rep 2, line 8, day55, batch 1

city: Singapore

first: Yow-Yong

last: Tan

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

description:
Library name: Sample 26
D55_TFL8B

data_processing:
Genome indexes were generated using STAR v2.7.4a with Homo_sapiens.GRCh38.r110 genome before mapping sequencing reads.
The aligned sequencing reads were then counted by using HTseq before differential expression analysis using DESeq2
Assembly: Homo_sapiens.GRCh38.r110
Supplementary files format and content: CSV file includes raw counts for all samples with column name listed in the description

source_name: in vitro differentiated neurons

growth_protocol: Isogenic control (XCL-1, SC-001-1V) neuron and Tau overexpression neurons were cultured and differentiated according to manufacturer’s protocols (XCell Science Inc). NSCs were seeded at a density of 0.04×10^6 cells/cm2 on poly-ornithine (20 µg/mL) & laminin (10 µg/mL)-coated plates in NSC maintenance media on Day 0 (D0). Cells were then replenished with neuronal induction media on Day 1, 3 and 5. On Day 6 (D6), neuronal precursor cells (NPCs) were harvested and replated on poly-ornithine/laminin-coated wells with similar density in neuronal maturation medium. Neurons were cultured for designated duration with media change every alternate Day.

extract_protocol:
Total RNA from biological replicates were isolated using RNAzol®RT (Sigma-Aldrich).
Poly-A enriched libraries were prepared and sequenced by NovogeneAIT (Singapore)  via NovaSeq PE150 service according to company protocols.

value: in vitro differentiated neurons

value: Tau441 overexpression


title: BBR_3_zone2_2

description:
Library name: sample131
DSP-1001660015391-D-D01


title: Tau441 overexpression neuron, biol rep 3, line 8, day55, batch 1

description:
Library name: Sample 27
D55_TFL8C


title: Tau441 overexpression neuron, biol rep 1, line 8, day55, batch 1

description:
Library name: Sample 25
D55_TFL8A


title: BBR_3_zone1_2

description:
Library name: sample130
DSP-1001660015391-D-C12


title: Tau441 overexpression neuron, biol rep 3, line 20, day55, batch 2

description:
Library name: Sample 24
D55_TFL20C


title: BBR_3_zone3_1

description:
Library name: sample129
DSP-1001660015391-D-C11


title: BBR_3_zone2_1

description:
Library name: sample128
DSP-1001660015391-D-C10


title: BBR_3_zone1_1

description:
Library name: sample127
DSP-1001660015391-D-C09


title: Tau441 overexpression neuron, biol rep 2, line 20, day55, batch 2

description:
Library name: Sample 23
D55_TFL20B


title: Rb1_3_zone3_3

description:
Library name: sample126
DSP-1001660015391-D-C08

value: Ginsenoside Rb1


title: Tau441 overexpression neuron, biol rep 1, line 20, day55, batch 2

description:
Library name: Sample 22
D55_TFL20A


title: Rb1_3_zone2_3

description:
Library name: sample125
DSP-1001660015391-D-C07


title: Tau11i overexpression neuron, biol rep 2, line 6, day55, batch 1

description:
Library name: Sample 19
D55_T11i6B

value: Tau11i overexpression


title: Rb1_3_zone1_3

description:
Library name: sample124
DSP-1001660015391-D-C06


title: BBR_3_zone3_3

description:
Library name: sample135
DSP-1001660015391-D-D05


title: Tau11i overexpression neuron, biol rep 2, line 25, day55, batch 2

description:
Library name: Sample 16
D55_T11i25B


title: Rb1_3_zone2_2

description:
Library name: sample122
DSP-1001660015391-D-C04


title: BBR_3_zone3_2

description:
Library name: sample132
DSP-1001660015391-D-D02