title: JP7 Normoxia TIFM Replicate 3

description: Library name: FN3


title: Anti-IL17A-Ab treated 3, macrophage

status: Public on Apr 15 2026

type: SRA

city: Indianapolis

first: Santhosh Kumar

last: Pasupuleti

state: Indiana

department: Pediatrics

country: USA

institute: Indiana University School of Medicine

description: Library name: IL-17_3_macrophage

library_source: transcriptomic

data_processing:
The RNA-seq reads were mapped to the mouse genome mm10 using a STAR (v2.7.2a) RNA-seq aligner with the following parameter: “–outSAMmapqUnique” Uniquely mapped sequencing reads were assigned to GENCODE M22 gene using featureCounts (v2.0.1) with the following parameter: “-s 0 -p -Q 10 -O.”
Assembly: GRCm38/mm10
Supplementary files format and content: readCounts

molecule: polyA RNA

organism: Mus musculus

source_name: Visceral Adipose Tissue

growth_protocol: Leptin-deficient LepOb/Ob (Ob/Ob) mice (stock no. 000632) on a C57BL/6J background was obtained from The Jackson Laboratory. Wild-type (WT) C57BL/6 control mice and Shp2E76K/+;LysM-Cre⁺ mice (C57BL/6 background) were generated at the Indiana University School of Medicine core facility. Mice used in this study were approximately 12–14 weeks of age and included both males and females. Animals were maintained under standard housing conditions (12-hour light/12-hour dark cycle), group-housed by age, sex, and genotype, and provided food and water ad libitum. Experimental groups were matched for age and sex. We did not observe any difference in function or phenotypes between males and females.

extract_protocol:
Total RNA was isolated from bone marrow (BM) cells and adipose tissue macrophages (ATMs) collected from vehicle control and three treatment groups (n = 3 mice per group) using the Qiagen RNeasy Plus Micro Kit, following the manufacturer’s instructions. RNA quality was assessed using an Agilent Bioanalyzer, and samples with RNA integrity number (RIN) > 8 were used for downstream library preparation.
Paired-end RNA-seq libraries were prepared at the Indiana University Genomics Core Facility using standard Illumina protocols. Sequencing was performed on an Illumina NovaSeq X Plus platform. Each experimental group included three biological replicates, with approximately 30 million reads generated per sample. Library type - Unstranded (RSeQC: 1++,1--,2+-,2-+; 1+-,1-+,2++,2--)

treatment_protocol: The CD45.2+ donor BM cells from Shp2E76K/+;LysM-Cre+ mice were mixed with age matched Boy/J CD45.1+ competitor BM donor cells (with an equal number of viable total BM cells, 500K:500K). Recipient mice (Ob/Ob and WT) were lethally irradiated (700 cGy + 400 cGy) one day prior to transplantation (intravenous tail injection) of donor cell. At 8 weeks post-transplantation, the Ob/Ob recipient mice were then randomized and treated for 30 days with Vehicle, Beinaglutide, a GLP-1R agonist (3 mg/kg, s.c.), an anti–IL-17A antibody (200 μg/mouse, i.p., three times weekly), or the combination. Mice were harvested after 30 days of drug treatment.

tag: tissue

value: Visceral Adipose Tissue

tag: cell type

value: Macrophages

tag: genotype

tag: treatment

value: Anti-IL17A-Ab treated

tag: batch

value: Batch 1


title: wildtype, L1 stage, set 3, rep 2

city: Bethesda

first: Katherine

last: McJunkin

state: Maryland

address: 50 South Dr, Building 50 Room 3148

institute: NIDDK/ NIH

description: Library name: sAG419

library_source: other

data_processing:
Adaptor trimming with cutadapt(ver 5.0) with the -q 20 flag
Mapping with bowtie2 (ver. 2.5.3) with --no-unal --end-to-end –sensitive -U flags
BAM indexing with samtools (ver 1.21)
Raw counts generated from htseq (ver. 2.0.4) with --mode union --nonunique fraction -a 0 flags
Assembly: WS280
Supplementary files format and content: Matrix of raw counts from Htseq output

molecule: other

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: C. elegans were grown at 20C on NGM plates.

extract_protocol:
Total RNA was extracted using Trizol.
Libraries were prepared using the NEB small RNA kit with a modified protocol.

value: Whole worm

value: wild type


title: Anti-IL17A-Ab treated 2, macrophage

description: Library name: IL-17_2_macrophage


title: JP7 Normoxia TIFM Replicate 1

city: Farmington

first: Yasir

last: Suhail

state: Connecticut

address: 263 Farmington Avenue

department: BME

institute: UCHC

description: Library name: FN1

data_processing:
Aligned and transcript counts using Salmon
Assembly: Grch38
Supplementary files format and content: Reads estimation per transcript
Supplementary files format and content: Reads per gene

organism: Homo sapiens

extract_protocol:
Standard total RNA extraction using established laboratory protocols.
Standard RNA-seq library preparation using established commercial kits and manufacturer protocols.

tag: cell line

value: Cancer Cell

value: Normoxia

tag: medium

value: TIFM


title: Heart_FP66_24-hours

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

description: Library name: 104

data_processing:
Adapters were trimmed and low-quality reads (N20 threshold) were filtered using a custom quality control pipeline. FASTQC was used to evaluate read quality metrics.
Trimmed reads were mapped to mature miRNAs in miRBase v21 using Bowtie v1.0.0, allowing one mismatch.
Reads were also mapped to the mm9 reference genome (UCSC) for validation. Only reads mapping to annotated miRNAs were retained.
Read counts were normalized using TMM (Trimmed Mean of M-values) via edgeR (Bioconductor).
Differential expression was assessed using two-way ANOVA across dose and timepoint groups. PCA and clustering were used for exploratory analysis.
Assembly: Mus musculus mm9 (UCSC)
Supplementary files format and content: Processed data includes normalized miRNA counts for each sample across cortex, heart, and lung tissues. File format: .xlsx  with miRNAs as rows and samples as columns.

molecule: total RNA

source_name: Heart

growth_protocol: Adult male SKH-1 Elite mice (Charles River, strain code 477) were housed in standard vivarium conditions with food and water provided ad libitum. All procedures were conducted in AAALAC-accredited facilities under IACUC-approved protocols.

extract_protocol:
Tissues were homogenized in TRIzol Reagent (Invitrogen) and total RNA, including small RNAs, was extracted using the miRNeasy Mini Kit (QIAGEN) following the manufacturer’s protocol. RNA quality was assessed using NanoDrop, Qubit, and Agilent Tapestation 2200.
Small RNA libraries were prepared using the Illumina TruSeq Small RNA Sample Prep Kit. 3′ and 5′ adapters were ligated to RNA, followed by reverse transcription, PCR amplification, and gel-based size selection. Libraries were pooled and sequenced on an Illumina NextSeq 500 to generate 50 bp single-end reads.

treatment_protocol: Mice were administered subcutaneous fentanyl citrate at one of three doses: HNLD (62 mg/kg), LD10 (110 mg/kg), or LD50 (135 mg/kg). Sham controls received vehicle only. Mice were euthanized at 0h (40 min), 6h, 24h, or 7d post-injection for tissue collection.

value: Heart

tag: strain

value: SKH-1 Elite

tag: dose

tag: timepoint

value: 24 hours


title: wildtype, L1 stage, set 3, rep 3

description: Library name: sAG512


title: wildtype, L1 stage, set 3, rep 1

description: Library name: sAG377


title: Heart_FP64_24-hours

description: Library name: 103


title: JP7 Hypoxia TIFM Replicate 3

description: Library name: FH3

value: Hypoxia


title: Old 3

city: Bunkyo-ku

first: Satoshi

last: Kofuji

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Institute of Science Tokyo

description: Library name: Sample 9

data_processing:
DRAGEN Bio-IT Platform v4.3.6
Adaptor sequence was not removed. Sequence reads were mapped to Nothobranchius furzeri.Nfu 20140520.dna.toplevel.fa.gz release 112 using DRAGEN.
Read count extraction and normalization were performed using DRAGEN
Assembly: Nothobranchius furzeri.Nfu 20140520.dna.toplevel.fa.gz release 112
Supplementary files format and content: Tab-delimited text files for both gene expression and transcript expression include TPM values and read counts in each sample.

organism: Nothobranchius furzeri

source_name: Liver

extract_protocol:
Total RNA was purified using TRIzol Reagent (15596018, Invitrogen) according to the manufacturer’s instructions. Extracted RNA was incubated with DNase I (2270B; Takara, Shiga, Japan) to degrade the genomic DNA and further purified using RNeasy Mini Kits (74104; QIAGEN). The quality of RNA was initially assessed by electrophoresis on a 1.5% agarose gel, and subsequently by absorption spectrophotometry.
RNA libraries for RNA-seq were prepared using SMART-Seq mRNA Kit following manufacturer's protocols.

value: Liver

value: GRZ

value: Wild type

value: 23 to 24 weeks old


title: GLP1R agonist treated 3, macrophage

description: Library name: GLP1_3_macrophage

value: Visceral Adipose Tissue

value: GLP1R agonist treated


title: JP7 Hypoxia TIFM Replicate 2

description: Library name: FH2


title: Anti-IL17A-Ab treated 1, macrophage

description: Library name: IL-17_1_macrophage

value: Macrophages

value: Anti-IL17A-Ab treated


title: Heart_FP63_24-hours

description: Library name: 102


title: Old 2

description: Library name: Sample 8


title: GLP1R agonist treated 2, macrophage

description: Library name: GLP1_2_macrophage

value: Batch 1


title: THP-1 WT cells replicate 3

type: genomic

first: David

middle: M

last: Aronoff

address: 545 Barnhill Dr. EH 305

department: Department of Medicine

description: Cell free DNA from WT cells

hyb_protocol: Genomic DNA was subjected to bisulfite conversion and was amplified, fragmented and hybridized to human Infinium MethylationEPIC v2.0 BeadChip microarray (Illumina)

scan_protocol: Imaged with BeadArray reader with recommended illumina settings

data_processing: Raw IDAT files were processed using the R package SeSAMe (v1.22.2).

label: Cy3 and Cy5

molecule: genomic DNA

label_protocol: Standard Illimuna protocol

growth_protocol: THP-1 WT or FOLR2 KO cells were passaged and PMA treated in RPMI +10% FBS +1% antibiotic/antimycotic at 37C with 5% humidity.

extract_protocol: DNA was extracted from PMA treated cells with Qiagen QIAamp DNA Mini kit and concentration was measured with a Nanodrop spectrophotometer.

value: Monocyte/macrophage

value: WT

value: Unstimulated


title: Old 1

description: Library name: Sample 7


title: Hep3B Normoxia Control Replicate 3

description: Library name: A5

value: Cancer Cell

value: Normoxia

value: Control


title: THP-1 FOLR2 KO cells replicate 3

description: Cell free DNA from FRB-KO cells

value: FOLR2 KO


title: GLP1R agonist treated 1, macrophage

description: Library name: GLP1_1_macrophage


title: Hep3B Normoxia Control Replicate 2

description: Library name: A3


title: Vehicle 3, macrophage

description: Library name: Veh_3_macrophage

value: Vehicle


title: Adult 3

description: Library name: Sample 6

value: Liver

value: 12 weeks old


title: Heart_FP60_7-days

description: Library name: 99

value: Heart

value: SKH-1 Elite

value: 7 days


title: Vehicle 2, macrophage

description: Library name: Veh_2_macrophage

value: Visceral Adipose Tissue


title: THP-1 FOLR2 KO cells replicate 1

description: Cell free DNA from FRB-KO cells


title: Adult 2

description: Library name: Sample 5

value: GRZ

value: Wild type


title: Heart_FP59_7-days

description: Library name: 98


title: Hep3B Normoxia Control Replicate 1

description: Library name: A1


title: Adult 1

description: Library name: Sample 4


title: Hep3B Hypoxia Control Replicate 3

description: Library name: A6

value: Hypoxia


title: Wild type 3, macrophage

description: Library name: WT_3_macrophage

value: Macrophages

value: Batch 1


title: Heart_FP58_24-hours

description: Library name: 97

value: LOEL

value: 24 hours


title: Hep3B Hypoxia Control Replicate 2

description: Library name: A4

value: Cancer Cell


title: Vehicle 1, macrophage

description: Library name: Veh_1_macrophage


title: Heart_FP61_7-days

description: Library name: 100


title: Heart_FP57_24-hours

description: Library name: 96


title: Young 2

description: Library name: Sample 2

value: 6 weeks old


title: Young 3

description: Library name: Sample 3


title: Wild type 2, macrophage

description: Library name: WT_2_macrophage


title: THP-1 FOLR2 KO cells replicate 4

description: Cell free DNA from FRB-KO cells

value: Monocyte/macrophage

value: FOLR2 KO

value: Unstimulated


title: Wild type 1, macrophage

description: Library name: WT_1_macrophage


title: JP7 Hypoxia TIFM Replicate 1

description: Library name: FH1

value: TIFM


title: Heart_FP62_24-hours

description: Library name: 101

value: Heart


title: Young 1

description: Library name: Sample 1

value: Liver


title: Bon1 Normoxia Control Replicate 2

description: Library name: B3

value: Normoxia

value: Control


title: THP-1 WT cells replicate 1

description: Cell free DNA from WT cells

value: WT


title: Bon1 Normoxia Control Replicate 3

description: Library name: B5


title: GLP1R agnoist and Anti-IL17A-ab treated 3, BM

description: Library name: Combo_3_BM

source_name: Bone Marrow

value: Bone Marrow

value: Whole bone marrow cells

value: GLP1R agnoist and Anti-IL17A-ab treated


title: Heart_FP56_24-hours

description: Library name: 95

value: SKH-1 Elite


title: DRG CHS Sensitization (from 2 mice)

city: Toulouse

first: Lilian

last: Basso

address: INSERM UMR1291 – CNRS UMR5051 - University Toulouse III CHU Purpan – BP 3028

country: France

institute: INFINITY INSERM U1291

hyb_protocol: The Xenium samples underwent multiple rounds of fluorescent probe hybridization, imaging, and probe removal. The Xenium Analyzer captured a Z-stack of images every cycle and in every channel, which needed to be processed and stitched to build a spatial map of the transcripts across the tissue section. Decoding of transcripts was performed using a Xenium codebook ? a collection of codewords that were assigned to genes in the gene panel. In order to assign mRNAs to cells, the spatial boundaries of cells were defined by nuclear expansion. The image volumes from all cycles and channels were then aligned and stitched to build a coherent three-dimensional dataset of probe signals, which were decoded into transcript identities using a codebook mapping unique optical signatures (codewords) to genes. To assign transcripts to individual cells, nuclei were first segmented (via DAPI staining) and then cell boundaries were inferred by expanding each nucleus isotropically (up to ~15 µm) or until encountering adjacent cells, producing a 2 D projection of cell masks onto which the decoded transcripts were mapped

scan_protocol: Xenium In Situ Analyzer

data_processing: Data processed using Xenium Ranger software, Seurat (v4.4.0), and Xenium Spatial Analysis Toolkit (v0.1.0).

source_name: DRG sensibilized

label_protocol: Xenium Mouse Probe Set

extract_protocol: 10 µm-thick cryostat sections were prepared from PFA-fixed tissue embedded in OCT compound for Xenium analysis.

value: back skin


title: GLP1R agnoist and Anti-IL17A-ab treated 2, BM

description: Library name: Combo_2_BM

value: Batch 1


title: Hep3B Hypoxia Control Replicate 1

description: Library name: A2

value: Cancer Cell

value: Hypoxia


title: Heart_FP55_0-hour

description: Library name: 94

value: 0 hour


title: DRG CHS Challenge (from 2 mice)

source_name: DRG CHS D4


title: ATF3DTA D64 (mouse421)

source_name: Back skin CHS D64


title: Bon1 Hypoxia Control Replicate 3

description: Library name: B6


title: GLP1R agnoist and Anti-IL17A-ab treated 1, BM

description: Library name: Combo_1_BM


title: Heart_FP53_7-days

description: Library name: 92

value: LOEL

value: 7 days


title: THP-1 FOLR2 KO cells replicate 2

description: Cell free DNA from FRB-KO cells

value: Monocyte/macrophage

value: FOLR2 KO

value: Unstimulated


title: Anti-IL17A-Ab treated 3, BM

description: Library name: IL-17_3_BM

value: Anti-IL17A-Ab treated


title: Heart_FP54_24-hours

description: Library name: 93

value: Heart

value: 24 hours


title: Heart_FP52_7-days

description: Library name: 91


title: Bon1 Normoxia Control Replicate 1

description: Library name: B1

value: Normoxia

value: Control


title: Heart_FP51_24-hours

description: Library name: 90


title: ATF3DTA D64 (mouse417)


title: THP-1 WT cells replicate 4

description: Cell free DNA from WT cells

value: WT


title: THP-1 WT cells replicate 2

description: Cell free DNA from WT cells


title: Bon1 Hypoxia Control Replicate 2

description: Library name: B4


title: ATF3DTA D64 (mouse416)


title: Bon1 Hypoxia Control Replicate 1

description: Library name: B2


title: GLP1R agonist treated 3, BM

description: Library name: GLP1_3_BM

value: Bone Marrow

value: Whole bone marrow cells

value: GLP1R agonist treated


title: CT D64 (mouse419)

value: back skin


title: ATF3DTA D64 (mouse414)


title: Heart_FP49_6-hours

description: Library name: 89

value: SKH-1 Elite

value: 6 hours


title: Anti-IL17A-Ab treated 1, BM

description: Library name: IL-17_1_BM

value: Batch 1


title: Heart_FP44_6-hours

description: Library name: 85


title: Vehicle 3, BM

description: Library name: Veh_3_BM

value: Vehicle


title: HBEC_U2AF1wt-S34F_RiboSeq_Disome_Rep2

first: Gloria

last: R Garcia

email: gloria.garcia@nih.gov, garciagr@vt.edu

address: Bldg 41, rm B303

institute: NIH

description:
Library name: Sample_11
Ribosome profiling (Ribo-seq), disome fraction.

data_processing:
Raw sequencing data were deposited as FASTQ files. No processed data files are included in this submission.
Assembly: hg19
Supplementary files format and content: Gene-level ribosome footprint coverage values generated by StringTie from Ribo-seq data.
Library strategy: Ribo-Seq

molecule: cytoplasmic RNA

source_name: Lung

growth_protocol: HBEC lines were cultured in Keratinocyte Serum Free Media supplemented with bovine pituitary extract and EGF as prescribed by the manufacturer (Invitrogen, Carlsbad, CA) at 37 oC and 5% CO2

extract_protocol:
Ribosome-protected RNA fragments were isolated from cycloheximide-treated human bronchial epithelial cells following RNase I digestion of lysates and sucrose cushion ultracentrifugation. RNA fragments associated with monosomes and disomes were recovered from ribosomal pellets using the mirVana microRNA isolation kit (Thermo Fisher Scientific).
Ribosome-protected RNA fragments were converted into sequencing libraries by ligation of 3′ and 5′ adapters, reverse transcription, PCR amplification, and size selection of monosome and disome footprints, following established ribosome profiling protocols.

value: Lung

value: epithelial cell


title: HBEC_U2AF1wt-S34F_RiboSeq_Monosome_Rep2

description:
Library name: Sample_8
Ribosome profiling (Ribo-seq), monosome fraction.


title: Heart_FP47_0-hour

description: Library name: 87

value: LOEL

value: 0 hour


title: Heart_FP43_7-days

description: Library name: 84

value: Heart

value: 7 days


title: CT D64 (mouse420)


title: HBEC_U2AF1wt-S34F_RiboSeq_Disome_Rep1

description:
Library name: Sample_10
Ribosome profiling (Ribo-seq), disome fraction.


title: Anti-IL17A-Ab treated 2, BM

description: Library name: IL-17_2_BM

value: Anti-IL17A-Ab treated


title: GLP1R agonist treated 1, BM

description: Library name: GLP1_1_BM


title: Heart_FP45_6-hours

description: Library name: 86


title: Heart_FP42_6-hours

description: Library name: 83


title: Vehicle 1, BM

description: Library name: Veh_1_BM


title: HBEC_U2AF1wt-S34F_RiboSeq_Monosome_Rep1

description:
Library name: Sample_7
Ribosome profiling (Ribo-seq), monosome fraction.


title: GLP1R agonist treated 2, BM

description: Library name: GLP1_2_BM


title: CT D64 (mouse412)


title: Heart_FP41_7-days

description: Library name: 82


title: Heart_FP48_0-hour

description: Library name: 88


title: HBEC_U2AF1wt-wt_RiboSeq_Disome_Rep3

description:
Library name: Sample_6
Ribosome profiling (Ribo-seq), disome fraction.


title: CT D64 (mouse413)


title: HBEC_U2AF1wt-wt_RiboSeq_Disome_Rep2

description:
Library name: Sample_5
Ribosome profiling (Ribo-seq), disome fraction.


title: HBEC_U2AF1wt-S34F_RiboSeq_Monosome_Rep3

description:
Library name: Sample_9
Ribosome profiling (Ribo-seq), monosome fraction.


title: HBEC_U2AF1wt-S34F_RiboSeq_Disome_Rep3

description:
Library name: Sample_12
Ribosome profiling (Ribo-seq), disome fraction.


title: ATF3DTA D21 (mouse449)

source_name: Back skin CHS D21


title: ATF3DTA D21 (mouse444)


title: HBEC_U2AF1wt-wt_RiboSeq_Disome_Rep1

description:
Library name: Sample_4
Ribosome profiling (Ribo-seq), disome fraction.


title: Vehicle 2, BM

description: Library name: Veh_2_BM


title: Wild type 3, BM

description: Library name: WT_3_BM


title: Heart_FP40_7-days

description: Library name: 81


title: CT2 (mouse 69)

source_name: Back skin CHS D4


title: Wild type 2, BM

description: Library name: WT_2_BM


title: GINIP-DTR2 (mouse 70)


title: CT D21 (mouse466)


title: Heart_FP39_24-hours

description: Library name: 80

value: 24 hours


title: HBEC_U2AF1wt-wt_RiboSeq_Monosome_Rep3

description:
Library name: Sample_3
Ribosome profiling (Ribo-seq), monosome fraction.


title: Wild type 1, BM

description: Library name: WT_1_BM


title: Heart_FP38_6-hours

description: Library name: 79


title: HBEC_U2AF1wt-wt_RiboSeq_Monosome_Rep2

description:
Library name: Sample_2
Ribosome profiling (Ribo-seq), monosome fraction.


title: In vitro-cultured primitive macrophage progenitors (PMPs) after 12 days under no doxycycline (control) conditions

city: Piscataway

first: Ziyuan

last: Ma

state: NJ

address: 604 Allison Rd

department: Cell Biology and Neuroscience

institute: Rutgers University

description:
Library name: PMP-12d-no-dox
10x Genomics 3' NextGEM v3.1

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were aligned to the human GRCh38 reference genome using Cell Ranger (v9.0.1).
Assembly: GRCh38
Supplementary files format and content: Filtered gene expression count matrix generated by Cell Ranger, stored in HDF5 format.

source_name: H1 ESC

growth_protocol: Human primitive macrophage progenitors (PMPs) were generated from the CRISPR-Cas9-mediated doxycycline-inducible hNEUROG2 expression H1 ESC line using a previously established protocol. Yolk sac embryoid bodies (YS-EBs) were generated by treating them with mTeSR 1 medium (STEMCELL Technologies) supplemented with bone morphogenetic protein 4 (BMP4, 50 ng/ml), vascular endothelial growth factor (VEGF, 50 ng/ml), and stem cell factor (SCF, 20 ng/ml) for 6 days. To induce myeloid differentiation, the YS-EBs were plated on dishes with X-VIVO 15 medium (Lonza) supplemented with interleukin-3 (IL-3, 25 ng/ml) and macrophage colony-stimulating factor (M-CSF, 100 ng/ml). Four to six weeks after plating, human PMPs emerged in the supernatant and continued to be produced for more than three months.

extract_protocol:
Single nuclei were prepared using Nuclei PURE Prep kit (Sigma) following the manufacturer’s protocols.
Isolated nuclei suspensions were loaded onto the Chromium Controller for snRNA-seq library preparation. Libraries from 12-day samples were generated using the Chromium Next GEM Single Cell 3′ Kit v3.1, 5-day samples were processed using the Chromium GEM-X Single Cell 3′ Kit v4 in combination with the Dual Index Kit TT Set A, following the manufacturer’s protocols. Library quality and fragment size distributions were assessed using an Agilent 2100 Bioanalyzer. Sequencing was performed on an Illumina NovaSeq 6000 system using S4 flow cells.

treatment_protocol: Cultured PMP cells were treated with doxycycline (2 μg/mL) for 5 or 12 days.

value: H1 ESC

value: Primitive macrophage progenitors (PMPs)

value: 12-day untreated control


title: GINIP-DTR1 (mouse 67)


title: Heart_FP33_6-hours

description: Library name: 78


title: CT D21 (mouse465)


title: Heart_FP32_0-hour

description: Library name: 77


title: Donor 330

type: RNA

city: Dallas

first: Douglas

last: Strand

state: TX

address: 5323 Harry Hines Blvd JA5.150 JA5.150

department: Urology

institute: UT Southwestern Medical Center

hyb_protocol: Hybridization, imaging, and washing was performed on the Xenium Analyzer.

scan_protocol: Xenium in situ analyzer

data_processing: Data processed using Xenium Onboard Analysis, followed by filtering and clustering with the Python modules Scanpy and SpatialData.

label: xenium

source_name: female urethra

label_protocol: Xenium panel hMulti_v1 + 100 custom genes (see gene_panel.json file for full specification)

extract_protocol: 10 µm FFPE sections were mounted on Xenium slides. Manufacturer recommendations for sample processing and operation of the Xenium analyzer were followed for downstream sample preparation and data collection.

tag: Sex

value: female

tag: orientation

value: sagittal


title: Heart_FP29_6-hours

description: Library name: 75

value: SKH-1 Elite


title: TIM045X-048X

city: Cincinnati

first: Timothy

last: Phoenix

state: OH

address: 231 Albert Sabin Way, MSB 3005M

department: Division of Pharmaceutical Sciences

institute: University of Cincinnati

description:
Library name: sample_045-048
10X Genomics

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were carried out in Cell Ranger v9.0.0 (10X Genomics, https://www.10xgenomics.com/support/software/cell-ranger/latest)
Samples were multiplexed using GEM-X Flex chemistry. Raw sequencing files are shared across multiple samples; sample identity is resolved via probe barcode as indicated in supplemental file.
Assembly: Mus musculus mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Glioma tumor

extract_protocol:
Cells were isolated using the GEM-X Flex Sample Preparation v2 kit (10x Genomics, #PN-1000781)
Libraries were prepared using the 10x Genomics Chromium GEM-X Flex platform. Sequencing was performed in paired-end mode. Read 1 contains cell barcode and UMI sequences, while Read 2 contains cDNA inserts representing captured transcripts.

value: Glioma tumor


title: Donor 216

value: transverse


title: HBEC_U2AF1wt-wt_RiboSeq_Monosome_Rep1

description:
Library name: Sample_1
Ribosome profiling (Ribo-seq), monosome fraction.


title: CT1 (mouse 68)

value: back skin


title: Heart_FP30_0-hour

description: Library name: 76


title: rna-VNO-Tex15KO-7134-102125

first: Kevin

last: Monahan

department: Molecular Biology and Biochemistry

description:
Library name: VNO.Tex15KO_4.0
VNO bulk RNA-seq from an adult Tex15 knockout mouse

data_processing:
Adapters were removed from sequencing data using Trim Galore (v0.6.5) and Cutadapt (v5.1).
STAR (v2.7.11b) was used to align trimmed reads to the mouse genome (mm10). Transcriptome alignment used a custom gtf annotation file based upon ENSEMBL release GRCm38.102, but updated to include expert curated olfactory receptor and vomeronasal receptor gene annotation from Barnes et al 2020 and  Dietschi et al 2022, respectively.
Bigwig signal tracks (.bw) were generated with Deeptools bamCoverage (v3.5.5) (--minMappingQuality 30 --binSize 1 -p 24 --normalizeUsing BPM).
Assembly: mm10
Supplementary files format and content: Bam files of aligned reads
Supplementary files format and content: Bigwig files of RNA-seq signal.

source_name: Vomeronasal Organ

extract_protocol:
The vomeronasal organ was dissected, chopped into pieces, and then RNA was extracted using Trizol. The extracted RNA was purified using the Zymo Research Direct-zol RNA Miniprep Kits (Cat# R2050). The RNA isolate was assessed on a Thermo Fisher Scientific Nanodrop One for concentration. It was then quality controlled for RIN in an Agilent Tapestation 4150.
Samples which had >7 RIN were sent to Admera (South Plainfield, NJ, USA) for DNAse treatment, PolyA selection, library preparation (NEB Ultra II Directional RNA) and sequencing (Illumina 2x150).

treatment_protocol: Adult mice were sacrificed using CO2 followed by cervical dislocation.

value: Vomeronasal Organ

value: m

tag: age (weeks)


title: In vitro-cultured primitive macrophage progenitors (PMPs) following 12 days of doxycycline-induced NEUROG2 expression

description:
Library name: PMP-12d-with-dox
10x Genomics 3' NextGEM v3.1

value: CRISPR-Cas9-mediated doxycycline-inducible hNEUROG2 expression

value: 12-day doxycycline treatment


title: TIM055-66

description:
Library name: sample_049-60
10X Genomics


title: rna-VNO-Tex15KO-7131-101725

description:
Library name: VNO.Tex15KO_2.0
VNO bulk RNA-seq from an adult Tex15 knockout mouse


title: Heart_FP25_0-hour

description: Library name: 73

value: Heart

value: LOEL

value: 0 hour


title: In vitro-cultured primitive macrophage progenitors (PMPs) after 5 days under no doxycycline (control) conditions

description:
Library name: PMP-5d-no-dox
10x Genomics 3' GEM-X v4

value: 5-day untreated control


title: Heart_FP27_7-days

description: Library name: 74

value: 7 days


title: rna-VNO-Tex15HET-7137-101725

description:
Library name: VNO.Tex15Het_4.0
VNO bulk RNA-seq from an adult Tex15 heterozygous mouse

value: f


title: Heart_FP24_7-days

description: Library name: 72


title: rna-VNO-Tex15KO-7136-101725

description:
Library name: VNO.Tex15KO_1.0
VNO bulk RNA-seq from an adult Tex15 knockout mouse


title: In vitro-cultured primitive macrophage progenitors (PMPs) following 5 days of doxycycline-induced NEUROG2 expression

description:
Library name: PMP-5d-with-dox
10x Genomics 3' GEM-X v4

value: H1 ESC

value: Primitive macrophage progenitors (PMPs)

value: 5-day doxycycline treatment


title: rna-VNO-Tex15KO-7132-101725

description:
Library name: VNO.Tex15KO_3.0
VNO bulk RNA-seq from an adult Tex15 knockout mouse


title: Donor 93

source_name: prostatic urethra

value: male

value: sagittal


title: rna-VNO-Tex15HET-7135-101725

description:
Library name: VNO.Tex15Het_3.0
VNO bulk RNA-seq from an adult Tex15 heterozygous mouse


title: shCtr-A

city: Jinan City

first: kainan

last: wu

state: Shandong

address: No. 107, Wenhua West Road, Lixia District, Jinan City, Shandong Province, China

country: China

institute: DeparQilu Hospital of Shandong University

description:
Library name: sample19
shCtr-A
All Comparisons.xlsx

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs.
circRNA: The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
Assembly: UCSC HG19
Supplementary files format and content: All_methylated_sites.circRNA.xlsx
Supplementary files format and content: All Comparisons.xlsx

source_name: FaDu

extract_protocol:
The concentration of RNA in each sample was measured using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). The OD260/OD280 ratio was used as an indicator of RNA purity. RNA samples were considered pure if the OD260/OD280 ratio ranged from 1.8 to 2.1, with the corresponding QC Results marked as "Pass". Denaturing agarose gel electrophoresis was performed to assess RNA integrity and genomic DNA (gDNA) contamination. Library quality was evaluated using an Agilent 2100 Bioanalyzer.
Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina Novaseq instrument with 150bp paired end reads

value: FaDu

value: hypopharyngeal squamous cell carcinoma

value: WT

value: Blank control


title: rna-VNO-Tex15HET-6416-41825

description:
Library name: VNO.Tex15Het_1.0
VNO bulk RNA-seq from an adult Tex15 heterozygous mouse

value: Vomeronasal Organ

value: m


title: E19.5 Semi-allogeneic Pregnancy Placental Mononuclear Cells, Batch 2

city: Yerevan

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Yerevan

address: Kogbatsi 1

department: Research and Development

country: Armenia

institute: PerikLab

description: Library name: Batch_2_Pla_19_A

data_processing:
The fast module of SeekSoulTools was employed to map raw FASTQ files to the mm10 reference genome, generating 10X-compatible feature, barcode, and matrix files containing gene-level RNA data.
Assembly: mm10 (https://seekgene-public.oss-cn-beijing.aliyuncs.com/software/data/reference/mm10.tar.gz)
Supplementary files format and content: 10X-like feature, barcode, and matrix files containing RNA data.
To quantify isoform-level expression, a Salmon-Alevin adaptation specifically tailored for scFAST-seq data was used to generate cell-by-isoform matrices (https://github.com/Perik-Zavodskii/IsoCaller-scFAST-seq-SeekOneDD).
Assembly: Ensembl release 115 cDNA reference (https://ftp.ensembl.org/pub/release-115/fasta/mus_musculus/cdna/ and https://app.flow.bio/data/657359233329314859/).
Supplementary files format and content: 10X-like feature, barcode, and matrix files containing Isoform data.

source_name: Placenta

extract_protocol:
For placental mononuclear cell isolation, fetuses with attached placentas were obtained and transferred to sterile Petri dishes, and placentas were carefully dissected from the embryos. Placentas from each individual mouse were pooled and placed in cold RPMI-1640 medium supplemented with antibiotics and then dissociated into single-cell suspensions using the SeekMate Tissue Dissociation A Pro kit (K01801-08, SeekGene, China) according to the manufacturer’s instructions. The resulting suspensions were washed in 5-10 mL phosphate-buffered saline and subjected to density gradient centrifugation using Ficoll-Urografin (density 1.119 g/mL) for 30 min at 322 × g. Mononuclear cells were collected and washed twice with PBS prior to downstream analyses.
The SeekOne® DD Single Cell Full-length RNA Transcriptome-seq Kit (Protocol v1.2) was utilized for scFAST-seq library construction.

value: Mononuclear cells

value: Placenta

tag: gestation day

tag: pregnancy type

value: Semi-Allogeneic

tag: instrument

value: SeekOne DD


title: E19.5 Syngeneic Pregnancy Placental Mononuclear Cells, Batch 2

description: Library name: Batch_2_Pla_19_S

value: Syngeneic


title: Heart_FP23_24-hours

description: Library name: 71

value: Heart

value: SKH-1 Elite

value: 24 hours


title: rna-VNO-Tex15HET-6349-42525

description:
Library name: VNO.Tex15Het_2.0
VNO bulk RNA-seq from an adult Tex15 heterozygous mouse

value: f


title: Donor 202

value: male

value: transverse


title: shCtr-C

description:
Library name: sample21
shCtr-C
All Comparisons.xlsx

value: FaDu


title: shCtr-B

description:
Library name: sample20
shCtr-B
All Comparisons.xlsx

value: hypopharyngeal squamous cell carcinoma


title: Heart_FP21_0-hour

description: Library name: 69

value: 0 hour


title: Heart_FP22_6-hours

description: Library name: 70

value: 6 hours


title: E12.5 Syngeneic Pregnancy Placental Mononuclear Cells, Batch 1

description: Library name: Batch_1_Pla_12_S


title: E19.5 Semi-allogeneic Pregnancy Placental Mononuclear Cells, Batch 1

description: Library name: Batch_1_Pla_19_A


title: Sh3-2B

description:
Library name: sample17
sh3-2B
All Comparisons.xlsx

value: IGF2BP3 knockdown


title: Sh3-2A

description:
Library name: sample16
sh3-2A
All Comparisons.xlsx


title: Heart_FP20_0-hour

description: Library name: 68


title: Heart_FP19_24-hours

description: Library name: 67


title: E12.5 Semi-allogeneic Pregnancy Placental Mononuclear Cells, Batch 1

description: Library name: Batch_1_Pla_12_A


title: Sh3-1C

description:
Library name: sample15
sh3-1C
All Comparisons.xlsx


title: Heart_FP17_7-days

description: Library name: 66

value: 7 days


title: Tfh cells from DKO-severe Foxp3-Cre Tet2/3fl/fl mice-2

city: La Jolla

first: Anjana

last: Rao

state: California

address: 9420 Athena Circle

department: Department of Signaling and Gene Expression

institute: La Jolla Institute for Immunology

description: Library name: Tfh cells from DKO-severe Foxp3-Cre Tet2/3fl/fl-2

library_source: genomic

data_processing:
Data were processed following the duet analysis pipeline v1.4.1.
Downstream analysis of the data was performed as in Füllgrabe J et al. Simultaneous sequencing of genetic and epigenetic bases in DNA. Nat Biotechnol. 2023 Oct;41(10):1457–64.
Assembly: mm10
Supplementary files format and content: Modified base calls

source_name: spleen and peripheral lymph nodes

extract_protocol:
genomic DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen, #69504).
The duet multiomics solution evoC method (6-base sequencing) was performed according to the manufacturer’s instructions (duet exoC User guide v.3), using 60-70 ng of sonicated genomic DNA as starting material (n=2). Libraries were sequenced at the UCSD Institute for Genomic Medicine Genomics Center using Illumina NovaSeq X Plus pair end 150 bp platform.

value: spleen and peripheral lymph nodes

value: splenocytes and lymphocytes

value: Foxp3Cre Tet2/3 flox/flox (DKO-moderate)


title: primed Foxp3Cre Bcl6fl/fl (Bcl6FC) mouse 2

first: Prasida

last: Holla

state: IN

address: 1044 W walnut St

department: Pediatric Infectious Diseases

description: Library name: pB2_db-pass

data_processing:
Raw BCR sequences were annotated and assembled using TRUST4
Fasta files from the TRUST4 output were aligned to mouse germline BCRs using the Immcantation framework's changeo/IgBLAST tool via the Singularity container
Assembly: mm10/ GRCm38
Supplementary files format and content: The data in the *dp-pass.tsv files is derived from alignment of fasta files containing TRUST4 outputs to germline B cell receptor sequences from https://www.imgt.org/ using the Immcantation framework's changeo/IgBLAST tool. The format is Adaptive Immune Receptor Repertoire (AIRR) files - https://www.antibodysociety.org/the-airr-community/airr-data-commons/.

source_name: mesenteric lymph node

growth_protocol: Mice were housed in Indiana Universty animal facility

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro (Qiagen)
per manufacturer's instructions (Takara Bio SMART-seq Mouse BCR)

treatment_protocol: either untreated or primed with ovalbumin (Sigma) plus 10 μg of cholera toxin (CT)

value: mesenteric lymph node

value: Germinal center B cells

value: Foxp3CreYFPBcl6fl/fl  C57BL/6


title: primed Foxp3Cre Bcl6fl/fl (Bcl6FC) mouse 3

description: Library name: pB3_db-pass

value: ovalbumin (Sigma) plus 10 μg of cholera toxin (CT)


title: Sh3-1B

description:
Library name: sample14
sh3-1B
All Comparisons.xlsx


title: Sh3-2C

description:
Library name: sample18
sh3-2C
All Comparisons.xlsx


title: primed ç mouse 1

description: Library name: pB1_db-pass


title: Tfh cells from DKO-severe Foxp3-Cre Tet2/3fl/fl mice-1

description: Library name: Tfh cells from DKO-severe Foxp3-Cre Tet2/3fl/fl-1


title: Cortex_FPB2_6-hours

description: Library name: 64

source_name: Cortex

value: Cortex

value: SKH-1 Elite


title: primed wild type mouse 3

description: Library name: pWT3_db-pass

value: Foxp3Cre-YFP (Foxp3-wt) C57BL/6


title: Heart_FP16_7-days

description: Library name: 65

source_name: Heart

value: Heart


title: shCtr-C IP

description:
Library name: sample12
shCtr-C
All_methylated_sites.circRNA.xlsx

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs.
circRNA: The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
Assembly: UCSC HG19
Supplementary files format and content: All_methylated_sites.circRNA.xlsx
Supplementary files format and content: All Comparisons.xlsx
Library strategy: MeRIP-Seq

value: FaDu

value: WT

value: Blank control


title: Naïve CD4+ T cells from Foxp3Cre WT mice-2

description: Library name: Naïve CD4+ T cells from Foxp3Cre WT-2

value: Foxp3Cre WT


title: primed wild type mouse 1

description: Library name: pWT1_db-pass


title: Naïve CD4+ T cells from Foxp3Cre WT mice-1

description: Library name: Naïve CD4+ T cells from Foxp3Cre WT-1


title: naïve Foxp3Cre Bcl6fl/fl (Bcl6FC) mouse 3

description: Library name: nB3_db-pass

value: untreated


title: Cortex_FP95_0-hour

description: Library name: 62

value: 200uL Ringer's

value: Control

value: 0 hour


title: primed wild type mouse 2

description: Library name: pWT2_db-pass


title: Cortex_FP96_0-hour

description: Library name: 63


title: naïve Foxp3Cre Bcl6fl/fl (Bcl6FC) mouse 2

description: Library name: nB2_db-pass


title: Sh3-1A

description:
Library name: sample13
sh3-1A
All Comparisons.xlsx

value: hypopharyngeal squamous cell carcinoma

value: IGF2BP3 knockdown


title: Cortex_FP94_24-hours

description: Library name: 61

value: 24 hours


title: shCtr-B IP

description:
Library name: sample10
shCtr-B
All_methylated_sites.circRNA.xlsx


title: shCtr-C Input

description:
Library name: sample11
shCtr-C
All_methylated_sites.circRNA.xlsx


title: naïve Foxp3Cre Bcl6fl/fl (Bcl6FC) mouse 1

description: Library name: nB1_db-pass

value: mesenteric lymph node

value: Germinal center B cells

value: Foxp3CreYFPBcl6fl/fl  C57BL/6


title: 5w-AR113Q4

city: Ann Arbor

first: Andrew

middle: P

last: Lieberman

state: MI

address: 1150 W Medical Center Dr.

institute: University of Michigan

description:
Library name: 12625-CK-7
12625-CK_gene_expected_count.csv

data_processing:
Reads trimmed using CutAdapt v2.3 (files with 07587-ZY*) or v4.8 (all others).
FastQC v0.11.8 used to ensure data quality.
Fastq Screen v0.15.3 used to screen for various types of contamination.
Reads mapped to GRCm38 using STAR v2.7.8a and assigned count estimates to genes with RSEM v1.3.3.
Assembly: GRCm38 (ENSEMBL)
Supplementary files format and content: .csv files have compiled RSEM counts with gene name annotation, separated by timepoint (5, 26, or 52 weeks were all distinct sequencing projects).

source_name: Tibialis anterior

growth_protocol: Mice aged to 5 weeks (files starting with 12625-CK*), 26 weeks (files starting with 11413-CK*), or 52 weeks (files starting with 07587-ZY*) prior to tissue collection. Library titles named reflecting age of tissue collection (5w, 26w, or 52w).

extract_protocol:
Mice were euthanized at 5, 26, or 52 weeks, and tibialis anterior was dissected and flash-frozen. Total RNA was then extracted using TRIzol, chloroform, and isopropanol. 500 ng RNA per sample was used for library prep and sequencing.
RNA libraries for RNA-seq were prepared by the University of Michigan Advanced Genomics Core, using the Illumina platform with manufacturer's protocols for polyA-enrichment.

treatment_protocol: For 52w project only (files starting with 07587-ZY*): Male wild-type C57BL6/J mice were treated between weeks 26 and 52 of age, once weekly, with subcutaneous injection of 25 mg/kg AR-directed anti-sense oligonucleotide (ASO) dissolved in sterile PBS, or vehicle.

value: Tibialis anterior

value: Skeletal muscle

tag: age


title: naïve wild type mouse 3

description: Library name: nWT3_db-pass

tag: tissue

value: Foxp3Cre-YFP (Foxp3-wt) C57BL/6


title: 5w-WT3

description:
Library name: 12625-CK-5
12625-CK_gene_expected_count.csv

tag: cell type

value: wild-type


title: naïve wild type mouse 2

description: Library name: nWT2_db-pass

tag: genotype


title: 5w-AR113Q2

description:
Library name: 12625-CK-4
12625-CK_gene_expected_count.csv


title: Cortex_FP93_24-hours

description: Library name: 60

value: Cortex

value: SKH-1 Elite

tag: treatment


title: shCtr-A IP

description:
Library name: sample8
shCtr-A
All_methylated_sites.circRNA.xlsx

value: FaDu

value: WT

value: Blank control


title: shCtr-B Input

description:
Library name: sample9
shCtr-B
All_methylated_sites.circRNA.xlsx


title: Flesh_D6_Ctrl_Rep3

status: Public on Apr 20 2026

city: Fargo

first: Tadeu

middle: dos Reis de

last: Oliveira

state: ND

address: 1616 Albrecht Blvd. North

department: Edward T. Schafer Agricultural Research Center

institute: USDA-Agricultural Research Service

description: Library name: PPP2_83

data_processing:
Paired-end reads obtained from the Novaseq 6000 system were processed using Trimmomatic to trim low-quality bases and remove adapter sequences, applying the parameters HEADCROP:10, SLIDINGWINDOW:4:15, and MINLEN:36. Trimmed reads were aligned to the Solanum tuberosum genome assembly version 6.1 (DM1-3516 R44) using HISAT2 (--dta). The resulting SAM files were converted to BAM format, sorted, and indexed using SAMtools. Transcript abundance was quantified with StringTie (-e, -B flags) using the reference genome annotation in GFF3 format. Gene and transcript count matrices were generated with the prepDE.py3 script.
Assembly: The Solanum tuberosum genome assembly version 6.1 was used for read alignment and analysis. The genome assembly, annotation, and related resources are available in the SpudDB database (Pham et al., 2020; https://spuddb.uga.edu/).
Supplementary files format and content: The processed data files include tab-delimited text files containing gene and transcript count matrices (gene_count_matrix.csv and transcript_count_matrix.csv). These files provide quantified expression levels for differential expression analysis, generated using the prepDE.py3 script based on StringTie outputs.

organism: Solanum tuberosum

source_name: Flesh

extract_protocol:
RNA extraction and purification were performed using the Qiagen RNeasy Plant Mini Kit, following the method described by Rubio-Piña & Zapata-Pérez (2011) for plant tissues rich in polysaccharides and polyphenols. RNA integrity was confirmed using an Agilent 2100 Bioanalyzer.
RNA-seq

value: Flesh

value: Russet Burbank (Solanum tuberosum L.)

value: Control


title: 5w-WT2

description:
Library name: 12625-CK-3
12625-CK_gene_expected_count.csv


title: Cortex_FP92_24-hours

description: Library name: 59

value: 200uL Ringer's


title: Cortex_FP91_24-hours

description: Library name: 58

value: 24 hours


title: shCtr-A Input

description:
Library name: sample7
shCtr-A
All_methylated_sites.circRNA.xlsx

value: hypopharyngeal squamous cell carcinoma


title: 5w-AR113Q1

description:
Library name: 12625-CK-2
12625-CK_gene_expected_count.csv


title: 5w-AR113Q3

description:
Library name: 12625-CK-6
12625-CK_gene_expected_count.csv


title: naïve wild type mouse 1

description: Library name: nWT1_db-pass

value: mesenteric lymph node

value: Germinal center B cells

value: untreated


title: Cortex_FP88_0-hour

description: Library name: 57

value: 0 hour


title: Sh3-2C IP

description:
Library name: sample6
sh3-2C
All_methylated_sites.circRNA.xlsx

value: IGF2BP3 knockdown


title: JC-M3

city: Kaohsiung

first: Chia-Jung

last: Li

state: Kaohsiung

address: No.386, Dazhong 1st Rd., Zuoying Dist., No.386, Dazhong 1st Rd., Zuoying Dist.

country: Taiwan

institute: Kaohsiung Veterans General Hospital

description:
Library name: SAMPLE 3
Column name in processed_data_matrix.txt: JC_WT_P_M3

data_processing:
Raw FASTQ files were quality-checked using FastQC (v0.11.9).
Sequence reads were aligned to the mouse reference genome (mm10) using STAR aligner (v2.7.9a).
Gene-level quantification was performed using featureCounts to generate the raw count matrix.
Assembly: Mouse mm10 (GRCm38)
Supplementary files format and content: A tab-delimited text file containing raw read counts and normalized TPM values for all samples.

source_name: Tumor

growth_protocol: JC cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cultured cells using Trizol reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions. RNA quality was assessed using an Agilent 2100 Bioanalyzer.
Libraries were prepared using the Illumina Stranded mRNA Prep kit. mRNA was enriched using oligo(dT) magnetic beads, followed by fragmentation, cDNA synthesis, adapter ligation, and PCR amplification.

treatment_protocol: Parental JC cells (JC-P) were isolated from orthotopic tumors 14 days after injection into the mammary fat pad. JC-M3 cells were established through three iterative cycles of tail vein injection (5x10^5 cells) followed by isolation of lung metastases using 1 mg/mL type I collagenase.

value: Tumor

value: JC

value: epithelial-like cell

value: metastasis


title: Sh3-2C Input

description:
Library name: sample5
sh3-2C
All_methylated_sites.circRNA.xlsx

value: FaDu


title: Cortex_FP87_0-hour

description: Library name: 56

data_processing:
Adapters were trimmed and low-quality reads (N20 threshold) were filtered using a custom quality control pipeline. FASTQC was used to evaluate read quality metrics.
Trimmed reads were mapped to mature miRNAs in miRBase v21 using Bowtie v1.0.0, allowing one mismatch.
Reads were also mapped to the mm9 reference genome (UCSC) for validation. Only reads mapping to annotated miRNAs were retained.
Read counts were normalized using TMM (Trimmed Mean of M-values) via edgeR (Bioconductor).
Differential expression was assessed using two-way ANOVA across dose and timepoint groups. PCA and clustering were used for exploratory analysis.
Assembly: Mus musculus mm9 (UCSC)
Supplementary files format and content: Processed data includes normalized miRNA counts for each sample across cortex, heart, and lung tissues. File format: .xlsx  with miRNAs as rows and samples as columns.

value: Cortex

value: SKH-1 Elite


title: JC-P

description:
Library name: SAMPLE 2
Column name in processed_data_matrix.txt: JC_WT_P_M3

value: WT


title: Sh3-2B IP

description:
Library name: sample4
sh3-2B
All_methylated_sites.circRNA.xlsx


title: 26w-AR113Q4

description:
Library name: 11413-CK-12
11413-CK_gene_expected_count.4v4.csv

value: Tibialis anterior

value: Skeletal muscle


title: JC-WT

description:
Library name: SAMPLE 1
Column name in processed_data_matrix.txt: JC_WT_P_M3


title: 26w-AR113Q3

description:
Library name: 11413-CK-11
11413-CK_gene_expected_count.4v4.csv


title: Cortex_FP85_6-hours

description: Library name: 54

value: 200uL Ringer's

value: Control

value: 6 hours


title: Sh3-2B Input

description:
Library name: sample3
sh3-2B
All_methylated_sites.circRNA.xlsx

value: hypopharyngeal squamous cell carcinoma


title: 5w-WT1

description:
Library name: 12625-CK-1
12625-CK_gene_expected_count.csv

value: wild-type


title: Sh3-2A IP

description:
Library name: sample2
sh3-2A
All_methylated_sites.circRNA.xlsx


title: 26w-AR113Q2

description:
Library name: 11413-CK-10
11413-CK_gene_expected_count.4v4.csv


title: Cortex_FP84_7-days

description: Library name: 53

value: 7 days


title: 26w-AR113Q1

description:
Library name: 11413-CK-09
11413-CK_gene_expected_count.4v4.csv


title: Cortex_FP82_7-days

description: Library name: 51


title: Cortex_FP83_7-days

description: Library name: 52


title: T3KO_1_2

city: Shanghai

first: Jieyuan

last: Xue

address: 280 South Chongqing Road

institute: Shanghai Jiao Tong University

description: Library name: T3KO_1_2

data_processing:
FastQC (Version 0.12.1) was used for quality control of FastQ.gz files.
HISAT2 (Version 2.2.1) was used for alignment against the mouse reference genome (mm39).
featureCounts (Version 2.0.6) was used to count aligned reads.
Assembly: mm39
Supplementary files format and content: csv file includes raw counts for each sample

source_name: heart

extract_protocol:
RNA were extracted from heart tissue using Trizol method.
RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer's recommendations. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to themanufacturer's instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated.

value: heart


title: Cortex_FP86_6-hours

first: Aarti

last: Gautam

description: Library name: 55

extract_protocol:
Tissues were homogenized in TRIzol Reagent (Invitrogen) and total RNA, including small RNAs, was extracted using the miRNeasy Mini Kit (QIAGEN) following the manufacturer’s protocol. RNA quality was assessed using NanoDrop, Qubit, and Agilent Tapestation 2200.
Small RNA libraries were prepared using the Illumina TruSeq Small RNA Sample Prep Kit. 3′ and 5′ adapters were ligated to RNA, followed by reverse transcription, PCR amplification, and gel-based size selection. Libraries were pooled and sequenced on an Illumina NextSeq 500 to generate 50 bp single-end reads.


title: Sh3-2A Input

description:
Library name: sample1
sh3-2A
All_methylated_sites.circRNA.xlsx

value: IGF2BP3 knockdown


title: T3KO_1_3

description: Library name: T3KO_1_3


title: 26w-WT3

description:
Library name: 11413-CK-03
11413-CK_gene_expected_count.4v4.csv


title: T158M-MU-E2KO replicate 2

city: Houston

first: Hu

last: Chen

address: 1250 Moursund St,

institute: Baylor College of Medicine

description: Library name: HPT-11

data_processing:
Adapter sequences were removed from raw sequencing reads using Trimmomatic v0.39 at default parameters.
Trimmed reads were aligned to GRCh38.p12 version 28 human genome assembly from GENCODE using STAR v2.7.9.a using all default parameters except –sjdbOverhang149.
Finally, differential gene expression analyses on the read counts were performed using DESeq2 in R environment.
Assembly: GRCh38
Supplementary files format and content: The number of reads mapped to each gene using the "--quantMode GeneCounts" option in STAR during mapping.

source_name: iPSC-derived neurons

growth_protocol: iPSC-derived neurons (NGN2- and NPC-derived) were cultured on Matrigel-coated 24-well plates in Neuronal Differentiation Media (NDM) until the time of harvesting for RNA extraction

extract_protocol:
RNA was extracted from iPSC-derived neurons using the Rneasy Mini Kit (Qiagen, Cat #74106) and 1ug was sent for RNA-sequencing library prep
Librabry prep was performed by Azenta/Genewiz using polyA selection

value: iPSC-derived neurons

value: iPSC-derived NGN2-iNeurons

value: MECP2E2KO/T158M-E2KO (T158M-MECP2 expressed; homozygous E2KO)


title: T158M-MU-E2KO replicate 3

description: Library name: HPT-12


title: WT_3

description: Library name: WT_3


title: 26w-WT4

description:
Library name: 11413-CK-04
11413-CK_gene_expected_count.4v4.csv


title: 26w-WT2

description:
Library name: 11413-CK-02
11413-CK_gene_expected_count.4v4.csv


title: T3KO_1_1

description: Library name: T3KO_1_1


title: Cortex_FP78_6-hours

address: 503 Robert Grant Avenue

description: Library name: 49


title: WT_2

description: Library name: WT_2


title: T158M-MU-E2KO replicate 1

description: Library name: HPT-09


title: Cortex_FP81_7-days

description: Library name: 50


title: 26w-WT1

description:
Library name: 11413-CK-01
11413-CK_gene_expected_count.4v4.csv


title: WT_1

description: Library name: WT_1


title: Cortex_FP74_0-hour

description: Library name: 47

value: 0 hour


title: T158M-MU replicate 2

description: Library name: HPT-07

value: MECP2+/T158M (T158M-MECP2 expressed)


title: Mus musculus, splenocytes, 3-4 months, Female, Sepsis (CLP+7dDCS), id: YFB6S7E

city: Gainesville

first: Jaimar

last: Rincon

state: FL

address: 1600 SW Archer Road

department: Departament of Surgery

institute: University of Florida

description:
Library name: YFB6S7E
10X Genomics

data_processing:
Cell Ranger Single-Cell Software v 7.0.1 (10X Genomics) was used to obtain FASTQ files from the Illumina base call files. The reads were aligned to the mm10 mouse transcriptome reference using “intronic reads included” mode, with an expected cell count of 10,000, and transcript expression was quantified at the single-cell level, generating gene-cell count matrices.
The Cell Ranger generated count matrices were imported into R (v4.3.2) and analyzed using the Seurat (v5.0.1) package (PMID: 37231261). Quality control (QC) steps were applied to remove low-quality cells (cells expressing > 10% mitochondrial transcripts or number of unique genes < 200) and doublets (number of unique genes > 6000). Gene expression data were log normalized and scaled. Principal Component Analysis (PCA) was performed based on the top 2,000 most variable genes. To account for batch effects across different samples, data integration was performed using the Harmony (v1.2.0) package (PMID: 31740819), using the top 50 principal components (PCs) to align datasets and reduce batch-specific variations. A shared nearest neighbor graph was constructed using 30 nearest neighbors based on the top 30 PCs. Further, cell clusters were detected based on the Louvain algorithm and were visualized in Uniform Manifold Approximation and Projection (UMAP) embeddings computed from the top 30 PCs.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Processed single-cell RNA-seq data are provided in HDF5 format (.h5) as generated by the Cell Ranger pipeline. Each file contains the filtered gene-cell expression matrices, along with associated barcodes and gene annotations output by Cell Ranger.

source_name: spleen

extract_protocol:
Splenocytes were obtained and counts were quantified using Cellometer™ Auto 2000 Cell Viability Counter (Nexcelom Bioscience, Lawrence, MA). A million cell concentrations with a minimum of 85% cell viability were obtained for scRNASeq using Chromium X instrument (10X Genomics, Pleasonton, CA).
Libraries were prepared with the 10X’s Chromium Next GEM Single Cell 5’ v2 kit profiling 10,000 cells per sample. To ensure quality during library preparation RNA integrity and dsDNA insert were assessed using the Tapestation 4200 (Agilent, Santa Clara, CA) and Qubit 4 (Invitrogen, Carlsbad, CA). Final concentration of the library pool was measured with the NEBNext Library Quant Kit (New England Biolabs, Ipswich, MA). Libraries were sequenced at a minimum depth of 20,000 read pairs per cell on an Illumina Novaseq X plus Platform (Illumina, San Diego, CA).

treatment_protocol: Naïve and septic, young adult (3-4 months) and older adult (18-24 months) female and male C57BL/6 (B6) mice were used for all studies. Sepsis was induced using the cecal ligation and puncture with daily chronic stress (CLP+DCS) as published model. Seven days post- CLP+DCS (CLP+DCS 7d) animals were euthanized to harvest splenocytes.

value: spleen

value: B6 strain

value: splenocytes

value: Female

value: 3-4 months

tag: disease group

value: Sepsis (CLP+7dDCS)


title: Mutant low‑yield sample of replicate 2 for mice in group 2

first: Kaiwen

last: Deng

state: Michigan

address: 3305 NCRC Building 520

description: Library name: 5830-SS-3_M-low_rep2

data_processing:
Both rounds of the experiments follow the same processing pipeline supported by the Bioinformatics Core of the University of Michigan Medical School’s Biomedical Research Core Facilities (RRID:SCR_019168)
A) The reads were trimmed using Cutadapt v2.3 (Martin, 2011). B) FastQC v0.11.8 was used to ensure the quality of data (Andrews, 2010). C) Fastq Screen v was used to screen for various types of contamination (Wingett and Andrews, 2018). D) Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq. E) Multiqc v1.7 compiled the results from several of these tools and provided a detailed and comprehensive quality control report (Ewels et al., 2016).
Assembly: GRCm38 (ENSEMBL)
Supplementary files format and content: Tab-deliminate tables in .txt files. They contain the matrices of raw counts from the two groups of RNA-seq experiments
Supplementary files format and content: CSV files recording the sample information. They are used to map the sample IDs to treatment groups

source_name: Fetal liver

extract_protocol:
Total RNA was extracted using RNeasy® Micro Kit (Qiagen, Cat 74004).
This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq). BCL Convert Conversion Software v3.9.3 (Illumina) was used to generate de-multiplexed Fastq files.

value: Fetal liver

value: M-lowyield


title: Mus musculus, splenocytes, 3-4 months, Female, Sepsis (CLP+7dDCS), id: YFB6S7C

description:
Library name: YFB6S7C
10X Genomics


title: T158M-MU replicate 1

description: Library name: HPT-05

tag: cell line


title: T158M-MU replicate 3

description: Library name: HPT-08


title: Mus musculus, splenocytes, 3-4 months, Female, Sepsis (CLP+7dDCS), id: YFB6S7B

description:
Library name: YFB6S7B
10X Genomics


title: Isogenic Control (T158M-WT) replicate 3

description: Library name: HPT-04

value: MECP2+/T158M (WT MECP2 expressed)


title: Mutant low‑yield sample of replicate 1 for mice in group 2

description: Library name: 5830-SS-1_M-low_rep1


title: Cortex_FP77_6-hours

description: Library name: 48

value: Cortex

value: SKH-1 Elite

value: 200uL Ringer's

value: Control

value: 6 hours


title: Cortex_FP73_6-hours

description: Library name: 46


title: Mutant low‑yield sample of replicate 3 for mice in group 2

description: Library name: 5830-SS-12_M-low_rep3


title: Cortex_FP72_6-hours

description: Library name: 45


title: Mutant sample of replicate 2 for mice in group 2

description: Library name: 5830-SS-10_M_rep2

value: M


title: Cortex_FP71_0-hour

description: Library name: 44

value: 0 hour


title: Isogenic Control (T158M-WT) replicate 1

description: Library name: HPT-01

value: iPSC-derived neurons

value: iPSC-derived NGN2-iNeurons


title: Cortex_FP69_0-hour

description: Library name: 43


title: Mus musculus, splenocytes, 3-4 months, Male, Sepsis (CLP+7dDCS), id: S7YM4

description:
Library name: S7YM4
10X Genomics

value: spleen

value: B6 strain

value: Male


title: Isogenic Control (T158M-WT) replicate 2

description: Library name: HPT-02


title: Mus musculus, splenocytes, 3-4 months, Male, Sepsis (CLP+7dDCS), id: S7YM3

description:
Library name: S7YM3
10X Genomics

value: splenocytes

value: 3-4 months


title: Mus musculus, splenocytes, 3-4 months, Male, Sepsis (CLP+7dDCS), id: S7YM2

description:
Library name: S7YM2
10X Genomics

value: Sepsis (CLP+7dDCS)


title: Mutant sample of replicate 1 for mice in group 2

description: Library name: 5830-SS-6_M_rep1

value: Fetal liver


title: iEC, WT3, DMSO, rep3

city: Greifswald

first: Robin

middle: A.

last: Pilz

address: Fleischmannstr. 43

department: Institute for Human Genetics

country: Germany

institute: University Medicine Greifswald

description:
Library name: WT3-ctrl
CCM3KOvsWT_DMSO_Differential_expression_analysis_table.csv
WT_semaxinibvsWT_DMSO_Differential_expression_analysis_table.csv

data_processing:
Read trimming was performed with Trimmomatic v.0.36.
Mapping to GRCh38 was performed with STAR aligner v.2.5.2b.
Unique gene hit counts were extracted with featureCounts from the Subread package v.1.5.2.
Assembly: GRCh38
Supplementary files format and content: Comma-separated values files include normalized counts, log2 fold changes, and (adjusted) p-values for differentially expressed genes.

growth_protocol: Cells were maintained in EndoGRO-MV medium (Merck Millipore) supplemented with 1 ng/ml fibroblast growth factor 2 (FGF-2) (Miltenyi Biotec).

extract_protocol:
RNA was harvested using TRIzol reagent (Thermo Fisher Scientific) and extracted with the Direct-zol RNA MiniPrep Plus Kit (Zymo Research).
mRNA sequencing via polyA selection

treatment_protocol: 10 µM of semaxinib or 0.1% of DMSO

value: iPSC-derived endothelial cells

value: WT

value: DMSO


title: Wildtype sample of replicate 3 for mice in group 2

description: Library name: 5830-SS-9_WT_rep3


title: Mutant sample of replicate 3 for mice in group 2

description: Library name: 5830-SS-15_M_rep3


title: Mus musculus, splenocytes, 3-4 months, Male, Sepsis (CLP+7dDCS), id: S7YM1

description:
Library name: S7YM1
10X Genomics


title: iEC, CCM3 KO3, DMSO, rep3

description:
Library name: KO3-ctrl
CCM3KOvsWT_DMSO_Differential_expression_analysis_table.csv
CCM3KO_semaxinibvsCCM3KO_DMSO_Differential_expression_analysis_table.csv

value: CCM3 KO


title: Cortex_FP67_0-hour

institute: WRAIR

description: Library name: 41

value: Cortex

value: SKH-1 Elite


title: Mus musculus, splenocytes, 3-4 months, Female, Sepsis (CLP+7dDCS), id: S7YF4

description:
Library name: S7YF4
10X Genomics

value: Female


title: Wildtype sample of replicate 2 for mice in group 2

description: Library name: 5830-SS-8_WT_rep2


title: iEC, WT3, semaxinib, rep3

description:
Library name: WT3-comp
CCM3KOvsWT_semaxinib_Differential_expression_analysis_table.csv
WT_semaxinibvsWT_DMSO_Differential_expression_analysis_table.csv

value: semaxinib


title: Cortex_FP68_6-hours

description: Library name: 42

value: 6 hours


title: Cortex_FP66_24-hours

description: Library name: 40

value: 24 hours


title: Mus musculus, splenocytes, 3-4 months, Female, Sepsis (CLP+7dDCS), id: S7YF3

description:
Library name: S7YF3
10X Genomics

value: spleen


title: iEC, CCM3 KO3, semaxinib, rep3

description:
Library name: KO3-comp
CCM3KOvsWT_semaxinib_Differential_expression_analysis_table.csv
CCM3KO_semaxinibvsCCM3KO_DMSO_Differential_expression_analysis_table.csv


title: Wildtype sample of replicate 1 for mice in group 2

description: Library name: 5830-SS-7_WT_rep1


title: Mutant sample of replicate 3 for mice in group 1

description: Library name: 8816-SS-10_M_rep3

value: M


title: Mus musculus, splenocytes, 3-4 months, Female, Sepsis (CLP+7dDCS), id: S7YF2

description:
Library name: S7YF2
10X Genomics

value: B6 strain


title: iEC, WT2, DMSO, rep2

description:
Library name: WT2-ctrl
CCM3KOvsWT_DMSO_Differential_expression_analysis_table.csv
WT_semaxinibvsWT_DMSO_Differential_expression_analysis_table.csv


title: Cortex_FP64_24-hours

description: Library name: 39


title: Cortex_FP63_24-hours

description: Library name: 38


title: Mutant sample of replicate 2 for mice in group 1

description: Library name: 8816-SS-9_M_rep2


title: iEC, CCM3 KO2, DMSO, rep2

description:
Library name: KO2-ctrl
CCM3KOvsWT_DMSO_Differential_expression_analysis_table.csv
CCM3KO_semaxinibvsCCM3KO_DMSO_Differential_expression_analysis_table.csv


title: Mus musculus, splenocytes, 3-4 months, Female, Sepsis (CLP+7dDCS), id: S7YF1

description:
Library name: S7YF1
10X Genomics

value: splenocytes


title: Wildtype sample of replicate 3 for mice in group 1

description: Library name: 8816-SS-4_WT_rep3


title: Cortex_FP61_7-days

description: Library name: 36

value: 7 days


title: Cortex_FP62_24-hours

description: Library name: 37


title: Mus musculus, splenocytes, 3-4 months, Male, Sepsis (CLP+7dDCS), id: S7080923-YM1

description:
Library name: S7080923-YM1
10X Genomics

value: Male

value: 3-4 months

value: Sepsis (CLP+7dDCS)


title: iEC, WT2, semaxinib, rep2

description:
Library name: WT2-comp
CCM3KOvsWT_semaxinib_Differential_expression_analysis_table.csv
WT_semaxinibvsWT_DMSO_Differential_expression_analysis_table.csv

value: iPSC-derived endothelial cells

value: WT


title: iEC, CCM3 KO2, semaxinib, rep2

description:
Library name: KO2-comp
CCM3KOvsWT_semaxinib_Differential_expression_analysis_table.csv
CCM3KO_semaxinibvsCCM3KO_DMSO_Differential_expression_analysis_table.csv

value: CCM3 KO


title: Mus musculus, splenocytes, 18-24 months, Female, Sepsis (CLP+7dDCS), id: S7080923-OF1

description:
Library name: S7080923-OF1
10X Genomics

value: 18-24 months


title: Cortex_FP60_7-days

description: Library name: 35

value: Cortex

value: SKH-1 Elite


title: Wildtype sample of replicate 2 for mice in group 1

description: Library name: 8816-SS-3_WT_rep2

value: Fetal liver


title: iEC, WT1, DMSO, rep1

description:
Library name: WT1-ctrl
CCM3KOvsWT_DMSO_Differential_expression_analysis_table.csv
WT_semaxinibvsWT_DMSO_Differential_expression_analysis_table.csv

value: DMSO


title: Mus musculus, splenocytes, 18-24 months, Male, Sepsis (CLP+7dDCS), id: S-082923-OM5

description:
Library name: S-082923-OM5
10X Genomics


title: Mus musculus, splenocytes, 18-24 months, Male, Sepsis (CLP+7dDCS), id: S-082923-OM4

description:
Library name: S-082923-OM4
10X Genomics


title: Cortex_FP59_7-days

description: Library name: 34


title: Mutant sample of replicate 1 for mice in group 1

description: Library name: 8816-SS-8_M_rep1


title: iEC, CCM3 KO1, DMSO, rep1

description:
Library name: KO1-ctrl
CCM3KOvsWT_DMSO_Differential_expression_analysis_table.csv
CCM3KO_semaxinibvsCCM3KO_DMSO_Differential_expression_analysis_table.csv


title: Cortex_FP58_24-hours

description: Library name: 33

value: LOEL

value: 24 hours


title: Mus musculus, splenocytes, 18-24 months, Male, Sepsis (CLP+7dDCS), id: S-082923-OM3

description:
Library name: S-082923-OM3
10X Genomics

value: spleen


title: iEC, WT1, semaxinib, rep1

description:
Library name: WT1-comp
CCM3KOvsWT_semaxinib_Differential_expression_analysis_table.csv
WT_semaxinibvsWT_DMSO_Differential_expression_analysis_table.csv

value: semaxinib


title: Mus musculus, splenocytes, 18-24 months, Male, Sepsis (CLP+7dDCS), id: S-082923-OM2

description:
Library name: S-082923-OM2
10X Genomics

value: B6 strain

value: splenocytes


title: iEC, CCM3 KO1, semaxinib, rep1

description:
Library name: KO1-comp
CCM3KOvsWT_semaxinib_Differential_expression_analysis_table.csv
CCM3KO_semaxinibvsCCM3KO_DMSO_Differential_expression_analysis_table.csv


title: Mus musculus, splenocytes, 18-24 months, Male, Sepsis (CLP+7dDCS), id: S-082923-OM1

description:
Library name: S-082923-OM1
10X Genomics

value: Male


title: TYMP_2

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

description: Library name: Sample 4

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 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp.ensembl.org/pub/release-112/gtf/homo_sapiens/Homo_sapiens.GRCh38.112.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: File include Count and FPKM values for each sample

source_name: HaCaT

growth_protocol: The human keratinocyte cell line HaCaT was purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China).

extract_protocol:
After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The HaCaT cells were seeded into 6-well plates and were transfected with stable overexpression-lentivirus to estabilish TYMP overexpression cell lines. The differentally expressed genes by TYMP overexpression were screened by RNA sequencing. The transcriptome sequencing studies were performed by deep sequencing, using Illumina NovaSeq 6000.

value: HaCaT

value: TYMP overexpression


title: Cortex_FP56_24-hours

city: Silver Spring

description: Library name: 31


title: Cortex_FP55_0-hour

description: Library name: 30

value: 0 hour


title: Mus musculus, splenocytes, 18-24 months, Female, Sepsis (CLP+7dDCS), id: S-082923-OF3

description:
Library name: S-082923-OF3
10X Genomics

value: Female

value: Sepsis (CLP+7dDCS)


title: TYMP_1

description: Library name: Sample 3


title: Mus musculus, splenocytes, 18-24 months, Female, Sepsis (CLP+7dDCS), id: S-082923-OF2

description:
Library name: S-082923-OF2
10X Genomics

value: 18-24 months


title: Wildtype sample of replicate 1 for mice in group 1

description: Library name: 8816-SS-2_WT_rep1

value: WT


title: Cortex_FP54_24-hours

description: Library name: 29

value: Cortex

value: SKH-1 Elite


title: NC_2

description: Library name: Sample 2

value: NC


title: Cortex_FP53_7-days

description: Library name: 28

value: LOEL

value: 7 days


title: Mus musculus, splenocytes, 18-24 months, Female, Sepsis (CLP+7dDCS), id: S-082923-OF1

description:
Library name: S-082923-OF1
10X Genomics

value: spleen


title: NC_1

description: Library name: Sample 1


title: HLF siSBNO1#2 replicate 3

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

description: HLF were transfected with siSBNO1#2 targeting human SBNO1, replicate 3

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data was analyzed with a commercial software called JMP Genomics, version 15, from SAS. Gene expression profiling was performed using arrays of Human Clariom D from Thermo Fischer Scientific. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: HLF cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: HLF cells were cultured in Dulbecco’s Modified Eagle’s Medium.

extract_protocol: Total RNA was extracted using the Macherey-Nagel RNA Extraction Kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions.

treatment_protocol: siRNA-mediated knockdown was performed using Lipofectamine RNAiMAX Transfection Reagent (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions.

value: liver cancer cell line


title: RPMI8226 cells,shDKC1_3

city: jinan

first: chenxi

last: sun

address: 247th of Beiyuan Road

institute: The Second Qilu Hospital of Shandong University

description: Library name: Sample 6

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome hg38 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

source_name: bone marrow

extract_protocol:
Total RNA was extracted with an RNA extraction kit (Fastagen Biotech Co., RNAfast200)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

value: multiple myeloma cells

value: DKC1 knockdown


title: Cortex_FP57_24-hours

description: Library name: 32

value: 24 hours


title: Cortex_FP51_24-hours

description: Library name: 26


title: RPMI8226 cells,shDKC1_2

description: Library name: Sample 5


title: Mus musculus, splenocytes, 3-4 months, Male, Naive, id: NYM3

description:
Library name: NYM3
10X Genomics

value: B6 strain

value: splenocytes

value: Male

value: 3-4 months

value: Naive


title: Mus musculus, splenocytes, 3-4 months, Male, Naive, id: NYM4

description:
Library name: NYM4
10X Genomics


title: HLF siSBNO1#1 replicate 2

description: HLF were transfected with siSBNO1#1 targeting human SBNO1, replicate 2


title: RPMI8226 cells,shDKC1_1

description: Library name: Sample 4


title: Mus musculus, splenocytes, 3-4 months, Male, Naive, id: NYM2

description:
Library name: NYM2
10X Genomics


title: Cortex_FP52_7-days

description: Library name: 27


title: Cortex_FP48_0-hour

description: Library name: 24

value: 0 hour


title: HLF siSBNO1#1 replicate 3

description: HLF were transfected with siSBNO1#1 targeting human SBNO1, replicate 3


title: Mus musculus, splenocytes, 3-4 months, Male, Naive, id: NYM1

description:
Library name: NYM1
10X Genomics


title: RPMI8226 cells,MOCK3

description: Library name: Sample 3

value: WT


title: Cortex_FP49_6-hours

description: Library name: 25

value: Cortex

value: SKH-1 Elite

value: 6 hours


title: HLF siSBNO1#1 replicate 4

description: HLF were transfected with siSBNO1#1 targeting human SBNO1, replicate 4


title: Mus musculus, splenocytes, 3-4 months, Female, Naive, id: NYF4

description:
Library name: NYF4
10X Genomics

value: Female


title: Cortex_FP47_0-hour

description: Library name: 23

value: LOEL


title: HLF siSBNO1#2 replicate 4

description: HLF were transfected with siSBNO1#2 targeting human SBNO1, replicate 4

value: liver cancer cell line


title: RPMI8226 cells,MOCK2

description: Library name: Sample 2

value: bone marrow


title: Mus musculus, splenocytes, 3-4 months, Female, Naive, id: NYF3

description:
Library name: NYF3
10X Genomics

value: spleen


title: Cortex_FP45_6-hours

description: Library name: 22


title: HLF NTC replicate 3

description: HLF were transfected with the non-targeting control (NTC) siRNA, replicate 3


title: Mus musculus, splenocytes, 3-4 months, Female, Naive, id: NYF2

description:
Library name: NYF2
10X Genomics


title: HLF NTC replicate 4

description: HLF were transfected with the non-targeting control (NTC) siRNA, replicate 4


title: Cortex_FP43_7-days

description: Library name: 20

value: 7 days


title: HLF siSBNO1#1 replicate 1

description: HLF were transfected with siSBNO1#1 targeting human SBNO1, replicate 1


title: HLF siSBNO1#2 replicate 2

description: HLF were transfected with siSBNO1#2 targeting human SBNO1, replicate 2


title: Arabidopsis nac42-L2 (SALK_078841) grown in mediterranean climate infected by S. sclerotiorum replicate 3

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

institute: INRAE

description: Library name: AthMutZClimat3-FRT3

data_processing:
HiSeq control software 2.2.58, RTA 1.18.64.0, Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genomes using the RNA-seq analysis function described in the pipeline https://doi.org/10.5281/zenodo.1400710) using the nf-core framework (https://github.com/nf-core/rnaseq).
Assembly: Arabidopsis thalinia (Araport11), Sclerotinia sclerotiorum strain 1980 (Derbyshire et al., 2017)
Supplementary files format and content: tab-delimited text files include raw read count per gene

organism: Arabidopsis thaliana

source_name: Front zone of lesion - Plants grown in mediterranean climate

growth_protocol: Plants were grown in jiffy pots for 35 days in Percival E41-L3 and E41-L2PLT growth cabinets at day temperatures of 23°C (mediterranean), 20°C (temperate), night temperatures of 7°C (mediterranean), 9°C (temperate), with a 13 hour light period at intensity of 120 μmol/m²/s.

extract_protocol:
The border (ring of ~5mm wide) of disease lesions were collected with a scalpel at 30 hours post inoculation (hpi) for temperate and mediterranean acclimation and 48 hpi for continental acclimation,  and frozen in liquid nitrogen. Samples were ground with metal beads (2.5 mm) in a Retschmill apparatus (24hertz for 2x1min). RNA was extracted using the RNAplus kit (Macherey Nagel) following the manufacturer’s instructions. A Turbo DNAse treatment (Ambion) was applied to remove genomic DNA. The quality and concentrations of RNAs preparations were assessed with an Agilent Bioanalyzer using the Agilent RNA 6000 Nano kit
HiSeq SBS Kit v4

treatment_protocol:
S. sclerotiorum strain 1980 was subcultured on Potato Dextrose Agar plates at 22°C. For inoculations, a 5-mm wide agar plug containing actively growing S. sclerotiorum mycelium was placed on the adaxial surface of leaves on 5-week old plants. Inoculations were performed on detached leaves under constant 21°C temperature, constant light (120 μmol/m²/s) and 90% relative humidity.
Temperate acclimation consisted in growth for 35 days under cycles of 13 hours at 20°C (day) followed by 11 hours at 9°C (night); mediterranean acclimation consisted in growth for 35 days under cycles of 13 hours at 23°C (day) followed by 11 hours at 7°C (night)

value: leaves of 5-week old plants

value: inoculated

tag: time

value: mediterranean


title: 4_MG_ColIV

city: Amsterdam

first: Jeen

last: Engelenburg

address: Meibergdreef 47

country: Netherlands

institute: Netherlands Institute for Neuroscience

description: Library name: 105193-001-021

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and BclConvert v3.10.5
Quality control was performed using FastQC (version 0.11.9). Adapter sequences were trimmed using fastp (version 0.23.2).
Reads were mapped to the human GRCh38.p13 genome using STAR2 (version 2.7.10) on default settings. Feature counts of reads mapped to genes were determined using HTSeq (version 2.0.2).
Resulting counts were analyzed separately using R (version 4.3.1) and Bioconductor.
Assembly: hg38
Supplementary files format and content: tab-delimited text file including raw counts of each sample

source_name: MG

extract_protocol:
Total RNA was isolated with the RNeasy MicroKit according to the manufacturer’s instructions (Qiagen).
The NEBNext Low Input RNA Library Prep Kit for Illumina was used to process the sample(s). The sample preparation was performed according to the protocol "NEBNext Low Inputr RNA Library Prep Kit for Illumina" (NEB #E6420S/L).

tag: donor

value: MG

value: ColIV

tag: cell number

tag: diagnosis

value: PSP

tag: batch


title: RPMI8226 cells,MOCK1

description: Library name: Sample 1

value: multiple myeloma cells


title: Cortex_FP42_6-hours

description: Library name: 19

tag: strain

tag: dose

tag: timepoint


title: 2_T8_Accutase

description: Library name: 105193-001-020

value: Accutase

value: MS

tag: Sex


title: HLF NTC replicate 1

description: HLF were transfected with the non-targeting control (NTC) siRNA, replicate 1


title: Mus musculus, splenocytes, 3-4 months, Female, Naive, id: NYF1

description:
Library name: NYF1
10X Genomics

value: B6 strain

value: splenocytes

value: 3-4 months

value: Naive


title: Cortex_FP44_6-hours

description: Library name: 21

value: Cortex

value: SKH-1 Elite

value: 6 hours


title: HLF NTC replicate 2

description: HLF were transfected with the non-targeting control (NTC) siRNA, replicate 2

value: liver cancer cell line


title: Arabidopsis nac42-L2 (SALK_078841) grown in mediterranean climate infected by S. sclerotiorum replicate 2

description: Library name: AthMutZClimat3-FRT2

value: leaves of 5-week old plants


title: Mus musculus, splenocytes, 3-4 months, Male, Sepsis (CLP+7dDCS), id: 24-S-YM2

description:
Library name: 24-S-YM2
10X Genomics

value: spleen

value: Male

value: Sepsis (CLP+7dDCS)


title: 1_T8_ColIVInh

description: Library name: 105193-001-019

value: ColIVInh

value: AD


title: Arabidopsis nac42-L2 (SALK_078841) grown in mediterranean climate infected by S. sclerotiorum replicate 1

description: Library name: AthMutZClimat3-FRT1

value: inoculated

value: mediterranean


title: Arabidopsis nac42-L2 (SALK_078841) grown in temperate climate infected by S. sclerotiorum replicate 3

description: Library name: AthMutZClimat1-FRT3

source_name: Front zone of lesion - Plants grown in temperate climate

value: temperate


title: Cortex_FP41_7-days

description: Library name: 18

value: 7 days


title: Cortex_FP40_7-days

description: Library name: 17

value: LOEL


title: Mus musculus, splenocytes, 3-4 months, Male, Sepsis (CLP+7dDCS), id: 24-S-YM1

description:
Library name: 24-S-YM1
10X Genomics

value: B6 strain

value: splenocytes

value: 3-4 months


title: Mus musculus, splenocytes, 18-24 months, Female, Sepsis (CLP+7dDCS), id: 24-S-OF4

description:
Library name: 24-S-OF4
10X Genomics

value: Female

value: 18-24 months


title: Cortex_FP39_24-hours

description: Library name: 16

value: Cortex

value: SKH-1 Elite

value: 24 hours


title: 2_T8_ColIV

description: Library name: 105193-001-018

value: ColIV

value: MS


title: Arabidopsis nac42-L2 (SALK_078841) grown in temperate climate infected by S. sclerotiorum replicate 2

description: Library name: AthMutZClimat1-FRT2

value: leaves of 5-week old plants


title: 2_MG_Accutase

description: Library name: 105193-001-017

value: MG

value: Accutase


title: Arabidopsis nac42-L2 (SALK_078841) grown in temperate climate infected by S. sclerotiorum replicate 1

description: Library name: AthMutZClimat1-FRT1

value: inoculated


title: Mus musculus, splenocytes, 3-4 months, Male, Naive, id: 24-N-YM3

description:
Library name: 24-N-YM3
10X Genomics

value: spleen

value: Male

value: Naive


title: 2_MG_ColIV

description: Library name: 105193-001-016


title: Arabidopsis nac42-L1 (SALK_016619C) grown in mediterranean climate infected by S. sclerotiorum replicate 3

description: Library name: AthMutEClimat3-FRT3

value: mediterranean


title: Mus musculus, splenocytes, 3-4 months, Male, Naive, id: 24-N-YM1

description:
Library name: 24-N-YM1
10X Genomics

value: B6 strain

value: splenocytes


title: 3_MG_Accutase

description: Library name: 105193-001-015

value: AD


title: Cortex_FP38_6-hours

description: Library name: 15

value: LOEL

value: 6 hours


title: Mus musculus, splenocytes, 3-4 months, Female, Naive, id: 24-N-YF2

description:
Library name: 24-N-YF2
10X Genomics

value: Female

value: 3-4 months


title: Cortex_FP32_0-hour

description: Library name: 13

value: Cortex

value: SKH-1 Elite

value: 0 hour


title: Mus musculus, splenocytes, 3-4 months, Female, Naive, id: 24-N-YF1

description:
Library name: 24-N-YF1
10X Genomics


title: 3_T8_ColIVInh

description: Library name: 105193-001-014

value: ColIVInh


title: Arabidopsis nac42-L1 (SALK_016619C) grown in mediterranean climate infected by S. sclerotiorum replicate 2

description: Library name: AthMutEClimat3-FRT2

value: leaves of 5-week old plants


title: Arabidopsis nac42-L1 (SALK_016619C) grown in temperate climate infected by S. sclerotiorum replicate 3

description: Library name: AthMutEClimat1-FRT3

value: inoculated

value: temperate


title: Arabidopsis nac42-L1 (SALK_016619C) grown in mediterranean climate infected by S. sclerotiorum replicate 1

description: Library name: AthMutEClimat3-FRT1


title: 3_MG_ColIV

description: Library name: 105193-001-013

value: MG

value: ColIV

value: Male


title: Mus musculus, splenocytes, 18-24 months, Male, Naive, id: 24-N-OM3

description:
Library name: 24-N-OM3
10X Genomics

value: spleen

value: B6 strain

value: 18-24 months

value: Naive


title: Cortex_FP29_6-hours

description: Library name: 11

value: 6 hours


title: Mus musculus, splenocytes, 18-24 months, Male, Naive, id: 24-N-OM2

description:
Library name: 24-N-OM2
10X Genomics

value: splenocytes


title: 4_MG_Accutase

description: Library name: 105193-001-012

value: Accutase

value: PSP

value: Female


title: Cortex_FP27_7-days

description: Library name: 10

value: Cortex

value: SKH-1 Elite

value: 7 days


title: 2_T8_ColIVInh

description: Library name: 105193-001-011

value: ColIVInh

value: MS


title: Arabidopsis nac42-L1 (SALK_016619C) grown in temperate climate infected by S. sclerotiorum replicate 2

description: Library name: AthMutEClimat1-FRT2

value: leaves of 5-week old plants

value: inoculated

value: temperate


title: Cortex_FP33_6-hours

description: Library name: 14

value: LOEL


title: Mus musculus, splenocytes, 18-24 months, Male, Naive, id: 24-N-OM1

description:
Library name: 24-N-OM1
10X Genomics

value: spleen

value: B6 strain

value: Male


title: Cortex_FP30_0-hour

description: Library name: 12

value: 0 hour


title: Callus, 12DAC, replicate 3

city: Seoul

first: Soon Hyung

last: Bae

state: South Korea

address: Gwanak-ro 1, Gwanak-gu

country: South Korea

institute: Seoul National University

description:
RNA-seq_raw_counts.tsv
RNA-seq_TPM_normalized.tsv

data_processing:
Reads were mapped to TAIR10 reference genome using STAR (v2.7.10a) with “--pOverlapNbasesMin 12 --peOverlapMMp 0.1 --twopassMode Basic” options.
Raw counts were obtained from STAR (v2.7.10a) with "--quantMode GeneCounts" option.
RSEM (v1.3.1) was used to quantify transcript abundance to obtain TPM values.
Assembly: TAIR10
Supplementary files format and content: Tab-separated values file includes raw counts for each sample
Supplementary files format and content: Tab-separated values file includes TPM values for each sample

source_name: leaf explant-derived callus

extract_protocol:
Total RNA was extracted from calli using TransZol Up according to the manufacturer’s recommendations.
RNA-seq libraries were constructed from 1 μg total RNA using the TruSeq RNA library kit.

value: leaf explant-derived callus


title: Cortex_FP25_0-hour

description: Library name: 9


title: Arabidopsis nac42-L1 (SALK_016619C) grown in temperate climate infected by S. sclerotiorum replicate 1

description: Library name: AthMutEClimat1-FRT1


title: 3_T8_ColIV

description: Library name: 105193-001-010

value: ColIV

value: AD


title: Mus musculus, splenocytes, 18-24 months, Female, Naive, id: 24-N-OF3

description:
Library name: 24-N-OF3
10X Genomics

value: splenocytes

value: Female

value: 18-24 months

value: Naive


title: Cortex_FP24_7-days

description: Library name: 8

value: Cortex

value: SKH-1 Elite

value: 7 days


title: Mus musculus, splenocytes, 18-24 months, Female, Naive, id: 24-N-OF2

description:
Library name: 24-N-OF2
10X Genomics


title: Callus, 12DAC, replicate 2


title: 3_MG_ColIVInh

description: Library name: 105193-001-008

value: MG

value: ColIVInh


title: Cortex_FP23_24-hours

description: Library name: 7

value: 24 hours


title: Mus musculus, splenocytes, 18-24 months, Female, Naive, id: 24-N-OF1

description:
Library name: 24-N-OF1
10X Genomics

value: spleen


title: 1_T8_Accutase

description: Library name: 105193-001-009

value: Accutase


title: Callus, 12DAC, replicate 1


title: 1_MG_ColIV

description: Library name: 105193-001-007

value: Male


title: Callus, 7DAC, replicate 3


title: Mus musculus, splenocytes, 18-24 months, Male, Sepsis (CLP+7dDCS), id: 0614S7-OM2

description:
Library name: 0614S7-OM2
10X Genomics

value: B6 strain

value: Sepsis (CLP+7dDCS)


title: 4_MG_ColIVInh

description: Library name: 105193-001-006

value: PSP


title: Cortex_FP20_0-hour

description: Library name: 4

value: 0 hour


title: Etching_3

city: Kodaira

first: Lili

last: Quan

address: 4-1-1 Ogawa-Higashi

department: National Institute of Neuroscience

institute: National Center of Neurology and Psychiatry

description:
Library name: Etching_3
Etching_raw_count.tsv

data_processing:
The generated reads were mapped to the rat reference genome (Rn6) or human reference genome (hg19) using TopHat (version 2.1.1) after adapter trimming by Trimmomatic.
Assembly: Rn6, hg19
Supplementary files format and content: Etching_raw_count.tsv
Supplementary files format and content: Dimemorfan_raw_count.tsv

organism: Rattus norvegicus

source_name: Rat prefrontal cortex

extract_protocol:
Total RNA was isolated from rat primary oligodendrocytes or iPSC-derived oligodendrocytes using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
Full-length cDNA was synthesized from total RNA using a SMART-Seq stranded (TaKaRa) according to manufacturer instructions. An Illumina library was prepared using a Nextera XT DNA Library Prep Kit (Illumina) according to SMART-seq kit instructions. Sequencing was performed using an Illumina NovaSeq 6000 sequencer (Illumina) in the 101-base single end mode for rat samples and DNBSEQ-G400 sequencer (MGI) in a single-end mode (150 bp) for human samples.

value: Rat prefrontal cortex

value: primary cell

value: oligodendrocytes


title: Mus musculus, splenocytes, 3-4 months, Male, Naive, id: 0614N-YM1

description:
Library name: 0614N-YM1
10X Genomics

value: splenocytes

value: 3-4 months

value: Naive


title: Cortex_FP21_0-hour

description: Library name: 5

source_name: Cortex

value: Cortex

value: SKH-1 Elite


title: Mus musculus, splenocytes, 18-24 months, Male, Naive, id: 0614N-OM2

description:
Library name: 0614N-OM2
10X Genomics

value: 18-24 months


title: Callus, 7DAC, replicate 2

value: leaf explant-derived callus


title: Etching_1

description:
Library name: Etching_1
Etching_raw_count.tsv


title: 1_T8_ColIV

description: Library name: 105193-001-005

value: ColIV

value: AD


title: Cortex_FP22_6-hours

description: Library name: 6

value: 6 hours


title: 3_T8_Accutase

description: Library name: 105193-001-004

value: Accutase

value: Male


title: Cortex_FP16_7-days

description: Library name: 1

value: 7 days


title: Input_2

city: Fuzhou

first: Ying

state: Fujian

address: No. 2, Xueyuan Road, University Town

institute: Fuzhou University

description: Library name: Input_2

data_processing:
Adapter trimming and quality filtering used Trimmomatic v0.36 to remove low-quality bases and adapters.
All datasets (RIP-seq and T&T-seq) were aligned to the human reference genome (hg38) using HISAT2 v2.1.0.
Reads were assembled and quantified by featureCounts (v1.6.5).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include TPM values for each Sample

source_name: human embryonic stem cell

growth_protocol: H9 human embryonic stem cells (hESCs) were maintained in Knockout DMEM supplemented with 20% Knockout Serum Replacement (KSR), 25 μg/mL basic fibroblast growth factor (bFGF), 1× Penicillin-Streptomycin, 1× GlutaMAX, and 1× Non-Essential Amino Acids (NEAA), cultured on mitomycin-C-inactivated mouse embryonic fibroblast (MEF) feeder layers in a humidified atmosphere with 5% CO₂ at 37°C.

extract_protocol:
For T&T-seq transcriptome RNA extraction, 100,000 oocyte-like cells (OLCs) were lysed in 2 μL aliquot, mixed with 1 mL TRIzol Reagent (Invitrogen #15596026), vortexed, incubated 5 min at RT, followed by chloroform addition (200 μL), centrifugation (12,000 × g, 15 min, 4°C), isopropanol precipitation (500 μL, 10 min RT), ethanol wash (75%), and resuspension in 11 μL nuclease-free water for storage at -80°C. For T&T-seq translatome RNA extraction, 8 μL lysate from 100,000 OLCs underwent ribosome capture using RiboLace Beads (Immagina) with 70-min rotation at 4°C, washed twice with W-Buffer, dissociated in 1% SDS + Proteinase K (37°C, 30 min), then extracted identically to transcriptome RNA including TRIzol/chloroform separation and overnight ethanol precipitation before resuspension. For RIP-seq RNA extraction, 1,000,000 OLCs were lysed in RIP buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) with protease/RNase inhibitors, precleared with Protein G Dynabeads (Thermo #10004D), immunoprecipitated with 5 μg BOLL antibody (Proteintech #13720-1-AP) overnight at 4°C followed by 4-h bead binding, washed four times with lysis buffer, resuspended in 1 mL TRIzol for RNA isolation via chloroform/isopropanol method, and eluted in 20 μL nuclease-free water. All RNA extracts were stored at -80°C pending library construction.
RNA libraries for T&T-seq and RIP-seq were prepared using SMART-Seq2 library construction strategy.

treatment_protocol: H9 hESCs were seeded at 50% confluency on Matrigel-coated plates and pretreated with 50 ng/mL BMP4 in differentiation medium for 1 hour prior to transduction with BOLL-overexpressing lentivirus (or p2k7 empty vector control) for 24 hours, followed by medium replacement, blasticidin selection (2 μg/mL for 3 days), and continued culture in differentiation medium until analysis at day 6 post-transduction.

value: human embryonic stem cell

value: 4% input RNA from total RNA of BMP4-treated, BOLL-overexpressing OLCs.


title: NT_2

description:
Library name: NT_2
Etching_raw_count.tsv

value: Rat prefrontal cortex

value: primary cell


title: 2_MG_ColIVInh

description: Library name: 105193-001-003

value: MG

value: ColIVInh

value: MS

value: Female


title: Input_1

description: Library name: Input_1


title: Etching_2

description:
Library name: Etching_2
Etching_raw_count.tsv

value: oligodendrocytes


title: NT_1

description:
Library name: NT_1
Etching_raw_count.tsv


title: Cortex_FP17_7-days

description: Library name: 2

value: Cortex

value: SKH-1 Elite


title: 1_MG_Accutase

description: Library name: 105193-001-002