title: Testis,replicate 2

city: nanjing

first: yutong

last: li

state: jiangsu

address: No. 818, Tianyuan East Road

institute: Nanjing medical university

description:
Library name: Sample4
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation weremade using the Cell Ranger software v7.1.0(https://support.10xgenomics.com/single-cell-geneexpression/software/pipelines/latest/what-is-cell-ranger）
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: primary cell

extract_protocol:
Single cells were isolated according to a previous protocol56 with slight modifications. Briefly, decapsulated mouse testes and day 21 TOs were collected and washed twice in HBSS (Gibco, 14175095). Testes and TOs were digested in 3 mL of MEMα containing 1 mg/ml collagenase I (Sigma, C5138) and 5 µg/ml deoxyribonuclease I (Sigma, DN25), gently triturated 50 times and incubated for 8 min at 37°C. The dispersed tissue was then centrifuged at 600×g for 5 min and digested with 0.25% trypsin/EDTA and DNase I at 37°C with gentle agitation for 4 min. The enzymatic reaction was neutralized by the addition of FBS at a final concentration of 10%. The cells were then filtered through a 40 µm filter to remove cell aggregates. Cell viability was examined by a 0.4% trypan blue exclusion assay (Thermo Fisher Scientific, 15250061) in a Neubauer chamber (Neubauer, Blaubrand, Germany). The viability of the cells exceeded 90%, and the aggregation rate was less than 5%. The cell suspension was washed twice with DPBS (calcium- and magnesium-free PBS) and resuspended in DPBS + 0.04% BSA at a cell concentration of 1000 cells/µL.
With the use of a Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000268), the SIC single-cell suspension (700-1200 living cells per ml as determined by the CellDrop FL Cell Counter) was loaded onto a Chromium Single Cell Chip (Chromium Single Cell G Chip Kit, 10x Genomics, PN-1000120) according to the manufacturer’s instructions, for co-encapsulation with barcoded Gel Beads at a target capture rate of $6000 individual cells per sample. We lysed captured cells and released RNA was barcoded through reverse-transcription in individual single-cell gel beads in the emulsion (GEMS). In each droplet, complementary DNA (cDNA) was generated and amplified through reverse-transcription on a T100 PCR Thermal Cycler (Bio Rad) at 53 C for 45 min, followed by 85 C for 5 min and a hold at 4 C. Then, cDNA concentration and quality were assessed using Qubit Fluorometer (Thermo Scientific) and bioanalyzer 2100 (Agilent), respectively. According to the manufacturer’s introduction, scRNA-seq libraries were constructed and sequenced to a depth of $40000 reads per cell on illumina platform by Annoroad Gene Technology Co., Ltd.

value: Testis

value: unsorted


title: Testis,replicate 1

status: Public on Jan 28 2026

type: SRA

country: China

description:
Library name: Sample3
10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type


title: testicular organoids (TOs),replicate 2

description:
Library name: Sample2
10x Genomics


title: Healthy MPCs in CKD serum biological replicate 1

city: Lexington

first: Alexander

middle: Romano

last: Keeble

state: KY

address: 900 S Limestone st

country: USA

institute: University of Kentucky

description: Library name: H_A

library_source: transcriptomic

data_processing:
Raw FASTQ  files underwent pre-alignment quality control and alignment at novagene using the GRCh38/HG38 reference genome. Differential gene expression analysis was performed in R (v4.4.2) using the DeSeq2 package was calculated comparing CKD and control samples. Raw p-values were adjusted for multiple testing using the Benjamini-Hochberg false discovery rate (FDR) step-up method. FDR-adjusted p values less than 0.05 and log2 fold change values <0.5 or >0.5 were used as significance cutoffs.
Assembly: hg38
Supplementary files format and content: tab-delimited excel files include raw counts for each sample

organism: Homo sapiens

source_name: Skeletal muscle

growth_protocol: MPCs were purified from muscle biopsies from Control participants or patients with CKD following overnight incubation in sterile 1% glucose at 4°C. Biopsy samples collected at Albert Einstein College of Medicine were shipped overnight on wet ice to the University of Kentucky; samples collected from both institutions were incubated ~24hr in sterile 1% glucose at 4°C prior to isolation per our prior methods. Briefly, muscles were minced in F10 containing 10% fetal bovine serum, dispase II (2.4 U/ml; Roche Applied Science, Indianapolis, IN, USA) and collagenase D (1 mg/ml; Sigma-Aldrich, St. Louis, MO, USA). The muscle slurry was incubated with agitation for 60 minutes at 37°C. Enzymes were subsequently refreshed and the muscle slurry was incubated with agitation for an additional 30 minutes. The muscle slurry was then filtered through a 40 μm filter and then spun at 500 g for 5 min to pellet cells. Cells were then plated on 10cm cell culture plates (Corning Primaria) and MPCs were isolated through multiple rounds of pre-plating until purity was reached  (Control: 92%, CKD: 89%, P = .55). MPCs were maintained in growth medium composed of Ham’s F10 (cat#11550043), 20% fetal bovine serum, 1% pen-streptavidin, and 5ng/ml basic fibroblast growth factor (bFGF). MPCs for RNA sequencing experiments were cultured in 10% control or CKD human serum. Media was refreshed every other day.

extract_protocol:
MPCs used for RNA sequencing were cultured for 4 days in 10% serum obtained from control participants or from patients with late stage CKD. Total RNA was extracted from primary MPCs by pipetting Trizol TRI Reagent (#R2050-1-200, Zymo Research) onto wells and manual scraping. RNA was isolated using the Direct-zol RNA Miniprep kit (#R2051, Zymo Research) per manufacturer’s instructions. RNA concentration and quality (average RIN: 9.7) was assessed with an RNA Nano chip kit on a bioanalyzer by the University of Kentucky Genomics Core Laboratory.
Six hundred nanograms of total RNA was sent to Novogene for library construction and sequencing on an NovaSeq PE150 system using a paired-end 150 bp dual-indexing protocol.

value: Skeletal muscle

tag: cell line

value: Primary myogenic progenitor cells


title: C6_Replication_146

type: genomic

city: Potsdam

first: Amandeep

last: Singh

state: Brandenburg

address: Arthur-Scheunert-Allee 114-116

department: EOD

country: Germany

institute: German Institute of Human Nutrition

hyb_protocol: The bisulfite treatment and hybridisation was carried out by Life & Brain GmbH

scan_protocol: iscan, carried out by Life & Brain GmbH

data_processing: ChAMP package in R environment

label: other

molecule: genomic DNA

source_name: Blood cells

label_protocol: Labeling was carried out by Life & Brain GmbH

extract_protocol: precipitation with sodium acetate

treatment_protocol: Genomic DNA was extracted from blood cells.

tag: Sex

value: M

value: Blood cells


title: C3_Replication_139


title: C6_Replication_144


title: C6_Replication_142

value: F


title: Healthy MPCs in control serum biological replicate 2

description: Library name: ESRD_CMB


title: C5_Replication_136


title: C5_Replication_141


title: C6_Replication_140


title: C5_Replication_138


title: testicular organoids (TOs),replicate 1

description:
Library name: Sample1
10x Genomics


title: C6_Replication_133


title: Transbronchial lung biopsy 9 replicate 1

city: New York

first: David

last: Zhang

state: NY

address: 650 W 168th Street, Room 905, New York, NY 10032

institute: Columbia University in the City of New York

description: Library name: CL37 replicate 1

data_processing:
Cellranger was used to construct feature matrices using standard protocols. Cells were filtered using Subset function to remove those with >10% mitochondrial genes and 7500 genes expressed and 40000 transcripts identified. Sample-level datasets were integrated using reciprocal PCA. NormalizeData function was used to log normalize data and the ScaleData function was used to regress out the number of UMIs and percentage of mitochondrial genes. Principal component analysis was performed using RunPCA and Louvain clustering was performed using the FindNeighbors and FindClusters functions. UMAP embeddings were calculated using RunUMAP for visualization. Correlation plots of the proportion of cell clusters in control and COVID-19 samples were graphed using R package CorrPlot.
Assembly: scRNA
Supplementary files format and content: .h5 files in the format "sample_name_filtered_feature_bc_matrix.h5"

molecule: polyA RNA

source_name: Lung

extract_protocol:
A cell suspension was prepared from transbronchial lung biopsies by digestion in 1.4ml DMEM containing 0.3 mg/μl liberase (Sigma), 70 μg/μl elastase (Worthington) and 3 U/ml dispase II (Sigma) at 37o C for 45 min, followed by the addition of 10μl DNAse (2.7 U/μl; Qiagen), 1μl 1M DTT, and 2μl 0.5M EDTA, and incubation for an additional 15 min. The cell suspension was strained through a 100-μm filter, centrifuged at 300xg for 10min, and resuspended in ~200μl residual buffer plus 10μl DNAse. Red blood cells were lyzed by adding 1ml ACK buffer (Gibco) and incubating on ice for 2 min. Following the addition of 10ml PBS with 1% BSA, centrifugation and resuspension in ~200μl residual buffer plus 10μl DNAse, the cells were blocked with FcR Blocking Reagent (Miltenyi) and stained 1:100 with CD326(EpCAM)-AF488 (Invitrogen), CD31-APC (Biolegend), CD45-APC (Biolegend), and CD235a-PE (Biolegend) for 1hr at 4 o C, strained through a 100-μm filter, and flow sorted on a BD Influx fluorescence-activated cell sorter (FACS). We positively sorted for complex, singlet cells and negatively sorted for DAPI and PE, which removed the dead cells and any remaining red blood cells. The FACS-sorted cells were collected as three populations: CD326/EpCAM positive (epithelial), CD31/CD45 positive (immune and endothelial), and those negative for either AF488 or APC fluorophore signals (enriched for fibroblasts). Using the cell count numbers obtained by FACS, each of the three populations of cells were mixed 1:1:1, using the population with the fewest number of cells as the limiting factor
10,000 cells were loaded on a 10X Genomics flow cell for encapsulation in individual droplets for lysis, reverse transcription, and barcoding of cDNA, followed by sequencing on an Illumina NovaSeq 6000. We performed additional quality control by visualizing transcript count, gene count, and percent mitochondrial genes for each cell cluster and by each sample.

value: Lung

value: Lung epithelial, immune, and mesenchymal cells


title: CKD MPCs in control serum biological replicate 1

description: Library name: CKD_A


title: Transbronchial lung biopsy 12

description: Library name: CL40


title: Transbronchial lung biopsy 11

description: Library name: CL39


title: Transbronchial lung biopsy 10

description: Library name: CL38


title: Transbronchial lung biopsy 9 replicate 3

description: Library name: CL37 replicate 3


title: Transbronchial lung biopsy 8 replicate 3

description: Library name: CL36 replicate 3


title: C5_Replication_135


title: Transbronchial lung biopsy 8 replicate 2

description: Library name: CL36 replicate 2


title: C6_Replication_134


title: Transbronchial lung biopsy 8 replicate 1

description: Library name: CL36 replicate 1


title: Transbronchial lung biopsy 9 replicate 2

description: Library name: CL37 replicate 2


title: C5_Replication_128


title: C5_Replication_132


title: C5_Replication_131


title: C6_Replication_129


title: C3_Replication_127


title: C5_Replication_130


title: C6_Replication_125


title: Transbronchial lung biopsy 6 replicate 4

description: Library name: CL34 replicate 4


title: Transbronchial lung biopsy 7 replicate 3

description: Library name: CL35 replicate 3


title: Transbronchial lung biopsy 7 replicate 1

description: Library name: CL35 replicate 1


title: Transbronchial lung biopsy 7 replicate 4

description: Library name: CL35 replicate 4


title: Transbronchial lung biopsy 6 replicate 3

description: Library name: CL34 replicate 3


title: Transbronchial lung biopsy 6 replicate 2

description: Library name: CL34 replicate 2


title: Transbronchial lung biopsy 7 replicate 2

description: Library name: CL35 replicate 2


title: C3_Replication_123


title: Transbronchial lung biopsy 5 replicate 3

description: Library name: CL33 replicate 3


title: Transbronchial lung biopsy 5 replicate 4

description: Library name: CL33 replicate 4


title: C6_Replication_121


title: C6_Replication_118


title: C6_Replication_120


title: Transbronchial lung biopsy 4 replicate 4

description: Library name: CL32 replicate 4


title: C3_Replication_119


title: Transbronchial lung biopsy 5 replicate 1

description: Library name: CL33 replicate 1


title: C5_Replication_124


title: C3_Replication_116


title: C3_Replication_115


title: C3_Replication_117


title: Transbronchial lung biopsy 4 replicate 3

description: Library name: CL32 replicate 3


title: Transbronchial lung biopsy 5 replicate 2

description: Library name: CL33 replicate 2


title: C5_Replication_122


title: C5_Replication_113


title: Transbronchial lung biopsy 4 replicate 1

description: Library name: CL32 replicate 1


title: C3_Replication_112


title: C3_Replication_126


title: Transbronchial lung biopsy 3 replicate 5

description: Library name: CL31 repliate 5


title: C5_Replication_137


title: C6_Replication_114


title: Transbronchial lung biopsy 3 replicate 4

description: Library name: CL31 repliate 4


title: Transbronchial lung biopsy 4 replicate 2

description: Library name: CL32 replicate 2


title: C3_Replication_111


title: Transbronchial lung biopsy 6 replicate 1

description: Library name: CL34 replicate 1


title: Transbronchial lung biopsy 3 replicate 3

description: Library name: CL31 repliate 3


title: Transbronchial lung biopsy 2 replicate 3

description: Library name: CL30 replicate 3


title: Transbronchial lung biopsy 3 replicate 1

description: Library name: CL31 repliate 1


title: C5_Replication_109


title: Transbronchial lung biopsy 3 replicate 2

description: Library name: CL31 repliate 2


title: C6_Replication_110


title: C5_Replication_108


title: Transbronchial lung biopsy 2 replicate 2

description: Library name: CL30 replicate 2


title: C5_Replication_105


title: Transbronchial lung biopsy 2 replicate 1

description: Library name: CL30 replicate 1


title: Transbronchial lung biopsy 1

description: Library name: CL29


title: C6_Replication_106


title: C3_Replication_103


title: C6_Replication_104


title: si-NAT10-2.Input

city: Jinan

first: Yunhong

state: Shandong

address: No. 4655, Daxue Road, Changqing District, Jinan, Shandong

institute: Shandong University of Traditional Chinese Medicine

description: Library name: sample2-2

data_processing:
Briefly, Paired-end reads were harvested from sequencer, and were quality controlled by Q30 and FastQC. After 3' adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).  .
After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Acetylated sites on RNAs (peaks) were identified by MACS software.
Differentially acetylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.
GO and Pathway enrichment analysis were performed by the differentially acetylated protein coding genes
Assembly: hg38
Supplementary files format and content: The file contains the information and annotation of RNA modification peaks identified in each sample

source_name: HUVEC

extract_protocol:
RNA was extracted using trizol reagent
Total RNA was subjected to immunoprecipitation with the GenSeq&ac4C RIP Kit (GenSeqInc.) by following the manufacturer's instructions. Briefly, RNA was randomlyfragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the ac4Cantibody by rotating at room temperature for 1 h. The RNA fragments were incubated with thebead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes werewashed for several times, and then, captured RNA was eluted from the complexes and purified. RNAlibraries for IP and input samples were then constructed with GenSeq Low Input Whole RNA LibraryPrep Kit(GenSeq Inc.) by following the manufacturer's instructions.

value: HUVEC

value: Endothelial cells

tag: treatment

value: Transfect the cells with si-NAT10

tag: batch


title: si-NAT10-2.IP

description: Library name: sample2-1


title: C6_Replication_107


title: NC-1.Input

description: Library name: sample1-2

value: Transfect the cells with NC


title: C3_Replication_102


title: C6_Replication_98


title: C6_Replication_101


title: C3_Replication_100


title: C3_Replication_99


title: P-hep-orgs, FFAs, Day10, rep1

city: Guangzhou

first: Changlu

last: Qin

address: No. 382, Outer Ring Road, Higher Education Mega Center, Xiaoguwei Subdistrict, Panyu District, Guangzhou City, Guangdong Province

institute: South China University of Technology

description:
Library name: Sample10
Day10_counts_matrix.txt

data_processing:
Sequencing was performed by Novogene (Beijing, China) on an Illumina HiSeq X-Tensequencer with 150 bp paired-end sequencing reaction. Differentially expressed genes (DEGs) were analyzed by DESeq2 using counts. Genes with P value ≤ 0.05 and fold change ≥ 1.5 was identified as DEGs.
Assembly: GRCh38
Supplementary files format and content: txt file include raw counts for each sample

source_name: Polarized Hepatocyte Organoids

extract_protocol:
Total RNA of organoids were extracted using RNAiso Plus kit according to the manufacturer’s instructions.
The cDNA libraries for RNA sequencing were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB).

value: H9 differentiated cells

value: Polarized Hepatocyte Organoids

value: FFAs, Day10


title: P-hep-orgs, Control, Day10, rep3

description:
Library name: Sample9
Day10_counts_matrix.txt

value: Control, Day10


title: P-hep-orgs, FFAs, Day10, rep3

description:
Library name: Sample12
Day10_counts_matrix.txt


title: NC-1.IP

description: Library name: sample1-1


title: C6_Replication_97


title: P-hep-orgs, Control, Day10, rep1

description:
Library name: Sample7
Day10_counts_matrix.txt


title: P-hep-orgs, Control, Day10, rep2

description:
Library name: Sample8
Day10_counts_matrix.txt


title: P-hep-orgs, FFAs, Day10, rep2

description:
Library name: Sample11
Day10_counts_matrix.txt


title: C5_Replication_93


title: C6_Replication_96


title: P-hep-orgs, Control, Day2, rep3

description:
Library name: Sample3
Day2_counts_matrix.txt

value: Control, Day2


title: C3_Replication_92


title: P-hep-orgs, FFAs, Day2, rep1

description:
Library name: Sample4
Day2_counts_matrix.txt

value: FFAs, Day2


title: C5_Replication_91


title: C6_Replication_94


title: P-hep-orgs, FFAs, Day2, rep3

description:
Library name: Sample6
Day2_counts_matrix.txt


title: C5_Replication_90


title: C3_Replication_88


title: Sheared,24hr,rep2

city: Norfolk

first: Michael

last: Henry

state: Virgina

address: 700 W Olney Rd, PO Box 1980

department: Department of Biomedical and Translational Sciences

institute: Eastern Virginia Medical School at Old Dominion University

description:
Library name: Sample17
S24C

data_processing:
Sequencing alignment was done using STAR Align against the ensembl reference library GRCh38.p13
Aligned BAM files were processed using DESeq2 in R using Rstudio to determine differential gene expression
Assembly: GRCh38.p13
Supplementary files format and content: .csv file of raw counts for all samples used for DESeq2 analysis, gene ids are in h38 format
Supplementary files format and content: .csv file of the comparison between sheared and static samples at 3 hours, gene ids are in h38 format
Supplementary files format and content: .csv file of the comparison between sheared and static samples at 12 hours, gene ids are in h38 format
Supplementary files format and content: .csv file of the comparison between sheared and static samples at 24 hours, gene ids are in h38 format

molecule: cytoplasmic RNA

growth_protocol: PC-3 cells were grown in DMEM/F12 supplemented with 10% FBS and 1x NEAA until time of the experiment. During experiment, the cells were in DMEM with supplemented with 1x insulin-transferrin-selenium and 5 mg/mL of bovine serum albumin

extract_protocol:
Cytosolic RNA was extracted by lysis in RLN buffer (50mM Tris-HCl pH=8, 140m NaCl, 1.5mM MgCl2, 0.5% NP-40) for 5 minutes, follwed by centrifugation at 12,000g for 5 minutes. Trizol was then added to the supernatant and the Direct-zol RNA Purification Kit (R2050, ZYMO Research) was used according to the manufacturer's guidelines.
Sequencing and library contruction was performed by Novogene Co

treatment_protocol: PC-3 cells were detached from the tissue culture plate and suspended to a concenctration of 2x10^6 cells/mL before being exposed to fluid shear stress by passaged through a 5mL syringe and 30G 1/2 inch needled at a flow rate of 250μL/sec. The samples that were exposed to fluid shear stress are identified as sheared, while the corresponding controls were held in suspension during the shear stress exposure. After exposure, cells were plated in poly-HEMA coated 12 wells at a density of 1x10^6 cells/mL and sampled either 3, 12, or 24 hours after shear stress exposure

value: Prostate cancer

value: FSS exposure

tag: time after_exposure

tag: biological replicate_for_time_point


title: Sheared,24hr,rep1

description:
Library name: Sample16
S24A


title: P-hep-orgs, Control, Day2, rep2

description:
Library name: Sample2
Day2_counts_matrix.txt


title: Sheared,12hr,rep1

description:
Library name: Sample13
S12A


title: C5_Replication_83


title: Sheared,12hr,rep2

description:
Library name: Sample14
S12B


title: C5_Replication_84

value: M


title: C6_Replication_95

value: Blood cells


title: Static_control,24hr,rep3

description:
Library name: Sample9
U24D

value: Static


title: C5_Replication_81

value: F


title: Static_control,24hr,rep2

description:
Library name: Sample8
U24C


title: Sheared,3hr,rep2

description:
Library name: Sample11
Shear3B


title: Sheared,3hr,rep1

description:
Library name: Sample10
Shear3A


title: C5_Replication_86


title: C6_Replication_89


title: P-hep-orgs, Control, Day2, rep1

description:
Library name: Sample1
Day2_counts_matrix.txt


title: Sheared,24hr,rep3

description:
Library name: Sample18
S24D


title: P-hep-orgs, FFAs, Day2, rep2

description:
Library name: Sample5
Day2_counts_matrix.txt


title: C3_Replication_77


title: C3_Replication_79


title: C6_Replication_80


title: C3_Replication_78


title: C5_Replication_75


title: C6_Replication_74


title: C5_Replication_85


title: Static_control,24hr,rep1

description:
Library name: Sample7
U24A


title: Static_control,3hr,rep3

description:
Library name: Sample3
Static3D


title: C5_Replication_87


title: C6_Replication_82


title: C3_Replication_72


title: Static_control,3hr,rep2

description:
Library name: Sample2
Static3B


title: C6_Replication_76


title: Sheared,12hr,rep3

description:
Library name: Sample15
S12C


title: Static_control,12hr,rep1

description:
Library name: Sample4
U12A


title: Sheared,3hr,rep3

description:
Library name: Sample12
Shear3D


title: Static_control,12hr,rep3

description:
Library name: Sample6
U12C


title: C5_Replication_67


title: C6_Replication_68


title: C3_Replication_73


title: Static_control,12hr,rep2

description:
Library name: Sample5
U12B


title: C5_Replication_69


title: C3_Replication_70


title: C3_Replication_64


title: C3_Replication_71


title: Resistenz pSCC Cera rep2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description: Library name: DX312_313433_25R134-2_S85_L000

data_processing:
Adapter and low quality reads were trimmed with Trimmomatic (v0.39).
Reads were aligned to hg38 reference genome and read-per-gene were quantified using STAR (v2.7.11b).
Assembly: hg38
Supplementary files format and content: raw read count per gene in tab delimited format

source_name: bladder cancer (SCC)

growth_protocol: Primary bladder cancer cells were cultured at 37°C, 5% CO₂, and 70% humidity in MEBM medium supplemented with 1× B27, amphotericin B, penicillin–streptomycin, EGF (20 ng/mL), heparin (4 mg/mL), FGF (20 ng/mL), gentamicin (35 mg/mL), rho kinase inhibitor (500 nM), and embedded in 2% Matrigel.

extract_protocol:
Total RNA was extracted using the NucleoSpin® RNA Plus Kit (Macherey-Nagel, cat. no. 740984.50) following the manufacturer’s instructions. RNA concentration was measured using a NanoDrop® ND-1000 spectrophotometer (ThermoFisher).
Libraries were prepared using the Illumina® Stranded TruSeq® RNA sample preparation kit, starting with 1 µg total RNA. mRNA was poly-A selected, purified, fragmented, reverse transcribed with random primers, followed by second strand cDNA synthesis. After end repair, A-tailing, and adapter ligation, libraries were purified and amplified by 15 PCR cycles.

treatment_protocol: p-SCCATRi models were cultured with a final ATR inhibitor concentration of 0.60 µM, whereas corresponding control p-SCCDMSO models were maintained in medium containing 0.1% DMSO.

value: bladder cancer (SCC)

value: primary cell culture

tag: genotype

value: ATR inhibitor (Ceralasertib, AZD6738)


title: C6_Replication_65


title: Resistenz pSCC DMSO rep2

description: Library name: DX312_313432_25R134-1_S84_L000

value: DMSO


title: TO_VehicleControl_Rep3

city: Philadelphia

first: Kellie

last: Jurado

state: Pennsylvania

address: 3400 Civic Center Blvd, Building 421

department: Microbiology

institute: University of Pennsylvania

description: Library name: MerlinoIL27_16

data_processing:
Mapped raw reads to human reference transcriptome using Kallisto
Calculated transcript abundances with kallisto and converted to count matrix with tximport
Counts per million normalization with EdgeR
Differential gene expression with limma
Functional enrichment with GSEA and msigndbr
Assembly: hg38
Supplementary files format and content: log2 CPM-scaled count matrix, gene symbols by sample names

source_name: trophoblast organoids derived from primary human placentas

extract_protocol:
Direct-zol RNA Miniprep kit (Zymo Research, R2050)
Illumina stranded total RNA Prep kit with Ribo-Zero, NovaSeq 6000 SP Reagent Kit v1.5, 200 cycles (Illumina, #20040719)

value: Cytokine stimulation

tag: cytokine

value: Vehicle control


title: TO_IL27stim_Rep3

description: Library name: MerlinoIL27_17

value: trophoblast organoids derived from primary human placentas


title: TO_antiIFNL1/3_Rep3

description: Library name: MerlinoIL27_15

value: neutralizing antibody

tag: antibody

value: anti-IFNL1 and anti-IFNL3


title: Static_control,3hr,rep1

description:
Library name: Sample1
Static3A


title: C3_Replication_63


title: TO_IFNL1/3stim_Rep3

description: Library name: MerlinoIL27_18


title: C3_Replication_61


title: C3_Replication_62


title: Resistenz pSCC Cera rep1

description: Library name: A006850326_211118_S43_L000


title: TO_IFNL1/3stim_Rep2

description: Library name: MerlinoIL27_12


title: C6_Replication_66


title: C3_Replication_60


title: C3_Replication_58


title: TO_IsotypeControl_Rep3

description: Library name: MerlinoIL27_13

value: isotype control


title: C5_Replication_59


title: TO_IsotypeControl_Rep2

description: Library name: MerlinoIL27_7


title: TO_antiIL27_Rep3

description: Library name: MerlinoIL27_14


title: Resistenz pSCC DMSO rep1

description: Library name: A006850326_211116_S42_L000


title: TO_antiIL27_Rep2

description: Library name: MerlinoIL27_8


title: TO_IFNL1/3stim_Rep1

description: Library name: MerlinoIL27_6


title: TO_antiIFNL1/3_Rep2

description: Library name: MerlinoIL27_9


title: C5_Replication_54


title: C5_Replication_56


title: TO_VehicleControl_Rep2

description: Library name: MerlinoIL27_10


title: TO_VehicleControl_Rep1

description: Library name: MerlinoIL27_4


title: C5_Replication_55


title: C6_Replication_57


title: C6_Replication_52


title: TO_IL27stim_Rep1

description: Library name: MerlinoIL27_5


title: C6_Replication_53


title: C3_Replication_51


title: TO_IsotypeControl_Rep1

description: Library name: MerlinoIL27_1


title: TO_antiIFNL1/3_Rep1

description: Library name: MerlinoIL27_3


title: C3_Replication_49


title: TO_antiIL27_Rep1

description: Library name: MerlinoIL27_2


title: C3_Replication_50


title: C3_Replication_48


title: WT HeLa, BMN673 treated

city: Shanghai

first: Yihao

last: Wang

state: State

address: Zhizaoju Road 833, Shanghai

department: Department of Ophthalmology

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

description:
Library name: Tmem
WT HeLa, BMN673 treated

library_source: genomic

data_processing:
ChIP-seq libraries were sequenced using the Illumina NovaSeq 6000 platform.
Raw reads were aligned to the reference genome hg19 using Bowtie2 (v2.4.4) with default parameters.
Duplicate reads were removed using Picard Tools (v2.27.4).
Peaks were called with MACS2 (v2.2.7.1; q-value < 0.05).
Assembly: hg19
Supplementary files format and content: bigwig file

source_name: HeLa cell line

growth_protocol: HeLa cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Treated HeLa cells were cross-linked with 1% formaldehyde for 10 min at room temperature, quenched with 125 mM glycine, and washed with ice-cold PBS. Cells were lysed in SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1) supplemented with protease inhibitors, and chromatin was sheared to 200–500 bp fragments using a Covaris S220 sonicator (peak power: 75 W, duty factor: 20%, cycles/burst: 200, duration: 15 min). Sheared chromatin was diluted 10-fold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl) and pre-cleared with Protein G magnetic beads (Thermo Fisher, #88847) for 1 h at 4°C. Immunoprecipitation was performed overnight at 4°C using 10 µl of STING antibody (Abcam, #ab239074). Antibody-chromatin complexes were captured with Protein G beads, washed sequentially with low-salt, high-salt, LiCl, and TE buffers, and eluted in elution buffer (1% SDS, 0.1 M NaHCO3). Cross-links were reversed by incubating at 65°C overnight with 200 mM NaCl. DNA was purified using the QIAquick PCR Purification Kit (Qiagen, #28104).
Libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit (NEB, #E7645S) following manufacturer instructions.

treatment_protocol: HeLa cells were treated with 20 μM BMN673 for 24 hours. ChIP-seq was performed to profile genome-wide binding of STING in HeLa cell line treated with 20 μM BMN673 for 24 h.

value: HeLa cell line

value: cervical cancer cell line

value: wild-type

value: BMN673 (20 μM) for 24 hours


title: C5_Replication_47

value: Blood cells


title: STING WT, BMN673 treated, rep2

description:
Library name: WY_2
STING_WT_Raw_Count.txt

data_processing:
RNA libraries were sequenced using the Illumina NovaSeq 6000 platform.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (v 0.6.6).
Trimmed sequence reads were mapped to GRCh37/hg19 using Hisat2 tool (v 2.2.1).
Read count extraction for each gene was performed by featureCounts (v 2.0.1).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include count values for each Sample

extract_protocol:
RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies). 3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) following manufacturer's protocols.

treatment_protocol: STING knockout (STING KO) HeLa cell line was engineered using CRISPR. STING wild-type (WT) and STING knockout (KO) HeLa cells were treated with 20 μM BMN673 or PBS for 24 hours.

value: STING wild-type (WT)


title: STING WT, BMN673 treated, rep1

description:
Library name: WY_1
STING_WT_Raw_Count.txt


title: C5_Replication_46

value: F


title: C5_Replication_45


title: STING WT, Non-treated, rep2

description:
Library name: WN_2
STING_WT_Raw_Count.txt

value: PBS for 24 hours


title: STING KO, Non-treated, rep1

description:
Library name: BN_1
STING_KO_Raw_Count.txt

source_name: STING KO HeLa cell line

value: STING KO HeLa cell line

value: STING knockout (KO)


title: C6_Replication_43


title: C5_Replication_42


title: RNAseq,S5

first: wenchen

last: luo

address: Dongan Road

institute: Fudan University

description: Library name: Sample10

data_processing:
Raw FASTQ reads were trimmed using Trim Galore and transcript quantification was performed using Salmon in the quasi-mapping mode.
Assembly: hg38
Supplementary files format and content: RNA count matrix at the gene level.

source_name: patients with sepsis

extract_protocol:
For RNA-seq,total RNA was extracted using the RNAprep Pure Cell/Bacteria Kit (TIANGEN; DP430) following the manufacturer’s protocol.
For RNA-seq, the extracted RNA was utilized for library construction with the Illumina TruSeq Stranded Total RNA Library Prep Kit. The library was sequenced using paired-end 150-bp reads.

value: PBMCs

value: patients with sepsis


title: C3_Replication_44


title: STING KO, BMN673 treated, rep1

description:
Library name: BY_1
STING_KO_Raw_Count.txt


title: STING KO, Non-treated, rep2

description:
Library name: BN_2
STING_KO_Raw_Count.txt


title: C5_Replication_37


title: RNAseq,S2

description: Library name: Sample7


title: C5_Replication_41


title: STING WT, Non-treated, rep1

description:
Library name: WN_1
STING_WT_Raw_Count.txt


title: TO_IL27stim_Rep2

description: Library name: MerlinoIL27_11

value: Cytokine stimulation


title: STING KO, BMN673 treated, rep2

description:
Library name: BY_2
STING_KO_Raw_Count.txt


title: C6_Replication_39


title: C5_Replication_33


title: C3_Replication_35


title: RNAseq,S1

description: Library name: Sample6


title: RNAseq,C5

description: Library name: Sample5

source_name: nonseptic control

value: nonseptic control


title: C5_Replication_38


title: C3_Replication_40


title: C6_Replication_34


title: RNAseq,S4

description: Library name: Sample9


title: C5_Replication_32


title: RNAseq,S3

description: Library name: Sample8


title: C3_Replication_28


title: FOXRED1-NC-3

city: Changsha

first: Huaiyuan

last: Liang

address: 183 Renmin Middle Road

institute: Institute of Urological Cancer, Central South University

description: Library name: Sample 24

data_processing:
Total RNA qualification
Assembly: hg38,mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: esophagus

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

value: esophagus

value: Esophageal adenocarcinoma cells

value: the control group of knockdown FOXRED1 by shRNA

value: transfection infection


title: RNAseq,C2

description: Library name: Sample2


title: C3_Replication_36


title: C3_Replication_30


title: RNAseq,C1

description: Library name: Sample1


title: C6_Replication_23


title: FOXRED1-sh-2

description: Library name: Sample 20

value: the treat group of knockdown FOXRED1 by shRNA


title: FOXRED1-NC-2

description: Library name: Sample 23


title: RNAseq,C3

description: Library name: Sample3


title: C3_Replication_31


title: FOXRED1-sh-1

description: Library name: Sample 19


title: C6_Replication_24


title: C6_Replication_29


title: C5_Replication_27


title: RNAseq,C4

description: Library name: Sample4


title: YY2-sh-3

description: Library name: Sample 15

value: the treat group of knockdown YY2 by shRNA


title: C3_Replication_21


title: C3_Replication_26


title: YY2-NC-2

description: Library name: Sample 17

value: the control group of knockdown YY2 by shRNA


title: YY2-NC-1

description: Library name: Sample 16


title: C3_Replication_22

value: Blood cells


title: YY2-sh-2

description: Library name: Sample 14


title: YY2-NC-3

description: Library name: Sample 18


title: FOXRED1-sh-3

description: Library name: Sample 21


title: C5_Replication_19


title: C5_Replication_20


title: C5_Replication_25


title: YY2-sh-1

description: Library name: Sample 13


title: C3_Replication_18


title: TRIM15-EV-2

description: Library name: Sample 11

value: the control group of overexpress TRIM15 by transfecting plasmids


title: FOXRED1-NC-1

description: Library name: Sample 22


title: TRIM15-EV-3

description: Library name: Sample 12


title: C3_Replication_16

value: F


title: TRIM15-OE-3

description: Library name: Sample 9

value: the treat group of overexpress TRIM15 by transfecting plasmids


title: C6_Replication_17


title: C6_Replication_15


title: TRIM15-EV-1

description: Library name: Sample 10


title: C3_Replication_13


title: TRIM15-OE-1

description: Library name: Sample 7


title: ND-2

description: Library name: Sample 5

value: ND mouse

value: feed


title: C6_Replication_12


title: C3_Replication_9


title: ND-1

description: Library name: Sample 4


title: C5_Replication_7


title: HFD-3

description: Library name: Sample 3

value: HFD mouse


title: HFD-2

description: Library name: Sample 2


title: C6_Replication_6


title: hiPSC-cardiomyocyte, icell, 25 Gy, day 14, biol rep 6

city: Saint Louis

first: Shuhua

last: Fu

state: MO

address: 660 S. Euclid Avenue Campus Box 8103

institute: Washington University in St. Louis

description: Library name: lib167

data_processing:
Raw reads of RNA-seq libraries were processed using the RNA-seq pipeline (https://github.com/Zhang-lab/RNA-seq_QC_analysis) which consists of data processing, quality control, integrative analysis, and data visualization.
Assembly: human genome hg38 with gene annotation ENCODE V27. mouse genome mm10 with gene annotation ENCODE M20.
Supplementary files format and content: TXT format, readcount table

growth_protocol: iCell Cardiomyocytes^2 were maintained per the manufacturer's instructions.  GCaMP6 hiPSC-CMs were differentiated into cardiomyocytes via GSK-3 inhibition/Wnt activation followed by TNKS inhibition/Wnt inhibition, followed by purification via lactate-mediated metabolic selection, and were then maintained in RPMI 1640 + 2% B-27 Supplement at 37 C with 5% CO2.

extract_protocol:
Cell preparation, antibody binding, tagmentation, and DNA extraction and purification were performed using the Active Motif CUT&Tag kit (Active Motif, 53171) according to the manufacturer’s instructions. The following antibodies were used: H3K27me3 (Active Motif, 39155), H3K27ac (Active Motif, 39685), H3K4me3 (Active Motif, 39159), H3K4me1 (Cell Signaling Technology, 5326), or IgG isotype control (Cell Signaling Technology, 66362S).
cDNA libraries were constructed using the Active Motif CUT&Tag kit with Nextera primers per manufacturer's instructions.

treatment_protocol: IR treatment was performed using the small animal radiation research platform (SARRP, Xstrahl Inc.). hiPSC-CMs received 25 Gy to the entire cell culture surface area. Radiation was delivered at a 3.9 Gy/min dose rate in a single fraction of 25 Gy.

value: hiPSC-cardiomyocytes

value: WT

value: 25 Gy IR


title: C5_Replication_14


title: hiPSC-cardiomyocyte, GCaAMP, 25 Gy, day 1, biol rep 2

description: Library name: lib260


title: C6_Replication_10


title: C5_Replication_8


title: C5_Replication_11


title: hiPSC-cardiomyocyte, GCaAMP, 25 Gy, day 14, biol rep 3

description: Library name: lib270


title: TRIM15-OE-2

description: Library name: Sample 8

value: esophagus


title: C6_Replication_1


title: ND-3

description: Library name: Sample 6

value: Esophageal adenocarcinoma cells


title: AAD

city: Shijiazhuang

first: siming

last: Bu

state: CHINA

address: Zhongshan East Road

institute: Hebei Medical university

description: Library name: 23R3761

data_processing:
DNBelab C Series Single-Cell RNA Analysis Software
Filtering will be conducted from three aspects: the UMI count of individual droplets, the number of genes detected in individual droplets, and the proportion of mitochondrial-related genes.
Assembly: mm10
Supplementary files format and content: matrix.mtx.gz,barcodes.tsv.gz,features.tsv.gz
Supplementary files format and content: conmatrix.mtx.gz,conbarcodes.tsv.gz,confeatures.tsv.gz

source_name: aortic tissues

extract_protocol:
Use scissors to divide the vascular tissue into small pieces. Wash the tissue with PBS three times. Add digestive enzymes to the test tube to obtain a single-cell suspension. Cell viability should be above 80% and have good monodispersity with low impurity content. Generally, the cell concentration should be controlled above 205 cells/uL, and the number of cells should be more than 100,000.
By utilizing the different nucleic acid sequence sizes contained in the large and small magnetic beads, separate libraries are independently constructed:Large magnetic bead library: Release the cDNA carrying Cell Barcode and UMI, after reverse transcription and amplification, add sequencing adapters to construct a transcriptome library; Small magnetic bead library: Extract the Oligo index information, generate an index library, which is used to locate the droplet position and verify the uniqueness of the tags.

value: aortic tissues


title: hiPSC-cardiomyocyte, GCaAMP, 25 Gy, day 1, biol rep 3

description: Library name: lib268


title: HFD-1

description: Library name: Sample 1


title: hiPSC-cardiomyocyte, GCaAMP, 25 Gy, day 28, biol rep 3

description: Library name: lib269


title: mPFC samples collected from four WT mices at ZT20

city: GuangZhou

first: Haobin

last: CEN

address: 232 Outer Ring East Road, University Town, Panyu District, Guangzhou City

institute: Guangzhou University of Chinese Medicine

description:
Library name: Sample1
10x Genomics

data_processing:
The analysis pipeline comprised the following key steps. First, raw sequencing data were processed for quality, aligned, and quantified to generate a gene-cell matrix. After quality filtering, data were normalized, scaled, and reduced via PCA. Initial cell-type annotation was performed on UMAP visualizations using known marker genes. Next, neuronal cells were isolated, re-processed, and sub-clustered with graph-based methods, visualized on a dedicated UMAP. Cluster distributions between WT and Npas2 KO conditions were then compared. Subsequently, differential expression analysis between genotypes was conducted. Finally, the significant genes were analyzed for KEGG pathway enrichment, and enriched pathways were ranked by adjusted p-value.
Assembly: Mouse mm10
Supplementary files format and content: Gene metadata.xlsx

source_name: Brian, mPFC

growth_protocol: All mice were maintained on a 12 h light/dark cycle, with lights on at 6:00 AM (ZT0) and lights off at 6:00 PM (ZT12) and had free access to water and food, unless otherwise specified.

extract_protocol:
Medial prefrontal cortex (mPFC) tissues were harvested from four Npas2 KO mice and four wild-type littermate control mice at ZT20. To minimize individual biological variance and ensure sufficient nuclear yield, tissues from mice of the same genotype were pooled prior to dissociation.Nuclei were isolated using the Shbio Cell Nuclear Isolation Kit (Shibio, Cat# 52009-10) in conjunction with NP-40 lysis buffer to facilitate efficient membrane lysis while preserving nuclear integrity. The pooled tissues were homogenized according to the manufacturer’s instructions. The resulting homogenate was filtered to remove cellular debris, and the nuclei were recovered through centrifugation.
Single-nucleus libraries were then constructed using the 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kit v3.1, followed by high-depth sequencing on the Illumina NovaSeq 6000 platform with a paired-end 150 bp (PE150) configuration.

treatment_protocol: To investigate the molecular basis of nap behavior, all mice were sacrificed at circadian time ZT20. The medial prefrontal cortex (mPFC) was rapidly dissected on ice and immediately processed for nuclei isolation or flash-frozen in liquid nitrogen and stored at -80℃ until further processing.

value: Brian, mPFC

value: Wild-type

value: male

value: mixed simple

tag: time


title: hiPSC-cardiomyocyte, GCaAMP, 25 Gy, day 28, biol rep 2

description: Library name: lib266


title: hiPSC-cardiomyocyte, GCaAMP, 25 Gy, day 28, biol rep 1

description: Library name: lib258


title: hiPSC-cardiomyocyte, GCaAMP, 25 Gy, day 1, biol rep 1

description: Library name: lib254


title: hiPSC-cardiomyocyte, GCaAMP, 25 Gy, day 14, biol rep 2

description: Library name: lib259


title: C3_Replication_3

value: Blood cells


title: 3 Month, 5xFAD positive, rep2

city: Charlottesville

first: Harald

last: Sontheimer

state: VA

address: 409 Lane Rd

department: Neuroscience

institute: University of Virginia

description:
Library name: 20698
14_3M_5xFADplus_20698_005_188_S143_L001

data_processing:
FastQC v0.11.5 - Quality Control
Cutadapt v3.4 - Adapter Trimming
STAR v2.7.9a - Read Alignment
featureCounts v2.0.6 - Count Generation
Assembly: GRCm39
Supplementary files format and content: .csv of raw gene counts

source_name: Brain tissue - CA2 region

extract_protocol:
To isolate the CA2 area of the hippocampus for the bulk sequencing, we prepared 500 µm acute coronal brain slices as described previously.25 Slices were transferred to a Petri dish containing cold carbogen-bubbled (95% O2 + 5% CO2) cutting solution. Slices with hippocampus were visualized under a dissection microscope, and the CA2 area was anatomically identified by the neurons with larger cell bodies than CA1 neurons and with an intermediate cell density between loosely packed CA3 and more densely packed CA1 neurons.26 Using a tissue puncher (Ted Pella #15116-1 ID 1 mm), we isolated the CA2 area and snap-froze it.
All samples were immediately lysed and homogenized using plastic tissue grinders before being stored in pre-chilled tubes at −80°C for a minimum of 24 h. RNA isolation was carried out on thawed samples using a TRIzol Plus RNA Purification Kit (Cat#12183555, Invitrogen). Following purification and nanodrop sample verification, samples were sent to the Yale Center for Genome Analysis (New Haven, CT), where they underwent mRNA (Poly A) library preparation and sequencing on an Illumina NovaSeq 6000.

value: Brain tissue - CA2 region

value: C57BL/6, 5xFAD Positive


title: hiPSC-cardiomyocyte, GCaAMP, 25 Gy, day 14, biol rep 1

description: Library name: lib249


title: hiPSC-cardiomyocyte, GCaAMP, 25 Gy, day 7, biol rep 1

description: Library name: lib252


title: C5_Replication_2

value: F


title: hiPSC-cardiomyocyte, GCaAMP, sham, day 1, biol rep 3

description: Library name: lib267

value: Sham


title: C6_Replication_4


title: Control

description: Library name: 23R1936


title: 3 Month, 5xFAD negative, rep4

description:
Library name: 20769
12_3M_5xFADminus_20769_029_164_S141_L001

value: C57BL/6, 5xFAD Negative


title: 3 Month, 5xFAD positive, rep4

description:
Library name: 20691
16_3M_5xFADplus_20691_076_117_S145_L001


title: hiPSC-cardiomyocyte, GCaAMP, 25 Gy, day 7, biol rep 2

description: Library name: lib253


title: C3_Replication_5


title: mPFC samples collected from four Npas2 KO mices at ZT20

description:
Library name: Sample2
10x Genomics

value: NPAS2 Knockout


title: 3 Month, 5xFAD negative, rep1

description:
Library name: 20770
9_3M_5xFADminus_20770_065_128_S138_L001


title: 3 Month, 5xFAD negative, rep2

description:
Library name: 20790
10_3M_5xFADminus_20690_053_140_S139_L001


title: hiPSC-cardiomyocyte, GCaAMP, 25 Gy, day 7, biol rep 3

description: Library name: lib264

value: hiPSC-cardiomyocytes


title: 3 Month, 5xFAD positive, rep3

description:
Library name: 20697
15_3M_5xFADplus_20697_088_105_S144_L001


title: 3 Month, 5xFAD negative, rep3

description:
Library name: 20692
11_3M_5xFADminus_20692_041_152_S140_L001


title: 3 Month, 5xFAD positive, rep1

description:
Library name: 20768
13_3M_5xFADplus_20768_017_176_S142_L001


title: 7 Month, 5xFAD positive, rep 3

description:
Library name: 20254
7_7M_5xFADplus_20254_089_104


title: 7 Month, 5xFAD positive, rep 2

description:
Library name: 20444
6_7M_5xFADplus_20444_006_187_S135_L001


title: hiPSC-cardiomyocyte, GCaAMP, sham, day 1, biol rep 2

description: Library name: lib265

value: WT


title: hiPSC-cardiomyocyte, GCaAMP, sham, day 28, biol rep 3

description: Library name: lib271


title: hiPSC-cardiomyocyte, GCaAMP, sham, day 14, biol rep 2

description: Library name: lib257


title: 7 Month, 5xFAD positive, rep 4

description:
Library name: 20440
8_7M_5xFADplus_20440_077_116_S137_L001


title: hiPSC-cardiomyocyte, GCaAMP, sham, day 14, biol rep 3

description: Library name: lib263


title: hiPSC-cardiomyocyte, GCaAMP, sham, day 14, biol rep 1

description: Library name: lib256


title: hiPSC-cardiomyocyte, GCaAMP, sham, day 7, biol rep 1

description: Library name: lib251


title: hiPSC-cardiomyocyte, GCaAMP, sham, day 7, biol rep 3

description: Library name: lib262


title: hiPSC-cardiomyocyte, GCaAMP, sham, day 28, biol rep 1

description: Library name: lib250


title: hiPSC-cardiomyocyte, GCaAMP, sham, day 1, biol rep 1

description: Library name: lib248


title: 7 Month, 5xFAD negative, rep 4

description:
Library name: 20382
4_7M_5xFADminus_20382_030_163_S133_L001


title: hiPSC-cardiomyocyte, icell, 25 Gy, day 14, biol rep 5

description: Library name: lib213

source_name: iCell Cardiomyocytes^2

value: iCell Cardiomyocytes^2

value: 25 Gy IR


title: S140: Contralateral TG mRNA of TRPM3 null mouse, day 11 post SHAM operation

city: Leuven

first: Andrei

last: Segal Stanciu

address: Herestraat 49/801

department: Cellular and Molecular Medicine

country: Belgium

institute: KU Leuven

description: Library name: S140

data_processing:
Reads were aligned against the mouse GENCODE gene set release M28 using the STAR aligner (v2.7.10b) and gene and isoform expression levels were estimated using the RSEM (v1.3.1) software package
Assembly: GENCODE M28 (GRCm39)
Supplementary files format and content: RSEM 1.3.1 output; tab-delimited expression estimates (expected count, TPM, FPKM)

source_name: Trigeminal ganglion

extract_protocol:
InnuPREP RNA Mini Kit 2.0 (Innuscreen GmbH, Berlin).
Illumina TruSeq® Stranded mRNA Sample Prep Kit

value: Trigeminal ganglion

value: KO

value: Day 11, right, SHAM


title: hiPSC-cardiomyocyte, icell, 25 Gy, day 14, biol rep 4

description: Library name: lib211


title: S141: Ipsilateral TG mRNA of wild type mouse, day 25 post CCI operation

description: Library name: S141

value: Day 25, left, CCI


title: hiPSC-cardiomyocyte, GCaAMP, sham, day 28, biol rep 2

description: Library name: lib261


title: hiPSC-cardiomyocyte, icell, 25 Gy, day 1, biol rep 1

description: Library name: lib201


title: 7 Month, 5xFAD negative, rep 1

description:
Library name: 20441
1_7M_5xFADminus_20441_066_127


title: hiPSC-cardiomyocyte, icell, 25 Gy, day 14, biol rep 2

description: Library name: lib169


title: 7 Month, 5xFAD positive, rep 1

description:
Library name: 20443
5_7M_5xFADplus_20443_018_175_S134_L001


title: S136: Ipsilateral TG mRNA of wild type mouse, day 3 post SHAM operation

description: Library name: S136

value: Day 3, left, SHAM


title: S137: Ipsilateral TG mRNA of wild type mouse, day 3 post SHAM operation

description: Library name: S137


title: S135: Contralateral TG mRNA of TRPM3 null mouse, day 18 post CCI operation

description: Library name: S135

value: Day 18, right, CCI


title: 7 Month, 5xFAD negative, rep 2

description:
Library name: 20253
2_7M_5xFADminus_20253_054_139_S131_L001


title: S138: Ipsilateral TG mRNA of wild type mouse, day 11 post CCI operation

description: Library name: S138

value: Day 11, left, CCI


title: hiPSC-cardiomyocyte, icell, 25 Gy, day 14, biol rep 3

description: Library name: lib195


title: S139: Ipsilateral TG mRNA of wild type mouse, day 11 post CCI operation

description: Library name: S139


title: hiPSC-cardiomyocyte, icell, 25 Gy, day 7, biol rep 6

description: Library name: lib217


title: hiPSC-cardiomyocyte, icell, 25 Gy, day 14, biol rep 1

description: Library name: lib168


title: hiPSC-cardiomyocyte, GCaAMP, sham, day 7, biol rep 2

description: Library name: lib255


title: hiPSC-cardiomyocyte, icell, 25 Gy, day 1, biol rep 3

description: Library name: lib207


title: 7 Month, 5xFAD negative, rep 3

description:
Library name: 20442
3_7M_5xFADminus_20442_042_151_S132_L001

value: Brain tissue - CA2 region


title: S99: Contralateral TG mRNA of wild type mouse, day 42 post SHAM operation

description: Library name: S99

value: Day 42, right, SHAM


title: S134: Contralateral TG mRNA of TRPM3 null mouse, day 11 post CCI operation

description: Library name: S134

value: Day 11, right, CCI


title: hiPSC-cardiomyocyte, icell, 25 Gy, day 1, biol rep 2

description: Library name: lib205


title: S98: Ipsilateral TG mRNA of wild type mouse, day 42 post SHAM operation

description: Library name: S98

value: Day 42, left, SHAM


title: S97: Contralateral TG mRNA of wild type mouse, day 42 post SHAM operation

description: Library name: S97


title: S96: Ipsilateral TG mRNA of wild type mouse, day 42 post SHAM operation

description: Library name: S96


title: hiPSC-cardiomyocyte, icell, 25 Gy, day 7, biol rep 2

description: Library name: lib199


title: S94: Ipsilateral TG mRNA of wild type mouse, day 42 post SHAM operation

description: Library name: S94


title: hiPSC-cardiomyocyte, icell, 25 Gy, day 7, biol rep 3

description: Library name: lib203


title: hiPSC-cardiomyocyte, icell, sham, day 1, biol rep 2

description: Library name: lib206

value: Sham


title: S95: Contralateral TG mRNA of wild type mouse, day 42 post SHAM operation

description: Library name: S95


title: hiPSC-cardiomyocyte, icell, sham, day 1, biol rep 3

description: Library name: lib208


title: hiPSC-cardiomyocyte, icell, 25 Gy, day 7, biol rep 1

description: Library name: lib197


title: hiPSC-cardiomyocyte, icell, sham, day 1, biol rep 1

description: Library name: lib202


title: S93: Contralateral TG mRNA of wild type mouse, day 42 post CCI operation

description: Library name: S93

value: Day 42, right, CCI


title: S92: Ipsilateral TG mRNA of wild type mouse, day 42 post CCI operation

description: Library name: S92

value: Day 42, left, CCI


title: S91: Contralateral TG mRNA of wild type mouse, day 42 post CCI operation

description: Library name: S91

value: WT


title: hiPSC-cardiomyocyte, icell, 25 Gy, day 7, biol rep 5

description: Library name: lib215

value: iCell Cardiomyocytes^2

value: hiPSC-cardiomyocytes


title: hiPSC-cardiomyocyte, icell, sham, day 14, biol rep 4

description: Library name: lib196


title: S9: Ipsilateral TG mRNA of TRPM3 null mouse, day 11 post SHAM operation

description: Library name: S9

value: Trigeminal ganglion

value: Day 11, left, SHAM


title: hiPSC-cardiomyocyte, icell, sham, day 14, biol rep 5

description: Library name: lib212


title: hiPSC-cardiomyocyte, icell, sham, day 14, biol rep 6

description: Library name: lib214


title: S90: Ipsilateral TG mRNA of wild type mouse, day 42 post CCI operation

description: Library name: S90


title: hiPSC-cardiomyocyte, icell, sham, day 14, biol rep 2

description: Library name: lib171


title: hiPSC-cardiomyocyte, icell, sham, day 14, biol rep 3

description: Library name: lib172


title: S88: Ipsilateral TG mRNA of TRPM3 null mouse, day 42 post SHAM operation

description: Library name: S88

value: KO


title: hiPSC-cardiomyocyte, icell, 25 Gy, day 7, biol rep 4

description: Library name: lib209

value: 25 Gy IR


title: hiPSC-cardiomyocyte, icell, sham, day 7, biol rep 6

description: Library name: lib218


title: S89: Contralateral TG mRNA of TRPM3 null mouse, day 42 post SHAM operation

description: Library name: S89


title: hiPSC-cardiomyocyte, icell, sham, day 14, biol rep 1

description: Library name: lib170


title: S86: Contralateral TG mRNA of TRPM3 null mouse, day 42 post CCI operation

description: Library name: S86


title: S87: Contralateral TG mRNA of TRPM3 null mouse, day 42 post SHAM operation

description: Library name: S87


title: S85: Ipsilateral TG mRNA of TRPM3 null mouse, day 42 post CCI operation

description: Library name: S85


title: S84: Contralateral TG mRNA of TRPM3 null mouse, day 42 post CCI operation

description: Library name: S84


title: hiPSC-cardiomyocyte, icell, sham, day 7, biol rep 5

description: Library name: lib216


title: hiPSC-cardiomyocyte, icell, sham, day 7, biol rep 3

description: Library name: lib204


title: hiPSC-cardiomyocyte, GCaMP, 25 Gy, day1, biol rep 1

description: Library name: lib225

data_processing:
Raw ATAC-seq reads were aligned to the human (hg38) or mouse (mm10) reference genome and processed using AIAP, which includes four key steps: data processing, quality control, integrative analysis, and data visualization.
To generate a unified peak set, narrow peak files from all ATAC-seq libraries were merged using the merge function in the BEDTools suite.
Read counts for each ATAC-seq peak were quantified using the BEDTools coverage command.
To correct batch effects in read counts, RUVr normalization (RUVSeq R package, k = 2) was applied.
Assembly: hg38 and mm10
Supplementary files format and content: bigWig: dense, continuous data used in genome browser track
Supplementary files format and content: txt: normalized read counts of OCRs


title: S8: Contralateral TG mRNA of TRPM3 null mouse, day 3 post CCI operation

description: Library name: S8

value: Day 3, right, CCI


title: hiPSC-cardiomyocyte, GCaMP, 25 Gy, day1, biol rep 2

description: Library name: lib232


title: S83: Ipsilateral TG mRNA of TRPM3 null mouse, day 42 post CCI operation

description: Library name: S83


title: S82: Contralateral TG mRNA of TRPM3 null mouse, day 42 post CCI operation

description: Library name: S82


title: hiPSC-cardiomyocyte, icell, sham, day 7, biol rep 2

description: Library name: lib200


title: S80: Ipsilateral TG mRNA of TRPM3 null mouse, day 42 post SHAM operation

description: Library name: S80


title: S81: Ipsilateral TG mRNA of TRPM3 null mouse, day 42 post CCI operation

description: Library name: S81


title: hiPSC-cardiomyocyte, icell, sham, day 7, biol rep 1

description: Library name: lib198


title: S79: Contralateral TG mRNA of wild type mouse, day 42 post CCI operation

description: Library name: S79


title: hiPSC-cardiomyocyte, GCaMP, 25 Gy, day14, biol rep2

description: Library name: lib230


title: S78: Ipsilateral TG mRNA of wild type mouse, day 42 post CCI operation

description: Library name: S78


title: hiPSC-cardiomyocyte, icell, sham, day 7, biol rep 4

description: Library name: lib210


title: S75: Contralateral TG mRNA of wild type mouse, day 42 post SHAM operation

description: Library name: S75


title: S73: Contralateral TG mRNA of wild type mouse, day 42 post SHAM operation

description: Library name: S73


title: hiPSC-cardiomyocyte, GCaMP, 25 Gy, day14, biol rep3

description: Library name: lib240


title: S77: Contralateral TG mRNA of wild type mouse, day 42 post SHAM operation

description: Library name: S77


title: S76: Ipsilateral TG mRNA of wild type mouse, day 42 post SHAM operation

description: Library name: S76


title: hiPSC-cardiomyocyte, GCaMP, 25 Gy, day28, biol rep 1

description: Library name: lib227


title: S72: Ipsilateral TG mRNA of wild type mouse, day 42 post SHAM operation

description: Library name: S72


title: hiPSC-cardiomyocyte, GCaMP, 25 Gy, day28, biol rep 2

description: Library name: lib234


title: S71: Contralateral TG mRNA of TRPM3 null mouse, day 42 post SHAM operation

description: Library name: S71


title: S74: Ipsilateral TG mRNA of wild type mouse, day 42 post SHAM operation

description: Library name: S74


title: hiPSC-cardiomyocyte, GCaMP, sham, day1, biol rep 2

description: Library name: lib233


title: hiPSC-cardiomyocyte, GCaMP, 25 Gy, day28, biol rep 3

description: Library name: lib244


title: hiPSC-cardiomyocyte, GCaMP, 25 Gy, day14, biol rep1

description: Library name: lib223


title: hiPSC-cardiomyocyte, GCaMP, 25 Gy, day7, biol rep 1

description: Library name: lib228


title: hiPSC-cardiomyocyte, GCaMP, 25 Gy, day7, biol rep 2

description: Library name: lib236


title: S69: Contralateral TG mRNA of wild type mouse, day 18 post CCI operation

description: Library name: S69

value: Day 18, right, CCI


title: hiPSC-cardiomyocyte, GCaMP, sham, day14, biol rep 2

description: Library name: lib231


title: hiPSC-cardiomyocyte, GCaMP, sham, day14, biol rep 1

description: Library name: lib224


title: hiPSC-cardiomyocyte, GCaMP, sham, day1, biol rep 1

description: Library name: lib226


title: hiPSC-cardiomyocyte, GCaMP, sham, day14, biol rep 3

description: Library name: lib241


title: hiPSC-cardiomyocyte, GCaMP, sham, day28, biol rep 2

description: Library name: lib245


title: S64: Contralateral TG mRNA of wild type mouse, day 18 post CCI operation

description: Library name: S64


title: S63: Contralateral TG mRNA of wild type mouse, day 18 post SHAM operation

description: Library name: S63

value: Day 18, right, SHAM


title: hiPSC-cardiomyocyte, GCaMP, sham, day7, biol rep 1

description: Library name: lib229


title: S7: Ipsilateral TG mRNA of TRPM3 null mouse, day 3 post CCI operation

description: Library name: S7

value: Day 3, left, CCI


title: hiPSC-cardiomyocyte, iCell, 25 gy, day1, biol rep 3

description: Library name: lib187


title: S66: Ipsilateral TG mRNA of wild type mouse, day 18 post CCI operation

description: Library name: S66

value: Day 18, left, CCI


title: S62: Ipsilateral TG mRNA of wild type mouse, day 18 post SHAM operation

description: Library name: S62

value: Day 18, left, SHAM


title: S6: Contralateral TG mRNA of TRPM3 null mouse, day 3 post SHAM operation

description: Library name: S6

value: Day 3, right, SHAM


title: S67: Contralateral TG mRNA of wild type mouse, day 18 post CCI operation

description: Library name: S67


title: hiPSC-cardiomyocyte, iCell, 25 Gy, day7, biol rep 1

description: Library name: lib177


title: hiPSC-cardiomyocyte, iCell, 25 gy, day1, biol rep 2

description: Library name: lib185


title: hiPSC-cardiomyocyte, iCell, 25 Gy, day14, biol rep 2

description: Library name: lib191


title: hiPSC-cardiomyocyte, iCell, sham, day14, biol rep 3

description: Library name: lib194

value: Sham


title: S65: Ipsilateral TG mRNA of wild type mouse, day 18 post CCI operation

description: Library name: S65


title: S56: Ipsilateral TG mRNA of wild type mouse, day 11 post SHAM operation

description: Library name: S56


title: S59: Contralateral TG mRNA of wild type mouse, day 18 post SHAM operation

description: Library name: S59


title: S70: Ipsilateral TG mRNA of TRPM3 null mouse, day 42 post SHAM operation

description: Library name: S70

value: Day 42, left, SHAM


title: hiPSC-cardiomyocyte, iCell, 25 Gy, day14, biol rep 3

description: Library name: lib193


title: S61: Contralateral TG mRNA of wild type mouse, day 18 post SHAM operation

description: Library name: S61


title: hiPSC-cardiomyocyte, iCell, 25 Gy, day7, biol rep 3

description: Library name: lib189


title: S68: Ipsilateral TG mRNA of wild type mouse, day 18 post CCI operation

description: Library name: S68


title: S60: Ipsilateral TG mRNA of wild type mouse, day 18 post SHAM operation

description: Library name: S60


title: S58: Ipsilateral TG mRNA of wild type mouse, day 18 post SHAM operation

description: Library name: S58


title: hiPSC-cardiomyocyte, iCell, sham, day1, biol rep 2

description: Library name: lib186


title: hiPSC-cardiomyocyte, GCaMP, sham, day28, biol rep 1

description: Library name: lib235


title: hiPSC-cardiomyocyte, iCell, sham, day14, biol rep 1

description: Library name: lib180


title: S55: Ipsilateral TG mRNA of wild type mouse, day 11 post SHAM operation

description: Library name: S55


title: S54: Ipsilateral TG mRNA of wild type mouse, day 11 post SHAM operation

description: Library name: S54


title: 154120, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 14, day, H3K4me1

description: Library name: 154120

data_processing:
Raw FASTQ reads from each biological replicate were quality-trimmed using Cutadapt (--quality-cutoff 15,10) to remove low-quality ends and then aligned to the hg38 reference genome using BWA.
The resulting BAM files were processed using methylQA in density mode without read extension (-E 0) to represent fragments accurately.
Enriched histone peaks were identified separately for each epigenetic modification using the callpeak function of MACS2 for H3K4me3, H3K27ac, H3K4me1 (-f BEDPE --nomodel --shift -100 --extsize 200 --broad), with input samples as controls and a q-value cutoff of 0.1.
Peaks were called by ChromHMM for H3K27me3.
Assembly: hg38
Supplementary files format and content: bigWig: peaks
Supplementary files format and content: bigWig: dense, continuous data used in genome browser track
Library strategy: CUT&Tag


title: hiPSC-cardiomyocyte, iCell, sham, day7, biol rep 1

description: Library name: lib176


title: S49: Contralateral TG mRNA of wild type mouse, day 11 post SHAM operation

description: Library name: S49

value: Day 11, right, SHAM


title: S53: Contralateral TG mRNA of wild type mouse, day 11 post CCI operation

description: Library name: S53

value: WT

value: Day 11, right, CCI


title: S48: Ipsilateral TG mRNA of wild type mouse, day 3 post CCI operation

description: Library name: S48


title: 154110, hiPSC-CM Cardiomyocyte, iCell, Sham, 14, day, H3K27me3

description: Library name: 154110

value: iCell Cardiomyocytes^2

value: hiPSC-cardiomyocytes


title: S57: Ipsilateral TG mRNA of wild type mouse, day 11 post CCI operation

description: Library name: S57

value: Trigeminal ganglion

value: Day 11, left, CCI


title: S47: Ipsilateral TG mRNA of wild type mouse, day 3 post CCI operation

description: Library name: S47


title: 154114, hiPSC-CM Cardiomyocyte, iCell, Sham, 14, day, H3K4me1

description: Library name: 154114


title: 154112, hiPSC-CM Cardiomyocyte, iCell, Sham, 14, day, H3K4me3

description: Library name: 154112


title: hiPSC-cardiomyocyte, iCell, sham, day7, biol rep 3

description: Library name: lib184


title: hiPSC-cardiomyocyte, iCell, sham, day7, biol rep 4

description: Library name: lib190


title: 154108, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 7, day, H3K4me1

description: Library name: 154108

value: 25 Gy IR


title: S51: Contralateral TG mRNA of wild type mouse, day 11 post SHAM operation

description: Library name: S51


title: hiPSC-cardiomyocyte, iCell, sham, day14, biol rep 2

description: Library name: lib192


title: S45: Ipsilateral TG mRNA of wild type mouse, day 3 post SHAM operation

description: Library name: S45

value: Day 3, left, SHAM


title: S5: Ipsilateral TG mRNA of TRPM3 null mouse, day 3 post SHAM operation

description: Library name: S5

value: KO


title: S50: Contralateral TG mRNA of wild type mouse, day 11 post SHAM operation

description: Library name: S50


title: 154104, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 7, day, H3K27me3

description: Library name: 154104


title: 154116, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 14, day, H3K27me3

description: Library name: 154116


title: hiPSC-cardiomyocyte, iCell, sham, day7, biol rep 2

description: Library name: lib178


title: S43: Contralateral TG mRNA of wild type mouse, day 3 post CCI operation

description: Library name: S43

value: Day 3, right, CCI


title: S42: Contralateral TG mRNA of wild type mouse, day 3 post CCI operation

description: Library name: S42


title: 154118, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 14, day, H3K4me3

description: Library name: 154118


title: S44: Contralateral TG mRNA of wild type mouse, day 3 post CCI operation

description: Library name: S44


title: S52: Contralateral TG mRNA of wild type mouse, day 11 post CCI operation

description: Library name: S52


title: S41: Contralateral TG mRNA of wild type mouse, day 3 post SHAM operation

description: Library name: S41


title: 154102, hiPSC-CM Cardiomyocyte, iCell, Sham, 7, day, H3K4me1

description: Library name: 154102


title: S40: Contralateral TG mRNA of wild type mouse, day 3 post SHAM operation

description: Library name: S40


title: S46: Ipsilateral TG mRNA of wild type mouse, day 3 post CCI operation

description: Library name: S46

value: Day 3, left, CCI


title: 154100, hiPSC-CM Cardiomyocyte, iCell, Sham, 7, day, H3K4me3

description: Library name: 154100


title: 154105, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 7, day, H3K27ac

description: Library name: 154105


title: 154092, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 1, day, H3K27me3

description: Library name: 154092


title: S39: Contralateral TG mRNA of wild type mouse, day 3 post SHAM operation

description: Library name: S39


title: 154094, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 1, day, H3K4me3

description: Library name: 154094


title: S4: Contralateral TG mRNA of TRPM3 null mouse, day 3 post SHAM operation

description: Library name: S4


title: S37: Contralateral TG mRNA of TRPM3 null mouse, day 25 post CCI operation

description: Library name: S37

value: Day 25, right, CCI


title: 154098, hiPSC-CM Cardiomyocyte, iCell, Sham, 7, day, H3K27me3

description: Library name: 154098


title: 154090, hiPSC-CM Cardiomyocyte, iCell, Sham, 1, day, H3K4me1

description: Library name: 154090


title: S34: Ipsilateral TG mRNA of TRPM3 null mouse, day 25 post SHAM operation

description: Library name: S34

value: Day 25, left, SHAM


title: S35: Ipsilateral TG mRNA of TRPM3 null mouse, day 25 post CCI operation

description: Library name: S35

value: Day 25, left, CCI


title: S36: Ipsilateral TG mRNA of TRPM3 null mouse, day 25 post CCI operation

description: Library name: S36


title: 154086, hiPSC-CM Cardiomyocyte, iCell, Sham, 1, day, H3K27me3

description: Library name: 154086

value: Sham


title: 154082, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 14, day, H3K4me3

description: Library name: 154082


title: 154084, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 14, day, H3K4me1

description: Library name: 154084


title: S33: Ipsilateral TG mRNA of TRPM3 null mouse, day 25 post SHAM operation

description: Library name: S33


title: 154081, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 14, day, H3K27ac

description: Library name: 154081


title: 154078, hiPSC-CM Cardiomyocyte, iCell, Sham, 14, day, H3K4me1

description: Library name: 154078


title: S30: Contralateral TG mRNA of TRPM3 null mouse, day 25 post SHAM operation

description: Library name: S30

value: Day 25, right, SHAM


title: S31: Ipsilateral TG mRNA of TRPM3 null mouse, day 25 post SHAM operation

description: Library name: S31


title: S32: Contralateral TG mRNA of TRPM3 null mouse, day 25 post CCI operation

description: Library name: S32


title: 154080, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 14, day, H3K27me3

description: Library name: 154080


title: S3: Ipsilateral TG mRNA of TRPM3 null mouse, day 3 post SHAM operation

description: Library name: S3


title: S38: Ipsilateral TG mRNA of TRPM3 null mouse, day 25 post CCI operation

description: Library name: S38


title: 154051, hiPSC-CM Cardiomyocyte, iCell, Sham, 1, day, H3K27ac

description: Library name: 154051


title: S28: Contralateral TG mRNA of TRPM3 null mouse, day 18 post CCI operation

description: Library name: S28

value: Day 18, right, CCI


title: 154043, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 14, day, IgG

description: Library name: 154043

value: WT


title: S27: Ipsilateral TG mRNA of TRPM3 null mouse, day 18 post CCI operation

description: Library name: S27

value: Day 18, left, CCI


title: S26: Contralateral TG mRNA of TRPM3 null mouse, day 18 post CCI operation

description: Library name: S26


title: 154052, hiPSC-CM Cardiomyocyte, iCell, Sham, 1, day, H3K4me3

description: Library name: 154052

value: iCell Cardiomyocytes^2


title: S25: Ipsilateral TG mRNA of TRPM3 null mouse, day 18 post CCI operation

description: Library name: S25


title: S29: Contralateral TG mRNA of TRPM3 null mouse, day 25 post SHAM operation

description: Library name: S29


title: 154040, hiPSC-CM Cardiomyocyte, iCell, Sham, 14, day, H3K4me3

description: Library name: 154040

value: hiPSC-cardiomyocytes


title: 154096, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 1, day, H3K4me1

description: Library name: 154096


title: 154042, hiPSC-CM Cardiomyocyte, iCell, Sham, 14, day, H3K4me1

description: Library name: 154042


title: 154044, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 14, day, H3K27me3

description: Library name: 154044


title: S24: Ipsilateral TG mRNA of TRPM3 null mouse, day 18 post CCI operation

description: Library name: S24

value: Trigeminal ganglion


title: 154039, hiPSC-CM Cardiomyocyte, iCell, Sham, 14, day, H3K27ac

description: Library name: 154039


title: 154106, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 7, day, H3K4me3

description: Library name: 154106


title: 154037, hiPSC-CM Cardiomyocyte, iCell, Sham, 14, day, IgG

description: Library name: 154037


title: S23: Contralateral TG mRNA of TRPM3 null mouse, day 18 post SHAM operation

description: Library name: S23

value: Day 18, right, SHAM


title: 154036, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 7, day, H3K4me1

description: Library name: 154036

value: 25 Gy IR


title: S21: Contralateral TG mRNA of TRPM3 null mouse, day 18 post SHAM operation

description: Library name: S21


title: 154032, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 7, day, H3K27me3

description: Library name: 154032


title: S22: Ipsilateral TG mRNA of TRPM3 null mouse, day 18 post SHAM operation

description: Library name: S22

value: Day 18, left, SHAM


title: S20: Ipsilateral TG mRNA of TRPM3 null mouse, day 18 post SHAM operation

description: Library name: S20

value: KO


title: S2: Contralateral TG mRNA of TRPM3 null mouse, day 3 post SHAM operation

description: Library name: S2

value: Day 3, right, SHAM


title: S18: Ipsilateral TG mRNA of TRPM3 null mouse, day 18 post SHAM operation

description: Library name: S18


title: 154028, hiPSC-CM Cardiomyocyte, iCell, Sham, 7, day, H3K4me3

description: Library name: 154028


title: 154038, hiPSC-CM Cardiomyocyte, iCell, Sham, 14, day, H3K27me3

description: Library name: 154038


title: S17: Ipsilateral TG mRNA of TRPM3 null mouse, day 11 post CCI operation

description: Library name: S17

value: Day 11, left, CCI


title: 154030, hiPSC-CM Cardiomyocyte, iCell, Sham, 7, day, H3K4me1

description: Library name: 154030


title: S19: Contralateral TG mRNA of TRPM3 null mouse, day 18 post SHAM operation

description: Library name: S19


title: MIA PaCa-2 shCLPX-1 rep2

first: Cai-guang

last: Yang

address: 555 Zuchongzhi Rd

institute: Shanghai Institute of Materia Medica

description: Library name: MIA_X1_2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human whole genome.
Transcripts per million (TPM) were calculated.
Assembly: Human NCBI genome build 38
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample.

source_name: MIA PaCa-2

growth_protocol: MIA PaCa-2 cells were maintained in DMEM supplemented with 10% FBS, 2.5% horse serum (GIBCO), 1 mM Sodium Pyruvate (Invitrogen) and 1% penicillin-streptomycin, and were cultured at 37 °C in a humidified, 5% CO2-containing atmosphere incubator (Thermo Scientific).

extract_protocol:
MIA PaCa-2 shNS and shCLPX-1 cells were collected and lysed using TRIzol reagent (Invitrogen) according to the manufacturer's instruction. All samples were frozen at -80 °C before RNA extraction and analysis. The following steps were conducted by Majorbio Bio-Pharm Technology Co., Ltd. (Shanghai, China). RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit (Illumina) using 1 mg of total RNA. Shortly, messenger RNA was isolated according to the polyA selection method using oligo(dT) beads and then fragmented by fragmentation buffer. Next, double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen) with random hexamer primers (Illumina).
The synthesized cDNA was subjected to end-repair, phosphorylation, and “A” base addition according to the library construction protocol.

value: MIA PaCa-2

value: pancreatic ductal adenocarcinoma epithelial cell line

value: CLPX knockdown


title: S128: Contralateral TG mRNA of TRPM3 null mouse, day 25 post SHAM operation

description: Library name: S128


title: 154033, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 7, day, H3K27ac

description: Library name: 154033


title: 154026, hiPSC-CM Cardiomyocyte, iCell, Sham, 7, day, H3K27me3

description: Library name: 154026

value: Sham


title: 154034, hiPSC-CM Cardiomyocyte, iCell, 25 Gy IR, 7, day, H3K4me3

description: Library name: 154034


title: S15: Ipsilateral TG mRNA of TRPM3 null mouse, day 11 post CCI operation

description: Library name: S15


title: S16: Contralateral TG mRNA of TRPM3 null mouse, day 11 post CCI operation

description: Library name: S16

value: Day 11, right, CCI


title: MIA PaCa-2 shCLPX-1 rep3

description: Library name: MIA_X1_3


title: S14: Contralateral TG mRNA of TRPM3 null mouse, day 11 post SHAM operation

description: Library name: S14

value: Day 11, right, SHAM


title: MIA PaCa-2 shNS rep3

description: Library name: MIA_NS_3

value: WT


title: MIA PaCa-2 shCLPX-1 rep1

description: Library name: MIA_X1_1


title: MIA PaCa-2 shNS rep2

description: Library name: MIA_NS_2


title: S13: Ipsilateral TG mRNA of TRPM3 null mouse, day 11 post SHAM operation

description: Library name: S13

value: Day 11, left, SHAM


title: Human iMPC-derived chondrocyte #3

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description: Library name: Sample 6

data_processing:
Quality control was first applied to raw RNA sequencing reads by tool FastQC.
Low-quality reads and adapter sequences were filtered out by the Trimmomatic tool.
Surviving reads were then aligned to human reference genome hg38 using STAR aligner, and gene counts were quantified.
Assembly: hg38
Supplementary files format and content: TAB

source_name: Cartilage

extract_protocol:
For bulk RNA‐seq experiments, cell pellets made by iMPCs or MSCs were induced in the chondrogenic medium (containing TGFβ3 or TGFβ+BMP4) for 56 days, and then lysed in QIAzol from the RNeasy Plus Mini Kit (Qiagen, Germantown, MD, USA) for RNA extraction. Extracted RNA were quantitated Qubit™ RNA BR Assay Kit (Thermo Fisher Scientific) followed by the RNA quality check using Fragment Analyzer (Agilent Technologies, Santa Clara, CA).
For each sample, RNA libraries were prepared from 500ng RNA using the KAPA mRNA HyperPrep Kit (Roche, Indianapolis, IN) according to manufacturer’s protocol, followed by quality check using Fragment Analyzer (Agilent Technologies) and fluorescent quantification on the Infinite F Nano + (Tecan, Männedorf, Switzerland). The libraries were normalized and pooled, and then sequenced using NovaSeq6000 platform (Illumina, San Diego, CA,) to an average of 50M 100PE reads.

value: Cartilage

value: female


title: S124: Contralateral TG mRNA of TRPM3 null mouse, day 25 post CCI operation

description: Library name: S124

value: Trigeminal ganglion

value: Day 25, right, CCI


title: MIA PaCa-2 shNS rep1

description: Library name: MIA_NS_1


title: S125: Ipsilateral TG mRNA of TRPM3 null mouse, day 25 post SHAM operation

description: Library name: S125

value: Day 25, left, SHAM


title: S127: Ipsilateral TG mRNA of TRPM3 null mouse, day 25 post SHAM operation

description: Library name: S127


title: Human iMPC-derived chondrocyte #2

description: Library name: Sample 5


title: Human MSC-derived chondrocyte #3

description: Library name: Sample 3


title: S123: Ipsilateral TG mRNA of TRPM3 null mouse, day 25 post CCI operation

description: Library name: S123

value: Day 25, left, CCI


title: S12: Contralateral TG mRNA of TRPM3 null mouse, day 11 post CCI operation

description: Library name: S12

value: KO


title: Human MSC-derived chondrocyte #1

description: Library name: Sample 1


title: S121: Contralateral TG mRNA of wild type mouse, day 25 post CCI operation

description: Library name: S121


title: Human MSC-derived chondrocyte #2

description: Library name: Sample 2


title: S126: Contralateral TG mRNA of TRPM3 null mouse, day 25 post SHAM operation

description: Library name: S126

value: Day 25, right, SHAM


title: S119: Ipsilateral TG mRNA of wild type mouse, day 25 post CCI operation

description: Library name: S119


title: Karpas-422 Ctrl 3

first: sun

last: Ruixin

address: Building 7, 277 South Chongqing Road

department: Biochemistry

institute: Shanghai Jiao Tong University, School of Medicine

description: Library name: sample9

data_processing:
Data analysis  Quality Control:  In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.  Alignment:  Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).  Expression analysis  In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.  Differential expression analysis  Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <= 0.05 to detect differential expressed ones.  GO and KEGG enrichment analysis GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less and equal than 0.05. And topGO was used to plot DAG. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.  Novel transcripts prediction  After assembling a transcriptome from one or more samples, Cuffcompare, a tool of Cufflinks v2.2.1, compared assembly to known transcripts. Then, novel transcripts can be predicted via results of Cuffcompare.  Alternative splicing analysis  Asprofile v1.0 is a suite of programs for extracting, quantifying and comparing alternative splicing (AS) events from RNA-seq data. It took a GTF transcript file created by Cufflinks as its input.  SNV analysis  Samtools v0.1.19 with command mpileup and Bcftools v0.1.19 were used to do SNV calling.  Differential exon usage  By differential exon usage (DEU), we mean changes in the relative usage of exons caused by the experimental condition. The relative usage of an exon is defined as number of transcripts from the gene that contain this exonnumber of all transcripts from the gene The basic concept can be summarized as follows. For each exon (or part of an exon) and each sample, we count how many reads map to this exon and how many reads map to any of the other exons of the same gene. We consider the ratio of these two counts, and how it changes across conditions, to infer changes in the relative exon usage. In the case of an inner exon, a change in relative exon usage is typically due to a change in the rate with which this exon is spliced into transcripts (alternative splicing). Note, however, that DEU is a more general concept than alternative splicing, since it also includes changes in the usage of alternative transcript start sites and polyadenylation sites, which can cause differential usage of exons at the 5’ and 3’ boundary of transcripts. To analysis DEU, we used Bioconductor package DEXSeq (V 1.21.1).  Principal component analysis  This is another way to visualize sample-to-sample distances. In this ordination method, the data points (here, the samples) are projected onto the 2D plane such that they spread out in the two directions that explain most of the differences. The x-axis is the direction that separates the data points the most. The values of the samples in this direction are written PC1. The y-axis is a direction (it must be orthogonal to the first direction) that separates the data the second most. The values of the samples in this direction are written PC2. The percent of the total variance that is contained in the direction is printed in the axis label. Note that these percentages do not add to 100%, because there are more dimensions that contain the remaining variance (although each of these remaining dimensions will explain less than the two that we see). This analysis has been dealt with R language with FPKM value as the input.
Assembly: GRCh38.107
Supplementary files format and content: csv files include FPKM values for each sample

growth_protocol: SUDHL8 and Karpas-422 cells were cultured in RPM 1640I supplemented with 20% Fetal Bovine Serum (FBS) and 100g/mL penicillin/streptomycin.

extract_protocol:
SUDHL8 and Karpas-422 cell suspension were washed twice with ice cold PBS and DNA was extracted using DNeasy Blood & Tissue Kit (#69504, Qiagen) per instruction manual DNA samples were end-repaired, A tailed, and adaptor ligated using TruSeq Nano DNA Sample Prep Kit (#FC-121-4002, Illumina)
Sequencing library was prepared by converting 10 ng DNA of each sample to phosphorylated blunt-end fragment. An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments, and Illumina's genomic adapters were ligated to the A tailed DNA fragments prior to subject to PCR amplification to enrich ligated fragments. The enriched product of ~200-1500 bp was size selected using AMPure XP beads. The library was denatured with 0.1M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell at 8pM concentration, amplified in situ using Cluster Kit.

treatment_protocol: GALNT3 was over expressed with the GALNT3 overexpression (OE) plasmid with a  control using the lenti virus systems. After 72hrs positive cells were selected and cutured with 20% FBS alongside 1% PS in 1640 RPMI medium. At a growth rate of 80 to 90% confluence the cells were harvested, washed and was prepared for RNA sequence following the manufactural protocol for RNA extraction

value: human DLBCL cells

value: Ctrl


title: Karpas-422 Ctrl 2

description: Library name: sample8


title: S118: Contralateral TG mRNA of wild type mouse, day 25 post SHAM operation

description: Library name: S118


title: Karpas-422 GALNT3-OE 2

description: Library name: sample11


title: S120: Contralateral TG mRNA of wild type mouse, day 25 post CCI operation

description: Library name: S120


title: S115: Contralateral TG mRNA of wild type mouse, day 25 post SHAM operation

description: Library name: S115


title: Karpas-422 Ctrl 1

description: Library name: sample7


title: Karpas-422 GALNT3-OE 3

description: Library name: sample12


title: S112: Contralateral TG mRNA of wild type mouse, day 11 post CCI operation

description: Library name: S112


title: SUDHL8 Ctrl3

description: Library name: sample3


title: S111: Contralateral TG mRNA of TRPM3 null mouse, day 3 post CCI operation

description: Library name: S111

value: Day 3, right, CCI


title: S122: Contralateral TG mRNA of wild type mouse, day 25 post CCI operation

description: Library name: S122


title: S113: Contralateral TG mRNA of TRPM3 null mouse, day 11 post CCI operation

description: Library name: S113


title: SUDHL8 Ctrl2

description: Library name: sample2


title: Human iMPC-derived chondrocyte #1

description: Library name: Sample 4


title: SUDHL8 GALNT3-OE 3

description: Library name: sample6


title: S116: Ipsilateral TG mRNA of wild type mouse, day 25 post SHAM operation

description: Library name: S116


title: S11: Ipsilateral TG mRNA of TRPM3 null mouse, day 11 post CCI operation

description: Library name: S11

value: Day 11, left, CCI


title: S117: Ipsilateral TG mRNA of wild type mouse, day 25 post CCI operation

description: Library name: S117


title: pre.21

city: Stockholm

first: Carolina

last: Nylén

address: Karolinska University Hospital

country: Sweden

institute: Karolinska Institutet

description: Library name: P30460_1036_S143_L007_Aligned.sortedByCoord.out.bam

data_processing:
Quality and adapter trimming of reads was performed using Cutadapt (v3·5). Sample quality was assessed using FastQC (v0·11·8) and MultiQC (v1·14). Reads were aligned to the Ensembl GRCh38/GRCm38 reference genome using STAR (v2·7·9d). Counts for each gene were obtained using featureCounts (v1·5·1).
Assembly: Ensembl GRCh38/GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

source_name: Vastus lateralis

extract_protocol:
Total RNA from skeletal muscle biopsies was isolated using E.Z.N.A. Total RNA Kit I, #R6834-02, Omega Bio-Tek, USA, and treated with E.Z.N.A. Tissue DNA kit, #D3396-02, Omega Bio-Tek, USA.
Libraries were generated using TruSeq Stranded Total RNA (Illumina) and sequenced on an Illumina Novaseq 6000 Sequencing System (Illumina).

value: Vastus lateralis

value: Female

tag: subjectid

tag: age

tag: time point

value: pre


title: Karpas-422 GALNT3-OE 1

description: Library name: sample10


title: S107: Ipsilateral TG mRNA of TRPM3 null mouse, day 3 post CCI operation

description: Library name: S107

value: Day 3, left, CCI


title: S109: Ipsilateral TG mRNA of TRPM3 null mouse, day 11 post CCI operation

description: Library name: S109


title: pre.19

description: Library name: P30460_1033_S140_L007_Aligned.sortedByCoord.out.bam


title: S110: Contralateral TG mRNA of TRPM3 null mouse, day 3 post CCI operation

description: Library name: S110


title: SUDHL8 GALNT3-OE 1

description: Library name: sample4


title: SUDHL8 GALNT3-OE 2

description: Library name: sample5


title: S114: Ipsilateral TG mRNA of wild type mouse, day 25 post SHAM operation

description: Library name: S114

value: WT


title: S103: Contralateral TG mRNA of wild type mouse, day 42 post CCI operation

description: Library name: S103

value: Day 42, right, CCI


title: SUDHL8 Ctrl1

description: Library name: sample1


title: pre.15

description: Library name: P30460_1027_S134_L007_Aligned.sortedByCoord.out.bam


title: pre.20

description: Library name: P30460_1034_S141_L007_Aligned.sortedByCoord.out.bam


title: post.21

description: Library name: P30460_1035_S142_L007_Aligned.sortedByCoord.out.bam

value: post


title: S100: Ipsilateral TG mRNA of wild type mouse, day 42 post CCI operation

description: Library name: S100

value: Trigeminal ganglion

value: Day 42, left, CCI


title: S108: Ipsilateral TG mRNA of wild type mouse, day 11 post CCI operation

description: Library name: S108


title: pre.16

description: Library name: P30460_1028_S135_L007_Aligned.sortedByCoord.out.bam


title: S106: Ipsilateral TG mRNA of TRPM3 null mouse, day 3 post CCI operation

description: Library name: S106


title: pre.17

description: Library name: P30460_1030_S137_L007_Aligned.sortedByCoord.out.bam


title: post.19

description: Library name: P30460_1032_S139_L007_Aligned.sortedByCoord.out.bam


title: S1: Ipsilateral TG mRNA of TRPM3 null mouse, day 3 post SHAM operation

description: Library name: S1

value: Day 3, left, SHAM


title: pre.13

description: Library name: P30460_1023_S130_L007_Aligned.sortedByCoord.out.bam


title: S10: Contralateral TG mRNA of TRPM3 null mouse, day 11 post SHAM operation

description: Library name: S10

value: Day 11, right, SHAM


title: S105: Contralateral TG mRNA of wild type mouse, day 42 post CCI operation

description: Library name: S105


title: post.17

description: Library name: P30460_1029_S136_L007_Aligned.sortedByCoord.out.bam


title: post.15

description: Library name: P30460_1026_S133_L007_Aligned.sortedByCoord.out.bam


title: post.13

description: Library name: P30460_1022_S129_L007_Aligned.sortedByCoord.out.bam


title: pre.14

description: Library name: P30460_1025_S132_L007_Aligned.sortedByCoord.out.bam


title: pre.12

description: Library name: P30460_1021_S128_L007_Aligned.sortedByCoord.out.bam


title: MYCN-nonamp/FGFR1-N546K, mouse_T4_14d

city: Cologne

first: Matthias

last: Fischer

address: Kerpener Str. 62

department: Department of Experimental Pediatric Oncology

institute: University Children’s Hospital of Cologne

description: Library name: T4_14d

data_processing:
Quantification of RNA sequencing data was carried out using Kallisto (version 0.44.0) with parameters --bootstrap-samples 100 --bias, and the GRCm38 reference genome. Raw Kallisto transcript level read counts were transformed to gene level counts using the R package tximport (version 1.20.0).
Normalization of Kallisto gene level read counts and further processing was carried out in R (version 4.2.2) using the package DESeq2 (version 1.32.0). Only genes with at least 10 reads in 8 mice were used for further analysis (8 being the size of the smallest subgroup of mice).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw read counts for each mouse
Supplementary files format and content: tab-delimited text file includes DESeq2 VST expression values for each mouse

source_name: Tumor

extract_protocol:
RNA isolation from fresh-frozen tissue was performed with TRIzol (Ambion). RNA concentration was measured by QubitTM Assay (Invitrogen) and quality was assessed by 2100 Bioanalzyer (Agilent).
Libraries were prepared using the Illumina Stranded TruSeq RNA sample preparation Kit. After library validation and quantification (Agilent Tape Station), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System.

value: Tumor

value: R26.FSF.FGFR1-N546K tg/wt, Th-IRES Cre tg/wt


title: pre.18

description: Library name: P30460_1031_S138_L007_Aligned.sortedByCoord.out.bam


title: MYCN-nonamp/FGFR1-N546K, mouse_T3_7d

description: Library name: T3_7d


title: S104: Ipsilateral TG mRNA of wild type mouse, day 42 post CCI operation

description: Library name: S104


title: S102: Ipsilateral TG mRNA of wild type mouse, day 42 post CCI operation

description: Library name: S102


title: adenoma tissue, colitis recovered

city: Cambridge

first: Surya

last: Nagaraja

state: MA

address: 7 Divinity Ave, Bauer 2nd Floor 208

department: HSCRB

institute: Harvard University

description: Library name: APC01-A1-7-B

data_processing:
BCLs were converted to fastqs using spaceranger mkfastq.
Fastqs  were processed using spaceranger count using probe set Visium_Mouse_Transcriptome_Probe_Set_v2.0_mm10-2020-A.csv and reference genome refdata-gex-mm10-2020-A
Counts were binned using 16 um bins.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tif: images from Visium slide imaging
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowers_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.parquet: parquet format of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Library strategy: Spatial Transcriptomics

source_name: colon

extract_protocol:
Tissue was processed as described in the Visium HD protocol with the following modifications: the OCT-embedded swiss rolls were sectioned on a cryostat at 10 μm thickness and mounted on a Fisherbrand™ Superfrost™ Plus glass slide. The slides were fixed using 4% PFA and stained using H&E method. During that process the wash buffers were supplemented with either ribonucleoside vanadyl complex or a commercial RNAse inhibitor. After imaging of the H&E staining, the samples were destained and permeabilized using 1% SDS and then pre-chilled 70% methanol.
Libraries were prepared per Visium HD protocol.

treatment_protocol: Colitis was induced in mice by admiinstering 1-1.5% DSS in drinking water for 3 cycles of 7 days on/ 10 days off. Tamoxifen was administered 21, 22 and 23 days following DSS cessation at 50 mg/kg. Tissue was collected 27 days following tamoxifen administration and fresh frozen as a swiss roll in OCT.

value: colon

value: colonic epithelium

value: colitis recovered, 27 days following 4OHT


title: adenoma tissue, control conditions

description: Library name: APC01-A1-13-B

value: control, 27 days following 4OHT


title: S101: Contralateral TG mRNA of wild type mouse, day 42 post CCI operation

description: Library name: S101


title: post.11

description: Library name: P30460_1019_S126_L007_Aligned.sortedByCoord.out.bam

value: Vastus lateralis


title: MYCN-nonamp/FGFR1-N546K, mouse_T2_7d

description: Library name: T2_7d


title: MYCN-nonamp/FGFR1-N546K, mouse_T15_14d

description: Library name: T15_14d


title: post.14

description: Library name: P30460_1024_S131_L007_Aligned.sortedByCoord.out.bam

value: Female


title: pre.11

description: Library name: P30460_1020_S127_L007_Aligned.sortedByCoord.out.bam

value: pre


title: MYCN-nonamp/FGFR1-N546K, mouse_T19_14d

description: Library name: T19_14d


title: post.10

description: Library name: P30460_1017_S124_L007_Aligned.sortedByCoord.out.bam


title: MYCN-nonamp/FGFR1-N546K, mouse_T21_14d

description: Library name: T21_14d