title: 252800524043_2_4_FP57L_24_hours

value: Sham

value: Fentanyl

value: Lungs


title: Mus musculus male 2

status: Public on Apr 15 2026

type: SRA

city: Memphis

first: Troy

last: Camarata

state: TN

address: 1003 Monroe Avenue

department: Biomedical Sciences

country: USA

institute: Baptist University College of Osteopathic Medicine

description:
Library name: M2
Mouse_Individual_Methylation.xlsx

library_source: genomic

data_processing:
Sequence quality and adapter trimming were performed using Fastqc and Fastp.
Sequence reads were aligned to the mouse or red-eared slider genome using Bismark.
Methylated cytosines were determined using MethyKit R package. MethylKit performed a Fisher’s test on the pooled sample and control groups, and an FDR-corrected P value threshold of ≤0.05 was considered significant for identifying differentially methylated cytosines (DMCs).
Assembly: T. scripta elegans: CAS_Tse_1.0; M. musculus: GRCm38
Supplementary files format and content: Quality control statistics for all sequenced samples in worksheet files
Supplementary files format and content: Genomic location, base calling, gene ID, reference ID, methylation location for each sample in worksheet files

molecule: genomic DNA

organism: Mus musculus

source_name: adult kidney cortex

extract_protocol:
Genomic DNA was extracted using the Monarch Genomic DNA Extraction Kit (New England Biolabs) following manufacturer’s instructions including proteinase K and RNase A incubations. For mice, outer cortical tissue was dissected in cold PBS followed by genomic DNA extraction. For adult turtle kidneys, surface convolutions or medullary tissue were dissected in cold PBS followed by extraction of genomic DNA.
Firstly, the genomic DNA spiked with lambda DNA were fragmented to 200-400 bp. The DNA fragments were bisulfite treatedto generate single strand DNA (ssDNA). During the bisulfite conversion, unmethylated cytosine were converted into uracil, whilemethylated cytosine staid unchanged. Methylation sequencing adapters were ligated, followed by double strand DNA synthesis. Thelibrary was ready after size selection and PCR amplification.

tag: tissue

value: adult kidney cortex

tag: Sex

value: male

tag: cell type

value: Mixed

tag: genotype

value: WT

tag: tissue type

value: Manual dissected cortical tissue


title: 252800524043_2_3_FP56L_24_hours

type: RNA

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

hyb_protocol: Hybridizations were performed using Agilent SurePrint G3 Mouse GE 8x60K microarrays following Agilent's Two-Color Microarray-Based Gene Expression protocol.

scan_protocol: Arrays were scanned using Agilent SureScan Microarray Scanner and features were extracted using Agilent Feature Extraction Software (v10.7).

data_processing: Data were processed using Feature Extraction Software. Log2 transformation and quantile normalization were applied where applicable.

molecule: total RNA

source_name: Agilent Universal Mouse Reference RNA

label_protocol: Purified RNA samples were labeled with Cy5 using the Agilent Low Input Quick Amp Labeling Kit. The reference RNA was labeled with Cy3.

extract_protocol: Total RNA was extracted from tissue samples using TRIzol reagent and miRNeasy Mini Kit (QIAGEN) following the manufacturer's instructions. Quality was assessed using NanoDrop, Qubit, and Tapestation 2200.

tag: time point

tag: treatment

source_name: Lungs


title: sibling biol rep1

city: Guangzhou

first: Zhibin

last: Huang

state: Guangdong Province

address: 382 Waihuan E Rd, Panyu District

department: School of Medicine

country: China

institute: South China University of Technology

description:
Library name: sample3
sib rep1

library_source: transcriptomic

data_processing:
Raw sequencing data underwent stringent quality control using fastp (v0.23.2). The cleaned reads were then aligned to the Danio rerio GRCz11 reference genome using STAR (v2.7.10a) with standard parameters. Gene-level read counts were generated using FeatureCounts (v2.0.1). The count matrix was input into R (v4.2.2) and analyzed with DESeq2 (v1.26.0) for normalization, identification of differentially expressed genes (DEGs), and sample-to-sample distance analysis. Functional enrichment analysis of KEGG pathways and Gene Ontology (GO) terms was performed on the significant DEGs using the R package ClusterProfiler (v4.6.2), with results visualized graphically.
Assembly: GRCz11
Supplementary files format and content: raw gene counts of tubgcp6 mutant and sibling countrol

organism: Danio rerio

source_name: whole embryos

growth_protocol: Zebrafish embroys were maintained in egg water in 28 °C till 7 dpf for sacrification.

extract_protocol:
Embryos from tubgcp6+/- intercrosses were genotyped at 7 dpf to identify mutants and  siblings. Then, total RNA was extracted from tubgcp6 mutants and their siblings using Trizol reagent (15596026, Invitrogen) according to the manufacturer’s instructions.
The RNA sequencing libraries were constructed by NEBNext® UltraTM RNA Library Prep Kit for Illumina® RNA (NEB; E7770)  according to the manufacturer’s instructions.

treatment_protocol: The embryos underwent no further treatment.

value: whole embryos

tag: strain

value: AB

tag: developmental stage

value: 7 dpf

value: sibling


title: shCTRshCTR_3h_rep1

city: Baltimore

first: Shuying

last: Sun

address: Hunterian 205

department: Physiology

institute: jhmi

description: Library name: YY85

data_processing:
Raw reads were trimmed using trim-galore (version 0.6.7) and aligned to human genome and transcriptome (hg38) using HISAT2 (version 2.2.1)
Cleaned reads were mapped to human GRCh38/hg38 and ERCC spike-in (Thermo Fisher Scientific, Cat. No. 4456740), seperately.
The number of unique reads mapped to GENCODE (https://www.gencodegenes.org/, version 38) annotated genes were counted using subread (version 2.0.1).
Raw reads were normalized by linear regression fitting of the RNA ERCC spike-in.
Assembly: GRCh38/hg38
Supplementary files format and content: txt file of raw reads quantified by subread (version 2.0.1) and used for DEseq2
Supplementary files format and content: txt file of reads normalized to ERCC spike-in reads

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Classic Neuronal Medium

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher), and RNA concentrations were determined with the Qubit RNA HS Assay Kit on a Qubit 4.0 Fluorometer
Libraries were prepared according to protocol accompanying the NEBNext® Ultra™ II Directional RNA Library Prep Kit (Cat. No. E7765) coupled with NEBNext Poly(A) mRNA Magnetic Isolation Module

treatment_protocol: Cells were transduced with shCTR or shTDP-43 for 8 days, and transduced with shCTR or shDCPS for 6 days. Cells were treated with 5μg/μL Actinomycin D for 0h, 3h, or 6h before harvesting.

tag: cell line

value: Day 14 neuron

value: control with shCTR transduction, actD treated for 3h

tag: batch


title: shCTRshCTR_0h_rep3

description: Library name: YY84

value: control with shCTR transduction, actD treated for 0h


title: Mus musculus male 4

description:
Library name: M4
Mouse_Individual_Methylation.xlsx


title: 252800524043_2_2_FP55L_0_hour_(40_mins_post)


title: Mus musculus male 1

description:
Library name: M1
Mouse_Individual_Methylation.xlsx


title: shCTRshCTR_0h_rep2

description: Library name: YY83


title: 252800524043_1_4_FP53L_7_days


title: WT-3-spleen

city: Shanghai

first: Shuang

last: Liu

address: 197 ruijin 2nd road

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description: Library name: Sample-12

data_processing:
Raw sequencing reads were quality-trimmed using Trimmomatic and aligned to the mouse reference genome (GRCm39) with HISAT2. Gene-level read counts were generated using featureCounts.
Assembly: Raw sequencing reads were quality-trimmed using Trimmomatic and aligned to the mouse reference genome (GRCm39) with HISAT2. Gene-level read counts were generated using featureCounts.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: spleen

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

value: spleen


title: 252800524043_2_1_FP54L_24_hours


title: shCTRshCTR_0h_rep1

description: Library name: YY82


title: tubgcp6 mutant biol rep1

description:
Library name: sample1
mut rep1

value: tubgcp6 mutant


title: WT-3-lung

description: Library name: Sample-11

source_name: lung

value: lung


title: 252800524043_1_3_FP52L_7_days

value: Sham

value: Fentanyl


title: 252800524043_1_2_FP51L_24_hours

value: Lungs


title: shTDP-43shDCPS_rep3

description: Library name: YY78

value: TDP-43 and DCPS double knockdown


title: WT-2-spleen

description: Library name: Sample-10


title: T3_10_2

city: Legnaro

first: Monica

last: Canton

state: Padova

address: Viale dell'Università, 16

department: DAFNAE

country: Italy

institute: University of Padova

data_processing:
reads quality-check using FastQC
alignments were performed with Hisat2
read counts with HTSeq
Differential expression analysis usignDESeq2 (v1.30)
Assembly: Vitis vinifera PN40024.v4
Supplementary files format and content: raw_counts.txt

organism: Vitis vinifera

source_name: buds

extract_protocol:
Spectrum™ Plant Total RNA Kit
Illumina TruSeq Stranded mRNA Library

value: buds

tag: node

tag: cultivar

value: Merlot

tag: phenological stages


title: WT-2-lung

description: Library name: Sample-9

value: WT


title: shTDP-43shDCPS_rep2

description: Library name: YY77


title: T3_10_1


title: T3_10_3


title: 252800524042_2_4_FP48L_0_hour_(40_mins_post)


title: shTDP-43shCTR_rep3

description: Library name: YY75

value: TDP-43 knockdown


title: T3_5_3


title: T3_5_2


title: 252800524042_2_1_FP44L_6_hours


title: shTDP-43shDCPS_rep1

description: Library name: YY76


title: T3_5_1


title: 252800524042_2_2_FP45L_6_hours


title: shTDP-43shCTR_rep1

description: Library name: YY73


title: 252800524042_2_3_FP47L_0_hour_(40_mins_post)


title: WT-1-lung

description: Library name: Sample-7


title: b3-3-lung

description: Library name: Sample-5

value: ITGB3 KO


title: 252800524043_1_1_FP49L_6_hours


title: shTDP-43shCTR_rep2

description: Library name: YY74


title: WT-1-spleen

description: Library name: Sample-8


title: T3_2_3


title: b3-3-spleen

description: Library name: Sample-6


title: T3_2_2


title: b3-2-spleen

description: Library name: Sample-4


title: shCTRshCTR_rep2

description: Library name: YY65

value: control with shCTR transduction


title: shCTRshCTR_rep3

description: Library name: YY66


title: T3_2_1


title: b3-2-lung

description: Library name: Sample-3


title: tubgcp6 mutant biol rep2

description:
Library name: sample2
mut rep2

value: whole embryos

value: AB

value: 7 dpf


title: 252800524042_1_2_FP41L_7_days


title: shCTRshCTR_rep1

description: Library name: YY64

value: Day 14 neuron


title: shTDP-43shDCPS_DDX6_rep3

description:
Library name: CHe-YX-43s-O1Y24
Y24_S31

library_source: other

data_processing:
The raw sequencing reads were trimmed with Cutadapt (version 5.0). Trimmed reads were first mapped to the human rRNA using bowtie2 (version 2.3.5.1) and ones mapped to rRNA were discarded in the downstream analysis.
Non-rRNA reads were then re-mapped to the human reference genome (hg38) using STAR.
Peaks were called strand-specifically using macs3 (version 3.0.2), given the input libraries as background.
All peak regions were merged and counted using subread (version 2.0.1).
Assembly: GRCh38/hg38
Supplementary files format and content: txt file of peak counts quantified by subread (version 2.0.1)

molecule: other

extract_protocol:
Cells were fixed, permeabilized, blocked, and incubated with anti-DDX6 (Millipore, Cat. No. SAB4200837) and Alexa Fluor 488 (ThermoFisher Scientific). pAG-RTase was added for in situ RT. After proteinase K digestion, nucleic acids were recovered by phenol-chloroform extraction.
RNA was digested with RNase H (NEB, Cat. No. M0297S) and RNase A/T1 (Thermo Fisher Scientific, Cat. No. EN0551), followed by biotinylated cDNA enrichment using Dynabeads MyOne Streptavidin C1 (ThermoFisher Scientific, Cat. No. 65001). Next, the 3′ cDNA adapter (5′Phos-8N-AGATCGGAAGAGGTCGTGT-3′SpC3) was ligated by T4 RNA ligase 1 (NEB, Cat. No. M0437M) at 25 °C for 16 hours, and cDNA was recovered with the elution buffer of 95% formamide and 10 mM EDTA (pH 8.0) by boiling at 95°C for 10 min, followed by ethanol precipitation. The library was PCR amplified and gel-purified.

treatment_protocol: Cells were transduced with shCTR or shTDP-43 for 8 days, and transduced with shCTR or shDCPS for 6 days.

tag: antibody


title: 252800524042_1_3_FP42L_6_hours


title: T2_10_3


title: 252800524042_1_4_FP43L_7_days


title: T2_10_2


title: b3-1-spleen

description: Library name: Sample-2

value: spleen


title: T2_10_1


title: Ldlr-_ET-hLDLR_mass_6

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

institute: San Raffaele Telethon Institute for Gene Therapy

description: Library name: LD27-6-mass

data_processing:
Raw sequencing reads were assessed for quality using FastQC (v0.11.6), and low-quality bases and adapter sequences were removed using Trim Galore (v0.6.6).
Cleaned reads were aligned to the Mus musculus reference genome (GRCm39) using STAR (v2.7.6a) with default parameters.
Gene-level read counts were quantified with the featureCounts function from the Subread package (v2.0.1).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: Liver with Tumor

extract_protocol:
Healthy liver tissues and liver masses were sent to Azenta for RNA extraction, library preparation and sequencing (Illumina NovaSeq platform, paired-end reads, 2 x 150 bp).
Healthy liver tissues and liver masses were sent to Azenta for RNA extraction, library preparation and sequencing (Illumina NovaSeq platform, paired-end reads, 2 x 150 bp).

value: Liver with Tumor

value: Ldlr-/-

value: male

value: ET-hLDLR


title: b3-1-lung

description: Library name: Sample-1

value: lung


title: shTDP-43shDCPS_DDX6_rep2

description:
Library name: CHe-YX-43s-O1Y23
Y23_S30

value: TDP-43 and DCPS double knockdown


title: Ldlr-_ET-hLDLR_mass_4

description: Library name: LD27-4-mass


title: shTDP-43shDCPS_DDX6_rep1

description:
Library name: CHe-YX-43s-O1Y22
Y22_S29


title: T2_5_3

value: buds


title: Ldlr-_ET-hLDLR_mass_3

description: Library name: LD27-3-mass2


title: 252800524041_2_1_FP32L_0_hour_(40_mins_post)

value: Sham

value: Fentanyl

value: Lungs


title: T2_5_2

value: Merlot


title: 252800524042_1_1_FP40L_7_days


title: 252800524041_1_4_FP30L_0_hour_(40_mins_post)


title: shTDP-43shDCPS_input_rep3

description:
Library name: CHe-YX-43s-O1Y21
Y21_S28


title: 252800524041_2_4_FP39L_24_hours


title: T2_5_1


title: shTDP-43shDCPS_input_rep1

description:
Library name: CHe-YX-43s-O1Y19
Y19_S26


title: 252800524041_2_3_FP38L_6_hours


title: shTDP-43shDCPS_input_rep2

description:
Library name: CHe-YX-43s-O1Y20
Y20_S27


title: 252800524041_2_2_FP33L_6_hours


title: T2_2_1


title: 252800524041_1_2_FP27L_7_days


title: T2_2_2


title: shTDP-43shCTR_DDX6_rep2

description:
Library name: CHe-YX-43s-O1Y17
Y17_S24

value: TDP-43 knockdown


title: shTDP-43shCTR_DDX6_rep1

description:
Library name: CHe-YX-43s-O1Y16
Y16_S23


title: T2_2_3


title: 252800524041_1_3_FP29L_6_hours


title: Ldlr-_ET-co.mLDLR_mass_2

description: Library name: LD18-2-MASS


title: shTDP-43shCTR_DDX6_rep3

description:
Library name: CHe-YX-43s-O1Y18
Y18_S25


title: T1_10_3


title: Ldlr-_ET-mLDLR_6

description: Library name: LD17-6

source_name: Liver

value: Liver

value: female

value: ET-mLDLR


title: Ldlr-_ET-co.mLDLR_mass_4

description: Library name: LD18-4-MASS


title: Ldlr-_ET-co.mLDLR_mass_6

description: Library name: LD18-6-MASS


title: shTDP-43shCTR_input_rep3

description:
Library name: CHe-YX-43s-O1Y15
Y15_S22

value: Day 14 neuron


title: Ldlr-_ET-co.mLDLR_5

description: Library name: LD18-5


title: shTDP-43shCTR_input_rep2

description:
Library name: CHe-YX-43s-O1Y14
Y14_S21


title: Ldlr-_ET-mLDLR_4

description: Library name: LD17-4


title: Ldlr-_ET-mLDLR_3

description: Library name: LD17-3


title: 252800524057_2_3_FP45H_6_hours

source_name: Heart

value: Heart


title: 252800524057_2_1_FP93H_24_hours


title: T1_10_1


title: T1_10_2


title: shTDP-43shCTR_input_rep1

description:
Library name: CHe-YX-43s-O1Y13
Y13_S20


title: WT_UT_13

description: Library name: LD17-13

value: WT

value: Untreated


title: shCTRshCTR_DDX6_rep3

description:
Library name: CHe-YX-43s-O1Y06
Y06_S13

value: control with shCTR transduction


title: 252800524041_1_1_FP25L_0_hour_(40_mins_post)


title: 252800524057_1_2_FP63H_24_hours


title: Ldlr-_ET-mLDLR_1

description: Library name: LD17-1

value: Ldlr-/-

value: male


title: shCTRshCTR_DDX6_rep2

description:
Library name: CHe-YX-43s-O1Y05
Y05_S12


title: shCTRshCTR_DDX6_rep1

description:
Library name: CHe-YX-43s-O1Y04
Y04_S11


title: 252800524057_1_3_FP78H_6_hours


title: T1_5_2


title: WT_UT_10

description: Library name: LD17-10


title: T1_5_1


title: 252800524057_2_2_FP48H_0_hour_(40_mins_post)


title: T1_5_3


title: WT_UT_11

description: Library name: LD17-11


title: T1_2_3


title: 252800524052_2_4_FP69H_0_hour_(40_mins_post)


title: shCTRshCTR_input_rep3

description:
Library name: CHe-YX-43s-O1Y03
Y03_S10


title: WT_UT_9

description: Library name: LD17-9


title: shCTRshCTR_input_rep2

description:
Library name: CHe-YX-43s-O1Y02
Y02_S9


title: T1_2_1


title: T1_2_2


title: Ldlr-_UT_13

description: Library name: LD27-13


title: Hindlimb Unloaded/PBA treated Sample 2

city: Mangalore

first: animikh

last: ray

state: Karnataka

address: Indoor Stadium Complex, Father Muller Campus, Kankanady,

country: India

institute: Father Muller Research center

description:
UP3_Kidney
Hindlimb unloaded mice with PBA treatment

data_processing:
Sequencing was carried out in an illumina platform using sequencing by synthesis paradigm
Following completion of sequencing, original base calling is performed using CASAVA base recognition to convert raw images into sequence reads. Raw data were stored in FASTQ file format containing sequence reads and corresponding base quality.
Raw sequencing data were processed to remove reads containing adapters . Reads with uncertain nucleotides constituting more than 10 percent of either read (N > 10%), reads containing low-quality nucleotides (Base Quality less than 5) constituting more than 50 percent of the read and sequencing artifacts. Cutadapt was used to filter the undesirable reads to obtain clean reads for further analysis.
The resulting clean reads were aligned using HISAT2. Mapped regions were classified as exons, introns, or intergenic regions. BAM files thus generated contained the mapping results and were viewed in an integrative genomics Viewer (IGV)
Assembled reads were annotated using blast. The gene expression level was evaluated based on the sum frequencies of compared reads. The gene expression level is considered equivalent to the read count. The obtained read count is normalized according to FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced), which yields transcript abundance estimation. Principal component analysis (PCA) was performed to evaluate intergroup differences and intragroup sample duplication. PCA analysis on the gene expression value (FPKM) of all samples was carried out. A co-expression Venn diagram was also constructed to represent a number of genes that are uniquely expressed within each group/sample, with the overlapping regions showing the number of genes that are co-expressed in two or more groups/samples.
Assembly: mm10
Supplementary files format and content: Processed data is in tab limited text format containing information like gene ID, normalized abundance of all the samples , gene name,chromosome information, gene start and end position, gene strand information, length, gene biotype, gene description, belonging to transcription factor family or not

molecule: cytoplasmic RNA

source_name: kidney

growth_protocol: All mice were kept in standard environmental conditions, including a room temperature of 25oC, 12 hours each of light/dark periods, and standard chow diet and water ad-libitum. Following conclusion of HU duration, mice were euthanized via cervical dislocation, and renal tissues were immediately excised and stored for histology and transcriptomic analysis. The University ACUC (Animal Care and Use Committee) approved the experimental protocol in agreement with accepted international standards

extract_protocol:
Renal tissue samples were collected from three cohorts of murine subjects (three replicates each of control, hind limb unloaded, hind limb unloaded, and PBA-treated mice, respectively). Total RNA was extracted using RNeasy®(Qiagen) following manufacturer’s protocol. Briefly approximately 30 mg of renal tissue was disrupted and homogenized, following which the lysate is centrifuged at 14000 RPM for 20 minutes. The supernatant that is thus obtained is transferred to gDNA spin column to remove genomic DNA content from the sample. The column is spun at 8000 RPM for 30 seconds, following which the supernatant is discarded, and the flowthrough is collected.  600 µl of 70% ethanol is added to the flowthrough to obtain RNA precipitate. 700 µl of sample, including precipitate to RNeasy spin column and centrifuged for 15 seconds at 10000 RPM, following which the flowthrough is discarded and purified RNA is obtained for further analysis
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platform, according to effective library concentration and data amount. The clustering of the index-coded samples was performed according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

treatment_protocol: We used four-month-old, male c57BL/6j mice for HU experiments. Mice were categorized into ground-based controls (GC), and HU mice treated with vehicle (HU) or 4PBA (HU-t, 100mg/kg/d via intraperitoneal injections) (n = 6-8 mice / group)

value: kidney

value: Hindlimb Unloaded/PBA Treated


title: Ldlr-_UT_12

description: Library name: LD27-12


title: Ldlr-_UT_11

description: Library name: LD27-11


title: Urethra, Donor 158

city: Dallas

first: Douglas

last: Strand

state: TX

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

department: Urology

institute: UT Southwestern Medical Center

description: Library name: D158UrFcol

library_source: transcriptomic single cell

data_processing:
10x Genomics cellranger mkfastq version 6.1.2 with default settings was used to demultiplex base call files.
10x Genomics cellranger count version 6.1.2 with default settings was used to align and count reads.
scDblFinder version 1.18.0 running on R version 4.4.1 was used for doublet detection.
Seurat version 5.1.0 running on R version 4.4.1 was used for filtering, normalization, dimensional reduction, clustering, and visualization.
Harmony version 1.2.0 running on R version 4.4.1 was used for batch correction.
Assembly: GRCh38
Supplementary files format and content: Sample-specific 10x Genomics formatted h5 file containing a cell x gene matrix for called cells (empty droplets removed).
Supplementary files format and content: RDS file containing a Seurat object corresponding to the fully processed annotated dataset.

source_name: urethra

extract_protocol:
Single-cell suspensions containing ~17400 cells were loaded on 10x Genomics Chromium single-cell Controller with 5’ paired-end library and gel bead kit according to manufacturer’s recommendations.
Libraries were created according to the manufacturer's instructions using the 10x Genomics Chromium Controller instrument and 5' paired-end library construction kit.

value: urethra


title: shCTRshCTR_input_rep1

description:
Library name: CHe-YX-43s-O1Y01
Y01_S8


title: WT_UT_8

description: Library name: LD17-8


title: Hindlimb Unloaded/PBA treated Sample 1

description:
UP1_K
Hindlimb unloaded mice with PBA treatment


title: 252800524052_2_3_FP71H_0_hour_(40_mins_post)

value: Sham

value: Fentanyl


title: SGC7901

city: guangzhou

first: xi

last: dongxin

address: No. 1, Xinzao Road, Xinzao Town, Panyu District, Guangzhou

institute: guangzhou medical university

description: Library name: sample 1

data_processing:
Once the raw sequencing data (RawData) is obtained, the data needs to be filtered, delinked, and processed for low-quality reads, followed by sequencing quality evaluation and ribosomal RNA removal to obtain high-quality data (CleanData). CleanData was aligned with the reference genome to obtain a BAM file.
For the detected mRNA, the gene expression level was further calculated and the differentially expressed genes between samples were analyzed, and the differentially expressed genes were analyzed by GeneOntology (GO) and KEGG pathway enrichment analysis.
For the detected lncRNAs, the expression of lncRNAs was calculated and the differentially expressed lncRNAs between samples were analyzed. Differential lncRNAs were selected for target gene prediction, GO analysis and KEGG pathway enrichment analysis were performed on target genes, and the potential functions of lncRNAs were explored.
Assembly: hg19
Supplementary files format and content: SGC7901--SGC7901_TM.all.gene.xls

source_name: gastric

growth_protocol: Human gastric cancer cell line SGC7901 was cultured in RPMI 1640 medium (Solarbio) supplemented with 10% fetal bovine serum (FBS, Biological Industries).  All the cells were digested with trypsin (containing EDTA, Solarbio) at a density of 80–90% for passaging at a 1:2 or 1:3 ratio and all the cells were cultured in a cell culture incubator (ESCO, Singapore) containing 5% CO2 at 37 °C.

extract_protocol:
Exosomes were isolated from the cell supernatants of SGC7901 cells. Cellular supernatant was mixed with RiboTMExosome Isolation Reagent and exosome isolation was performed according to the manufacturer’s instructions (Ribobio, China). Exosomal RNA was extracted by Magzol Reagent (Magen, China). The quantity of RNA yield was assessed by using the Qubit(Thermo Fisher Scientific, USA) and the Agilent 2200 TapeStation (Agilent Technologies, USA) .
rRNAs were removed fromExosomal RNA using QIAseqFastSelect RNA Removal Kit（QIAGEN，Germany）and fragmented to approximately 200bp. Subsequently, the RNAfragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext®Ultra™ RNA LibraryPrep Kit for Illumina (NEB, USA). The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit. The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).

value: gastric

value: Human gastric cancer cell

value: Non-endoplasmic reticulum stress


title: SGC7901_TM

description: Library name: sample 2

treatment_protocol: Exosomes were isolated from the cell supernatants of SGC7901 cells.

value: endoplasmic reticulum stress


title: Ldlr-_UT_10

description: Library name: LD27-10

value: Liver

value: female


title: Urethra, Donor 151

description: Library name: D151UrFcol


title: 252800524051_2_4_FP21H_0_hour_(40_mins_post)

value: Heart


title: Ldlr-_UT_7

description: Library name: LD27-7


title: Hindlimb Unloaded sample 2

description:
U6_K
Hindlimb unloaded mice

value: Hindlimb Unloaded


title: Hindlimb Unloaded sample 3

description:
U7_K
Hindlimb unloaded mice


title: 252800524052_1_3_FP24H_7_days


title: 252800524052_1_2_FP73H_6_hours


title: 252800524052_1_1_FP61H_7_days


title: 252800524052_2_2_FP68H_6_hours


title: 252800524051_2_3_FP96H_0_hour_(40_mins_post)


title: Stress-susceptible mouse3

city: Seoul

first: Dong-Joo

last: Hwang

address: 1239, Yangjae-daero, Songpa-gu

department: Institute of Sport Science

country: South Korea

institute: Korea National Sport University

description:
Library name: SUSSED3
Ventral hippocampus tissue in stress-susceptible mouse: SUSSED3

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform to generate 101 bp paired-end reads.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39(NCBI) whole genome using STAR
Calculation mapped reads using salmon
TMM + CPM calculation using conorm
Assembly: GRCm39
Supplementary files format and content: Tab-delimited text files contain Read count values for each sample.

source_name: Brain (ventral hippocampus)

growth_protocol: Naïve 8-week-old male C57BL/6J mice (Daehan Bio-Link, Chungbuk, Korea) were housed and acclimated to a controlled pathogen-free environment of animal facility at Korea National Sport University (KNSU) (12:12-h dark/ light cycle, 20°C ± 1°C, and 50% relative humidity) with ad libitum access to standard chow diet (SAFE R04-10, Aston Pharma, England) and distilled water.

extract_protocol:
RNA was extracted using a TaKaRa RNAiso Plus.
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

treatment_protocol: In brief, mice were individually placed in ventilated 50 mL polyethylene tubes to induce immobilization for 2 hours daily, from 10 a.m. to 12 p.m. (during the light cycle). This procedure was repeated for 14 consecutive days. Following two weeks of chronic restraint stress, stress-susceptible mice underwent a 2-week low-intensity treadmill exercise intervention, while control groups remained sedentary.

value: Brain (ventral hippocampus)

value: Wild-type

value: Restraint stress


title: Hindlimb Unloaded sample 1

description:
U4_K
Hindlimb unloaded mice


title: Stress-susceptible mouse2

description:
Library name: SUSSED2
Ventral hippocampus tissue in stress-susceptible mouse: SUSSED2


title: 252800524052_2_1_FP33H_6_hours


title: 252800524052_1_4_FP66H_24_hours


title: 252800524051_2_1_FP74H_0_hour_(40_mins_post)


title: Stress-susceptible mouse1

description:
Library name: SUSSED1
Ventral hippocampus tissue in stress-susceptible mouse: SUSSED1


title: Ground Control sample 3

description:
MC4_K
no treatment Grounded control mice

value: Ground control


title: Chronic,Day8,Rep2

city: New York

first: Jahan

last: Rahman

state: New York

address: 417 E 68th St

department: Center for Hematologic Malignancies

institute: Memorial Sloan Kettering

description: Library name: Sample_D8-Chr-2

data_processing:
RNA-seq samples were sequenced using the Illumina NovaSeq 6000 platform, generating 100-base pair paired-end reads. FASTQ files were quality-checked using FastQC v0.12.0 and trimmed with Trim Galore v0.6.10 to remove adapter sequences and read ends with Phred scores below 15. STAR v2.7.0a was used to align the FASTQ files to the mm10 reference genome. SAM files outputted by STAR were sorted using the sort function from Samtools v1.19.2, and indexed using the index function to generate BAM index files. A gene expression count matrix was generated using featureCounts v2.0.6, quantifying only read pairs that overlapped exons. Downstream differential gene expression analysis was performed using DESeq2 v1.42.0.
Assembly: hg38
Supplementary files format and content: tab-delimited gene-read count matrix for each sample: gene_count_matrix.txt

source_name: Primary Human CD8 T

extract_protocol:
Primary human T cells were activated and expanded with or without chronic stimulation. Following 2, 4, and 8 days of activation, biological triplicate wells were harvested.
RNA was extracted using a TRIzol-chloroform-based method2.  cDNA libraries were then prepared as instructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina) in accordance with the manufacturer's instructions and sequenced using Illumina NextSeq 500 generating 150-bp paired-end reads.

value: Primary Human CD8 T


title: Hindlimb Unloaded/PBA treated Sample 3

description:
UP6_Kidney
Hindlimb unloaded mice with PBA treatment

value: kidney

value: Hindlimb Unloaded/PBA Treated


title: Urethra, Donor 148

description: Library name: D148UrFcol

value: urethra


title: Urethra, Donor 149

description: Library name: D149UrFcol


title: 252800524051_1_4_FP91H_7_days

value: Sham

value: Fentanyl


title: Stress-susceptible mouse subjected to low-intensity exercise 2

description:
Library name: SUSLE2
Ventral hippocampus tissue in stress-susceptible mouse subjected to low-intensity exercise: SUSLE2

value: Restraint stress and low-intensity exercise


title: Ground Control sample 1

description:
MC1_K
no treatment Grounded control mice


title: memory TFH_TGF-beta_rep3

city: Hengyang

first: Yixin

last: Yang

address: 湖南省衡阳市蒸湘区常胜西路28号

department: Hengyang Medical School

institute: University of South China

description: Library name: T6

data_processing:
Raw sequencing reads in FASTQ format were processed using Fastp (v0.24.1) to remove technical sequences and low-quality bases.
Clean reads were aligned to the reference genome (Species_name, assembly version) using HISAT2 (v2.2.1), a splice-aware aligner.
Gene-level counts were quantified using HTSeq (v0.6.1). Reads overlapping exons were counted, and multi-mapping reads or reads overlapping multiple genes were excluded.
Assembly: GRCh38.107
Supplementary files format and content: txt files include raw counts and FPKM values for each sample.

source_name: peripheral blood

growth_protocol: TFH cells were maintained in complete RPMI medium (RPMI-1640 medium containing penicillin-streptomycin, 50 µM 2-mercaptoethanol, 1 mM sodium pyruvate, nonessential amino acids and 25 mM HEPES, pH7.2-7.5) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
TFH cells were fully dissolved with 1 mL of Trizol (Takara). 1 μg total RNA was used for the following library preparation.
For mRNA enrichment, poly(A) mRNA isolation was performed using Oligo(dT) beads. Alternatively, when the sample quality or experimental design necessitated, ribosomal RNA was depleted using rRNA removal methods to enrich for coding and non-polyadenylated transcripts. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA synthesis was carried out using reverse transcriptase, followed by second-strand cDNA synthesis. For strand-specific library construction, during the second-strand synthesis the standard dTTP was replaced with dUTP; subsequent treatment with USER enzyme selectively degrades the second strand prior to PCR amplification, thereby preserving strand information. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tail in a single reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers, and the PCR products were validated. Finally, libraries with different indexes were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2×150 paired-end (PE) configuration according to the manufacturer’s instructions.

treatment_protocol: TFH cells were stimulated with anti-human CD3/CD28 Dynabeads (Invitrogen) in the absence or presence of TGF-beta1 (10 ng/mL, PeproTech).

value: peripheral blood

value: TFH cells derived from memory TFH cells

value: wild type

value: anti-CD3/CD28 beads + TGF-beta


title: Stress-susceptible mouse subjected to low-intensity exercise 3

description:
Library name: SUSLE3
Ventral hippocampus tissue in stress-susceptible mouse subjected to low-intensity exercise: SUSLE3


title: Chronic,Day8,Rep1

description: Library name: Sample_D8-Chr-1


title: Ground Control sample 2

description:
MC3_Kidney
no treatment Grounded control mice


title: Chronic,Day8,Rep3

description: Library name: Sample_D8-Chr-3


title: Acute,Day8,Rep3

description: Library name: Sample_D8-Ac-3


title: Stress-susceptible mouse subjected to low-intensity exercise 1

description:
Library name: SUSLE1
Ventral hippocampus tissue in stress-susceptible mouse subjected to low-intensity exercise: SUSLE1


title: 252800524051_1_3_FP77H_6_hours

value: Heart


title: Acute,Day8,Rep2

description: Library name: Sample_D8-Ac-2


title: memory TFH_TGF-beta_rep2

address: 湖南省衡阳市蒸湘区常胜西路28号

description: Library name: T5


title: 252800524051_1_1_FP49H_6_hours


title: 252800524051_1_2_FP47H_0_hour_(40_mins_post)


title: 252800524047_2_4_FP81H_7_days


title: Acute,Day8,Rep1

description: Library name: Sample_D8-Ac-1


title: memory TFH_control_rep3

address: 湖南省衡阳市蒸湘区常胜西路28号

description: Library name: C6

value: anti-CD3/CD28 beads


title: memory TFH_TGF-beta_rep1

address: 湖南省衡阳市蒸湘区常胜西路28号

description: Library name: T4


title: Chronic,Day4,Rep3

description: Library name: Sample_D4-Chr-3


title: Sedentary mouse sample3

description:
Library name: SED3
Ventral hippocampus tissue in sedentary mouse: SED3

value: Brain (ventral hippocampus)

value: No treatment


title: Chronic,Day4,Rep1

description: Library name: Sample_D4-Chr-1


title: memory TFH_control_rep1

address: 湖南省衡阳市蒸湘区常胜西路28号

description: Library name: C4


title: Chronic,Day4,Rep2

description: Library name: Sample_D4-Chr-2


title: Sedentary mouse sample2

description:
Library name: SED2
Ventral hippocampus tissue in sedentary mouse: SED2

value: Wild-type


title: naïve-derived TFH_TGF-beta_rep3

address: 湖南省衡阳市蒸湘区常胜西路28号

description: Library name: T3

value: TFH cells derived from naive CD4+ T cells


title: OIR_VA2ab_4_P19

city: Yokohama

first: Hiroto

last: Abe

state: Kanagawa

address: 216 Totsuka-cho, Totsuka-ku

country: Japan

institute: Chugai Pharmaceutical. Co. Ltd.

description: Library name: R40

data_processing:
Reads were mapped to the mouse genome with RefSeq (GRCm38.p4) transcript annotation using STAR v2.7.10a (https://github.com/alexdobin/STAR). TPM (transcripts per million) values were calculated using RSEM v1.3.3 (https://github.com/deweylab/RSEM).
Assembly: GRCm38.p4
Supplementary files format and content: csv files include raw counts and TPM values for each sample

source_name: retina

extract_protocol:
Eyes were enucleated from the sacrificed control and OIR mice at P17 and P19, and the whole retinas were collected using dissecting forceps. One whole retina was used for total RNA extraction using Sepasol-RNA I Super G (Nacalai Tesque, 09379), and 4 independent samples were prepared for one condition.
Library generation was done using SMART-Seq mRNA (Takara Bio Inc.), IDT for Illumina - DNA/RNA UD Indexes, Tagmentation (Illumina, Inc., San Diego, CA, USA)), and Nextera XT DNA Library Prep Kit (Illumina).

value: retina


title: Acute,Day4,Rep3

description: Library name: Sample_D4-Ac-3

value: Primary Human CD8 T


title: Sedentary mouse sample1

description:
Library name: SED1
Ventral hippocampus tissue in sedentary mouse: SED1


title: 252800524047_1_4_FP52H_7_days


title: 252800524047_2_3_FP54H_24_hours


title: memory TFH_control_rep2

address: 湖南省衡阳市蒸湘区常胜西路28号

description: Library name: C5


title: OIR_VA2ab_3_P19

description: Library name: R39


title: OIR_VA2ab_2_P19

description: Library name: R38


title: OIR_VA2ab_1_P19

description: Library name: R37


title: 252800524047_2_2_FP38H_6_hours


title: naïve-derived TFH_TGF-beta_rep2

address: 湖南省衡阳市蒸湘区常胜西路28号

description: Library name: T2


title: 252800524047_2_1_FP85H_6_hours


title: OIR_A2ab_4_P19

description: Library name: R36


title: Acute,Day4,Rep1

description: Library name: Sample_D4-Ac-1


title: Activated,Day2,Rep3

description: Library name: Sample_D2-3


title: 252800524047_1_3_FP30H_0_hour_(40_mins_post)


title: naïve-derived TFH_control_rep3

address: 湖南省衡阳市蒸湘区常胜西路28号

description: Library name: C3


title: Acute,Day4,Rep2

description: Library name: Sample_D4-Ac-2


title: 252800524047_1_1_FP16H_7_days


title: Activated,Day2,Rep2

description: Library name: Sample_D2-2


title: OIR_A2ab_3_P19

description: Library name: R35


title: naïve-derived TFH_control_rep2

address: 湖南省衡阳市蒸湘区常胜西路28号

description: Library name: C2


title: naïve-derived TFH_control_rep1

address: 湖南省衡阳市蒸湘区常胜西路28号

description: Library name: C1


title: naïve-derived TFH_TGF-beta_rep1

address: 湖南省衡阳市蒸湘区常胜西路28号

description: Library name: T1


title: Activated,Day2,Rep1

description: Library name: Sample_D2-1


title: OIR_A2ab_1_P19

description: Library name: R33


title: 7242, Severe

city: Denver

first: Evans

last: Fernandez

state: CO

address: 1400 Jackson St.

institute: National Jewish

description: Library name: sev_7242

data_processing:
FASTQ files from the Illumina bcl2fastq V.2.17 converter were adapter trimmed using skewer V.0.2.2 and aligned to the hg19 human reference genome with the STAR aligner V.2.4.15 using Ensembl V.75 (http://ensembl.org) gene models.
Counts of uniquely mapped reads per gene were quantified using the Subread V.1.5.1 software.
Assembly: hg19
Supplementary files format and content: annotated_counts_geo.xlsx, gene-by-sample counts table, generated by the data processing steps listed.

source_name: PBMCs

extract_protocol:
PBMCs extracted from frozen cell pellets in whole blood
Extracted PBMCs were subjected to mRNA bead capture, quality control (Qiagen) and RNA-seq library build (Kapa Biosystems Inc). Libraries were QCed on the Bioanalyzer (Agilent Technologies) and sequenced on the Illumina 2500 at 1×50 bp (mean: 40 million standard error 12 million reads/sample).

value: PBMCs

tag: disease severity

value: Severe

value: F

tag: age


title: OIR_A2ab_2_P19

description: Library name: R34

tag: tissue


title: 7191, Severe

description: Library name: sev_7191

tag: Sex

value: M


title: OIR_Vab_4_P19

description: Library name: R32


title: HCM2

city: Houston

first: Yi

last: Zhao

state: Texas

address: 6770 Bertner Avenue

institute: The Texas Heart Institute at Baylor College of Medicine

description:
Library name: 2023_Pediatric1_DTuraga_P186
LV tissue from end stage P186 HCM heart at time of transplant, profiled by 10X Genomics 3'v3 snRNA-seq

data_processing:
Raw sequencing reads were aligned to the genome (build GRCh38) using the 10X Genomics toolkit CellRanger version 5.0.1 (cellranger count) with default parameters.
Assembly: GRCh38
Supplementary files format and content: TSV files: Tab-separated tables. MTX files: long-format matrix files. CSV files: comma-seperated tables.

molecule: nuclear RNA

source_name: Heart left ventricle

extract_protocol:
Cardiac tissue was collected from the LV free wall in the operating room at time of transplant. The sample was kept in cold saline on ice during transfer to the laboratory for preservation. It was carefully dissected into multiple aliquots, which were flash-frozen and stored at –80 °C. Nuclear isolation was performed. Briefly, frozen cardiac tissue was dissociated by using a Dounce homogenizer. Single nuclei were isolated via fluorescence-activated cell sorting.
SnRNA-seq was performed by using the 10X Genomics platform. Isolated nuclei were loaded into the 10X Genomics Chromium Controller to obtain the gel beads in emulsion. The sequencing libraries were then prepared according to the manufacturer’s protocols for the Single-cell 3’ Reagents Kits v3. Sequencing was performed by using the NovaSeq 6000 system.

value: Heart left ventricle

tag: cell type

value: Cardiac cells

value: female

tag: patient id


title: HCM3

description:
Library name: 2023_Pediatric1_DTuraga_P194
LV tissue from end stage P194 HCM heart at time of transplant, profiled by 10X Genomics 3'v3 snRNA-seq


title: 252800524047_1_2_FP57H_24_hours

source_name: Agilent Universal Mouse Reference RNA

value: Sham

value: Fentanyl


title: 252800524037_2_2_FP94H_24_hours

value: Heart


title: OIR_Vab_3_P19

description: Library name: R31


title: 252800524037_1_4_FP82H_7_days


title: 252800524037_2_1_FP17H_7_days


title: Recurrent_3

city: Chongqing

first: hui

last: li

state: Chongqing

address: No. 181 of Hanyu Road

department: Hepatobiliary Pancreatic Tumor Center

institute: Chongqing University Cancer Hospital

description: Library name: Sample 6

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Gene_Expression_Profiling.txt includes FPKM values for each Sample

source_name: tumor

extract_protocol:
Total RNA was extracted using Trizol Reagent (Invitrogen, USA). CircRNA high-throughputsequencing and analysiswere performed by NovogeneTechnologyCo., Ltd. (Beijing, China).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. In order to ensure the quality of the library, the library needs to be tested. After the construction of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

value: tumor


title: OIR_Vab_2_P19

description: Library name: R30


title: 252800524037_2_4_FP88H_0_hour_(40_mins_post)

data_processing: Data were processed using Feature Extraction Software. Log2 transformation and quantile normalization were applied where applicable.

extract_protocol: Total RNA was extracted from tissue samples using TRIzol reagent and miRNeasy Mini Kit (QIAGEN) following the manufacturer's instructions. Quality was assessed using NanoDrop, Qubit, and Tapestation 2200.


title: 252800524037_2_3_FP42H_6_hours


title: 6974, Severe

description: Library name: sev_6974


title: Recurrent_2

description: Library name: Sample 5


title: 252800524037_1_3_FP22H_6_hours


title: OIR_Vab_1_P19

description: Library name: R29


title: 7093, Severe

description: Library name: sev_7093


title: 6890, Severe

description: Library name: sev_6890


title: Primary_3

description: Library name: Sample 3


title: OIR_IgG_4_P19

description: Library name: R28


title: Recurrent_1

description: Library name: Sample 4


title: OIR_IgG_3_P19

description: Library name: R27


title: 6754, Severe

description: Library name: sev_6754


title: Primary_2

description: Library name: Sample 2


title: 252800524037_1_1_FP39H_24_hours


title: OIR_IgG_2_P19

description: Library name: R26


title: 5772, Severe

description: Library name: sev_5772


title: 6284, Severe

description: Library name: sev_6284


title: 252800524036_2_4_FP44H_6_hours


title: 252800524036_2_3_FP58H_24_hours


title: OIR_IgG_1_P19

description: Library name: R25


title: Primary_1

description: Library name: Sample 1


title: 252800524037_1_2_FP84H_7_days


title: nOIR_3_P19

description: Library name: R23


title: 6944, Severe

description: Library name: sev_6944


title: 252800524036_2_2_FP23H_24_hours


title: f2n11_csc1

city: Amman

first: Heba

last: Saadeh

state: Not Applicable

address: Queen Rania Street

country: Jordan

institute: The University of Jordan

description: Library name: Sample 3

data_processing:
Raw sequencing reads underwent quality control, trimming and alignment to the reference genome GRCh38 and genes and transcripts were assembled with StringTie. Abundance of gene/transcript was calculated as FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Kilobase Million)
Assembly: GRCh38
Supplementary files format and content: xlsx file that includes read counts, FPKM and TPM values for each sample

source_name: U87 MG

extract_protocol:
Total RNA was extracted using TRIzol® reagent (Invitrogen, USA) and purified with RNeasy® Micro Kit (QIAGEN, USA)
TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E

value: U87 MG

tag: genotype

value: Cancer stem cells

value: CD133 positive


title: 252800524036_2_1_FPB2H_6_hours

city: Silver Spring

first: Aarti

last: Gautam

institute: WRAIR

tag: time point


title: 5137, Severe

description: Library name: sev_5137


title: nOIR_2_P19

description: Library name: R22


title: f2n11_csc3

description: Library name: Sample 5

tag: treatment


title: nOIR_4_P19

description: Library name: R24


title: nOIR_1_P19

description: Library name: R21


title: 6969, Moderate

description: Library name: mod_6969

value: Moderate


title: u87_control3

description: Library name: Sample 2

value: CONTROL


title: 252800524036_1_4_FP67H_0_hour_(40_mins_post)


title: f2n11_csc2

description: Library name: Sample 4


title: u87_control2

description: Library name: Sample 1


title: 7283, Moderate

description: Library name: mod_7283


title: OIR_VA2ab_4_P17

description: Library name: R20

value: retina


title: 252800524036_1_3_FP92H_24_hours


title: HuCAFsNERS_3

description: Library name: sample6

data_processing:
After obtaining the sequencing data, the data were first filtered to obtain high-quality sequencing data (Clean Data), and then the high-quality sequencing data was compared to the reference genome of the species in this project, and gene expression quantification, GSEA, gene difference analysis, enrichment analysis and other analyses were carried out
Assembly: hg19
Supplementary files format and content: gene_count_matrix.xlsx
Supplementary files format and content: 1_genes_fpkm_expression.xlsx

extract_protocol:
Human gastric cancer cell line SGC7901 was cultured in RPMI 1640 medium (Solarbio) supplemented with 10% fetal bovine serum (FBS, Biological Industries). Primary human gastric cancer fibroblasts (h-CAFs, Procell) were cultured in RPMI 1640 medium (Solarbio) supplemented with 10% fetal bovine serum (FBS, Biological Industries). H-CAFs were cultured in human gastric cancer tissue fibroblast complete medium (Procell). Penicillin or streptomycin (Solarbio) was added to the above medium when necessary. All the cells were digested with trypsin (containing EDTA, Solarbio) at a density of 80–90% for passaging at a 1:2 or 1:3 ratio and all the cells were cultured in a cell culture incubator (ESCO, Singapore) containing 5% CO2 at 37 °C. Cocultured the h-CAFs with the supernatant of human gastric cancer cells stimulated by 5μg/ml TM to formulate the TME of ERS-GC.
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: gastric

value: SGC7901,primary human gastric cancer fibroblasts

value: Human gastric cancer cell ,primary human gastric cancer fibroblasts

value: WT

value: Non-endoplasmic reticulum stress


title: OIR_VA2ab_3_P17

description: Library name: R19


title: HuCAFsNERS_2

description: Library name: sample5


title: 252800524036_1_2_FP41H_7_days


title: 6050, Moderate

description: Library name: mod_6050

value: PBMCs

value: M


title: 6543, Moderate

description: Library name: mod_6543


title: 252800524029_2_4_FP95H_0_hour_(40_mins_post)

value: Sham


title: 252800524036_1_1_FP55H_0_hour_(40_mins_post)

value: Fentanyl


title: 5783, Moderate

description: Library name: mod_5783


title: HuCAFsERS_3

description: Library name: sample3

value: Endoplasmic reticulum stress (ERS)


title: 5818, Moderate

description: Library name: mod_5818

value: F


title: OIR_VA2ab_1_P17

description: Library name: R17


title: 252800524029_2_3_FP20H_0_hour_(40_mins_post)

value: Heart


title: HuCAFsERS_2

description: Library name: sample2


title: OIR_VA2ab_2_P17

description: Library name: R18


title: 5654, Moderate

description: Library name: mod_5654


title: 5630, Moderate

description: Library name: mod_5630


title: HuCAFsERS_1

description: Library name: sample1


title: OIR_A2ab_3_P17

description: Library name: R15


title: HuCAFsNERS_1

description: Library name: sample4


title: OIR_A2ab_4_P17

description: Library name: R16


title: 5599, Moderate

description: Library name: mod_5599


title: 252800524029_2_1_FP56H_24_hours


title: 252800524029_2_2_FP72H_6_hours


title: OIR_A2ab_2_P17

description: Library name: R14


title: 5690, Moderate

description: Library name: mod_5690


title: Huh7, COP1-siRNA

city: Daegu, Republic of Korea

first: EUN-HYE

last: JEON

address: 1095 Dalgubeol, Dalseo-gu

department: Molecular Medicine

institute: Keimyung University School of Medicine

description: Library name: Huh7-COP1

data_processing:
Raw reads underwent quality control using FastQC v0.11.7 and trimming with Trimmomatic v0.38. Reads were aligned to the GRCh38 genome using HISAT2 v2.1.0. Transcript assembly and quantification were performed using StringTie v2.1.3b. Normalized expression values were calculated as FPKM and TPM. Differential gene expression analysis was conducted using edgeR.
Assembly: Genome build: GRCh38; Annotation: NCBI release 109.20200522.
Supplementary files format and content: Processed data files are provided in Excel format, containing raw read counts, normalized expression values (FPKM and TPM), and differential expression analysis results including fold changes and p-values.

growth_protocol: All cell lines were incubated in a humidified incubator set to 37°C with 5% CO2. The cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (74134; Qiagen, Hilden, Germany)
Libraries were constructed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the TruSeq Stranded mRNA Reference Guide #1000000040498 v00. The process included poly(A)+ RNA purification, RNA fragmentation, reverse transcription to cDNA, adapter ligation, and PCR amplification with size selection for inserts of 200-400 bp.

treatment_protocol: To knockdown specific genes in HCC cells, cells were transfected with 20 nM of either negative control (NC) siRNA or COP1-specific siRNA using Lipofectamine 2000and Opti-MEM in a humidified incubator for 5 h. Cells were harvested 48 hours later.

value: Hepatocellular carcinoma

value: COP1 Knockdown


title: OIR_A2ab_1_P17

description: Library name: R13


title: 252800524029_1_3_FP43H_7_days

address: 503 Robert Grant Avenue


title: 4951, Moderate

description: Library name: mod_4951

value: Moderate


title: Huh7, NC-siRNA

description: Library name: Huh7-NC

value: NC-siRNA


title: 252800524029_1_2_FP25H_0_hour_(40_mins_post)


title: 7068, Moderate

description: Library name: mod_7068


title: OIR_Vab_4_P17

description: Library name: R12

value: retina


title: HepG2, COP1-siRNA

description: Library name: HepG2-COP1


title: OIR_Vab_3_P17

description: Library name: R11


title: HepG2, NC-siRNA

description: Library name: HepG2-NC


title: 252800524029_1_4_FP29H_6_hours


title: 252800524029_1_1_FP53H_7_days


title: OIR_Vab_2_P17

description: Library name: R10


title: 252800524051_2_2_FP87H_0_hour_(40_mins_post)


title: OIR_Vab_1_P17

description: Library name: R9


title: 6943, Moderate

description: Library name: mod_6943


title: Oocyte in situ Fresh and Frozen

first: Wen

last: Li

state: Shanghai

address: No.910 Hengshan Road

institute: International Peace Maternity and Child Health Hospital

description: Library name: Sample 7

data_processing:
For 10X genomic strategy: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1(https://support.10xgenomics.com/single-cell-gene- expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Homo sapiens (homo) hg18
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Oocyte

extract_protocol:
For 10X Genomics strategy, the fresh and vitrification-thawing processed human ovarian cortex were cut into pieces with very sharp knives, followed by dissociating in collagenase I solution(2mg/ml) for 45 minutes at 37°C. Before FACS, the Blood cells were depleted by Red Blood cells lysis buffer (BD Pharmingen). Cells were then labeled with DAPI (4',6-diamidino-2-phenylindole, Cat number: D9452, Sigma, 1:1000), and DAPI- cells (live cells) were sorted through a MoFlo FACS machine (MoFlo Astrios EQ, Beckman Coulter) directly into PBS containing 0.04% BSA. For Smartseq2 strategy, fresh and vitrification-thawing processed human ovarian cortex were cut into pieces with very sharp knives, followed by dissociating in collagenase I solution(2mg/ml) for 45 minutes at 37°C. RPMI 1640 medium containing 10% FBS was used to stop digestion. The resulting cell suspension was then transferred into a 3.5 cm dish. Then, oocytes were manually picked under a dissection microscope and transferred to a PBS drop (containing 0.1% BSA) by mouth pipetting. Finally, the oocytes were placed separately into an individual PCR tube with lysis buffer and stored at -80°C for subsequent experiments.
For 10X Genomics strategy based single-cell RNA sequencing, the single-cell RNA library was built via 10x Chromium platform, and FACS-enriched live ovarian cells were loaded per channel approximately. The libraries were built via the Chromium platform and Chromium Single Cell 3’ v2 chemistry. Finally, the libraries were loaded on an illumine NovaSeq 6000 System (Illumina, San Diego) with a PE150 sequencing strategy. For Smart-seq2 strategy based single-cell RNA sequencing, scRNA-seq libraries were constructed according to the published protocol with modifications [20b]. Brieﬂy, the constructed libraries of each oocyte will undergo preliminary screening through the marker genes (DDX4 for oocyte and NR5A2 for granulosa cells) of oocytes and granulosa cells via qPCR, aiming to exclude multi-cell samples. Then, the libraries were sequenced on an Illumina NovaSeq 6000 platform with a 150-bp paired-end read length by Novogene.

value: Oocyte


title: 6981, Moderate

description: Library name: mod_6981


title: OIR_IgG_4_P17

description: Library name: R8


title: Ovatian Cortex Frozen-3

description: Library name: Sample 6

source_name: Ovarian Cortex

value: Ovarian Cortex

value: Ovarian cells


title: 7167, Mild

description: Library name: mild_7167

value: Mild


title: 252800524028_2_4_FP86H_6_hours


title: 6542, Moderate

description: Library name: mod_6542


title: OIR_IgG_3_P17

description: Library name: R7


title: Ovatian Cortex Frozen-1

description: Library name: Sample 4


title: 7176, Mild

description: Library name: mild_7176


title: 252800524028_2_1_FP27H_7_days


title: OIR_IgG_2_P17

description: Library name: R6


title: 7044, Mild

description: Library name: mild_7044


title: Ovatian Cortex Frozen-2

description: Library name: Sample 5


title: Ovatian Cortex Fresh-3

description: Library name: Sample 3


title: 252800524028_2_2_FP64H_24_hours


title: 252800524028_2_3_FP83H_7_days


title: 252800524028_1_4_FP51H_24_hours


title: OIR_IgG_1_P17

description: Library name: R5


title: 7035, Mild

description: Library name: mild_7035


title: 252800524028_1_3_FP59H_7_days


title: 6857, Mild

description: Library name: mild_6857


title: Ovatian Cortex Fresh-2

description: Library name: Sample 2


title: Ovatian Cortex Fresh-1

description: Library name: Sample 1


title: 6015, Mild

description: Library name: mild_6015


title: nOIR_4_P17

description: Library name: R4


title: 6208, Mild

description: Library name: mild_6208


title: nOIR_3_P17

description: Library name: R3


title: nOIR_2_P17

description: Library name: R2


title: Reduction Mammoplasty

city: Singapore

first: Kanaga

last: Sabapathy

state: --None--

address: 11 Hospital Crescent

department: Division of Cellular & Molecular Research

country: Singapore

institute: National Cancer Centre Singapore

data_processing:
CeleScope® was used to generate a single-nucleus gene expression matrix file based on the raw FASTQ files aligned to the GRCh38 human reference genome.
Assembly: GRCh38

source_name: Reduction mammoplasty

extract_protocol:
Single nuclei were isolated from approximately 50 mg of frozen tissue for each tumor sample and 100 mg for each peri-tumoral and RM sample by Singleron Biotechnologies using the GEXSCOPE® Single Nucleus RNAseq kit. Single nuclei were partitioned into the SCOPE-microwell chip isolated mRNA from each nucleus was hybridized to unique nucleus-identifying tags barcode sequences on the bead in the same well.
The beads containing the hybridized mRNA were collected and reverse transcribed into cDNA. The resulting cDNA was then amplified by PCR, fragmented, ligated to adapters, and PCR amplified to construct a sequencing library suitable for the Illumina sequencing platform.
snRNA-seq

value: Reduction mammoplasty


title: Peritumor2

source_name: Peritumor

value: Peritumor


title: Tumor 2

source_name: Tumor

value: Tumor


title: Peritumor1


title: Spleen, Tex_CITE-seq_r2_ADT

city: Nutley

first: Haihui

last: Xue

state: NJ

address: 123 Metro Boulevard, Bldg. 123, Rm. 5527

department: Center for Discovery and Innovation

institute: Hackensack University Medial Center

description: Library name: Tex_CITE-seq_r2_ADT

data_processing:
The CITE-seq data were pre-processed with 10x "cellranger multi" pipeline with default parameter, with the help of 10x cloud analysis platform. Processed expression matrix (RNA part) and multiplexing assignment (ADT part) were provided as processed data. Individual cells with high quality on both RNA and ADT parts were kept for downstream analysis (RNA: ≥1000 covered genes. ADT: quality filtered by cellranger multi pipeline).
Assembly: mm10
Supplementary files format and content: For CITE-seq data, processed expression matrix (RNA part) and  cell multiplexing  assignment(ADT part) were provided as processed data.
Library strategy: CITE-seq

molecule: protein

source_name: spleen

growth_protocol: Naive P14 TCR transgenic CD8+ T cells were nucleofected with sgRNAs targeting Thy1 (as a negative control) and those targeting Id2. The nucleofected P14 cells were adoptively transferred into CD45-disparate recipients and subsequently infected with LCMV-Clone 13 to induce chronic viral infection. On day 8 post-infection,  Tim3+Slamf6- P14 cells were sorted and purified as effector exhausted CD8+ T (Tex-eff) cells, while Tim3−Slamf6+ P14 cells were sorted and purified as precursors to stem-like exhausted CD8+ T (Tex-prec) cells, and both subsets were used for ATAC-seq analysis. WT or CD4-Cre+ Id3 fl/fl mice were directed infected with LCMV-Clone 13 to induce chronic viral infection. On day 8 post-infection, antigen-specific CD8+ T cells were detected with GP33- MHC-I tetramer. Among tetramer+ cells,  Tim3+Slamf6- P14 cells were sorted and purified as effector exhausted CD8+ T (Tex-eff) cells, while Tim3−Slamf6+ P14 cells were sorted and purified as precursors to stem-like exhausted CD8+ T (Tex-prec) cells, and both subsets were used for ATAC-seq analysis.

extract_protocol:
Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) was performed on WT and ID3KO GP33-tetramer+ CD8+ T cells, or CD45.2+ sgThy1 and sgId2 P14 CD8+ T cells sorted on day 8 post-infection with LCMV- clone 13.
Construction of gene expression libraries and cell surface protein libraries was performed using the 10X Genomics Chromium Next GEM Single Cell 3’ library kit (PN-1000269), following the manufacturer's instructions. The resulting gene expression and cell multiplexing libraries  were combined at a molecular ratio of 9:1. Libraries were quantified using a KAPA Library Quantification Kit (KK4835), assessed for quality using an Agilent Tapestation, and then sequenced on Illumina’s NovaSeq X plus in paired-end read mode with the read length of 150 nucleotides at the Admera Health.

treatment_protocol: Sorted cells were used directly for downstream analyses without further treatment.

value: spleen

value: CD45.2+ CD8+ T cells

value: sgRNA targeting Thy1 and Id2

value: day 8 post-infection with LCMV Cl13


title: nOIR_1_P17

description: Library name: R1


title: Spleen, Tex_CITE-seq_r2_RNA

description: Library name: Tex_CITE-seq_r2_RNA


title: 252800524061_2_1_FP88C_0_hour_(40_mins_post)

value: Sham

source_name: Cortex

value: Fentanyl

value: Cortex


title: 5361, Mild

description: Library name: mild_5361

value: PBMCs

value: F


title: 252800524028_1_1_FP60H_7_days

source_name: Heart

value: Heart


title: 5171, Mild

description: Library name: mild_5171


title: 252800524061_2_3_FP17C_7_days


title: Spleen, Tex_CITE-seq_r1_ADT

description: Library name: Tex_CITE-seq_r1_ADT

value: Cd11a high,  GP33-tetramer+, CD8+ T cells

value: WT and Id3 KO with Cd4-Cre


title: 5113, Mild

description: Library name: mild_5113

value: M


title: 5272, Mild

description: Library name: mild_5272

value: Mild


title: 252800524061_1_4_FP47C_0_hour_(40_mins_post)


title: 252800524028_1_2_FP32H_0_hour_(40_mins_post)


title: 252800524061_2_4_FP71C_0_hour_(40_mins_post)


title: 4437, Mild

description: Library name: mild_4437


title: 252800524061_2_2_FP67C_0_hour_(40_mins_post)


title: G118E-E2KO; Clone#25; technical replicate 6

first: Hu

last: Chen

address: 1250 Moursund St,

department: Pediatrics

institute: Baylor College of Medicine

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

source_name: iPSC-derived neurons

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

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

value: iPSC-derived neurons

value: iPSC-derived NPC-iNeurons


title: TC71_shSTAG2_2_Rep2

city: Ann Arbor

first: Abhijit

last: Parolia

state: MI

address: 1500 E Medical Center Dr

institute: Michigan Medicine

description:
Library name: TC71_shSTAG2_2_Rep2
Poly(A)+Transcriptome
CPM_ValuesPolyA.csv

data_processing:
Libraries passing quality control were trimmed of sequencing adaptors and aligned to the human reference genome, GRCh38. Samples were demultiplexed into paired-end reads using Illumina’s bcl2fastq conversion software v2.20. The reference genome was indexed using bowtie2-build, and reads were aligned onto the GRCh38/hg38 human reference genome using TopHat2 with strand-specificity and allowing only for the best match for each read.
Assembly: hg38
Supplementary files format and content: CPM

source_name: Bone/soft tissue

growth_protocol: Ewing sarcoma cells (A673, TC71) were grown in DMEM and IMDM media with 10% FBS and Penicillin/Streptomycin respectively.

extract_protocol:
Qiagen mRNeasy RNA extraction kit
RNA-seq libraries were prepared using 200–1,000 ng of total RNA. RiboErase to enrich for mRNA, cDNA synthesis, end-repair, A-base addition, and ligation of the Illumina indexed adapters were performed according to the TruSeq RNA protocol (Illumina). Libraries were size selected for 250–300 bp cDNA fragments on a 3% Nusieve 3:1 (Lonza) gel, recovered using QIAEX II reagents (QIAGEN), and PCR amplified using Phusion DNA polymerase (New England Biolabs). Library quality was measured on an Agilent 2100 Bioanalyzer for product size and concentration. Paired-end libraries were sequenced with the Illumina HiSeq 2500, (2 × 100 nucleotide read length) with sequence coverage to 15–20M paired reads.

treatment_protocol: Cells were stably transduced with lentivirus containing non-targeting shRNA or STAG2 shRNA#1 and #2. Cells were treated with doxycycline prior to performing RNA-seq.  For siRNA-treated samples, cells were treated with 25nM of siRNA on two consecutive days. 72 hours later, cells were harvested for RNA processing.

value: Bone/soft tissue

value: EWS-FLI1 fusion positive Ewing sarcoma cell line.

value: Male

value: TC71 cells were stably transduced with lentivirus containing STAG2 shRNA#2. Cells were treated with doxycycline for 5 days prior to performing RNA-seq.


title: EPZ5676_rep3

first: chen

last: huan

address: guangzhou

institute: guangzhou laboratory

description: Library name: sample9

data_processing:
Sequenced reads were aligned to a transcriptome index generated from the GENCODE annotations transcriptome (Mm10) using RSEM, bowtie2
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw read counts and  TPM value for each Sample

source_name: Lung

extract_protocol:
Total RNA was extracted using TRIzol (TR118-200, MRC), 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries using the VAHTS® Universal V8 RNAseq Library Prep Kit for Illumina (NR605-02, Vazyme) according to the manufacturer's instructions.

value: Lung

tag: sample group

value: primary Lung cell


title: G118E-E2KO; Clone#25; technical replicate 5


title: Spleen, Tex_CITE-seq_r1_RNA

description: Library name: Tex_CITE-seq_r1_RNA

value: spleen

value: day 8 post-infection with LCMV Cl13


title: G118E-E2KO; Clone#25; technical replicate 4


title: EPZ5676_rep2

description: Library name: sample8


title: 252800524061_1_3_FP41C_7_days

value: Sham

value: Fentanyl

value: Cortex


title: TC71_shSTAG2_2_Rep1

description:
Library name: TC71_shSTAG2_2_Rep1
Poly(A)+Transcriptome
CPM_ValuesPolyA.csv


title: Tumor 1

value: Tumor


title: EPZ5676_rep1

description: Library name: sample7


title: G118E-E2KO; Clone#25; technical replicate 3


title: 252800524061_1_1_FP43C_7_days


title: 252800524061_1_2_FP19C_24_hours


title: G118E-E2KO; Clone#25; technical replicate 2


title: TC71_shSTAG2_1_Rep2

description:
Library name: TC71_shSTAG2_1_Rep2
Poly(A)+Transcriptome
CPM_ValuesPolyA.csv

value: TC71 cells were stably transduced with lentivirus containing STAG2 shRNA#1. Cells were treated with doxycycline for 5 days prior to performing RNA-seq.


title: 252800524060_2_3_FP87C_0_hour_(40_mins_post)


title: 252800524060_2_4_FP29C_6_hours


title: Control_rep3

description: Library name: sample6

value: 72h of in vitro culture in control


title: TC71_shSTAG2_1_Rep1

description:
Library name: TC71_shSTAG2_1_Rep1
Poly(A)+Transcriptome
CPM_ValuesPolyA.csv


title: TC71_shNC_Rep2

description:
Library name: TC71_shNC_Rep2
Poly(A)+Transcriptome
CPM_ValuesPolyA.csv

value: TC71 cells were stably transduced with lentivirus containing non-targeting shRNA. Cells were treated with doxycycline for 5 days prior to performing RNA-seq


title: G118E; Clone#20; technical replicate 6

value: iPSC-derived neurons


title: 252800524060_2_2_FP39C_24_hours


title: G118E-E2KO; Clone#25; technical replicate 1

value: iPSC-derived NPC-iNeurons


title: 252800524060_2_1_FP23C_24_hours


title: Control_rep2

description: Library name: sample5


title: TC71_shNC_Rep1

description:
Library name: TC71_shNC_Rep1
Poly(A)+Transcriptome
CPM_ValuesPolyA.csv

value: Bone/soft tissue


title: A673_shSTAG2_2_Rep2

description:
Library name: A673_shSTAG2_2_Rep2
Poly(A)+Transcriptome
CPM_ValuesPolyA.csv

value: EWS-FLI1 fusion positive Ewing sarcoma cell line.

value: Female

value: A673 cells were stably transduced with lentivirus containing STAG2 shRNA#2. Cells were treated with doxycycline for 10 days prior to performing RNA-seq.


title: G118E; Clone#20; technical replicate 5


title: Control_rep1

description: Library name: sample4

value: Lung


title: G118E; Clone#20; technical replicate 4


title: E11.5_lung_rep1

description: Library name: sample1

value: primary Lung cell


title: E11.5_lung_rep3

description: Library name: sample3


title: E11.5_lung_rep2

description: Library name: sample2


title: G118E; Clone#20; technical replicate 3


title: A673_shSTAG2_2_Rep1

description:
Library name: A673_shSTAG2_2_Rep1
Poly(A)+Transcriptome
CPM_ValuesPolyA.csv


title: G118E; Clone#20; technical replicate 2


title: Bri 7

city: Jinan

first: Jing

last: Cai

state: Shandong

address: 4 Duanxing West Road

department: Shandong Provincial ENT Hospital

institute: Shandong University

description: Library name: Sample 17

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Assembly: mm10
Supplementary files format and content: tab-delimted files include read count for each sample

source_name: cochlear cells

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

value: cochlear cells

value: interstitial cells

value: WT

value: intraperitoneal injections of 1 mg/kg brimonidine prior to noise exposure


title: G118E; Clone#20; technical replicate 1


title: A673_shSTAG2_1_Rep2

description:
Library name: A673_shSTAG2_1_Rep2
Poly(A)+Transcriptome
CPM_ValuesPolyA.csv

value: A673 cells were stably transduced with lentivirus containing STAG2 shRNA#1. Cells were treated with doxycycline for 10 days prior to performing RNA-seq.


title: 252800524060_1_4_FP54C_24_hours

value: Sham

value: Fentanyl

value: Cortex


title: A673_shSTAG2_1_Rep1

description:
Library name: A673_shSTAG2_1_Rep1
Poly(A)+Transcriptome
CPM_ValuesPolyA.csv


title: 252800524060_1_3_FP95C_0_hour_(40_mins_post)


title: 252800524060_1_2_FP40C_7_days


title: A673_shNC_Rep2

description:
Library name: A673_shNC_Rep2
Poly(A)+Transcriptome
CPM_ValuesPolyA.csv

value: A673 cells were stably transduced with lentivirus containing non-targeting shRNA. Cells were treated with doxycycline for 10 days prior to performing RNA-seq


title: 252800524056_2_3_FP27C_7_days


title: Isogenic Control (WT); Clone#42; technical replicate 6

value: iPSC-derived neurons


title: 252800524056_2_4_FP77C_6_hours


title: 252800524056_2_2_FP16C_7_days


title: Bri 4

description: Library name: Sample 14


title: A673_shNC_Rep1

description:
Library name: A673_shNC_Rep1
Poly(A)+Transcriptome
CPM_ValuesPolyA.csv


title: Bri 6

description: Library name: Sample 16


title: Bri 5

description: Library name: Sample 15


title: Isogenic Control (WT); Clone#42; technical replicate 5

value: iPSC-derived NPC-iNeurons


title: Isogenic Control (WT); Clone#42; technical replicate 4


title: A673_sgSA2_siNC_72_H_Rep2

description:
Library name: A673_sgSA2_siNC_72_H_Rep2
RiboErase
CPM_Values_RiboErase.csv

value: Bone/soft tissue

value: A673 cells were treated with STAG2-targeting guide RNA followed by non-targeting siRNA. Cells were cultured for 72 hours with siRNA prior to RNA harvest.


title: 252800524060_1_1_FP69C_0_hour_(40_mins_post)


title: Bri 3

description: Library name: Sample 13


title: Isogenic Control (WT); Clone#42; technical replicate 3


title: 252800524056_2_1_FP61C_7_days


title: Zeb1Prx1 MSC rep2

city: NanJing

first: Chuyue

last: Pan

address: 639 Longmian Ave.

institute: China Pharmaceutical University

description:
Library name: KO_rep2
Primary MSCs from Zeb1Prx1 mice

data_processing:
Clean data were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include read counts (or FPKM) values for each Sample.

source_name: compact bone

extract_protocol:
The femurs and tibias were excised into bone chips and digested for 1 h with collagenase Ⅱ. Bone chips were then cultured in α-MEM supplemented with 10% FBS at 37 °C in a 5% CO2 incubator. Cells were sorted by GFP fluorescent signal to isolate Prx1+ MSCs
PCR products were purified by AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system. A TruSeq PE Cluster Kit v3-cBot-HS (Illumina) was used to cluster the index-coded samples. 150 bp paired-end reads were generated on an Illumina Novaseq platform.

value: compact bone

value: Prx1+ MSCs

value: Prx1-Cre+; ROSA-YFP; Zeb1fl/fl

value: untreated


title: A673_sgSA2_siNC_72_H_Rep1

description:
Library name: A673_sgSA2_siNC_72_H_Rep1
RiboErase
CPM_Values_RiboErase.csv

value: EWS-FLI1 fusion positive Ewing sarcoma cell line.

value: Female


title: Isogenic Control (WT); Clone#42; technical replicate 2


title: Bri 2

description: Library name: Sample 12

value: cochlear cells

value: interstitial cells

value: WT


title: A673_sgSA2_siFL1_72H_Rep1

description:
Library name: A673_sgSA2_siFL1_72H_Rep1
RiboErase
CPM_Values_RiboErase.csv

value: A673 cells were treated with STAG2-targeting guide RNA followed by siRNA against FLI1. Cells were cultured for 72 hours with siRNA prior to RNA harvest.


title: A673_sgSA2_siFL1_72H_Rep2

description:
Library name: A673_sgSA2_siFL1_72H_Rep2
RiboErase
CPM_Values_RiboErase.csv


title: Bri 1

description: Library name: Sample 11

value: intraperitoneal injections of 1 mg/kg brimonidine prior to noise exposure


title: 252800524056_1_4_FP32C_0_hour_(40_mins_post)

value: Sham

value: Fentanyl

value: Cortex


title: Isogenic Control (WT); Clone#42; technical replicate 1

value: iPSC-derived neurons

value: iPSC-derived NPC-iNeurons


title: A673_sgNC_siNC_72_H_Rep2

description:
Library name: A673_sgNC_siNC_72_H_Rep2
RiboErase
CPM_Values_RiboErase.csv

value: Bone/soft tissue

value: A673 cells were treated with non-targeting guide RNA followed by non-targeting siRNA. Cells were cultured for 72 hours with siRNA prior to RNA harvest.


title: NE 7

description: Library name: Sample 10

value: exposed to broadband noise, 8–16 kHz, at 100 dB SPL for 2 hours


title: NE 6

description: Library name: Sample 9


title: A673_sgNC_siNC_72_H_Rep1

description:
Library name: A673_sgNC_siNC_72_H_Rep1
RiboErase
CPM_Values_RiboErase.csv


title: 252800524056_1_2_FP60C_7_days


title: G118E-E2KO; Clone#21; technical replicate 4


title: NE 4

description: Library name: Sample 7


title: G118E-E2KO; Clone#21; technical replicate 5


title: 252800524056_1_3_FP91C_24_hours


title: A673_sgNC_siFL1_72H_Rep2

description:
Library name: A673_sgNC_siFL1_72H_Rep2
RiboErase
CPM_Values_RiboErase.csv

value: A673 cells were treated with non-targeting guide RNA followed by siRNA against FLI1. Cells were cultured for 72 hours with siRNA prior to RNA harvest.


title: NE 5

description: Library name: Sample 8


title: G118E-E2KO; Clone#21; technical replicate 3


title: 252800524056_1_1_FP74C_0_hour_(40_mins_post)


title: NE 2

description: Library name: Sample 5


title: NE 3

description: Library name: Sample 6


title: G118E-E2KO; Clone#21; technical replicate 2


title: G118E-E2KO; Clone#21; technical replicate 6


title: G118E-E2KO; Clone#21; technical replicate 1


title: A673_sgNC_siFL1_72H_Rep1

description:
Library name: A673_sgNC_siFL1_72H_Rep1
RiboErase
CPM_Values_RiboErase.csv


title: 252800524055_2_4_FP25C_0_hour_(40_mins_post)


title: A673_shSTAG2_48_d10_Rep2

description: Library name: A673_shSTAG2_48_d10_Rep2

data_processing:
The program bwa mem was run for alignment.Alignments were then filtered using both samtools (quality score cutoff of 20) and picard MarkDuplicates (removed duplicates and chrM). Peaks were called using macs2. Blacklisted regions were removed
Assembly: hg38
Supplementary files format and content: macs peak beds, bigwigs

growth_protocol: Ewing sarcoma cells(A673 were grown in DMEM with 10% FBS and Penicillin/Streptomycin.

extract_protocol:
ATAC-seq was performed as previously described in Buenrostro et al. 2013 Nat Methods. In brief, 50,000 cancer cells were washed in cold PBS and resuspended in cytoplasmic lysis buffer (CER-I from the NE-PER kit, Invitrogen, cat. no. 78833). This single-cell suspension was incubated on ice for 5 min. The lysate was centrifuged at 1,300g for 5 min at 4 °C. Nuclei were resuspended in 50μl of 1× TD buffer, then incubated with 0.5-3μl Tn5 enzyme (depending on the cell line) for 30 min at 37 °C (Nextera DNA Library Preparation Kit; cat. no. FC-121-1031). Samples were immediately purified by Qiagen minElute column and PCR-amplified with the NEBNext High-Fidelity 2X PCR Master Mix (NEB; cat. no. M0541L) following the original protocol27. qPCR was used to determine the optimal PCR cycles to prevent over-amplification. The amplified library was further purified by Qiagen minElute column and SPRI beads (Beckman Coulter; cat. no. A63881).
The tagmented adapter-ligated DNA was immediately purified by Qiagen minElute column and PCR-amplified with the NEBNext High-Fidelity 2X PCR Master Mix (NEB; cat. no. M0541L) following the original protocol. qPCR was used to determine the optimal PCR cycles to prevent over-amplification. The amplified library was further purified by Qiagen minElute column and SPRI beads (Beckman Coulter; cat. no. A63881). ATAC-seq libraries were sequenced on the Illumina HiSeq 2500 (125-nucleotide read length, paired end).

treatment_protocol: Cells were stably transduced with lentivirus containing non-targeting shRNA or STAG2 shRNA. Cells were treated with doxycycline for 10 days prior to performing ATAC-seq.

value: Ewing Sarcoma

value: A673 cells were stably transduced with lentivirus containing STAG2 shRNA#1. Cells were treated with doxycycline for 10 days prior to performing ATAC-seq.


title: A673_shSTAG2_48_d10_Rep3

description: Library name: A673_shSTAG2_48_d10_Rep3

value: Female


title: 252800524055_2_1_FP62C_24_hours


title: 252800524055_2_3_FP63C_24_hours


title: NE 1

description: Library name: Sample 4

value: cochlear cells


title: 252800524055_2_2_FP68C_6_hours


title: controll 3

description: Library name: Sample 3

value: interstitial cells

value: control


title: G118E; Clone#15; technical replicate 6


title: 252800524055_1_2_FP52C_7_days


title: controll 2

description: Library name: Sample 2

value: WT


title: 252800524055_1_4_FP48C_0_hour_(40_mins_post)


title: G118E; Clone#15; technical replicate 5


title: A673_shSTAG2_16_d10_Rep3

description: Library name: A673_shSTAG2_16_d10_Rep3

value: A673 cells were stably transduced with lentivirus containing STAG2 shRNA#2. Cells were treated with doxycycline for 10 days prior to performing ATAC-seq.


title: G118E; Clone#15; technical replicate 4


title: A673_shSTAG2_16_d10_Rep2

description: Library name: A673_shSTAG2_16_d10_Rep2


title: controll 1

description: Library name: Sample 1


title: A673_shSTAG2_48_d10_Rep1

description: Library name: A673_shSTAG2_48_d10_Rep1


title: 252800524055_1_3_FP83C_7_days

value: Sham


title: A673_shSTAG2_16_d10_Rep1

description: Library name: A673_shSTAG2_16_d10_Rep1


title: G118E; Clone#15; technical replicate 3


title: snRNA-AR113Q3

first: Andrew

middle: P

last: Lieberman

address: 1150 W Medical Center Dr.

institute: University of Michigan

description:
Library name: 08363-CK-8
10x Genomics with CellRanger output; features.tsv identical for all samples

data_processing:
BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files.
Reads were mapped to the transcriptome mm10 with the pipeline cellranger-7.1.0.
Assembly: mm10
Supplementary files format and content: *barcodes.tsv is the list of barcodes for each of the paired-end runs for reconstruction from the sparse matrix format.
Supplementary files format and content: *features.tsv is the list of genes, using ENSEMBL stable gene IDs and gene names, for reconstruction from the sparse matrix format.
Supplementary files format and content: *matrix.mtx has the row index, column index, and gene counts for reconstruction from the sparse matrix format.

source_name: Tibialis anterior

growth_protocol: Male C57BL/6J mice, three WT and three AR113Q, were aged to 52 weeks.

extract_protocol:
Mice were euthanized at 52 weeks and tibialis anterior was dissected and flash-frozen for storage. Nuclei were then isolated with the 10X Chromium Nuclei Isolation kit and suspended in individual droplets. Approximately 10,000 nuclei per sample were sent through the 10X platform for sequencing.
RNA libraries were prepared by the University of Michigan Advanced Genomics Core, with the pool subjected to 2 x 150bp paired-end sequencing per manufacturer's instructions (Illumina NovaSeq).

value: Tibialis anterior

value: Skeletal muscle


title: G118E; Clone#15; technical replicate 2

value: iPSC-derived neurons


title: A673_shNC_d10_Rep3

description: Library name: A673_shNC_d10_Rep3

value: A673 cells were stably transduced with lentivirus containing non-targeting shRNA. Cells were treated with doxycycline for 10 days prior to performing ATAC-seq.


title: 252800524054_2_3_FP57C_24_hours

source_name: Agilent Universal Mouse Reference RNA

value: Fentanyl

value: Cortex


title: Isogenic Control (WT); Clone#32; technical replicate 6

value: iPSC-derived NPC-iNeurons


title: A673_shNC_d10_Rep1

description: Library name: A673_shNC_d10_Rep1

value: Bone/soft tissue


title: G118E; Clone#15; technical replicate 1


title: Isogenic Control (WT); Clone#32; technical replicate 5


title: snRNA-AR113Q1

description:
Library name: 08363-CK-6
10x Genomics with CellRanger output; features.tsv identical for all samples


title: 252800524054_2_4_FP22C_6_hours


title: snRNA-AR113Q2

description:
Library name: 08363-CK-7
10x Genomics with CellRanger output; features.tsv identical for all samples


title: hCO, d7tic

city: Atlanta

first: Emily

middle: Jane

last: Hill

state: Georgia

address: 615 Michael Street

institute: Emory University

description:
Library name: Sample 115
CMO sequence CGGATTCCACATCAT

data_processing:
Bulk sequencing of 40 million paired-end reads per sample was completed using the Illumina-based platform. FASTQ files were evaluated for quality using FastQC and then mapped to the human genome (hg19), using the Spliced Transcripts Alignment to a Reference (STAR) aligner with the paired-end option. The featureCounts package was used to generate a raw counts data matrix from mapped reads. After generating the filtered, raw counts data matrices, we used DESeq2 to normalize the matrices and perform differential gene expression-based statistics. scRNAseq: Fastq sequencing files were processed through CellRanger.
Assembly: hg19
Supplementary files format and content: Bulk RNAseq: tab-delimited/comma-delimited text file that includes raw counts for each sample and .bam files.
Supplementary files format and content: scRNAseq: matrix, barcode, and features files for each sample

source_name: human cortical organoid

growth_protocol: Human cortical organoids (hCOs): Following 3D formation, hCOs were treated daily in neural induction media (DMEM/F12, KSR, NEAA, Glutamax, Pen/Strep, Beta-mercaptoethanol) supplemented with Dorsomorphin (Sigma, Cat. 142  P5499-25MG, 5 μM) and SB-431542 (Selleck Chemicals, Cat. S1067, 10 μM) for 6 days.  Following this treatment, hCOs were treated daily with neural media supplemented with EGF (R&D Systems, Cat. 236-EG-01M, 20 ng/mL) and FGF2 (R&D Systems, Cat. 233-FB-01M, 20 ng/mL) for 10 days, and every other day for days 16-24. At day 25, hCOs were treated every other day with neural media supplemented with BDNF (PeproTech, Cat. 450-02- 1mg, 20 ng/mL) and NT-3 (R&D Systems, Cat. 267-N3-005/CF, 20 ng/mL) to promote differentiation of progenitors. From day 43 onwards, hCOs were fed every 3 days with neural media only. hCOs were cultured in Neurobasal-A media supplemented with B27-A, 1% penicillin-streptomycin, and 1% GlutaMAX. hCOs were incubated in 10cm low-adherence cell culture dish at 37°C and 5% CO2.

extract_protocol:
Bulk RNAseq: RNA was extracted from the cells using a RNeasy Micro Kit (Qiagen, 74004) following the manufacturer’s instructions. scRNAseq: hCOs were dissociated and cells were prepared for library creation according to the 10X Genomics Chromium Next-GEM Single Cell 3' kit manufacturer's protocol (10X Genomics, 1000268). scRNAseq: hCOs were dissociated and cells were prepared for library creation according to the 10X Genomics Chromium Next-GEM Single Cell 3' kit manufacturer's protocol (10X Genomics, 1000268).
Bulk RNAseq: The SMART-Seq® v4 PLUS Kit (Takara Bio) was used following the manufacturer's instructions. scRNAseq: Libraries were created according to the 10X Genomics Chromium Next Gem Single Cell 3' kit manufacturer's protocol.

treatment_protocol: hCOs were treated with either control Neurobasal-A media or Neurobasal-A supplemented with TNF-α (30ng/mL, Cell Signaling Technology, 16769S), IL-1α (3ng/mL,Sigma-Aldrich, I2778), and C1q (400ng/mL, EMD Millipore, 204876).

value: human cortical organoid

value: TIC


title: hCO, d1control + hCO, d1tic, multiplexed

description:
Library name: Sample 114
CMO sequence AAGATGAGGTCTGTG, multiplexed CMO sequence AAGCTCGTTGGAAGA

value: control, TIC multiplexed


title: snRNA-WT2

description:
Library name: 08363-CK-2
10x Genomics with CellRanger output; features.tsv identical for all samples

value: wild-type


title: 252800524054_2_2_FP82C_7_days

state: MD


title: 252800524054_2_1_FP42C_6_hours


title: snRNA-WT1

description:
Library name: 08363-CK-1
10x Genomics with CellRanger output; features.tsv identical for all samples


title: hCO, d84tic, rep2

description: Library name: Sample 14

value: astrocyte


title: A673_shNC_d10_Rep2

description: Library name: A673_shNC_d10_Rep2

value: Ewing Sarcoma

value: Female


title: Isogenic Control (WT); Clone#32; technical replicate 3


title: 252800524055_1_1_FP24C_7_days


title: Isogenic Control (WT); Clone#32; technical replicate 4


title: 52w-ASO4

description:
Library name: 07587-ZY-24
07587-ZY_gene_expected_count.csv

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

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

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

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

value: ASO


title: snRNA-WT3

description:
Library name: 08363-CK-3
10x Genomics with CellRanger output; features.tsv identical for all samples


title: hCO, d84tic, rep1

description: Library name: Sample 13


title: Isogenic Control (WT); Clone#32; technical replicate 2


title: 52w-ASO3

description:
Library name: 07587-ZY-23
07587-ZY_gene_expected_count.csv


title: hCO, d31tic, rep3

description: Library name: Sample 12


title: 252800524054_1_4_FP30C_0_hour_(40_mins_post)

value: Sham


title: 252800524054_1_3_FP58C_24_hours


title: 252800524054_1_1_FP72C_6_hours


title: 252800524054_1_2_FP92C_24_hours


title: 252800524040_2_4_FP49C_6_hours


title: 52w-ASO2

description:
Library name: 07587-ZY-22
07587-ZY_gene_expected_count.csv

value: Tibialis anterior


title: hCO, d31tic, rep2

description: Library name: Sample 11


title: hCO, d31tic, rep1

description: Library name: Sample 10


title: hCO, d7tic, rep3

description: Library name: Sample 9


title: hCO, d7tic, rep2

description: Library name: Sample 8


title: G118E-E2KO; Clone#25; 2month; technical replicate 2

value: iPSC-derived NGN2-iNeurons


title: G118E-E2KO; Clone#25; 2month; technical replicate 4

value: iPSC-derived neurons


title: G118E-E2KO; Clone#25; 2month; technical replicate 3


title: 52w-AR113Q3

description:
Library name: 07587-ZY-19
07587-ZY_gene_expected_count.csv

value: Skeletal muscle

value: vehicle


title: 52w-AR113Q2

description:
Library name: 07587-ZY-18
07587-ZY_gene_expected_count.csv


title: Isogenic Control (WT); Clone#32; technical replicate 1


title: G118E-E2KO; Clone#21; 2month; technical replicate 4


title: G118E-E2KO; Clone#25; 2month; technical replicate 1


title: 252800524053_1_1_FP21C_0_hour_(40_mins_post)

value: Fentanyl

value: Cortex


title: 52w-AR113Q4

description:
Library name: 07587-ZY-20
07587-ZY_gene_expected_count.csv


title: 52w-ASO1

description:
Library name: 07587-ZY-21
07587-ZY_gene_expected_count.csv


title: 252800524040_2_3_FP45C_6_hours


title: G118E-E2KO; Clone#21; 2month; technical replicate 3


title: hCO, d1tic, rep3

description: Library name: Sample 6


title: 52w-WT4

description:
Library name: 07587-ZY-16
07587-ZY_gene_expected_count.csv


title: 252800524040_1_3_FP85C_6_hours