title: IFN gamma-treated WT Developing Oligodendrocytes [HS-2]

data_processing:
Beta galactosidase gene quantification: map reads to gene reference, counts reads per sample and cross reference to metadata
QC of raw data
Map reads to reference genome (STAR)
Quantify gene expression (featureCounts) on Ensembl gene annotations
Quantify isoform expression against isoform transcriptome annotation (Kallisto)
Normalize gene expression to counts per million units (CPM) (EdgeR)
Average gene expression across sample groups
Principle component analysis and plot of log-scaled CPMs to assess sample clustering and outliers
Differental expression - Three way ANOVA: FDR correction to adjust for multiple testing, output is p-values and q-values (FDRs)
Pairwise comparisons: FDR correction for each comparison, output is log2 fold-change, log2 CPM, p-value, and q-value
Genome_build: mm
Supplementary_files_format_and_content: txt

extract_protocol:
Total OPC RNA was extracted using the Rneasy mini columns kit (Qiagen, Crawley, UK) and treated with Dnase I (Qiagen). RNA concentration and purity were determined by Nanodrop spectrophotometry and QC. RNA quality was determined using Agilent Bioanalyzer RNA Analysis (Agilent Technologies, Santa Clara, CA, USA) and QC.
Expression wa analyzed by sequencing using Illumina HiSeQ technology (Illumina Next Generation Sequencing Services, University of Chicago). Raw data was processed by the University of Illinois in Chicago Bioinformatics Core.

value: Whole brain

value: Developing oligodendrocyte


title: KB39_20_HB13

status: Public on Dec 31 2025

type: SRA

city: Mancehster

first: Kiran

last: Batta

address: Paterson Building, Wilmslow Rd

department: Division of Cancer Research

country: United Kingdom

institute: University of Manchester

description: Library name: KB39_20_lib

library_source: transcriptomic

data_processing:
Sample libraries were prepared by 3’ Quantseq (Lexogen) protocol and were sequenced using the Novaseq (Illumina) platform. Basecalls were converted to fastq files using bcl2fastq (Illumina). Fastq files were aligned to GRCh38 using Star aligner (version 2.5.1b; Ensembl85). BAM alignments were quantified in R (version 3.6.1) using featureCounts from the Rsubread library (version 2.0.1) and the Ensemble GTF annotation (Homo_sapiens.GRCh38.85.gtf). Differential expression (DE) was evaluated comparing the gene level integer read count data for between patient/sample groups using the DESeq2.v 1.26.0 Bioconductor package.   DESeq2 DEG estimation involves multiple steps. In brief, it uses normalization factor to model read counts to account for sequencing depth. Then it estimates gene-wise dispersions and perform shrinkage analysis to generate more accurate estimates of dispersion to model the counts. Finally, it fits the negative binomial model and performs hypothesis testing using the Wald test.
Assembly: GRCh38.85
Supplementary files format and content: DESeq2's output: Gene-by-gene log2fold change, adjusted p-value for the rejection of non-differential expression, and ormalised (TPM) transcript counts in tab-delimited format. Genes with an adjusted p-value > 0.5 have been removed, and all the results are sorted by increasing adjusted p-value.

molecule: polyA RNA

organism: Homo sapiens

source_name: Fresh peripheral blood

extract_protocol:
RNA was extracted from 5 x 105 granulocytes isolated from fresh healthy volunteer and CMML patient peripheral blood using RNeasy Micro Plus kit (QIAGEN, 74034), according to manufacturer’s recommendations.
3' Quantseq (Lexogen)

tag: tissue

value: Fresh peripheral blood

tag: group

value: Healthy Old


title: icSHAPE, U-2 OS, Whole Cell, Untreated, NAIN3, biological replicate 1

city: Singapore

first: Jovi

last: Lim

address: 60 Biopolis St

country: Singapore

institute: Genome Institute of Singapore

description: Library name: U2OS_Untreated_NAIN3_rep1

data_processing:
Briefly, icSHAPE libraries were de-duplicated and adapter-trimmed. Remaining reads were mapped to genome. RT stops and base coverage were called out for each nucleotide. Genomic coordinates were converted to transcript coordinate for downstream analysis.
Assembly: ENSEMBL GRCh38 release 98
Supplementary files format and content: Processed data consists of icSHAPE reactivity for all detected transcripts in each sample i.e. files ending with "shape.txn.txt". Each row in the files represent one transcript. Each entry (tab delimited) in each row represent the reactivity of each nucleotide. SPLASH txt files contain the information of all detected chimeras in each sample. eCLIP txt.gz files contain the enriched windows for each sample (refer to software Skipper for details https://doi.org/10.1016/j.xgen.2023.100317). Translation Efficiency data are recorded in "tpm_te.csv"  files. Transcript per million (TPM) was quantified for each gene. Translation efficiency was quantified by dividing TPM of Ribo-seq samples with that of RNA-seq.

molecule: total RNA

source_name: Bone

extract_protocol:
RNA was harvested using TRIzol/TRIzol LS reagent following manufacturer's instructions. The amount of 500ng and 1,500ng RNA were used for generating icSHAPE and SPLASH libraries, repectively. For SRSF1 eCLIP libraries, cells were fixed with UV (254nm, 400mJ/cm^2) in prior to proceeding to immunoprecipitation and library preparation.
icSHAPE library preparation was carried out according to the protocol described before (Flynn, et al, 2016); SPLASH library preparation was performed according to the protocol described before (Aw, et al, 2016); eCLIP library preparation was performed according to the protocol described before (Blue, et al, 2022).

value: Bone

tag: cell line

value: U-2 OS

tag: cell type

value: Osteosarcoma

tag: genotype

tag: treatment


title: icSHAPE, U-2 OS, Whole Cell, NaAsO2, DMSO, biological replicate 1

description: Library name: U2OS_NaAsO2_DMSO_rep1

value: DMSO


title: Vehicle-1

city: Xi'an

first: XIAN

last: GUO

address: Xinyi Road

country: China

institute: Air Force Medical University

description: Library name: Vehicle-1

data_processing:
The reads were aligned to the human genome hg19 for all the samples. lncRNA-seq: differential gene expression analysis was performed using DESeq2 package in R .
Assembly: hg19
Supplementary files format and content: differential gene expression analysis result

source_name: human aortic smooth muscle cell

extract_protocol:
Refer to the instruction manual of Trizol (Invitrogen, CA, USA) to extract total RNA.RNA contamination was assessed by 1.5% agarose gel.
After the RNA sample passed the test, rRNA was removed from it. The remaining RNA was then fragmented using a fragmentation buffer. The fragmented RNA was used as a template for reverse transcription with 6nt random hexamers to synthesize the first - strand cDNA. The second - strand cDNA was synthesized by adding buffer, dNTPs (with dTTP replaced by dUTP), DNA polymerase I, and RNase H. After purification, end - repair, A - tailing, and sequencing adapter ligation, the double - stranded cDNA was degraded with USER enzyme and enriched by PCR. Finally, the PCR products were purified using AMPure XP Beads to obtain the final strand - specific libraries.

value: human aortic smooth muscle cell


title: Untreated WT Developing Oligodendrocytes [HS-1]

city: Chicago

first: Brian

last: Popko

state: IL

address: 303 E. Chicago Avenue

department: Neurology

country: USA

institute: Northwestern University

organism: Mus musculus

growth_protocol: Cells were acquired through isolation and immunopanning purification of oligodendrocyte progenitor cells (OPCs) from 6 day old mouse pup brain cortices. OPCs were initially grown in proliferation media, taken through 2 passage cycles at 37 C, and allowed to differentiate for 12-14 hours. Plates were then randomly designated for treatment.

treatment_protocol: Both experimental groups were treated with either IFN-gamma (200 U/ml) or thapsigargin (Sigma, 200 uM) and RNA was extracted at designated timepoints throughout the treatment process.

tag: strain background

value: wild type

tag: treatment timepoint

value: 1 hour


title: H3K27ac_Vehicle

description: Library name: H3K27ac_Vehicle

library_source: genomic

data_processing:
Trimmomatic was used with parameters ILLUMINACLIP:NexteraPE-PE.fa:2:30:10:8:true and MINLEN:8.
FastQC was used to assess the quality of paired - end raw data.
Trimmed reads were mapped to the human (hg19) genome using Bowtie2 v2.3.3 with standard settings for paired reads.
Peaks were called using macs3 with default settings. Detected peaks were visualized using deeptools. Downstream analyses were performed using DiffBind 3.2.4.
Assembly: hg19
Supplementary files format and content: bed format of each samples
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
100,000 cells were harvested and centrifuged for 3 min at 600×g at room temperature. Cells were washed twice in 300 μL Wash Buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail) by gentle pipetting. 10 μL of activated concanavalin A - coated magnetic beads were added per sample and incubated at RT for 10 min. The unbound supernatant was removed, and bead - bound cells were resuspended in 50 μL Dig - wash Buffer (20mM HEPES pH 7.5; 150mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin) containing 2mM EDTA and a 1:50 dilution of the appropriate primary antibody. Primary antibody incubation was performed on a rotating platform for 2 h at RT. Then the liquid was removed on the magnet stand. An appropriate secondary antibody (Goat anti - Rabbit IgG or Rabbit Anti - Mouse IgG) was diluted 1:50 in 50μL of Dig - Wash buffer, and cells were incubated at RT for 1 h. For constructing the negative control library (IgG), only the secondary antibody was added without the primary antibody. Cells were washed twice using the magnet stand for 1 min in 500 μL Dig - Wash buffer to remove unbound antibodies. A 1:200 dilution of pG - Tn5 adapter complex (~0.04 μM) was prepared in Dig - 300 Buffer (0.01% Digitonin, 20mM HEPES, pH 7.5, 300mM NaCl, 0.5mM Spermidine, 1× Protease inhibitor cocktail). After removing the liquid, 100 μL was added to the cells with gentle vortexing and incubated with pG - Tn5 at RT for 1 h. Cells were washed twice for 1 min in 500 μL Dig - 300 Buffer to remove unbound pG - Tn5 protein. Next, cells were resuspended in 300 μL Tagmentation buffer (10mM MgCl2 in Dig - 300 Buffer) and incubated at 37 °C for 1 h. To stop tagmentation, 10 μL of 0.5M EDTA, 3 μL of 10% SDS, and 2.5 μL of 20 mg/mL Proteinase K were added to 300 μL of sample, which was incubated at 55 °C for 1h, purified using phenol - chloroform - isoamyl alcohol and ethanol, washed with 100% ethanol, and suspended in water. The DNA was amplified by PCR as follows: 3 min at 72 °C, 30 s at 98 °C, followed by 16 cycles of 15 s at 98 °C, 30 s at 60 °C, and 30 s at 72 °C, with a final extension at 72 °C for 3 min. Finally, the amplified DNA was purified using Ampure XP beads. Libraries were sequenced on the Illumina Nova - seq platform.
Libraries were sequenced on the Illumina Nova - seq platform


title: THPIL4DGlng3

city: San Francisco

first: Robert

last: Raffai

state: California

address: 4150 Clement St

department: Surgery

institute: University of California San Francisco

description: Library name: EXR-RRAFF1exRNAcarrierSEQTHPIL4DGlng3-BS

data_processing:
All small RNAseq FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/. Long RNAseq FASTQ files were processed through Jensen Pipeline
Assembly: smallRNAseq aligned in hg19, longRNAseq aligned in hg38
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: cell culture

extract_protocol:
RNA Isolation method was . RNA Isolation kit was Norgen and Qiagen minElute.
Library construction kit was NEXTflex (Bioo). Samples were not multiplexed. Type of Starting Material was total RNA.

value: cell culture

tag: condition

value: Acute monocytic leukemia

tag: anatomical location

value: Blood cell

tag: rna source

value: extracellular exosome

tag: rna isolation kit

value: Norgen


title: QOG10t13AXlng

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG10t13AXlng-BS

source_name: Plasma

value: Plasma

value: Healthy Subject

value: Entire cardiovascular system


title: KB39_19_BC1216

description: Library name: KB39_19_lib

value: Fresh peripheral blood

value: CMML


title: THPIL4DGlng1

description: Library name: EXR-RRAFF1exRNAcarrierSEQTHPIL4DGlng1-BS


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-40]

data_processing:
QC of raw data
Map reads to reference genome (STAR)
Quantify gene expression (featureCounts) on Ensembl gene annotations
Quantify isoform expression against isoform transcriptome annotation (Kallisto)
Normalize gene expression to counts per million units (CPM) (EdgeR)
Average gene expression across sample groups
Principle component analysis and plot of log-scaled CPMs to assess sample clustering and outliers
Differental expression: Two way ANOVA: FDR correction to adjust for multiple testing, output is p-values and q-values
Pairwise comparisons: FDR correction for each comparison, output is log2 fold-change, log2 CPM, p-value, and q-value
Genome_build: mm
Supplementary_files_format_and_content: counts

treatment_protocol: Experimental groups were treated with either IFN-gamma (200 U/ml) or thapsigargin (Sigma, 200 uM) and RNA was extracted at designated timepoints throughout the treatment process. Untreated controls were extracted at the same timepoints.

value: Wild-type

tag: age

value: 6-7 days

value: Interferon-gamma (200 U/ml)

value: 48 hours

value: Whole brain

value: Developing oligodendrocyte


title: QOG10t13MAlngB

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG10t13MAlngB-BS


title: THPIL4DGlng2

description: Library name: EXR-RRAFF1exRNAcarrierSEQTHPIL4DGlng2-BS


title: KB39_18_BC1188

description: Library name: KB39_18_lib


title: QOG10t13MAlngA

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG10t13MAlngA-BS


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-38]

value: 24 hours


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-39]


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-37]


title: KB39_16_YHB2

description: Library name: KB39_16_lib

value: Healthy Young


title: QOG10t13ROlng

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG10t13ROlng-BS


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-36]

value: 8 hours


title: KB39_15_HB11

description: Library name: KB39_15_lib

value: Healthy Old


title: QOG6t9AXlng

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG6t9AXlng-BS

value: extracellular exosome


title: QOG6t9MAlngB

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG6t9MAlngB-BS

value: Norgen


title: icSHAPE, U-2 OS, Whole Cell, Untreated, DMSO, biological replicate 1

description: Library name: U2OS_Untreated_DMSO_rep1

value: Bone

value: U-2 OS

value: Osteosarcoma

value: DMSO


title: KB39_14_BC986

description: Library name: KB39_14_lib

value: Fresh peripheral blood

value: CMML


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-35]

value: Wild-type

value: 6-7 days


title: QOG6t9MAlngA

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG6t9MAlngA-BS

value: Plasma

value: Healthy Subject

value: Entire cardiovascular system


title: QOG6t9ANlng

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG6t9ANlng-BS


title: KB39_17_RNA_BC999_T7

description: Library name: KB39_17_lib


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-34]

value: Interferon-gamma (200 U/ml)

value: 1 hour

value: Whole brain

value: Developing oligodendrocyte


title: KB39_12_BC612

description: Library name: KB39_12_lib


title: QOG6t9ROlng

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG6t9ROlng-BS

value: extracellular exosome


title: KB39_13_BC830

description: Library name: KB39_13_lib


title: KB39_11_YHB5

description: Library name: KB39_11_lib

value: Healthy Young


title: Q11t4MAlng2

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ11t4MAlng2-BS

value: Norgen


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-33]


title: Q15t12ROlng

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ15t12ROlng-BS


title: QOG10t13ANlng

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG10t13ANlng-BS


title: KB39_09_BC1239

description: Library name: KB39_09_lib


title: Q15t12MAlng

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ15t12MAlng-BS


title: KB39_10_HB14

description: Library name: KB39_10_lib

value: Healthy Old


title: Q15t12ANlng

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ15t12ANlng-BS


title: Q11t4ROlng2

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ11t4ROlng2-BS


title: Thapsigargin-treated WT Developing Oligodendrocytes [BP-31]

value: Thapsigargin (200 uM)

value: 8 hours


title: Q11t4AXlng2

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ11t4AXlng2-BS


title: Thapsigargin-treated WT Developing Oligodendrocytes [BP-30]


title: Q11t4ANlng2

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ11t4ANlng2-BS


title: KB39_08_YHB3

description: Library name: KB39_08_lib

value: Fresh peripheral blood


title: Q11t4AXlng1

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ11t4AXlng1-BS


title: Thapsigargin-treated WT Developing Oligodendrocytes [BP-29]


title: Q11t4ANlng1

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ11t4ANlng1-BS


title: Q15t12AXlng

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ15t12AXlng-BS


title: Untreated WT Developing Oligodendrocytes [BP-28]

value: 48 hours


title: Q11t4ROlng1

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ11t4ROlng1-BS


title: KB39_07_BC1115

description: Library name: KB39_07_lib

value: CMML


title: Q11t4MAlng1

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ11t4MAlng1-BS


title: Thapsigargin-treated WT Developing Oligodendrocytes [BP-32]

value: Wild-type

value: 6-7 days


title: Untreated WT Developing Oligodendrocytes [BP-27]


title: QOG6t9ANsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG6t9ANsm-BS

value: Plasma

value: Healthy Subject

value: Norgen and Qiagen minElute


title: KB39_06_YHB4

description: Library name: KB39_06_lib


title: QOG10t13ROsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG10t13ROsm-BS

value: Entire cardiovascular system


title: KB39_05_BC1223

description: Library name: KB39_05_lib


title: DG5t7AXsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQDG5t7AXsm-BS


title: QOG6t9AXsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG6t9AXsm-BS


title: Q11t4ROsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ11t4ROsm-BS


title: Untreated WT Developing Oligodendrocytes [BP-26]

value: 24 hours

value: Whole brain


title: KB39_04_BC1206

description: Library name: KB39_04_lib


title: LDLANsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQLDLANsm-BS

value: extracellular exosome


title: VLDLANsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQVLDLANsm-BS


title: KB39_03_YHB1

description: Library name: KB39_03_lib

value: Healthy Young


title: Untreated WT Developing Oligodendrocytes [BP-25]

value: Developing oligodendrocyte


title: EENorEluAXsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQEENorEluAXsm-BS


title: Untreated WT Developing Oligodendrocytes [BP-24]


title: DG10t12ANsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQDG10t12ANsm-BS


title: Untreated WT Developing Oligodendrocytes [BP-23]


title: DG5t7MAsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQDG5t7MAsm-BS


title: KB39_01_BC1172

description: Library name: KB39_01_lib


title: VLDLAXsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQVLDLAXsm-BS


title: LDLAXsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQLDLAXsm-BS


title: KB39_02_HB10

description: Library name: KB39_02_lib

value: Healthy Old


title: Untreated WT Developing Oligodendrocytes [BP-22]

value: 1 hour


title: DG8t9ROsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQDG8t9ROsm-BS


title: DG10t12AXsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQDG10t12AXsm-BS


title: Hacat cell, CT3

city: SHENZHEN

first: JIANGMING

last: ZHONG

address: Shennan rd 9996, 518000, Shenzhen, Guangdong, P.R. China.

institute: Shenzhen Hujia Technology Co., Ltd.

description: Library name: SAMPLE9

data_processing:
The workflow for mRNA library preparation and sequencing involves several key steps: first, the purity of total RNA is assessed using NanoDrop One, while its integrity is evaluated with either an Agilent 2100 Bioanalyzer or an FA 471 Fragment Analyzer; subsequently, mRNA is enriched and purified from eukaryotic total RNA using the VAHTS mRNA Capture Beads Kit; the enriched mRNA is then fragmented into insert sizes of 250–450 bp via ion-mediated fragmentation; first-strand cDNA is synthesized using the fragmented RNA as a template, followed by second-strand cDNA synthesis, end repair, and dA-tailing; universal adapters are ligated to the ds cDNA, which is then purified using magnetic beads and size-selected to obtain fragments ranging from 250–350 bp; the fragments are amplified by PCR with dual-indexed primers for sample identification, and the final library is purified using a 0.9X bead cleanup to remove adapter dimers; library quality is assessed using Qubit 4.0, LabChip, FA Fragment Analyzer, or ABI QuantStudio 12K qPCR; finally, the qualified library is sequenced on the Illumina NovaSeq 6000 platform using paired-end (PE) sequencing technology.
After the samples were subjected to sequencing on the instrument, BCL image files were generated. These files were then converted by the Illumina bcl2fastq software to produce the raw data in Fastq format.
The sequencing data includes adapter-contaminated and low-quality reads that may adversely affect downstream bioinformatics analysis. To address this, the data were filtered using fastp v0.23.2, with filtering parameters following the software's recommended settings for optimal performance.
The low-quality-filtered reads were subsequently processed with SortMeRNA v4.3.4 to remove ribosomal RNA (rRNA) sequences.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skin

growth_protocol: Hacat cell were maitained in DMEM supplemented wth 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TransZol Up Plus RNA Kit (Transgen).2 ug of total RNA was used for the construction of sequencing ibraries.
Library construction using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina kit

value: skin

value: Hacat

value: Human Keratinocyte cell

value: WT

value: UVA(5 J/cm2) and CT treated


title: Untreated WT Developing Oligodendrocytes [BP-21]

value: Wild-type

value: 6-7 days


title: Hacat cell, CT2

description: Library name: SAMPLE8


title: RNezmidANsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQERNezmidANsm-BS

value: Plasma

value: Healthy Subject


title: RNezmidAXsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQERNezmidAXsm-BS

value: Entire cardiovascular system

value: Norgen and Qiagen minElute


title: plazMAsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQplazMAsm-BS


title: Hacat cell, UVA3

description: Library name: SAMPLE6

value: UVA(5 J/cm2)


title: QOG10t13MAsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG10t13MAsm-BS

value: extracellular exosome


title: LPdepleteAXsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQLPdepleteAXsm-BS


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-18]

value: Interferon-gamma (200 U/ml)

value: 24 hours

value: Whole brain


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-19]

value: 48 hours

value: Developing oligodendrocyte


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-17]


title: Hacat cell, UVA2

description: Library name: SAMPLE5

value: skin

value: Hacat


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-20]


title: LPdepleteROsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQLPdepleteROsm-BS


title: Q11t4ANsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ11t4ANsm-BS


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-16]

value: 8 hours


title: Hacat cell, NC3

description: Library name: SAMPLE3

value: Human Keratinocyte cell

value: WT


title: Q11t4AXsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ11t4AXsm-BS


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-15]

value: Wild-type

value: 6-7 days


title: HDLANsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQHDLANsm-BS

value: Plasma

value: Healthy Subject


title: LPdepleteMAsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQLPdepleteMAsm-BS

value: Entire cardiovascular system

value: Norgen and Qiagen minElute


title: DG8t9ANsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQDG8t9ANsm-BS

value: extracellular exosome


title: Hacat cell, NC2

description: Library name: SAMPLE2


title: QOG6t9MAsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG6t9MAsm-BS


title: Hacat cell, NC1

description: Library name: SAMPLE1


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-14]

value: Interferon-gamma (200 U/ml)

value: 1 hour


title: Q11t4MAsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQQ11t4MAsm-BS


title: Hacat cell, CT1

description: Library name: SAMPLE7

value: UVA(5 J/cm2) and CT treated


title: RNezmidMAsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQERNezmidMAsm-BS


title: HDLAXsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQHDLAXsm-BS


title: EENorEluMAsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQEENorEluMAsm-BS


title: QOG10t13ANsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG10t13ANsm-BS


title: TCDEO_L

city: shenzhen

first: Huang

last: Yibin

address: Engineering Biological Industry Innovation Centre, No.229 Gongchang Road, Xinhu Street, Guangming District

institute: SynOrg Biotechnology (Shenzhen) Co., Ltd.

description:
Library name: Sample 3
Column name in TPM.gene.annotated.txt: TCDEO_L

data_processing:
Use cutadapt to remove splice sequences and filter out low-quality reads (reads less than 50nt in length, reads with an N-base ratio greater than 10%, rRNA sequences)
The reads obtained from the filtering of each sample were compared with the reference sequence (HUMAN GENCODE 34 GRCh37 (11.2019)) using the STAR software (mapping parameter: default)
Quantitative analyses were performed using featureCounts software, and gene expression quantification was performed in units of TPM (Transcripts Per kilobase of exon model per Million mapped reads).TPM takes into account the effects of sequencing depth and gene length on the count of reads and is corrected so that TPM can be compared between different genes in different samples.
Assembly: HUMAN GENCODE 34 GRCh37 (11.2019)
Supplementary files format and content: text file includes TPM vaules for each Sample

source_name: Thyroid cancer organoid

growth_protocol: TCDEO_E and TCDEO_L were maintained in advanced DMEM/F12 medium supplemented with  1 % Glutamax，1% Penicillin-Streptomycin，1% N2，10 μM SB202190，5 ng/mL FGF-2，100 ng/mL FGF-10，5 ng/mL EGF，100 ng/mL Noggin，100 ng/mL R-Spondin-1，10 mM Nicotinamide，500 nM A83-01，25 ng/mL HGF，10 μM Forskolin，5 μM Y-27632，1% B27

extract_protocol:
RNA was harvested using a total RNA extraction kit (Tiangen Biotech). 2 μg total RNA was used for the construction of sequencing libraries.
mRNAs with polyA tails were enriched by Oligo(dT) magnetic beads. The first strand of cDNA was synthesised in the 1st Strand Enzyme reverse transcriptase system using fragmented mRNA as template and random oligonucleotides as primers. The purified double-stranded cDNA was then end-repaired, A-tailed and ligated into sequencing junctions, and the 200-300bp cDNA was selected for PCR amplification and the PCR product was purified again to obtain the final library. After library construction, the libraries were quantified using a Qubit2.0 Fluorometer, diluted to 1.5 ng/ul, and the insert size of the libraries was checked using an Agilent 4200 TapeStation to ensure the quality of the libraries.

value: Thyroid cancer organoid

value: thyroid cancer tissue-derived primary cells


title: Thapsigargin-treated WT Developing Oligodendrocytes [BP-12]

value: Thapsigargin (200 uM)

value: Whole brain

value: Developing oligodendrocyte


title: DG8t9AXsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQDG8t9AXsm-BS


title: VLDLROsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQVLDLROsm-BS


title: VLDLMAsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQVLDLMAsm-BS


title: Thapsigargin-treated WT Developing Oligodendrocytes [BP-11]

value: 8 hours


title: TC_M

description:
Library name: Sample 1
Column name in TPM.gene.annotated.txt: TC_M

source_name: Thyroid cancer tissue

value: Thyroid cancer tissue

value: WT


title: Hacat cell, UVA1

description: Library name: SAMPLE4

value: skin

value: Hacat

value: Human Keratinocyte cell

value: UVA(5 J/cm2)


title: QOG10t13AXsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG10t13AXsm-BS

value: Plasma

value: Healthy Subject

value: Entire cardiovascular system

value: Norgen and Qiagen minElute


title: Thapsigargin-treated WT Developing Oligodendrocytes [BP-10]

value: Wild-type

value: 6-7 days

value: 1 hour


title: ZXB

city: Tianjin

first: Weiwei

last: Qian

address: 154 Anshan Road, Heping District

department: Department of Emergency

institute: Tianjin Medical University General Hospital

description: Library name: sample 6

data_processing:
To explore developmental dynamics, Monocle2 (v2.22.0) was applied to infer pseudotime trajectories of key immune cell subsets, including B cells, T cells, regulatory T cells (Tregs), and platelets, based on their transcriptional profiles.
Single-cell transcriptomic data were processed using the Seurat package (v5.0) in R. Low-quality cells were filtered out based on the following criteria: number of features < 200 or > 6000, and mitochondrial gene content > 15%.
Cell type annotation was conducted using a combination of GPTCelltype (v1.1.1), SingleR (v1.0.0), and scCATCH (v3.1.1), with reference to established marker gene databases and published literature.
Differentially expressed genes (DEGs) were identified using the wilcoxauc function from the RPresto package, with the significance threshold set at log₂ fold change > 0.25 and adjusted p < 0.05.
Cell–cell communication networks were predicted using CellphoneDB (v2.1.7) to identify significant ligand–receptor interactions, with a minimum expression threshold of 10% set for inclusion in downstream analyses.
Assembly: hg38

source_name: human whole blood cell

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent.The concentration of total RNA was measured by Qubit RNA HS assay kit.
The library was prepared by smart-seq method. Both the input samples without IP and the m6A IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.

value: non-survivor

tag: disease state

value: sepsis

value: human whole blood cell


title: Thapsigargin-treated WT Developing Oligodendrocytes [BP-9]

value: Thapsigargin (200 uM)

value: Whole brain

value: Developing oligodendrocyte


title: ZL

description: Library name: sample 5


title: DG10t12ROsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQDG10t12ROsm-BS

value: extracellular exosome


title: DG5t7ROsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQDG5t7ROsm-BS


title: LDLROsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQLDLROsm-BS


title: Untreated WT Developing Oligodendrocytes [BP-8]

value: 48 hours


title: DG10t12MAsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQDG10t12MAsm-BS


title: IFN gamma-treated WT Developing Oligodendrocytes [BP-13]

value: Interferon-gamma (200 U/ml)


title: LTL

description: Library name: sample 3

value: survivor


title: TCDEO_E

description:
Library name: Sample 2
Column name in TPM.gene.annotated.txt: TCDEO_E

value: Thyroid cancer organoid

value: thyroid cancer tissue-derived primary cells

value: WT


title: RNezmidROsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQERNezmidROsm-BS

value: Plasma

value: Healthy Subject

value: Entire cardiovascular system

value: Norgen and Qiagen minElute


title: EENorEluROsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQEENorEluROsm-BS


title: LJY

description: Library name: sample 2


title: Untreated WT Developing Oligodendrocytes [BP-5]

value: Wild-type

value: 6-7 days

value: 24 hours


title: DG1t4MAsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQDG1t4MAsm-BS


title: DG1t4ANsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQDG1t4ANsm-BS


title: HDLMAsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQHDLMAsm-BS


title: ICY

description: Library name: sample 1

value: sepsis

value: human whole blood cell


title: LDLMAsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQLDLMAsm-BS


title: LPdepleteANsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQLPdepleteANsm-BS


title: Untreated WT Developing Oligodendrocytes [BP-4]

value: 8 hours

value: Whole brain

value: Developing oligodendrocyte


title: DG1t4AXsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQDG1t4AXsm-BS

value: extracellular exosome


title: DG8t9MAsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQDG8t9MAsm-BS


title: H2030-Lbrm-siHMGB3 cells, biol rep 3

city: Shanghai

first: Huanhuan

last: Cui

address: 270 Dong'an Road

institute: Fudan University Shanghai Cancer Center

description:
Library name: H2030-Lbrm-si_biol rep 3
si1-3_fpkm
expression-raw-2.xls

data_processing:
1. Quality control Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis. 2. Reads mapping The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0). 3. Expression analysis: We used HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Assembly: GRCh38
Supplementary files format and content: expression-raw.xls
Supplementary files format and content: expression-raw-2.xls

extract_protocol:
The high brain metastasis derivative of H2030 cell line (H2030-Lbrm) were isolated from mouse metastatic brains derived from an experimental brain metastasis model using H2030 cells and further cultured in vitro. The cells were maintained in RPMI-1640 medium (C22400500BT, Gibco, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS) (A5669701, Gibco) at 37°C within a humidified incubator (Thermo Fisher Scientific, Waltham, MA, USA) containing 5% CO2. Cells in the logarithmic growth phase were selected for assays and confirmed as mycoplasma-free.
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina) Shanghai Personal Biotechnology Cp. Ltd.

value: LUAD


title: Untreated WT Developing Oligodendrocytes [BP-3]


title: H2030-Lbrm-siHMGB3 cells, biol rep 2

description:
Library name: H2030-Lbrm-si_biol rep 2
si1-2_fpkm
expression-raw-2.xls


title: Untreated WT Developing Oligodendrocytes [BP-2]

value: 1 hour


title: plazANsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQplazANsm-BS


title: H2030-Lbrm-siHMGB3 cells, biol rep 1

description:
Library name: H2030-Lbrm-si_biol rep 1
si1-1_fpkm
expression-raw-2.xls


title: LYL

description: Library name: sample 4

value: non-survivor


title: Untreated WT Developing Oligodendrocytes [BP-7]

value: 48 hours


title: Untreated WT Developing Oligodendrocytes [BP-1]


title: HDLROsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQHDLROsm-BS

value: Plasma


title: QOG6t9ROsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG6t9ROsm-BS

value: Healthy Subject


title: EENorEluANsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQEENorEluANsm-BS

value: Entire cardiovascular system


title: THPIL4DGsm2

description: Library name: EXR-RRAFF1exRNAcarrierSEQTHPIL4DGsm2-BS

value: cell culture

value: Acute Monocytic Leukemia

value: Blood cell

value: Norgen and Qiagen minElute


title: H2030-Lbrm-NC cells, biol rep 3

description:
Library name: H2030-Lbrm-NC_biol rep 3
NC-3_fpkm
expression-raw-2.xls

value: siNC


title: plazROsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQplazROsm-BS


title: QOG6t9DIFsm1

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG6t9DIFsm1-BS

value: Rectal Carcinoma

value: Region of rectum


title: H2030-Lbrm-NC cells, biol rep 2

description:
Library name: H2030-Lbrm-NC_biol rep 2
NC-2_fpkm
expression-raw-2.xls


title: QOG6t9DIFsm3

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG6t9DIFsm3-BS


title: THPIL4DGsm3

description: Library name: EXR-RRAFF1exRNAcarrierSEQTHPIL4DGsm3-BS


title: DG1t4ROsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQDG1t4ROsm-BS


title: Biological replicate 2 of hashtagged but pooled samples (HTO)

city: Rochester

first: Mark

middle: Ayor

last: Osabutey

state: New York

address: 601 Elmwood Avenue

institute: University of Rochester Medical Center

description:
Library name: Sample 2 HTO
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed with Cell Ranger v7.0.1 to generate fastq files, align reads to the mouse mm10 reference, and produce gene‑cell count matrices for 3′ gene expression libraries.
Hashtag oligonucleotide (HTO) counts were used for sample demultiplexing to assign cells to individual animals and remove doublets/unassigned cells, retaining singlet cells for analysis.
Assembly: 10X provided gex mm10-2020-A
Supplementary files format and content: Cell Ranger Feature Barcode Matrices (HDF5 format)
Supplementary files format and content: Barcode tags corresponding to the HTO are included within featref.csv

source_name: Hippocampus + overlying cortex

growth_protocol: Male and female C57BL/6J mice (Jackson Laboratory, stock no. 000664) were used. Mice were shipped two weeks prior to irradiation and housed 4–5 per cage under standard vivarium conditions at Brookhaven National Laboratory with a 12‑hour light/dark cycle and ad libitum access to food and water. After irradiation, animals were transferred to the University of Rochester and maintained under similar conditions. Female mice cycled naturally without estrous synchronization.

extract_protocol:
At 53 days post‑irradiation, mice were deeply anesthetized (ketamine/xylazine) and perfused. Hippocampus and overlying cortex were dissected and homogenized in FACS buffer (0.5% BSA in 1× PBS), filtered through a 70 μm strainer, and subjected to a 40% isotonic Percoll cleanup to remove myelin. Cells were Fc‑blocked and stained with CD11b‑FITC, 7AAD, and TotalSeq‑B hashtag antibodies (anti‑CD45 and anti‑MHC Class I). Live singlet CD11b+ microglia were sorted on a BD FACSAria II into PBS + 0.5% BSA and kept on ice until library preparation.
Sorted cells were processed using the 10x Genomics Chromium platform. Single‑cell gel bead‑in‑emulsions (GEMs) were generated and 3′ gene expression libraries were prepared using the Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 following the manufacturer’s protocol. Hashtag (feature barcode) libraries were generated using the 10x Genomics Feature Barcoding library preparation workflow. Libraries were quantified (Qubit) and quality‑checked (Bioanalyzer) prior to pooling.

treatment_protocol: Mice were placed in plexiglass chambers with 2–3 littermates per chamber and received 100 cGy whole‑body simplified 5‑ion galactic cosmic radiation simulation (GCRsim) using a 12 cm × 12 cm beam line at the NASA Space Radiation Laboratory (NSRL), Brookhaven National Laboratory. The beam sequence comprises high‑ and low‑energy protons, helium, oxygen, silicon, and iron ions delivered sequentially; the full exposure was completed within approximately 27–32 minutes. Sham controls underwent identical handling without irradiation.

value: Hippocampus + overlying cortex

value: Microglia

value: Myeloid cells

value: Sham + Irradiation

tag: batch

value: replicate 2

tag: library type

value: HTO


title: H2030-Lbrm-NC cells, biol rep 1

description:
Library name: H2030-Lbrm-NC_biol rep 1
NC-1_fpkm
expression-raw-2.xls

value: LUAD


title: Biological replicate 1 of hashtagged but pooled samples (HTO)

description:
Library name: Sample 1 HTO
10x Genomics

value: replicate 1


title: QOG6t9DIFsm2

description: Library name: EXR-RRAFF1exRNAcarrierSEQQOG6t9DIFsm2-BS

value: extracellular exosome


title: Biological replicate 2 of hashtagged but pooled samples (GEX)

description:
Library name: Sample 2 GEX
10x Genomics

value: mRNA


title: plazAXsm

description: Library name: EXR-RRAFF1exRNAcarrierSEQplazAXsm-BS

value: Plasma

value: Healthy Subject

value: Entire cardiovascular system


title: F2

city: Weifang

first: Wang

last: Guobao

address: No.5147 Dongfeng East Street

institute: Weifang University

description: Library name: D-F-2

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.
After removing adaptor and low-quality sequences, the clean reads were assembled into expressed sequence tag clusters (contigs) and de novo assembled into transcripts by Trinity (vesion: 2.4) with paired-end method. The longest transcript was selected as a unigene based on the similarity and length for subsequent analyses.
The FPKM measure was used to calculate expression of each gene of which read counts were determined by HTSeq-count. The biological duplication of samples was evaluated by principal component analysis (PCA) with R (v 3.2.0).
Assembly: De novo transcriptome
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Eumeta variegata

source_name: head

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: head

tag: Sex

value: female


title: F1

description: Library name: D-F-1

tag: tissue


title: Biological replicate 1 of hashtagged but pooled samples (GEX)

description:
Library name: Sample 1 GEX
10x Genomics


title: M2

description: Library name: D-M-2

value: male


title: Untreated WT Developing Oligodendrocytes [BP-6]

value: Wild-type

value: 6-7 days

value: 24 hours

value: Whole brain

value: Developing oligodendrocyte


title: F3

description: Library name: D-F-3


title: ageing Muscle Satellite Cells, hMG53, Rep3

city: Columbus

first: Jethro

middle: WANG

last: Zih-Shuo

state: Ohio

address: 460 W 12th Ave.

department: Department of Surgery

institute: Ohio State University

description:
Library name: MusSCs_hMG53_6
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: S6.sorted.bam

data_processing:
The libraries were sequenced on an Illumina platform (Next-Generation Sequencing) to generate 2×150 bp paired-end reads, with a depth of approximately 40 million reads per sample (20M in each direction).
Raw reads were aligned to the mouse reference genome (mm10) using STAR
Gene expression counts were quantified using featureCounts
Differential expression analysis was performed using EdgeR in R software. Gene expression levels were normalized using the TMM method.
Assembly: mm10
Supplementary files format and content: MG53_ageing_Mus_SCs_gene_counts_matrix.csv

source_name: ageing Muscle Satellite Cells

growth_protocol: Primary satellite cells were isolated from the hindlimb muscles of C57BL/6 mice. Cells were cultured in DMEM supplemented with 20% FBS and bFGF. Cells were maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from the collected cells using [填写试剂盒名称, e.g., TRIzol reagent or Qiagen RNeasy Mini Kit] following the manufacturer's instructions. RNA quality and integrity were assessed using an Agilent Bioanalyzer 2100.
RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit with Poly(A) mRNA Magnetic Isolation Module, following the "Low Input" protocol according to the manufacturer's instructions.

treatment_protocol: Cells were cultured to appropriate confluency and then treated with either recombinant human MG53 protein (rhMG53) or Bovine Serum Albumin (BSA) as a vehicle control for 72 hours.

value: ageing Muscle Satellite Cells

value: WT

value: Day 3


title: M3

description: Library name: D-M-3


title: H2030-Lbrm cells, biol rep 2

description:
Library name: H2030-Lbrm_biol rep 2
B5_2:fpkm
expression-raw.xls

value: LUAD


title: M1

description: Library name: D-M-1


title: H2030-Lbrm cells, biol rep 1

description:
Library name: H2030-Lbrm_biol rep 1
B5_1:fpkm
expression-raw.xls


title: ageing Muscle Satellite Cells, hMG53, Rep2

description:
Library name: MusSCs_hMG53_5
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: S5.sorted.bam


title: Brain, he rep6

city: changsha

first: Huilin

middle: huilin

last: Yang

state: huannan

address: Donghu Street

institute: Hunan Agricultural University

data_processing:
Illumina Novaseq platform were used for basecalling.
The clustering of the index-coded samples was performed on acBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS(Illumia) according to the manufacturer’s instructions.
After cluster generation, thelibrary preparations were sequenced on an Illumina Novaseq platformand150bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed throughin-house perl scripts. In this step, clean data (clean reads) were obtainedbyremoving reads containing adapter, reads containing N base and lowqualityreads from raw data. At the same time, Q20, Q30 and GC content thecleandata were calculated. All the downstream analyses were based on thecleandata with high quality.
The left files (read1 files) from all libraries_x0014__x001D_mples were pooled intoonebig left.fq file, and right files (read2 files) into one big right.fq file. Transcriptomeassembly was accomplished based on the left.fq and right.fq using Trinity with min_kmer_cov set to 2 by default and all other parameters set default.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

organism: Sinotaia aeruginosa

source_name: Brain

extract_protocol:
RNA was harvested using  Rneasy mini plus kit (Qiagen).
RNA  libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Brain

value: Medium concentration cadmium and medium concentration polystyrene


title: Brain, he rep5


title: ageing Muscle Satellite Cells, hMG53, Rep1

description:
Library name: MusSCs_hMG53_4
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: S4.sorted.bam


title: H2030 cells, biol rep 2

description:
Library name: H2030_biol rep 2
H2030_2:fpkm
expression-raw.xls


title: Liver, he rep3

source_name: Liver

value: Liver


title: Brain, he rep4


title: ageing Muscle Satellite Cells, BSA, Rep3

description:
Library name: MusSCs_BSA_3
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: S3.sorted.bam

value: BSA


title: H2030-Lbrm cells, biol rep 3

description:
Library name: H2030-Lbrm_biol rep 3
B5_3:fpkm
expression-raw.xls


title: ageing Muscle Satellite Cells, BSA, Rep2

description:
Library name: MusSCs_BSA_2
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: S2.sorted.bam


title: Liver, he rep1


title: Brain, ps rep4

value: Medium concentration polystyrene


title: Brain, ps rep6


title: ageing Muscle Satellite Cells, BSA, Rep1

description:
Library name: MusSCs_BSA_1
Column name in MG53_ageing_Mus_SCs_gene_counts_matrix: S1.sorted.bam


title: Brain, ps rep5


title: CT group_OT1 & Combo group_OT1 (merged data)

city: Chongqing

first: shuai

last: yue

state: Chongqing

address: Gaotanyan street

institute: army medical university

description:
Library name: Sample 4
BD Rhapsody platform ( 2 samples mixed by Sample Tags)

data_processing:
The output files produced from raw data were generated by Seven Bridges platform (https://velsera.com/bd-rhapsody/)
1. Multiplexing Strategy: We pooled multiple biological samples (e.g., "Ctrl group" and "Combo group") into single libraries using distinct barcodes (Sample Tags) to identify them. 2. File Relationship: For each library (e.g., Sample 1), two types of FASTQ files were generated that must be processed together:      "S" files (e.g., S1_R1/R2): These contain the Sample Tag reads required to demultiplex the biological samples.      "WTA" files (e.g., WTA-1_R1/R2): These contain the Whole Transcriptome Amplification (mRNA) reads.
Assembly: Mouse mm10
Supplementary files format and content: S1_Seurat.rds, S2_Seurat.rds, S3_Seurat.rds, S4_Seurat.rds

source_name: Tumor

extract_protocol:
To obtain P14/OT1 CD8 T cells in tumor, tumors were mechanically minced and digested using with 1 mg/mL collagenase I (Sigma, c0130) and mashed through filters. Then, lymphocytes were enriched using Percoll (GE Healthcare, 17-0891-09) density gradient. Next, lymphocytes were stained with flow cytometry antibodies specicifc for CD8, Va2, CD45.1, CD45.2, P14/OT1 cells were FACS-sorted.
The library preparation for single-cell RNA sequencing (scRNA-seq) using the BD Rhapsody platform according to manufacturer instructions. scRNA-seq begins with the capture of individual cells which employs microfluidic technology to isolate cells within nanowells. Once captured, each cell is lysed, and reverse transcription is performed to convert the RNA into complementary DNA (cDNA). During this process, unique molecular identifiers (UMIs) and cell barcodes are incorporated into each cDNA molecule, enabling accurate quantification and differentiation of transcripts from different cells. Following reverse transcription, the cDNA undergoes amplification through PCR to generate an adequate quantity of material for sequencing. The amplified cDNA is then processed to prepare sequencing libraries, which involves enzymatic fragmentation, adapter ligation, and purification steps to ensure that only the desired fragments are included in the final product. To confirm that the libraries meet the necessary standards for sequencing, quality and quantity assessments are conducted using methods such as bioanalyzer or Qubit. Finally, the libraries were sequenced using paired-end sequencing, with 150 nucleotides on each end, conducted in a single lane of a NovaSeq 6000 for each sample. Raw gene expression matrices were generated using the Cell Ranger pipeline (version 6.1.1), coupled with the mm10 genome annotation reference.

value: Tumor


title: Brain, cd rep6

value: Medium concentration of cadmium


title: Liver, ps rep1


title: DSP-1001660005602-D-C07_SR21-4053

city: New Haven

first: Thazin

middle: Nwe

last: Aung

address: 310 Cedar Street

institute: Yale University

description: Library name: DSP-1001660005602-D-C07

data_processing:
The sequencing data were processed with the GeoMx NGS Pipeline (DND) according to the GeoMx-DSP user manual (MAN-10153-01). Briefly, the pipeline was performed for trimming, merging, and aligning the reads to a list of indexing oligos to identify the source probe. The unique molecular identifier (UMI) region of each read was used to remove PCR duplicate reads. This program then converted FASTQ files to DCCs, i.e., converting reads into digital counts.
The zipped folder containing the DCC files were transferred back to GeoMx DSP to obtain the read counts.
After uploading the files to GeoMx DSP, the sequencing quality (quality control) allowed for specifying the parameters for evaluating the quality of NGS data and to qualify segments by number of cells or by area. Read counts were filtered setting the threshold for the limit of detection (LoD) in an ROI. This was defined based on the mean and standard deviation (s.d.) of 𝑙𝑜𝑔−10 normalized target group genes. The calculation is: LoD = mean + (2 × s.d.). A gene was filtered as detected only if it exceeded the LoD in at least 10% of all ROIs. ROIs that did not have the filtering criteria were excluded from further analyses
Assembly: hg19
Supplementary files format and content: CD45_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the leukocyte (CD45) compartment
Supplementary files format and content: CD68_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the macrophage (CD68) compartment
Supplementary files format and content: CK_0%filter_Greek.xlsx  contains raw, unnormalized read counts from the tumor (CK) compartment
Library strategy: Spatial Transcriptomics

source_name: Lung Cancer

extract_protocol:
day1:TMA slides were processed using the Nanostring GeoMx DSP manual slide preparation GeoMx-DSP protocol (MAN-10150-01). Antigen retrieval of the FFPE tissue was performed for 20 minutes followed by deparaffinization and rehydration.Then, the slides were incubated with proteinase K for 20 minutes and RNA probes were placed on slides for overnight in situ hybridization. day2:slides were washed to remove off-target probes for 90 minutes. Morphology markers: CD68 for macrophage compartment (Cy5-666 nm, excitation 645-19 nm, emission 683-30 nm), CD45 for lymphocyte compartment (Texas Red-615 nm, excitation 588-19 nm, emission 623-30 nm), S100B (Cy3-568 nm, excitation 538-19 nm, emission 564-15nm) for tumor compartment to identify the compartments and SYTO 13 for nuclear stain, were added for 1-hour incubation. Slides were loaded onto the GeoMx DSP instrument and after scanning, ROI (region of interest: i.e., CD45, CD68 and S100B) selection and probe collection were performed according to the GeoMx-DSP user manual protocol (MAN-10088-03). Samples were collected in a 96-well probe aspirate collection plate and each ROI representing a compartment from a patient tumor core was collected in a well.
GeoMx-DSP user manual (MAN-10117-01); Each GeoMx DSP aspirate in the plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. Prior to purification, PCR reactions were pooled into three mixtures, separating CD68, CD45 and S100B ROIs to generate three pooled libraries. The libraries were pooled in a biased manner designed to target the smallest ROI pool with 6 parts of reads for CD68, 3 parts of reads for CD45 and 1 part of reads for S100B. Illumina i5 x i7 system adapter sequences and unique dual sample indices are added when PCR is performed on the probe aspirates. Each photocleaved oligo in the GeoMx DSP collection plate contains a readout tag sequence identifier (RTS ID) that identifies the target. It also includes a unique molecular identifier (UMI), to remove PCR duplicates when converting reads to digital counts. Read 1 (SPR1) and Read 2 (SPR2) are binding sites for Illumina sequencing primers. The GeoMx Seq code primers that hybridize to SPR1 and SPR2 contain i5 or i7 indexing sequences as well as P5 or P7 sequences for binding to Illumina flow cells. Sequencing was performed in both lanes of an Illumina Nova-Seq 6000 S2 flow cell resulting of 3 billion reads

value: Lung Cancer

value: immunotherapy


title: Liver, ps rep3


title: Liver, ps rep2


title: DSP-1001660005602-D-C04_S21-12496

description: Library name: DSP-1001660005602-D-C04


title: DSP-1001660005602-D-C06_SR21-4053

description: Library name: DSP-1001660005602-D-C06


title: Ctrl group_OT1 & CT group_P14 (merged data)

description:
Library name: Sample 2
BD Rhapsody platform ( 2 samples mixed by Sample Tags)


title: H2030 cells, biol rep 3

description:
Library name: H2030_biol rep 3
H2030_3:fpkm
expression-raw.xls


title: Brain, cd rep5


title: DSP-1001660005602-D-C03_S21-12496

description: Library name: DSP-1001660005602-D-C03


title: Brain, cd rep4


title: Ctrl group_P14 & Combo group_P14 (merged data)

description:
Library name: Sample 1
BD Rhapsody platform ( 2 samples mixed by Sample Tags)


title: Liver, cd rep2


title: Liver, cd rep3


title: DSP-1001660005602-D-C02_S21-12496

description: Library name: DSP-1001660005602-D-C02


title: H2030 cells, biol rep 1

description:
Library name: H2030_biol rep 1
H2030_1:fpkm
expression-raw.xls


title: Liver, he rep2


title: Liver, cd rep1


title: DSP-1001660005602-D-C01_S21-12496

description: Library name: DSP-1001660005602-D-C01


title: Brain, ck rep6

value: No handling


title: OV group_P14 & OV group_OT1 (merged data)

description:
Library name: Sample 3
BD Rhapsody platform ( 2 samples mixed by Sample Tags)


title: DSP-1001660005602-D-B12_S20-27058

description: Library name: DSP-1001660005602-D-B12


title: DSP-1001660005602-D-C05_SR21-4053

description: Library name: DSP-1001660005602-D-C05


title: Liver, ck rep3


title: Mouse colon, WT, DSS-induced colitis, rep2

city: Nantong

first: Mengmeng

last: Sang

address: Qixiu

institute: Nantong Unversity

description:
Library name: WT2
Bulk RNA-seq of mouse colon tissue

data_processing:
Clean reads were aligned to the mouse reference genome using HISAT2 v2.0.5. Reference genome index was built prior to alignment.
Transcript assembly and quantification were performed using StringTie v1.3.3b in a reference-based approach.
Gene-level read counts were generated using featureCounts v1.5.0-p3. Gene expression levels were calculated as FPKM values.
Differential gene expression analysis was performed using DESeq2 with |log2 fold change| > 1 and false discovery rate (FDR) ≤ 0.05 as significance thresholds.
Assembly: Mus musculus reference genome (GRCm38/mm10).
Supplementary files format and content: Processed data files include gene-level expression matrices in TXT format containing FPKM values for each sample, and differential expression analysis results including log2 fold changes, p-values, and adjusted p-values.
Supplementary files format and content: gene_count.xls

source_name: colon

extract_protocol:
Distal colon tissues were collected immediately after euthanasia, snap-frozen in liquid nitrogen, and stored at −80°C. Total RNA was extracted from colon tissues using standard RNA extraction procedures. RNA integrity was assessed using the RNA Nano 6000 Assay Kit on the Agilent Bioanalyzer 2100 system.
Total RNA was used as input material for library preparation. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was performed using divalent cations under elevated temperature. First-strand cDNA synthesis was carried out using random hexamer primers and M-MuLV Reverse Transcriptase, followed by second-strand cDNA synthesis using DNA Polymerase I and RNase H. After end repair and A-tailing, sequencing adaptors were ligated. cDNA fragments of approximately 370–420 bp were selected using AMPure XP beads. Libraries were amplified by PCR, purified, and library quality was assessed on the Agilent Bioanalyzer 2100 system.Raw reads in FASTQ format were processed to remove adaptor sequences, reads containing poly-N, and low-quality reads using in-house Perl scripts. Clean reads were used for all downstream analyses.

treatment_protocol: Acute colitis was induced by administering 3% (w/v) dextran sulfate sodium (DSS, 36–50 kDa) in drinking water ad libitum for 7 consecutive days. Control and experimental mice were monitored daily and euthanized on day 7 for tissue collection.

value: colon

value: DSS


title: Liver, ck rep2


title: Brain, ck rep4


title: Mouse colon, WT, DSS-induced colitis, rep3

description:
Library name: WT3
Bulk RNA-seq of mouse colon tissue


title: Liver, ck rep1


title: DSP-1001660005602-D-B11_S20-27058

description: Library name: DSP-1001660005602-D-B11


title: hCOs, VN2004-inoculated, 3 days post-inoculation (historical HPAI H5N1)

city: Hamilton

first: Emmie

last: de Wit

state: MT

address: 903 S 4th St

institute: NIAID

description:
Library name: S9
influenza A/Vietnam/1203/2004 (H5N1) (NCBI taxid:284218)

data_processing:
Illumina bcl2fastq was used for demultiplexing. Reads were aligned to a combined human influenza A virus reference genome and unique molecular identifier counts were generated using PIPseeker v3.3 software (Fluent Biosciences).
Assembly: hg38
Supplementary files format and content: tab-separated matrix, genes, and barcodes files
Supplementary files format and content: h5ad AnnData file

organism:
Homo sapiens
Influenza A virus

extract_protocol:
Human cerebral organoids (hCOs) were dissociated into a single cell suspension as follows: one organoid per well was placed in a 24-well plate. hCOs were washed with Dulbecco’s Modified Eagle Medium/F-12 (Gibco). hCOs were incubated with 500 µl trypsin EDTA (Gibco), 500µl Accutase (MilliporeSigma), and 200 units of RNase inhibitor (Applied Biosystems) for 20 minutes at 37°C and 5% CO2. Every ten minutes, hCOs were gently agitated using a wide-bore P1000 pipette tip. If hCOs were not dissociated after twenty minutes, they were incubated for a further 5 minutes. Cells were filtered through a pre-wet 70 µm filter (pluriSelect) into stop solution (PBS + 20% FBS) and centrifuged at 200 x g for 5 minutes at 4°C. The cell pellet was resuspended in Cell Suspension Buffer (Fluent Biosciences), and filtered through a pre-wet 40 µm filter (pluriSelect). Cell concentration was determined using trypan blue and a manual hemocytometer.
The recommended 5,000 cell input was used for the PIPseq T2 protocol (Fluent Biosciences). Cells derived from 3 organoids per sample were pooled for scRNA-seq library construction. Libraries were prepared using PIPseq T2 3’ Single Cell RNA kit v4.0 PLUS (Fluent Biosciences) according to the manufacturer’s instructions. Samples were indexed using the PIPseq UDI-96 kit (Fluent Biosciences)

treatment_protocol: influenza A virus inoculation

value: human cerebral organoid


title: DSP-1001660005602-D-B09_S20-27058

description: Library name: DSP-1001660005602-D-B09


title: Mouse colon, ITGBL1 knockout, DSS-induced colitis, rep2

description:
Library name: KO 2
Bulk RNA-seq of mouse colon tissue

value: Itgbl1 -/-


title: hCOs, BR2007-inoculated, 1 day post-inoculation (seasonal influenza A virus)

description:
Library name: S6
influenza A/Brisbane/59/07 (H1N1) (NCBI taxid:504904)


title: hCOs, mMT2024-inoculated, 1 day post-inoculation (contemporary HPAI H5N1)

description:
Library name: S7
influenza A/mountain lion/Montana/2/2024 (H5N1) (EPI_ISL_19880418)


title: Mouse colon, ITGBL1 knockout, DSS-induced colitis, rep1

description:
Library name: KO 1
Bulk RNA-seq of mouse colon tissue


title: hCOs, mMT2024-inoculated, 3 days post-inoculation (contemporary HPAI H5N1)

description:
Library name: S5
influenza A/mountain lion/Montana/2/2024 (H5N1) (EPI_ISL_19880418)


title: hCOs, bOH2024-inoculated, 3 days post-inoculation (contemporary HPAI H5N1)

description:
Library name: S3
influenza A/bovine/Ohio/B24OSU-342/2024 (H5N1) (EPI_ISL_678615)


title: DSP-1001660005602-D-B07_S20-1194

description: Library name: DSP-1001660005602-D-B07


title: hCOs, bOH2024-inoculated, 1 day post-inoculation (contemporary HPAI H5N1)

description:
Library name: S2
influenza A/bovine/Ohio/B24OSU-342/2024 (H5N1) (EPI_ISL_678615)


title: DSP-1001660005602-D-B08_S20-1194

description: Library name: DSP-1001660005602-D-B08


title: Brain, ck rep5


title: CRR-3

city: xining

first: Shengrong

last: Xu

address: kunlun

institute: qinghai university

description: Library name: sample12

data_processing:
Reads with adapters at the 3′ end and low-quality reads were removed from the raw reads to obtain high-quality clean reads, which were assembled by de novo splicing using Trinity software to obtain transcripts
The longest transcript for each gene was selected as a reference sequence (unigene) for that gene
Using the transcriptome expression quantification software RSEM, clean reads for each sample were aligned to unigene reference sequences.
the number of reads aligned to individual genes was determined to calculate the FPKM value of each gene
Assembly: High-quality total RNA was used for the enrichment of mRNA with a poly-A structure
Supplementary files format and content: tab-delimited text file includes raw counts foe each sample

organism: Hansenia forbesii

source_name: root and canopy

extract_protocol:
Total RNA extracted using the Takara RNA extraction kit
The mRNA was subsequently fragmented (300 bp) to construct the mRNA library, which was sequenced on the Illumina HiSeq sequencing platform to generate 150 bp paired-end reads.

value: root and canopy

value: developmental stage

value: root and canopy cells

value: cultispecies

value: Secondary metabolic differences


title: DSP-1001660005602-D-B06_S20-1194

description: Library name: DSP-1001660005602-D-B06


title: hCOs, VN2004-inoculated, 1 day post-inoculation (historical HPAI H5N1)

description:
Library name: S1
influenza A/Vietnam/1203/2004 (H5N1) (NCBI taxid:284218)


title: Mouse colon, ITGBL1 knockout, DSS-induced colitis, rep3

description:
Library name: KO 3
Bulk RNA-seq of mouse colon tissue


title: CRR-2

description: Library name: sample11


title: DSP-1001660005602-D-B10_S20-27058

description: Library name: DSP-1001660005602-D-B10


title: CRL-2

description: Library name: sample8


title: Mouse colon, WT, DSS-induced colitis, rep1

description:
Library name: WT1
Bulk RNA-seq of mouse colon tissue

value: WT


title: Shank3_KO_Flu

first: Hanyu

last: Wang

address: Siping Road

institute: Tongji University

description:
Library name: Sample2
10× Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger (v9.0.0). The gene expression matrix was analyzed in Seurat (v4.0.0). Following normalization, single-cell and single-nucleus RNA sequencing (sc/sn-RNA seq) datasets were integrated with batch effect correction using Harmony (v1.0). Cells were clustered via a graph-based clustering algorithm and visualized via two-dimensional UMAP. Differentially expressed genes (DEGs) were identified with the FindMarkers function (Presto method), applying thresholds of |log₂(fold change)| > 0.58 and an adjusted P < 0.05 (Bonferroni correction). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the hypergeometric test in R (v4.0.3).
Cell-cell communication analysis was conducted using CellChat (v2.1.2).
Gene set variation analysis (GSVA) was performed with the GSVA package (v1.30.0) using gene sets from the KEGG and GO databases.
Pseudotime trajectories were constructed under an unsupervised framework using Monocle3 (v1.0.0).
Assembly: mm10
Supplementary files format and content: matrix tables with raw genes counts for every gene and every sample

extract_protocol:
All procedures for nucleus suspension preparation were performed on ice. Frozen tissue samples were minced in 1 mL of nuclear lysis buffer (NST), which contained 0.1% NP-40, 10 mM Tris-HCl (pH 7.4), 146 mM NaCl, 1 mM CaCl₂ , 21 mM MgCl₂ , and 1 U/μL RNase inhibitor (Thermo Scientific， Cat.No.EO0382). The lysis duration was 7 minutes. Complete cell lysis was confirmed by trypan blue staining and microscopic examination. Subsequently, 1 mL of ST Wash buffer (10 mM Tris-HCl, 146 mMNaCl, 1 mM CaCl₂ , 21 mM MgCl₂ , 0.01% BSA (MACS, Cat.No.1000076), and 40 U/mL RNase inhibitor was added. The lysate was filtered through a 40-µm cell strainer (Falcon, cat.no. 352340), and the filtrate was transferred to a 15 mL centrifuge tube. The strainer was rinsed with additional ST Wash buffer, and the rinse solution was combined with the nuclear filtrate. The mixture was centrifuged at 500 × g for 5 minutes at 4°C using a horizontal rotor. The nuclear pellet was resuspended in 5 mL of PBS containing 1% BSA, followed by another centrifugation step. Finally, nuclei were resuspended in 100 μL of PBS with 1% BSA. Nuclear viability and concentration were assessed via trypan blue staining and microscopic counting
Single-nucleus RNA sequencing libraries were prepared according to the manufacturer’s protocol for the 10× Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (Cat.no. PN-1000268). The constructed libraries were sequenced on the Illumina Nova 6000 PE150 platform for high-throughput sequencing.

value: Brain

value: fluconazole


title: CRR-1

description: Library name: sample10


title: hCOs, BR2007-inoculated, 3 days post-inoculation (seasonal influenza A virus)

description:
Library name: S8
influenza A/Brisbane/59/07 (H1N1) (NCBI taxid:504904)


title: Shank3_KO_MOCK

description:
Library name: Sample1
10× Genomics

value: MOCK


title: DSP-1001660005602-D-B05_S20-1194

description: Library name: DSP-1001660005602-D-B05


title: CRL-3

description: Library name: sample9


title: CVR-3

description: Library name: sample6


title: NEBNext-Mouse-stomach-1

first: Wen

last: Xiao

address: 320 Yueyang Road

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, CAS

description:
Library name: RPI9
Modeling for machine learning

data_processing:
Raw data (read1) were pre-processed using the FASTX Toolkit (v0.0.14). The first 70 bp of each read were retained, and low-quality sequences were filtered out (-q 20, -p 90). After quality filtering, adapter sequences were trimmed, requiring a minimum 10-nucleotide match at the 3' end. Reads without detected adapter or shorter than 32 bp were discarded. Only reads with "CGA" at positions 4-6 were retained, corresponding to the 5' random adapter. UMI extraction was performed with UMI_tools (v0.5.1) using the following parameters: extract --extract-method regex --bc-pattern="^(?P<umi_1>.{3})(?P<cell_1>.{3})(?P<umi_2>.{4})([A,T,C,G]{5,100})(?P<umi_3>.{4})$". Processed reads were aligned to the target genome using Bowtie (v1.2.1.1) with parameters --best -v 0. Duplicate reads were removed with UMI_tools using the following parameters: dedup --edit-distance-threshold 1 --soft-clip-threshold 0 --method adjacency. Unaligned reads were mapped to the spike-in reference sequences using Bowtie with parameters --best -v 1 --norc and de-duplicated in the same manner. Remaining unmapped reads were aligned to the isomiR reference library with the same parameters and de-duplicated. Molecules aligned to the genome were merged with isomiR molecules for downstream analysis. Molecules were annotated based on the following priority: mature miRNA > isomiR > tRNA > rRNA > snoRNA > snRNA > scRNA > scaRNA > YRNA > lncRNA > mRNA > piRNA > novel miRNA. Mature miRNA, isomiR, piRNA, and novel miRNA were annotated based on exact sequence and length matches, while other small RNA categories were aligned to known sequences using Bowtie with parameters -k=100 -v=0 -norc. Reads that aligned to the genome but lacked known annotations were classified as "others". The expression of molecules in each library was normalized using the standard curve generated from the external spike-ins.
Assembly: human:hg38;  mouse:mm10; crab-eating monkey:macFas5
Supplementary files format and content: absolute quantification of miRNA expression for each Sample

source_name: stomach

extract_protocol:
1 ml of Trizol reagent (Invitrogen) was added to lyse the cells completely. Subsequently, 200 µl of trichloromethane was added and mixed thoroughly. The solution was then centrifuged at 12,000 rpm for 15 min at 4°C. The upper aqueous phase (450 µl) was transferred into a new 1.5 ml EP tube, followed by the addition of 900 µl of absolute ethanol. The solution was mixed by inversion, left to stand at -30°C for 30 min, and then centrifuged again at 12,000 rpm for 15 min at 4°C, until a distinct precipitate formed at the bottom of the tube. After removing the supernatant, the pellet was washed twice with 80% ethanol, air-dried for 2-3 min at room temperature, and dissolved in DEPC-treated water. RNA concentration was measured using a Nanodrop spectrophotometer, and the sample was diluted to a concentration of 100 ng/µl.
100 ng RNA with 0.05 µl of 20 nM EM or RM spike-in control oligos was ligated to a 0.55 µM 3' randomized adapter using 25 U/µl T4 RNA ligase 2 truncated KQ (NEB) in 0.83X T4 RNA ligase reaction buffer (NEB), supplemented with 20% PEG 8000 (NEB) at 25°C overnight. The ligated RNA was then annealed with 1.28 µM RTP. To remove the 3’ adapter-RTP byproduct, 3.33 U/µl 5’ deadenylase (NEB) and 0.2 U/µl lambda exonuclease (NEB) were added, followed by incubation at 30°C for 1 h and 37°C for 2 h, respectively. Subsequently, the product was ligated to a 5’ randomized adapter using 0.4 U/µl of T4 RNA ligase 1 (NEB) in 0.74X T4 RNA ligase reaction buffer, supplemented with 0.7 mM ATP and 17.3% PEG 8000 (NEB) at 25°C for 1 h. Reverse transcription was carried out using 5 U/µl of ProtoScriptII reverse transcriptase (NEB) in 1X ProtoScriptII RT reaction buffer (NEB), containing 0.5 mM dNTPs (Promega) and 10 mM DTT (NEB), at 50°C for 1 h. The resulting cDNA was then amplified using 0.02 U/µl of KOD-Plus-Neo (TOYOBO) in 1X PCR Buffer for KOD-Plus-Neo (TOYOBO), along with 0.5 µM primers, 1.5 mM MgSO4 (TOYOBO), and 0.2 mM dNTPs (TOYOBO). After PCR amplification, the cDNA was gel-purified on a 6% polyacrylamide gel to remove adapter dimers and sequenced using the Illumina NovaSeq platform.

value: stomach

tag: libtype

value: NEBNext


title: DSP-1001660005602-D-B03_S19-26656

description: Library name: DSP-1001660005602-D-B03

value: Lung Cancer

value: immunotherapy


title: NEBNext-Mouse-lung-1

description:
Library name: RPI7
Modeling for machine learning

source_name: lung

value: lung


title: CRL-1

description: Library name: sample7

tag: cell line


title: NEBNext-Mouse-colon-1

description:
Library name: RPI6
Modeling for machine learning

value: colon


title: CVR-1

description: Library name: sample4

tag: cell type


title: NEBNext-Mouse-thymus-1

description:
Library name: RPI8
Modeling for machine learning

source_name: thymus

value: thymus


title: NEBNext-Mouse-liver-1

description:
Library name: RPI5
Modeling for machine learning

source_name: liver

value: liver


title: DSP-1001660005602-D-B04_S19-26656

description: Library name: DSP-1001660005602-D-B04


title: CVL-3

description: Library name: sample3

value: root and canopy

tag: genotype


title: DSP-1001660005602-D-B02_S19-26656

description: Library name: DSP-1001660005602-D-B02

tag: treatment


title: CVL-1

description: Library name: sample1

value: developmental stage


title: DSP-1001660005602-D-B01_S19-26656

description: Library name: DSP-1001660005602-D-B01


title: CVR-2

description: Library name: sample5

value: root and canopy cells


title: NEBNext-Mouse-heart-4

description:
Library name: RPI4
Modeling for machine learning

source_name: heart

value: heart


title: knee Infrapaterllar fat pad, SVF, Female (R1)

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

country: Germany

institute: Berlin Institute of Health, Charité Medical University of Berlin

description: Library name: A4499_RNA_64

data_processing:
Raw FASTQ data underwent standard quality control steps using FastQC, Dupradar, Qualimap, RNA_seqc and Preseq to assess read quality, followed by adapter and quality trimming with fastp. Low-quality bases (Q < 20) and reads shorter than 36 bp were removed to ensure high-quality data for subsequent analysis. Cleaned reads were aligned to the Cavia porcellus (guinea pig) reference genome (assembly Cavpor3.0, GCA_000151735.1) using the STAR aligner, v. 2.7.11a. The corresponding GTF annotation file was used to guide the alignment. Raw gene expression counts were generated using featureCounts, which assigned uniquely mapped reads to annotated genomic features. The data has been stored locally on an implementation of the SODAR system and is accessible through GEO under the identifier XXXX.
For purposes of PCA and visualization, raw counts were normalized using the Regularized Log Transformation (RLD) implemented in the DESeq2 R package, version 1.38. PCA was then performed on the RLD-transformed data to visualize global gene expression differences between the experimental groups.
Assembly: Cavpor3.0, GCA_000151735.1
Supplementary files format and content: Tab separated values (TSV), raw counts returned by featureCounts.

organism: Cavia porcellus

source_name: knee Infrapaterllar fat pad

extract_protocol:
RNA was harvested using RNeasy Mini Kit (QIAGEN).
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA protocol, following the manufacturer’s instructions. Poly(A)-selected RNA was used to construct strand-specific libraries with the NEBNext Ultra II Directional RNA Library Prep Kit.

value: knee Infrapaterllar fat pad

value: SVF

value: Female

tag: replicate


title: DSP-1001660005602-D-A12_S19-26268

description: Library name: DSP-1001660005602-D-A12


title: knee cartilage, CD31+ (SVF), Male (R3)

description: Library name: A4499_RNA_55

source_name: knee cartilage

value: knee cartilage

value: CD31+ (SVF)

value: Male


title: knee cartilage, SVF, Male (R3)

description: Library name: A4499_RNA_53


title: NEBNext-Mouse-brain-2

description:
Library name: RPI3
Modeling for machine learning

source_name: brain

value: brain

value: NEBNext


title: NEBNext-Mouse-muscle-1

description:
Library name: RPI2
Modeling for machine learning

source_name: muscle

value: muscle


title: DSP-1001660005602-D-A10_S19-26268

description: Library name: DSP-1001660005602-D-A10

value: Lung Cancer

value: immunotherapy


title: knee Infrapaterllar fat pad, CD31+ (SVF), Male (R3)

description: Library name: A4499_RNA_43


title: knee Infrapaterllar fat pad, CD31+ (SVF), Male (R4)

description: Library name: A4499_RNA_44


title: knee Infrapaterllar fat pad, SVF, Male (R3)

description: Library name: A4499_RNA_63


title: knee Infrapaterllar fat pad, CD31+ (SVF), Male (R1)

description: Library name: A4499_RNA_41


title: DSP-1001660005602-D-A09_S19-26268

description: Library name: DSP-1001660005602-D-A09


title: NEBNext-Mouse-pancreas-1

description:
Library name: RPI1
Modeling for machine learning

source_name: pancreas

value: pancreas


title: knee Infrapaterllar fat pad, SVF, Male (R2)

description: Library name: A4499_RNA_35


title: NEBNext-Mouse-ovary-1

description:
Library name: RPI17
Modeling for machine learning

source_name: ovary

value: ovary


title: DSP-1001660005602-D-A08_S19-21466

description: Library name: DSP-1001660005602-D-A08


title: knee Infrapaterllar fat pad, SVF, Male (R1)

description: Library name: A4499_RNA_33


title: NEBNext-Mouse-testis-2

description:
Library name: RPI16
Modeling for machine learning

source_name: testis

value: testis


title: DSP-1001660005602-D-A07_S19-21466

description: Library name: DSP-1001660005602-D-A07


title: knee Infrapaterllar fat pad, DPBS, Male (R3)

description: Library name: A4499_RNA_30

value: DPBS


title: NEBNext-Mouse-rectum-1

description:
Library name: RPI15
Modeling for machine learning

source_name: rectum

value: rectum


title: knee Infrapaterllar fat pad, DPBS, Female (R1)

description: Library name: A4499_RNA_32


title: knee Infrapaterllar fat pad, DPBS, Male (R1)

description: Library name: A4499_RNA_28


title: knee Infrapaterllar fat pad, DPBS, Male (R2)

description: Library name: A4499_RNA_29


title: DSP-1001660005602-D-A06_S19-21466

description: Library name: DSP-1001660005602-D-A06


title: NEBNext-Mouse-kidney-1

description:
Library name: RPI14
Modeling for machine learning

source_name: kidney

value: kidney


title: DSP-1001660005602-D-A11_S19-26268

description: Library name: DSP-1001660005602-D-A11

source_name: Lung Cancer


title: knee cartilage, CD31+ (SVF), Female (R1)

description: Library name: A4499_RNA_20


title: NEBNext-Mouse-breast-5

description:
Library name: RPI13
Modeling for machine learning

source_name: breast

value: breast


title: DSP-1001660005602-D-A05_S19-21466

description: Library name: DSP-1001660005602-D-A05


title: knee Infrapaterllar fat pad, CD31+ (SVF), Male (R2)

description: Library name: A4499_RNA_42

value: knee Infrapaterllar fat pad


title: knee cartilage, CD31+ (SVF), Male (R2)

description: Library name: A4499_RNA_18


title: NEBNext-Mouse-adipose-3

description:
Library name: RPI12
Modeling for machine learning

source_name: adipose

value: adipose


title: DSP-1001660005602-D-A04_S19-20906

description: Library name: DSP-1001660005602-D-A04


title: DSP-1001660005602-D-A03_S19-20906

description: Library name: DSP-1001660005602-D-A03


title: photoreceptor, Day 50, ZT20, rep 3

city: West Lafayette

first: Sarah

last: McGovern

state: IN

address: Department of Biochemistry

department: Biochemistry

institute: Purdue University

data_processing:
Adaptors trimmed using Trimmomatic
Alignment using HISAT2
SAM file processing using SAMtools
BigWigs generated using deepTools, CPM-normalized
Assembly: BDGP6.46 (GCA_000001215.4)
Supplementary files format and content: CPM-normalized BigWigs

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: Outer photoreceptors

growth_protocol: Drosophila were maintained in population cages in a 25°C incubator with a 12:12 hour light:dark cycle.

extract_protocol:
400 male flies in triplicate were collected at the indicated days post-eclosion (D10 and D50) and at the indicated Zeitgeber times (ZT0, ZT4, ZT8, ZT12, ZT16, ZT20). GFP-positive photoreceptor nuclei were immunoprecipitated using the nuclei immunoenrichment protocol (dx.doi.org/10.17504/protocols.io.buiqnudw), followed by RNA isolation and purification.
6 ng of nuclear RNA was used to prepare libraries using the Ovation® SoLo® RNA-Seq library preparation kit from Tecan with Drosophila AnyDeplete probes.

value: Outer photoreceptors

value: adult, day 50

tag: time

value: male


title: CVL-2

description: Library name: sample2

source_name: root and canopy

value: root and canopy

value: developmental stage

value: root and canopy cells

value: cultispecies

value: Secondary metabolic differences


title: NEBNext-Mouse-skin-5

description:
Library name: RPI11
Modeling for machine learning

source_name: skin

value: skin

value: NEBNext


title: knee cartilage, SVF, Female (R1)

description: Library name: A4499_RNA_16

value: knee cartilage

value: SVF

value: Female


title: NEBNext-Mouse-spleen-1

description:
Library name: RPI10
Modeling for machine learning

source_name: spleen

value: spleen


title: DSP-1001660005602-D-A02_S19-20906

description: Library name: DSP-1001660005602-D-A02

value: Lung Cancer

value: immunotherapy


title: DSP-1001660002551-C-H12_S19-12863

description: Library name: DSP-1001660002551-C-H12


title: knee cartilage, SVF, Male (R1)

description: Library name: A4499_RNA_10

value: Male


title: photoreceptor, Day 50, ZT20, rep 1

value: Outer photoreceptors


title: DSP-1001660002551-C-H11_S19-12863

description: Library name: DSP-1001660002551-C-H11


title: knee cartilage, DPBS, Male (R4)

description: Library name: A4499_RNA_07

value: DPBS


title: photoreceptor, Day 50, ZT16, rep 3

value: adult, day 50

value: male


title: DSP-1001660002551-C-H10_S19-12863

description: Library name: DSP-1001660002551-C-H10


title: photoreceptor, Day 50, ZT16, rep 2


title: DSP-1001660002551-C-H09_S19-12863

description: Library name: DSP-1001660002551-C-H09


title: photoreceptor, Day 50, ZT16, rep 1


title: knee cartilage, DPBS, Male (R2)

description: Library name: A4499_RNA_05


title: WT-ATAC-rep3.bigwig

first: Weiqi

last: Zhang

address: 280 South Chongqing Road, Shanghai, China

department: Shanghai Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: WT-ATAC-rep3

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Fastp（version 0.24.1）to be high quality clean data.  Reference genome sequences and gene model annotation files of relative species are downloaded from UCSC. Bowtie2-build is used to index reference genome sequence. Clean data is aligned to reference genome via software Bowtie2 (version 2.2.6). Use MACS[1](V2)  to analyze peaks quality control, peaks calling and peaks annotation.
Assembly: GRCm39/mm9
Supplementary files format and content: bigwig

extract_protocol:
For T-bet and  Foxp3 CUT&Tag assay, 2×10^5 WT and V408M Treg cells sorted as described  above from WT and V408M mice were prepared for each reaction. Treg cells were isolated and subjected to CUT&Tag profiling using the Vazyme CUT&Tag Kit (TD904-01) according to the manufacturer’s instructions. Briefly, purified Treg cells were incubated with primary antibodies, followed by binding of secondary antibody and pA-Tn5 transposase complex to enable site-specific tagmentation. After activation of transposase, genomic DNA fragments containing sequencing adapters were released and purified. For ATAC-seq, freshly isolated Treg cells were processed for nuclei preparation, followed by transposition using Tn5 transposase to simultaneously fragment accessible chromatin and insert sequencing adapters. Transposed DNA fragments were then purified and PCR-amplified to construct sequencing libraries.
CUT&Tag DNA samples were quantified using a Qubit 3.0 Fluorometer (Invitrogen) and qualified by Agilent Bioanalyzer 2100(Agilent Technologies). Next generation sequencing library preparations were constructed following the manufacturer’s protocol. For each sample, CUT&Tag product was used for library preparation. The CUT&Tag product was treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dAtailing in one reaction, followed by ligation to adaptors with a “T” base overhang. Adaptor-ligated DNA was then recovered using Beads. Each sample was then amplified by PCR using P5 and P7 primers, with both primers carrying sequences which can anneal with flowcell to perform bridge PCR and P7 primer carrying index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Agilent 2100 Bioanalyzer, and quantified by Qubit 3.0 Fluorometer. Then libraries with different indices were multiplexed and loaded on an Illumina Novaseq instrument according to manufacturer’s instruction.

value: primary T cell

value: splenic CD4+CD25+ Treg cells

value: Wild-type


title: KI-ATAC-rep3.bigwig

description: Library name: KI-ATAC-rep3

value: Foxp3V408M Knock-in


title: KI-ATAC-rep1.bigwig

description: Library name: KI-ATAC-rep1


title: KI-ATAC-rep2.bigwig

description: Library name: KI-ATAC-rep2


title: WT-ATAC-rep2.bigwig

description: Library name: WT-ATAC-rep2


title: DSP-1001660002551-C-H08_S18-565

description: Library name: DSP-1001660002551-C-H08


title: knee cartilage, DPBS, Male (R3)

description: Library name: A4499_RNA_06


title: photoreceptor, Day 50, ZT12, rep 3


title: knee cartilage, SVF, Male (R2)

description: Library name: A4499_RNA_11


title: knee cartilage, DPBS, Male (R1)

description: Library name: A4499_RNA_04


title: DSP-1001660002551-C-H07_S18-565

description: Library name: DSP-1001660002551-C-H07


title: photoreceptor, Day 50, ZT20, rep 2


title: knee cartilage, CD31+ (SVF), Male (R1)

description: Library name: A4499_RNA_17

value: CD31+ (SVF)


title: 02 KD (siRNA for PNN)

type: RNA

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description: The cells were treated with siRNA for PNN followed by culturing at 37°C for 2 days.

hyb_protocol: After fragmentation, biotin-labeled cRNA was hybridized to microarrays at 45°C for 16 h.

scan_protocol: Arrays were washed, stained with streptavidin-phycoerythrin, and scanned using a probe array scanner (Thermo Fisher Scientific).

data_processing: Data were processed using the GeneChip® Analysis Suite.

label: biotin

source_name: Normal human epidermal keratinocytes

label_protocol: Five hundred nanograms of total RNA were used to synthesize complementary RNA (cRNA) using the GeneChip® 3' IVT Express Kit (Thermo Fisher Scientific).

growth_protocol: Normal human epidermal keratinocytes (KK-4009; Kurabo Industries Ltd., Osaka, Japan) were cultured in Humedia-KG2 (Kurabo Industries Ltd, Osaka, Japan) supplemented with 20% FBS in a humidified atmosphere with 5% CO2. All experiments were carried out on cells at the third passage.

extract_protocol: Total RNA was prepared from normal human epidermal keratinocytes (KK-4009; Kurabo Industries Ltd., Osaka, Japan) using a method previously described [Makino et al., J Biol Chem. 2001 Dec 14;276(50):47445-52.] and was pretreated with DNase I (Roche Diagnostics, Basel, Schweiz). RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies). RNA samples with RIN (RNA integrity number) values >9.5 were considered acceptable.

treatment_protocol: The cells were transfected with siRNA duplexes (ambion, silencer select, Thermo Fisher Scientific K.K., Tokyo, Japan) by a reverse transfection method using Lipofectoamine RNAiMAX (Thermo Fisher Scientific, Inc., Waltham, MA, USA) according to the manufacturer’s instructions. Two days after the transfection, the cells were used for the experiments.

tag: gender

value: newborn

value: skin

tag: life span

value: third passage

tag: morphology

value: cobblestone appearance


title: WT-ATAC-rep1.bigwig

description: Library name: WT-ATAC-rep1

value: spleen


title: photoreceptor, Day 50, ZT12, rep 2


title: knee cartilage, PLX-PAD (1M), Female (R2)

description: Library name: A4499_RNA_50

value: knee cartilage

value: PLX-PAD (1M)

value: Female


title: DSP-1001660002551-C-H06_S18-565

description: Library name: DSP-1001660002551-C-H06

value: Lung Cancer

value: immunotherapy


title: photoreceptor, Day 50, ZT12, rep 1

value: Outer photoreceptors

value: adult, day 50


title: knee cartilage, PLX-PAD (1M), Male (R2)

description: Library name: A4499_RNA_49

value: Male


title: photoreceptor, Day 50, ZT8, rep 3

value: male


title: knee cartilage, PLX-PAD (2M), Female (R1)

description: Library name: A4499_RNA_15

value: PLX-PAD (2M)


title: 01 CTR (negative control siRNA)

description: The cells were treated with negative control siRNA followed by culturing at 37°C for 2 days.


title: photoreceptor, Day 50, ZT8, rep 2


title: KI-Tbet-rep1.bigwig

description: Library name: KI-Tbet-rep1

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Fastp（version 0.24.1）to be high quality clean data.  Reference genome sequences and gene model annotation files of relative species are downloaded from UCSC. Bowtie2-build is used to index reference genome sequence. Clean data is aligned to reference genome via software Bowtie2 (version 2.2.6). Use MACS[1](V2)  to analyze peaks quality control, peaks calling and peaks annotation.
Assembly: GRCm39/mm9
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

value: primary T cell

value: splenic CD4+CD25+ Treg cells

value: Foxp3V408M Knock-in


title: knee cartilage, PLX-PAD (2M), Male (R2)

description: Library name: A4499_RNA_13


title: WT-Tbet-rep3.bigwig

description: Library name: WT-Tbet-rep3

value: Wild-type


title: knee cartilage, PLX-PAD (2M), Male (R3)

description: Library name: A4499_RNA_14


title: DSP-1001660002551-C-H02_S17-9483

description: Library name: DSP-1001660002551-C-H02


title: photoreceptor, Day 50, ZT4, rep 3


title: knee cartilage, PLX-PAD (2M), Male (R1)

description: Library name: A4499_RNA_12


title: DSP-1001660002551-C-H03_S17-9483

description: Library name: DSP-1001660002551-C-H03


title: photoreceptor, Day 50, ZT4, rep 2


title: WT-Tbet-rep1.bigwig

description: Library name: WT-Tbet-rep1


title: photoreceptor, Day 50, ZT0, rep 3


title: knee cartilage, PLX-PAD (1M), Female (R1)

description: Library name: A4499_RNA_08


title: DSP-1001660002551-C-G12_S17-28460

description: Library name: DSP-1001660002551-C-G12


title: DSP-1001660002551-C-H05_S18-565

description: Library name: DSP-1001660002551-C-H05


title: KI-Foxp3-rep3.bigwig

description: Library name: KI-Foxp3-rep3


title: DSP-1001660002551-C-H01_S17-9483

description: Library name: DSP-1001660002551-C-H01


title: WT-Tbet-rep2.bigwig

description: Library name: WT-Tbet-rep2


title: photoreceptor, Day 50, ZT4, rep 1


title: DSP-1001660002551-C-G11_S17-28460

description: Library name: DSP-1001660002551-C-G11


title: KI-Tbet-rep2.bigwig

description: Library name: KI-Tbet-rep2


title: KI-Foxp3-rep2.bigwig

description: Library name: KI-Foxp3-rep2


title: KI-Tbet-rep3.bigwig

description: Library name: KI-Tbet-rep3


title: knee cartilage, DPBS, Male (R4)

description: Library name: A4499_RNA_07

value: DPBS


title: photoreceptor, Day 50, ZT0, rep 2


title: DSP-1001660002551-C-H04_S17-9483

description: Library name: DSP-1001660002551-C-H04


title: knee cartilage, DPBS, Male (R3)

description: Library name: A4499_RNA_06


title: DSP-1001660002551-C-G10_S17-28460

description: Library name: DSP-1001660002551-C-G10


title: photoreceptor, Day 50, ZT0, rep 1


title: knee cartilage, DPBS, Male (R2)

description: Library name: A4499_RNA_05


title: DSP-1001660002551-C-G09_S17-28460

description: Library name: DSP-1001660002551-C-G09


title: WT-Foxp3-rep3.bigwig

description: Library name: WT-Foxp3-rep3


title: photoreceptor, Day 10, ZT20, rep 3

value: adult, day 10


title: DSP-1001660002551-C-G08_S17-18548

description: Library name: DSP-1001660002551-C-G08


title: photoreceptor, Day 10, ZT20, rep 2


title: knee cartilage, DPBS, Male (R1)

description: Library name: A4499_RNA_04


title: knee cartilage, PLX-PAD (1M), Male (R1)

description: Library name: A4499_RNA_01


title: WT-Foxp3-rep2.bigwig

description: Library name: WT-Foxp3-rep2

value: spleen


title: DSP-1001660002551-C-G07_S17-18548

description: Library name: DSP-1001660002551-C-G07