title: Healthy mice LN 15,BCR

description: BD Rhapsody,BCR

value: No treatment


title: Cured PN 21,BCR

status: Public on Nov 14 2025

type: SRA

city: Suzhou

first: Mi

last: Liu

state: Jiangsu

address: 1435 of Yunxuan Lou, Du Shu Hu Xiao Qu,, Gong Ye Yuan Qu

department: Pharmaceutics

country: China

institute: Soochow University

description: BD Rhapsody,BCR

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8
We applied BD Genomics Rhapsody Analysis pipeline(https://bitbucket.org/CRSwDev/cwl/src/master/,V1.10.1)with default parameter toanalyzesingle-cellGEX,TCR/BCRsequencingdata,assemblecontigscorrespondingtorearrangedTCR/BCRchainmRNA.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files;filtered contig for TCR and BCR sequencing.

molecule: total RNA

organism: Mus musculus

source_name: Draning lymph nodes

extract_protocol:
Healthy mice, tumor-bearing mice treated with PBS, non-cured mice or cured mice were sacrifaced. Blood,Spleen and drainining lymph nodes were collected. PBMC, single cell suspension of splenocytes or single cell suspension of draining lymph node cells were prepared for single cell sequencing analysis
BD Rhapsody system and BD RhapsodyTM TCR/BCR Amplification kit(Cat.NO.633773) were used to capture the single cells and construct the scRNA-Seq libraries and V(D)J libraries.
scRNA-seq; scTCR-seq; scBCR-seq

treatment_protocol: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then these tumor-bearing mice were treated with nanovaccines or PBS. After nanovaccine treatment, non-cured mice were sacrificed and cured mice were sacrificed at different time (Freshly, 3 months or 8 months). In terms of cured mice sacrificed at 8 months, they were rechallenged with nanovaccines or cancer cells.

tag: tissue

value: Draning lymph nodes

tag: cell type

value: Draning lymph node cells

tag: genotype

tag: treatment

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with nanovaccines


title: Blood, DM1 patient, classic3

city: San José

first: Fernando

last: Morales

address: San Pedro de Montes de Oca

country: Costa Rica

institute: Universidad de Costa Rica

description:
Library name: CR70_BL
DM1 patient living in Costa Rica

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 for basecalling and demultiplexing
Raw sequence quality was assessed using FASTQC.
Reads passing quality control were mapped to the hg19 genome using Hisat2.
Percent splice in (PSI or Ψ) values were computed using MISO with hg19 v2.0 MISO annotations.
TPM were calculated using Kallisto
Assembly: hg19
Supplementary files format and content: txt format, TPM counts for all samples

organism: Homo sapiens

source_name: Blood

extract_protocol:
RNA samples used in this study were previously purified using TRIzol reagent (Thermo-Scientific, USA) from three different tissues (blood, skeletal muscle [tibialis anterior-TA], and skin) of the same DM1 patients.
RNA-seq libraries were constructed using the NEBNext Ultra II RNA library prep kit for Illumina (New England Biolabs, USA) with ribosomal RNA depletion (NEBNext rRNA depletion kit, New England Biolabs). Strand-specific RNA-seq libraries were sequenced using Illumina NextSeq 500 v2 with 75 nucleotide paired-end reads.

value: Blood


title: VLU1

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

country: USA

institute: University of Miami

data_processing:
Reads were aligned to the human genome reference index hg38 using STAR 2.7.3a
Gene counts were normalized to counts per million with a 0.0001 offset
Assembly: hg38
Supplementary files format and content: Tab delimited normalized counts file. Column 1 represents gene symbol and each subsequent column is gene counts normalized to counts per million with a 0.0001 offset for each sample

source_name: Healing ulcer

extract_protocol:
Total RNA was extracted using Rneasy Midi Kit (Qiagen)
Total RNA was prepped with the Tecan/Nugen Universal Plus Total RNASeq w/ Human AnyDepleteusing ~60ng via Qubit and 14 cycles PCR. Libraries were sequenced on Illumina Novaseq 6000

value: Healing ulcer


title: Fascia_acupuncture_scRNA2

city: Nanjing

first: ZhenWei

last: Zhang

address: No. 1 Weigang

department: veterinarian

institute: Nanjing Agricultural University

description:
Fascia_AC_2
10x Genomics

library_source: transcriptomic single cell

data_processing:
The reads were processed using the Cell Ranger V6.0.1 pipeline with default and recommended parameters. FASTQ files generated from Illumina sequencing output were aligned to the rat/human genome (version mRatBN7.2/GRCh38.p13) using the STAR algorithm. Subsequently, Gene-Barcode matrices were generated for each individual sample by counting Unique Molecular Identifiers (UMIs) and filtering non-cell associated barcodes. This resulted in a gene-barcode matrix containing the barcoded cells and gene expression counts.
Assembly: mRatBN7.2
Supplementary files format and content: 10X expression matrix generated by CellRanger V6.0.1

organism: Rattus norvegicus

source_name: subcutaneous fascia

extract_protocol:
The process of tissue dissociation and cell purification for single-cell RNA sequencing and fascia primary cell extraction was meticulously executed. The fascia was placed in a sterile culture dish containing 10 ml of 1x Dulbecco’s Phosphate-Buffered Saline (DPBS; Thermo Fisher, Cat. no. 14190144) on ice to eliminate the residual blood and adipose, followed by mincing on ice.We employed a specially formulated dissociation solution, composed of the collagenase type 4 (sigma-Aldrich, Cat. no. C5138), elastase (sigma-aldrich, Cat. no. e1250), and 10 ug/mL DNase I (Thermo Fisher, Cat. no. en0523) dissolved in PBS with 5% Fetal Bovine Serum (FBS; Thermo Fisher, Cat. no. SV30087.02), to digest the fascia. The fascia was dissociated at 37℃ with a shaking speed of 50 rpm for approximately 40 minutes. We collected the dissociated cells at 20-minute intervals to maximize cell yield and viability.Cell suspensions were filtered by the sequence of nylon cell strainer from 100μm to 40 μm, and residual red blood cells were eliminated using 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57). The dissociated cells were then washed with 1x DPBS containing 2% FBS. Cell viability was assessed using 0.4% Trypan blue staining and the Countess® II Automated Cell Counter (Thermo Fisher), all samples of suspension cells were filtered by Dead Cell Removal Kit (Miltenyi Biotec, Cat. No. 130-090-101), and only samples with >95 % living cells were used for next steps.Suspension cells were prepared for 10X library construction and 3’ sequencing, water-in-oil solution was prepared by the Chromium™ Single Cell Controller (10X Genomics).
The process of tissue dissociation and cell purification for single-cell RNA sequencing and fascia primary cell extraction was meticulously executed. The fascia was placed in a sterile culture dish containing 10 ml of 1x Dulbecco’s Phosphate-Buffered Saline (DPBS; Thermo Fisher, Cat. no. 14190144) on ice to eliminate the residual blood and adipose, followed by mincing on ice.We employed a specially formulated dissociation solution, composed of the collagenase type 4 (sigma-Aldrich, Cat. no. C5138), elastase (sigma-aldrich, Cat. no. e1250), and 10 ug/mL DNase I (Thermo Fisher, Cat. no. en0523) dissolved in PBS with 5% Fetal Bovine Serum (FBS; Thermo Fisher, Cat. no. SV30087.02), to digest the fascia. The fascia was dissociated at 37℃ with a shaking speed of 50 rpm for approximately 40 minutes. We collected the dissociated cells at 20-minute intervals to maximize cell yield and viability.Cell suspensions were filtered by the sequence of nylon cell strainer from 100μm to 40 μm, and residual red blood cells were eliminated using 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57). The dissociated cells were then washed with 1x DPBS containing 2% FBS. Cell viability was assessed using 0.4% Trypan blue staining and the Countess® II Automated Cell Counter (Thermo Fisher), all samples of suspension cells were filtered by Dead Cell Removal Kit (Miltenyi Biotec, Cat. No. 130-090-101), and only samples with >95 % living cells were used for next steps.Suspension cells were prepared for 10X library construction and 3’ sequencing, water-in-oil solution was prepared by the Chromium™ Single Cell Controller (10X Genomics).

value: subcutaneous fascia

value: dysentery


title: Muscle, DM1 patient, pediatric1

description:
Library name: CR69_SM
DM1 patient living in Costa Rica

source_name: Muscle

value: Muscle


title: Non-GCSCs 003 [miRNA]

first: Xiaowei

last: Chen

address: No.138 Xianlin Avenue, Qixia District

institute: Nanjing University of Chinese Medicine

description:
CSC-3N
miRNA_Expression_Summary.xlsx

data_processing:
Use the analysis process of Stringtie to quantify the expression of known genes and transcripts. Use Deseq2 software to analyze the differentially expressed genes between the case group and the control group in pairwise groups. Type is the screening result, and if pvalues<0.05 and | log2 (fold change) |>1 is the differential gene,
Assembly: hg38
Supplementary files format and content: mRNA_Expression_Summary.xlsx
Supplementary files format and content: circRNA_Expression_Summary.xlsx
Supplementary files format and content: lncRNA_Expression_Summary.xlsx
Supplementary files format and content: miRNA_Expression_Summary.xlsx

source_name: non-gastric cancer stem cells

extract_protocol:
Based on the inclusion-exclusion criteria, tumor tissues from three gastric cancer patients were collected and prepared into single-cell suspensions. Cells were labeled with antibodies against two gastric cancer stem cell surface markers, CD54 and CD44. The labeled cells were sorted by flow cytometric sorting technique to obtain CD54+ CD44+ double-positive cell subpopulation and CD54- CD44- double-negative cell subpopulation of gastric cancer stem cells (GCSCs) and non-gastric cancer stem cells (Non-GCSCs), respectively. Total RNA was extracted from GCSCs and Non-GCSCs with TRIzol reagent (Invitrogen, Carlsbad, CA, USA). Total RNA quality was assessed using agarose gel electrophoresis and quantified using a NanoDrop2000 spectrophotometer (Thermo Fisher Scientific, USA). The Agilent Bioanalyzer 2100 (Agilent Technologies, USA) was used to verify RNA integrity.
The fragmented RNA was used as a template for first strand cDNA synthesis, using random primers (Random Hexamers).The second strand of cDNA was synthesized using DNA polymerase and the double stranded cDNA was purified with magnetic beads (AMPure XP; Beckman Coulter,USA).Then addition of adenlylate 3′ ends, connection sequencing adapters, selection library size, PCR amplification and checking library quality were performed in turn.
The whole transcriptome sequencing project requires the construction of two sequencing libraries simultaneously, including a strand-specific library for rRNA removal and a small RNA library. The constructed library was sequenced using Illumina high-throughput sequencing platform according to standard protocol (Genesky Biotechnologies Inc., Shanghai, China). This study obtained the expression landscape of mRNAs, miRNAs, circRNAs, and lncRNAs from the same samples in the discovery set and conducted subsequent bioinformatics analysis.The cDNA library was sequenced on an Illumina NovaSeq 6000 sequencing platform to generate read pairs of 150 bp length.

value: non-gastric cancer stem cells


title: Fascia_acupuncture_scRNA1

description:
Fascia_AC_1
10x Genomics


title: Cured SP 13,BCR

description: BD Rhapsody,BCR

source_name: Spleen

value: Spleen

value: Splenocytes


title: Skin, DM1 patient, pediatric1

description:
Library name: CR69_SK
DM1 patient living in Costa Rica

source_name: Skin

value: Skin


title: Non-GCSCs 002 [miRNA]

description:
CSC-2N
miRNA_Expression_Summary.xlsx


title: Blood, DM1 patient, pediatric1

description:
Library name: CR69_BL
DM1 patient living in Costa Rica


title: Non-GCSCs 001 [miRNA]

description:
CSC-1N
miRNA_Expression_Summary.xlsx


title: Cured SP 12,BCR

description: BD Rhapsody,BCR


title: rat_fascia2

first: Haixiang

last: Huang

state: 江苏

address: No.1, Weigang, Xuanwu district

department: College of veterinary

description: 3' paired-end scRNA-seq

source_name: subcutanous fascia

extract_protocol:
The process of tissue dissociation and cell purification for single-cell RNA sequencing and SF primary cell extraction was meticulously executed. The SF and skin tissues were placed in a sterile culture dish containing 10 ml of 1x Dulbecco’s Phosphate-Buffered Saline (DPBS; Thermo Fisher, Cat. no. 14190144) on ice to eliminate the residual blood and adipose, followed by mincing on ice. We employed a specially formulated dissociation solution, composed of the collagenase type 4 (sigma-Aldrich, Cat. no. C5138), elastase (sigma-aldrich, Cat. no. e1250), and 10 ug/mL DNase I (Thermo Fisher, Cat. no. en0523) dissolved in PBS with 5% Fetal Bovine Serum (FBS; Thermo Fisher, Cat. no. SV30087.02), to digest the SF and skin. The SF and skin tissues were dissociated at 37℃ with a shaking speed of 50 r.p.m for approximately 40 minutes. We collected the dissociated cells at 20-minute intervals to maximize cell yield and viability. Cell suspensions were filtered by the sequence of nylon cell strainer from 100μm to 40 μm, and residual red blood cells were eliminated using 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57). The dissociated cells were then washed with 1x DPBS containing 2% FBS. Cell viability was assessed using 0.4% Trypan blue staining and the Countess® II Automated Cell Counter (Thermo Fisher), all samples of suspension cells were filtered by Dead Cell Removal Kit (Miltenyi Biotec, Cat. No. 130-090-101), and only samples with >95 % living cells were used for next steps. Suspension cells were prepared for 10X library construction and 3’ sequencing, water-in-oil solution was prepared by the Chromium™ Single Cell Controller (10X Genomics).
Beads, each carrying a unique molecular identifier (UMI) and cell barcodes, were loaded to near saturation, ensuring each cell was paired with a bead in a Gel Beads-in-emulsion (GEM). Following exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. The beads were then collected into a single tube for reverse transcription. During cDNA synthesis, each cDNA molecule was tagged at the 5’ end (corresponding to the 3’ end of a messenger RNA transcript) with a UMI and a cell label indicating its cell of origin. The 10x beads were then subjected to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All subsequent procedures, including library construction, were performed according to the standard manufacturer’s protocol (Chromium SingleCell 3ʹ v3.1). The sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on a NovaSeq6000 (Illumina) using 2x150 chemistry.

value: subcutanous fascia

value: WT


title: rat_fascia1

description: 3' paired-end scRNA-seq


title: Muscle, DM1 patient, classic23

description:
Library name: CR430_SM
DM1 patient living in Costa Rica


title: rat_skin2

description: 3' paired-end scRNA-seq

source_name: skin

value: skin


title: Blood, DM1 patient, classic23

description:
Library name: CR430_BL
DM1 patient living in Costa Rica


title: Cured SP 11,BCR

description: BD Rhapsody,BCR


title: GCSCs 002 [miRNA]

description:
CSC-2C
miRNA_Expression_Summary.xlsx

source_name: gastric cancer stem cells

value: gastric cancer stem cells


title: Treated not cured SP 10,BCR

description: BD Rhapsody,BCR


title: rat_skin1

description: 3' paired-end scRNA-seq


title: PBS treated SP 9,BCR

description: BD Rhapsody,BCR

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with PBS


title: Muscle, DM1 patient, pediatric4

description:
Library name: CR428_SM
DM1 patient living in Costa Rica


title: GCSCs 003 [miRNA]

description:
CSC-3C
miRNA_Expression_Summary.xlsx


title: Healthy mice SP 8,BCR

description: BD Rhapsody,BCR

value: No treatment


title: Non-GCSCs 003

description:
CSC-3N
mRNA_Expression_Summary.xlsx
circRNA_Expression_Summary.xlsx
lncRNA_Expression_Summary.xlsx


title: Cured SP 14,BCR

description: BD Rhapsody,BCR


title: DSP-1001660014619-C-A01

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description:
Library name: DSP-1001660014619-C-A01_NTC
spatial transcriptomic sequencing

data_processing:
Digital count conversion (.dcc) files were produced from fastq files using the GeoMx NGS Pipeline 2.3.3.10 desktop application.  Briefly, reads are trimmed to remove adapter sequences followed by merging paired-end reads. Stitched reads are then aligned to RTS-ID barcodes in the reference assay. PCR duplicates are removed by sorting on UMIs. Supplemental file Hs_R_NGS_WTA_v1.0 contains RTS-ID mapping.
Assembly: GRCh38.p13. Reads are aligned to GeoMx RTS_ID barcodes as part of the GeoMx NGS Pipeline to generate .dcc files
Supplementary files format and content: deduplicated read counts
Library strategy: Spatial Transcriptomics

organism: synthetic construct

source_name: lung

extract_protocol:
Sample extraction from tissue slides was performed on the GeoMx Digital Spatial Profiler
Samples were amplified, pooled, purified, and checked for quality control according to the GeoMx NGS Readout NGS Library Preparation and Sequencing protocols

tag: slide name

value: No Template Control

value: lung


title: Blood, DM1 patient, pediatric4

description:
Library name: CR428_BL
DM1 patient living in Costa Rica

value: Blood


title: DSP-1001660014618-B-A01

description:
Library name: DSP-1001660014618-B-A01_NTC
spatial transcriptomic sequencing


title: Cured PBMC 7,BCR

description: BD Rhapsody,BCR

value: PBMC

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with nanovaccines


title: Muscle, DM1 patient, classic22

description:
Library name: CR422_SM
DM1 patient living in Costa Rica


title: Non-GCSCs 002

description:
CSC-2N
mRNA_Expression_Summary.xlsx
circRNA_Expression_Summary.xlsx
lncRNA_Expression_Summary.xlsx


title: DSP-1001660014616-A-A01

description:
Library name: DSP-1001660014616-A-A01_NTC
spatial transcriptomic sequencing


title: Cured PBMC 6,BCR

description: BD Rhapsody,BCR


title: Skin, DM1 patient, classic22

description:
Library name: CR422_SK
DM1 patient living in Costa Rica


title: Non-GCSCs 001

description:
CSC-1N
mRNA_Expression_Summary.xlsx
circRNA_Expression_Summary.xlsx
lncRNA_Expression_Summary.xlsx


title: DSP-1001660011973-F-A01

description:
Library name: DSP-1001660011973-F-A01_NTC
spatial transcriptomic sequencing


title: Blood, DM1 patient, classic22

description:
Library name: CR422_BL
DM1 patient living in Costa Rica


title: Cured PBMC 5,BCR

description: BD Rhapsody,BCR


title: Cured PBMC 4,BCR

description: BD Rhapsody,BCR


title: Muscle, DM1 patient, Mild 4

description:
Library name: CR421_SM
DM1 patient living in Costa Rica


title: DSP-1001660011972-E-A01

description:
Library name: DSP-1001660011972-E-A01_NTC
spatial transcriptomic sequencing


title: DSP-1001660020373-D-A01

description:
Library name: DSP-1001660020373-D-A01_NTC
spatial transcriptomic sequencing


title: Treated not cured PBMC 3,BCR

description: BD Rhapsody,BCR


title: GCSCs 001 [miRNA]

description:
CSC-1C
miRNA_Expression_Summary.xlsx


title: Skin, DM1 patient, Mild 4

description:
Library name: CR421_SK
DM1 patient living in Costa Rica


title: GCSCs 001

description:
CSC-1C
mRNA_Expression_Summary.xlsx
circRNA_Expression_Summary.xlsx
lncRNA_Expression_Summary.xlsx


title: Blood, DM1 patient, Mild 4

description:
Library name: CR421_BL
DM1 patient living in Costa Rica


title: PBS treated PBMC 2,BCR

description: BD Rhapsody,BCR


title: DSP-1001660020372-E-A01

description:
Library name: DSP-1001660020372-E-A01_NTC
spatial transcriptomic sequencing


title: Input

city: Shijiazhuang

first: lingxiao

last: xing

state: hebei

address: 361 zhongshan Road

institute: hebei medical university

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg38 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control and an initial threshold q-value of 0.05 as cutoff
Assembly: GRCh38
Supplementary files format and content: bigwig files were generated using Deeptools(3.5.0),narrowPeak  file were generated using MACS2(2.2.7.1) (except for Input sample)

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

value: Human  NSCLC cell line

tag: chip antibody


title: Healthy mice PBMC 1,BCR

description: BD Rhapsody,BCR


title: Muscle, DM1 patient, classic21

description:
Library name: CR404_SM
DM1 patient living in Costa Rica

value: Muscle


title: DSP-1001660020370-C-A01

description:
Library name: DSP-1001660020370-C-A01_NTC
spatial transcriptomic sequencing


title: DSP-1001660020371-A-A01

description:
Library name: DSP-1001660020371-A-A01_NTC
spatial transcriptomic sequencing


title: Blood, DM1 patient, classic21

description:
Library name: CR404_BL
DM1 patient living in Costa Rica


title: Anti-flag (ETV4)

value: Sigma F1804


title: DSP-1001660015818-B-A01

description:
Library name: DSP-1001660015818-B-A01_NTC
spatial transcriptomic sequencing


title: Muscle, DM1 patient, classic20

description:
Library name: CR39_SM
DM1 patient living in Costa Rica


title: GCSCs 003

description:
CSC-3C
mRNA_Expression_Summary.xlsx
circRNA_Expression_Summary.xlsx
lncRNA_Expression_Summary.xlsx


title: CD11b+ cells, olaparib + MSA-2 2

city: Boston

first: Jean

last: Zhao

state: MA

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description: Column names: Gene,LD_001,LD_002,LD_003,LD_004,LD_005,LD_006,LD_007,LD_008,LD_009,LD_010,LD_011,LD_012

data_processing:
Data processing used the ampliSeqRNA plugin v5.12.0.1 available inside the Ion Torrent suite 5.12 for Ion torrent sequencing platform
with default settings for all steps
Assembly: Mouse 46k: WG00278_Reference, (WG00278_Designed2.bed);   Mouse transcriptome: AmpliSeq_Mouse_Transcriptome_v1.fasta, (AmpliSeq_Mouse_Transcriptome_V1_Designed.bed)
Supplementary files format and content: xls: Tab-separated values and matrix file

source_name: Ascites

growth_protocol: PBM and PBM-R tumors: about 0.2 million tumor cells were transplanted orthotopically into 6- to 8-week-old female syngeneic FVB/NJ mice to generated tumors for drug evaluation.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (QIAGEN, # 74134).
RNA libraries were prepared using Ampliseq Library Prep Kit following manufacturer's protocols for targeted amplicon amplification
Other: Mouse 46K, Ion AmpliSeq Panels Mouse 46K genes for transcriptome analysis of PBM and PBM-R tumors; Mouse transcriptome,  Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit for transcriptome analysis of myeloid cells.

treatment_protocol: PBM and PBM-R tumors: mice bearing orthotopic PBM tumors were treated with vehicle control or olaparib (50 mg/kg/day). Tumors were collected when mice reach humane endpoints. Myeloid cells: PBM-R tumor-bearing mice were treated with treated with control, olaparib, MSA-2 and MSA-2 in combination with MSA-2 for 24 hours. Olaparib (AZD2281) was administered daily by i.p. injection at a dose of 50mg/kg body weight. MSA-2 was administered every other day (three times a week, two weeks on followed by one week off) by i.p. injection at a dose of 25 mg/kg body weight. Myeloid cells enriched from ascites were subjected to transcriptome analysis.

value: Ascites

value: primary myeloid cells

value: Wild-type

value: Olaparib in combination with MSA-2


title: Cured LN 19,TCR

description: BD Rhapsody,TCR

value: Draning lymph nodes

value: Draning lymph node cells


title: DRG, Male, 24h, IL, rep 5

city: Würzburg

first: Robert

last: Blum

address: Josef-Schneider-Str. 11

department: Department of Neurology

country: Germany

institute: University Hospital Würzburg

description:
DRG_M_24h_IL_R5
RC29  IL - M 24h
Raw_count_table_2.csv

data_processing:
Base calling with Illumina NextSeq RTA v2.11.3 (NextSeq 500) and v3.9.25/v3.10.30 (NextSeq 2000)
FASTQ conversion with bcl2fastq v2.20.0.422/bcl-convert v4.0.3
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) v2.5 (parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) except for Male, 5W samples where read 3' ends were initially trimmed by 25 bases (parameters: -u -25 --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) to allow fair comparison with Male, 1W samples at 76 nt read length.
Alignment of trimmed reads to rat genome using STAR (Dobin et al., 2013) v2.7.2b with default parameters except for including transcript annotations from RefSeq annotation version 108 for mRatBN7.2
Calculation of read counts on exon level summarized for each gene (RefSeq annotation version 108 for mRatBN7.2) using featureCounts v1.6.4 from Subread package (Liao et al., 2014) (parameters: -s 2 -t exon -M -O --fraction)
Assembly: GCF_015227675.2/mRatBN7.2
Supplementary files format and content: Character (TAB) separated value file containing raw read counts

source_name: dorsal root ganglion (DRG)

extract_protocol:
Arturus PicoPure kit (with lysis at 30Hz for 2 mins in a Retsch Bead Mill)
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was ≥ 7,5. DNA libraries suitable for sequencing were prepared from 300-500 ng of total RNA with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions (1/2 volume). After 13-15 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~310 bp by electrophoresis on Agilent DNA 1000 Bioanalyzer microfluidic chips. Sequencing of pooled libraries, spiked with 1% PhiX control library, was performed at ~25 million reads/sample in single-end mode with 75 nt read length on the NextSeq 500 platform (Illumina) or 100 nt read lenght on the NextSeq 2000 platform (Illumina).

value: dorsal root ganglion (DRG)

tag: Sex

value: male

tag: time

value: Chronic Constriction Injury (CCI), ipsilateral side

tag: replicate

value: rep 5


title: GCSCs 002

description:
CSC-2C
mRNA_Expression_Summary.xlsx
circRNA_Expression_Summary.xlsx
lncRNA_Expression_Summary.xlsx

value: gastric cancer stem cells


title: CD11b+ cells, olaparib + MSA-2 1


title: DRG, Male, 24h, IL, rep 6

description:
DRG_M_24h_IL_R6
RC30  IL - M 24h
Raw_count_table_2.csv

value: rep 6


title: Skin, DM1 patient, classic20

description:
Library name: CR39_SK
DM1 patient living in Costa Rica

value: Skin


title: Cured LN 18,TCR

description: BD Rhapsody,TCR

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with nanovaccines


title: Muscle, DM1 patient, pediatric2

description:
Library name: CR375_SM
DM1 patient living in Costa Rica


title: Muscle, DM1 patient, classic19

description:
Library name: CR373_SM
DM1 patient living in Costa Rica


title: Treated not cured LN 17,TCR

description: BD Rhapsody,TCR


title: PBS treated LN 16,TCR

description: BD Rhapsody,TCR

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with PBS


title: DRG, Male, 24h, IL, rep 4

description:
DRG_M_24h_IL_R4
RC28  IL - M 24h
Raw_count_table_2.csv

value: rep 4


title: DRG, Male, 24h, IL, rep 3

description:
DRG_M_24h_IL_R3
RC27  IL - M 24h
Raw_count_table_2.csv

value: rep 3


title: CD11b+ cells, MSA-2 3

value: Ascites


title: CD11b+ cells, MSA-2 1

value: primary myeloid cells


title: Cured PN 21,TCR

description: BD Rhapsody,TCR


title: Healthy mice LN 15,TCR

description: BD Rhapsody,TCR

value: No treatment


title: CD11b+ cells, olaparib + MSA-2 3

value: Wild-type

value: Olaparib in combination with MSA-2


title: DRG, Male, 24h, IL, rep 2

description:
DRG_M_24h_IL_R2
RC26  IL - M 24h
Raw_count_table_2.csv

value: rep 2


title: Blood, DM1 patient, classic19

description:
Library name: CR373_BL
DM1 patient living in Costa Rica

value: Blood


title: Cured SP 14,TCR

description: BD Rhapsody,TCR

value: Spleen

value: Splenocytes


title: CD11b+ cells, olaparib 3

value: Olaparib


title: Cured LN 20,TCR

description: BD Rhapsody,TCR

value: Draning lymph nodes

value: Draning lymph node cells


title: Blood, DM1 patient, classic18

description:
Library name: CR363_BL
DM1 patient living in Costa Rica


title: DRG, Male, 24h, IL, rep 1

description:
DRG_M_24h_IL_R1
RC25  IL - M 24h
Raw_count_table_2.csv

value: dorsal root ganglion (DRG)

value: male

value: Chronic Constriction Injury (CCI), ipsilateral side

value: rep 1


title: CD11b+ cells, olaparib 2


title: DRG, Male, 24h, CL, rep 6

description:
DRG_M_24h_CL_R6
RC30  CL - M 24h
Raw_count_table_2.csv

value: Chronic Constriction Injury (CCI), contalateral side

value: rep 6


title: Cured SP 13,TCR

description: BD Rhapsody,TCR

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with nanovaccines


title: DRG, Male, 24h, CL, rep 5

description:
DRG_M_24h_CL_R5
RC29  CL - M 24h
Raw_count_table_2.csv

value: rep 5


title: Cured SP 12,TCR

description: BD Rhapsody,TCR


title: CD11b+ cells, olaparib 1

value: Ascites

value: primary myeloid cells

value: Wild-type


title: CD11b+ cells, control 3

value: Vehicle control


title: CD11b+ cells, MSA-2 2


title: DRG, Male, 24h, CL, rep 4

description:
DRG_M_24h_CL_R4
RC28  CL - M 24h
Raw_count_table_2.csv

value: rep 4


title: Skin, DM1 patient, classic19

description:
Library name: CR373_SK
DM1 patient living in Costa Rica

value: Skin


title: CD11b+ cells, control 2

description: Column names: Gene,LD_001,LD_002,LD_003,LD_004,LD_005,LD_006,LD_007,LD_008,LD_009,LD_010,LD_011,LD_012


title: Treated not cured SP 10,TCR

description: BD Rhapsody,TCR

value: Spleen

value: Splenocytes


title: Blood, DM1 patient, classic2

description:
Library name: CR30_BL
DM1 patient living in Costa Rica

value: Blood


title: PBS treated SP 9,TCR

description: BD Rhapsody,TCR

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with PBS


title: CD11b+ cells, control 1


title: PBM-R tumor 6

description: Column names: Gene, PBM_1, PBM_2, PBM_3, PBM_4, PBM_5, PBM_6, PBM_R_1, PBM_R_2, PBM_R_3, PBM_R_4, PBM_R_5, PBM_R_6

source_name: ovarian tumor

value: ovarian tumor

value: mouse tumor cells

value: Olaparib


title: DRG, Male, 24h, CL, rep 2

description:
DRG_M_24h_CL_R2
RC26  CL - M 24h
Raw_count_table_2.csv

value: dorsal root ganglion (DRG)

value: male

value: Chronic Constriction Injury (CCI), contalateral side

value: rep 2


title: DRG, Male, 24h, CL, rep 1

description:
DRG_M_24h_CL_R1
RC25  CL - M 24h
Raw_count_table_2.csv

value: rep 1


title: Muscle, DM1 patient, classic16

description:
Library name: CR291_SM
DM1 patient living in Costa Rica

value: Muscle


title: DRG, Male, 24h, CL, rep 3

description:
DRG_M_24h_CL_R3
RC27  CL - M 24h
Raw_count_table_2.csv

value: rep 3


title: Blood, DM1 patient, classic16

description:
Library name: CR291_BL
DM1 patient living in Costa Rica


title: Healthy mice SP 8,TCR

description: BD Rhapsody,TCR

value: No treatment


title: PBM-R tumor 5


title: Muscle, DM1 patient, classic2

description:
Library name: CR30_SM
DM1 patient living in Costa Rica


title: DRG, Female, 5W, IL, rep 6

description:
DRG_F_5W_IL_R6
RC38  IL - F 5W
Raw_count_table_2.csv

value: female

value: 5 weeks

value: Chronic Constriction Injury (CCI), ipsilateral side

value: rep 6


title: Cured PBMC 7,TCR

description: BD Rhapsody,TCR

value: Blood

value: PBMC

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with nanovaccines


title: Muscle, DM1 patient, classic15

description:
Library name: CR28_SM
DM1 patient living in Costa Rica


title: Muscle, DM1 patient, classic17

description:
Library name: CR311_SM
DM1 patient living in Costa Rica


title: PBM-R tumor 4

value: ovarian tumor

value: mouse tumor cells


title: Cured PBMC 6,TCR

description: BD Rhapsody,TCR


title: Cured SP 11,TCR

description: BD Rhapsody,TCR

value: Spleen

value: Splenocytes


title: Blood, DM1 patient, classic17

description:
Library name: CR311_BL
DM1 patient living in Costa Rica


title: DRG, Female, 5W, IL, rep 5

description:
DRG_F_5W_IL_R5
RC37  IL - F 5W
Raw_count_table_2.csv

value: dorsal root ganglion (DRG)

value: rep 5


title: Muscle, DM1 patient, classic14

description:
Library name: CR284_SM
DM1 patient living in Costa Rica


title: DRG, Female, 5W, IL, rep 4

description:
DRG_F_5W_IL_R4
RC35  IL - F 5W
Raw_count_table_2.csv

value: rep 4


title: DRG, Female, 5W, IL, rep 3

description:
DRG_F_5W_IL_R3
RC34  IL - F 5W
Raw_count_table_2.csv


title: PBM-R tumor 2

value: Olaparib


title: DRG, Female, 5W, IL, rep 2

description:
DRG_F_5W_IL_R2
RC33  IL - F 5W
Raw_count_table_2.csv

value: rep 2


title: PBM-R tumor 1


title: Treated not cured PBMC 3,TCR

description: BD Rhapsody,TCR


title: Cured PBMC 4,TCR

description: BD Rhapsody,TCR


title: Blood, DM1 patient, classic13

description:
Library name: CR279_BL
DM1 patient living in Costa Rica


title: Blood, DM1 patient, classic14

description:
Library name: CR284_BL
DM1 patient living in Costa Rica


title: DRG, Female, 5W, IL, rep 1

description:
DRG_F_5W_IL_R1
RC31  IL - F 5W
Raw_count_table_2.csv

value: rep 1


title: PBM tumor 6

description: Column names: Gene, PBM_1, PBM_2, PBM_3, PBM_4, PBM_5, PBM_6, PBM_R_1, PBM_R_2, PBM_R_3, PBM_R_4, PBM_R_5, PBM_R_6

value: Vehicle control


title: PBM tumor 5


title: Healthy mice PBMC 1,TCR

description: BD Rhapsody,TCR

value: No treatment


title: DRG, Female, 5W, CL, rep 6

description:
DRG_F_5W_CL_R6
RC38  CL - F 5W
Raw_count_table_2.csv

value: female

value: 5 weeks

value: Chronic Constriction Injury (CCI), contalateral side


title: DRG, Female, 5W, CL, rep 5

description:
DRG_F_5W_CL_R5
RC37  CL - F 5W
Raw_count_table_2.csv


title: PBS treated PBMC 2,TCR

description: BD Rhapsody,TCR

value: Blood

value: PBMC

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with PBS


title: PBM tumor 4

value: ovarian tumor

value: mouse tumor cells


title: PBM-R tumor 3


title: Blood, DM1 patient, classic11

description:
Library name: CR269_BL
DM1 patient living in Costa Rica


title: Cured PBMC 5,TCR

description: BD Rhapsody,TCR

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with nanovaccines


title: DRG, Female, 5W, CL, rep 4

description:
DRG_F_5W_CL_R4
RC35  CL - F 5W
Raw_count_table_2.csv

value: dorsal root ganglion (DRG)


title: Cured LN 20,GEX

description: BD Rhapsody,GEX

value: Draning lymph nodes

value: Draning lymph node cells


title: PBM tumor 3


title: DRG, Female, 5W, CL, rep 3

description:
DRG_F_5W_CL_R3
RC34  CL - F 5W
Raw_count_table_2.csv

value: rep 3


title: Skin, DM1 patient, classic10

description:
Library name: CR266_SK
DM1 patient living in Costa Rica

value: Skin


title: PBM tumor 1


title: Blood, DM1 patient, classic10

description:
Library name: CR266_BL
DM1 patient living in Costa Rica


title: Cured LN 19,GEX

description: BD Rhapsody,GEX


title: Muscle, DM1 patient, classic13

description:
Library name: CR279_SM
DM1 patient living in Costa Rica

value: Muscle


title: Muscle, DM1 patient, classic12

description:
Library name: CR272_SM
DM1 patient living in Costa Rica


title: Muscle, DM1 patient, classic9

description:
Library name: CR262_SM
DM1 patient living in Costa Rica


title: DRG, Female, 5W, CL, rep 1

description:
DRG_F_5W_CL_R1
RC31  CL - F 5W
Raw_count_table_2.csv

value: rep 1


title: Treated not cured LN 17,GEX

description: BD Rhapsody,GEX


title: Muscle, DM1 patient, classic11

description:
Library name: CR269_SM
DM1 patient living in Costa Rica


title: PBM tumor 2

value: Vehicle control


title: DRG, Female, 5W, CL, rep 2

description:
DRG_F_5W_CL_R2
RC33  CL - F 5W
Raw_count_table_2.csv

value: female

value: rep 2


title: Cured LN 18,GEX

description: BD Rhapsody,GEX


title: PBS treated LN 16,GEX

description: BD Rhapsody,GEX


title: Muscle, DM1 patient, classic8

description:
Library name: CR244_SM
DM1 patient living in Costa Rica


title: Blood, DM1 patient, classic9

description:
Library name: CR262_BL
DM1 patient living in Costa Rica


title: ND+CCl4_6

type: RNA

city: Daejeon

first: Tae-Su

last: Han

address: 125 Gwahak-ro

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description: Exosomal miRNA expression profiling of annotated miRNAs was performed on mouse serum samples from four groups: ND+oil (normal), WD+oil (NASH), ND+CCl₄ (cirrhosis), and WD+CCl₄ (HCC).

hyb_protocol: 3 µL of sample containing 100 ng of total RNA were used, a reporter and a capture probe were added and hybridized in the respective genes of interest, according to the manufacturer's instructions (NanoString Technologies).

scan_protocol: the cartridge containing immobilized and aligned reporter complexes were transferred to nCounter® Digital Analyzer (NanoString Technologies), with 280 fields of view. These results were tabulated in RCC (Reporter Code Count) format.

data_processing: Raw data were collected and pre-processed by nSolver™ Analysis Software v4.0 (NanoString Technologies), and further normalization by LoW CV method and differential expression analysis were performed in the R statistical environment (R-project v3.6.3; The R Foundation, Viena, Austria). The data were normalized using the housekeeping method by the NanoStringNorm package (Bioconductor). Normalized data were log2-transformed and used as input for the differential expression analysis.

source_name: Serum exosome

extract_protocol: Exosomal microRNAs (exo-miRNAs) were extracted from serum exosomes using miRNeasy micro kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Male C57BL/6N mice (Orientbio, Seongnam, Korea) were fed a normal chow diet (ND; LabDiet, St. Louis, MO, USA, Rodent diet 20, #5053) and normal tap water, or western diet (WD) containing high-fat diet (Teklad diets, Indianapolis, IN, USA, TD. 120528) and high sugar solution consisting of 23.1 g/L d-fructose (Sigma-Aldrich, St. Louis, MO, USA, F0127) and 18.9 g/L d-glucose (Sigma-Aldrich). Carbon tetrachloride (CCl4; Sigma-Aldrich, 289116-1L) or corn oil, a control vehicle, was intraperitoneally injected once weekly.

tag: strain

tag: sample

value: serum

tag: age

value: 40 weeks


title: WD+CCl4_6


title: Cured PN 21,GEX

description: BD Rhapsody,GEX


title: DRG, Female, 1W, IL, rep 6

description:
DRG_F_1W_IL_R6
RC50  IL - F 1W
Raw_count_table_2.csv

value: 1 week

value: Chronic Constriction Injury (CCI), ipsilateral side

value: rep 6


title: Skin, DM1 patient, classic8

description:
Library name: CR244_SK
DM1 patient living in Costa Rica


title: Healthy mice LN 15,GEX

description: BD Rhapsody,GEX

value: No treatment


title: DRG, Female, 1W, IL, rep 5

description:
DRG_F_1W_IL_R5
RC49  IL - F 1W
Raw_count_table_2.csv

value: rep 5


title: Blood, DM1 patient, classic8

description:
Library name: CR244_BL
DM1 patient living in Costa Rica

value: Blood


title: Cured SP 14,GEX

description: BD Rhapsody,GEX

value: Spleen

value: Splenocytes

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with nanovaccines


title: WD+oil_6


title: DRG, Female, 1W, IL, rep 4

description:
DRG_F_1W_IL_R4
RC48  IL - F 1W
Raw_count_table_2.csv

value: dorsal root ganglion (DRG)

value: rep 4


title: ND+oil_6


title: Cured SP 13,GEX

description: BD Rhapsody,GEX


title: Cured SP 12,GEX

description: BD Rhapsody,GEX


title: WD+CCl4_5


title: ND+CCl4_5


title: Blood, DM1 patient, congenital2

description:
Library name: CR218_BL
DM1 patient living in Costa Rica


title: DRG, Female, 1W, IL, rep 2

description:
DRG_F_1W_IL_R2
RC46  IL - F 1W
Raw_count_table_2.csv


title: DRG, Female, 1W, IL, rep 7

description:
DRG_F_1W_IL_R7
RC51  IL - F 1W
Raw_count_table_2.csv

value: rep 7


title: DRG, Female, 1W, IL, rep 1

description:
DRG_F_1W_IL_R1
RC45  IL - F 1W
Raw_count_table_2.csv

value: rep 1


title: Cured SP 11,GEX

description: BD Rhapsody,GEX


title: Muscle, DM1 patient, Mild3

description:
Library name: CR215_SM
DM1 patient living in Costa Rica

value: Muscle


title: WD+oil_5


title: Treated not cured SP 10,GEX

description: BD Rhapsody,GEX


title: Muscle, DM1 patient, classic1

description:
Library name: CR20_SM
DM1 patient living in Costa Rica


title: DRG, Female, 1W, CL, rep 7

description:
DRG_F_1W_CL_R7
RC51  CL - F 1W
Raw_count_table_2.csv

value: female

value: Chronic Constriction Injury (CCI), contalateral side


title: DRG, Female, 1W, CL, rep 6

description:
DRG_F_1W_CL_R6
RC50  CL - F 1W
Raw_count_table_2.csv


title: ND+oil_5

value: serum

value: 40 weeks


title: WD+CCl4_4


title: Skin, DM1 patient, classic1

description:
Library name: CR20_SK
DM1 patient living in Costa Rica

value: Skin


title: Blood, DM1 patient, classic1

description:
Library name: CR20_BL
DM1 patient living in Costa Rica


title: ND+CCl4_4


title: Muscle, DM1 patient, congenital2

description:
Library name: CR218_SM
DM1 patient living in Costa Rica


title: DRG, Female, 1W, CL, rep 5

description:
DRG_F_1W_CL_R5
RC49  CL - F 1W
Raw_count_table_2.csv

value: 1 week


title: Cured PBMC 7,GEX

description: BD Rhapsody,GEX

value: PBMC


title: Healthy mice SP 8,GEX

description: BD Rhapsody,GEX

value: No treatment


title: DRG, Female, 1W, IL, rep 3

description:
DRG_F_1W_IL_R3
RC47  IL - F 1W
Raw_count_table_2.csv

value: Chronic Constriction Injury (CCI), ipsilateral side

value: rep 3


title: Muscle, DM1 patient, classi7

description:
Library name: CR199_SM
DM1 patient living in Costa Rica


title: DRG, Female, 1W, CL, rep 4

description:
DRG_F_1W_CL_R4
RC48  CL - F 1W
Raw_count_table_2.csv


title: Cured PBMC 6,GEX

description: BD Rhapsody,GEX

value: Blood


title: WD+oil_4

description: Exosomal miRNA expression profiling of annotated miRNAs was performed on mouse serum samples from four groups: ND+oil (normal), WD+oil (NASH), ND+CCl₄ (cirrhosis), and WD+CCl₄ (HCC).


title: ND+oil_4


title: Blood, DM1 patient, classic7

description:
Library name: CR199_BL
DM1 patient living in Costa Rica


title: DRG, Female, 1W, CL, rep 3

description:
DRG_F_1W_CL_R3
RC47  CL - F 1W
Raw_count_table_2.csv


title: Cured PBMC 5,GEX

description: BD Rhapsody,GEX

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with nanovaccines


title: Muscle, DM1 patient, congenital1

description:
Library name: CR188_SM
DM1 patient living in Costa Rica


title: ND+CCl4_3


title: PBS treated SP 9,GEX

description: BD Rhapsody,GEX

value: Spleen

value: Splenocytes

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with PBS


title: Blood, DM1 patient, congenital1

description:
Library name: CR188_BL
DM1 patient living in Costa Rica


title: DRG, Female, 1W, CL, rep 2

description:
DRG_F_1W_CL_R2
RC46  CL - F 1W
Raw_count_table_2.csv

value: dorsal root ganglion (DRG)

value: rep 2


title: Cured PBMC 4,GEX

description: BD Rhapsody,GEX


title: DRG, Female, 1W, CL, rep 1

description:
DRG_F_1W_CL_R1
RC45  CL - F 1W
Raw_count_table_2.csv

value: female

value: rep 1


title: DRG, Male, 5W, IL, rep 5

description:
DRG_M_5W_IL_R5
CCI_5W_L4_IL_R5
Raw_count_table_1.csv

value: male

value: 5 weeks

value: rep 5


title: Skin, DM1 patient, classic6

description:
Library name: CR185_SK
DM1 patient living in Costa Rica

value: Skin


title: ND+oil_3

value: serum

value: 40 weeks


title: PBS treated PBMC 2,GEX

description: BD Rhapsody,GEX

value: PBMC


title: Muscle, DM1 patient, Mild2

description:
Library name: CR118_SM
DM1 patient living in Costa Rica

value: Muscle


title: Blood, DM1 patient, classic6

description:
Library name: CR185_BL
DM1 patient living in Costa Rica

value: Blood


title: Healthy mice PBMC 1,GEX

description: BD Rhapsody,GEX

value: No treatment


title: DRG, Male, 5W, IL, rep 4

description:
DRG_M_5W_IL_R4
CCI_5W_L4_IL_R4
Raw_count_table_1.csv

value: Chronic Constriction Injury (CCI), ipsilateral side

value: rep 4


title: WD+CCl4_2


title: DRG, Male, 5W, IL, rep 3

description:
DRG_M_5W_IL_R3
CCI_5W_L4_IL_R3
Raw_count_table_1.csv

value: rep 3


title: 6_Islets_Chow_Macro

city: Paris

first: Nicolas

last: Venteclef

address: 156 rue de Vaugirard

country: France

institute: Institut Necker Enfants Malades, INSERM U1151

data_processing:
Reads were mapped to the GRCm38 primary mouse genome assembly with STAR.
Assembly: GRCm38 primary mouse genome
Supplementary files format and content: Counts table was generated with featureCounts from subread-1.6.4 package

source_name: Islets

extract_protocol:
Total RNA was extracted using RNeasy Plus Micro Kit (QIAGEN Cat# 74034). 10 ng of total RNA was used.
RNA sequencing libraries were prepared using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech/Takara).

value: Islets

value: Macro

tag: batch

tag: diet

value: Chow


title: ND+CCl4_2


title: DRG, Male, 5W, IL, rep 2

description:
DRG_M_5W_IL_R2
CCI_5W_L4_IL_R2
Raw_count_table_1.csv

value: dorsal root ganglion (DRG)

value: rep 2


title: Muscle, DM1 patient, Mild1

description:
Library name: CR05_SM
DM1 patient living in Costa Rica


title: 6_Fat_Chow_Macro

source_name: Fat

value: Fat


title: WD+oil_2


title: DRG, Male, 5W, IL, rep 1

description:
DRG_M_5W_IL_R1
CCI_5W_L4_IL_R1
Raw_count_table_1.csv

value: male

value: 5 weeks

value: rep 1


title: 4_Fat_Chow_Macro


title: scRNAseq-297

city: Guangzhou

first: Binkui

last: Li

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

description: 10x Genomics

data_processing:
Raw reads of of human were aligned to the human genome (hg38), cells were called and gene expression matrices were generated for each sample by the cellranger count function with default parameters.
Assembly: hg38 for the row reads of human
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: biopsy of HCC

extract_protocol:
Fresh tissue was washed by DPBS and carefully chopped into small pieces, cell suspensions were produced by enzymatic digestion and centrifugation.
The library synthesis was conducted in accordance with the instructions of Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10× GENOMICS).

treatment_protocol: anti-PD1 therapy

value: HCC cells

value: biopsy of HCC


title: ND+oil_2

value: serum

value: 40 weeks


title: scRNAseq-296

description: 10x Genomics


title: DRG, Male, 5W, CL, rep 5

description:
DRG_M_5W_CL_R5
CCI_5W_L4_CL_R5
Raw_count_table_1.csv

value: Chronic Constriction Injury (CCI), contalateral side

value: rep 5


title: 4_Islets_Chow_Macro


title: Treated not cured PBMC 3,GEX

description: BD Rhapsody,GEX

source_name: Blood

value: Blood

value: PBMC

value: C57bl/6 mice were inoculated with B16F10 melanoma cancer cell, and then treated with nanovaccines


title: WD+CCl4_3

description: Exosomal miRNA expression profiling of annotated miRNAs was performed on mouse serum samples from four groups: ND+oil (normal), WD+oil (NASH), ND+CCl₄ (cirrhosis), and WD+CCl₄ (HCC).


title: DRG, Male, 5W, CL, rep 4

description:
DRG_M_5W_CL_R4
CCI_5W_L4_CL_R4
Raw_count_table_1.csv

value: rep 4


title: Mel92.1_ A366(1uM) Treated Replicate 2

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

description:
MEL-8
A366 (1uM) treated, 48 hours

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Genome_build: hg38
Supplementary_files_format_and_content: rsem_count.txt: Tab-delimited text file includes raw count values for each Sample.

source_name: Mel 92.1 cell line

growth_protocol: MP-41 and Mel 92.1 cells were grown in RPMI medium respectively with 10% Fetal bovine serum and Penicilline and Streptomycin at 37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacturer and then purified using RNeasy mini columns (Qiagen) as per the manufacturer's instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C. Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries. The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: MP-41 and Mel 92.1 cells were treated with EHMT2/G9a inhibitor (1 micromolar) UNC0642 and A366 for 48 hours, were harvested and were used for preparing the total RNA and to perform RNA Seq.


title: Mel92.1_ A366(1uM) Treated Replicate 3

description:
MEL-9
A366 (1uM) treated, 48 hours


title: 2_Fat_Chow_Macro

value: Macro

value: Chow


title: ND+CCl4_1


title: Mel92.1_ A366(1uM) Treated Replicate 1

description:
MEL-7
A366 (1uM) treated, 48 hours


title: DRG, Male, 5W, CL, rep 2

description:
DRG_M_5W_CL_R2
CCI_5W_L4_CL_R2
Raw_count_table_1.csv

value: dorsal root ganglion (DRG)

value: rep 2


title: WD+oil_3


title: 2_Islets_Chow_Macro

value: Islets


title: Pancreatic islets, chow diet, rep2

data_processing:
CellRanger mkfastq and count (10x Genomics) were used to align to the mouse genome (mm10) and generate gene-barcode matrices.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix output from CellRanger count

molecule: polyA RNA

source_name: pancreatic islets

extract_protocol:
Single cell solutions were obtained from pancreatic islets isolated from 6-8 C57BL/6J males as previously described. Immune cells were sort-purified as live DAPI-Epcam-CD45+ cells with a FACS ARIA III cell sorter (BD Biosciences) using FACS Diva software (BD Biosciences) and lysed for mRNA extraction. Sorted cells were then centrifuged at 300 rcf for 5 minutes and resuspended in PBS containing 0.04% of Ultrapure BSA (Invitrogen Cat# AM2616).
Cells were loaded on a Chromium Controller (10x Genomics) with a target output of 3000-4000 cells per condition and RNA-seq libraries were prepared with the Chromium Single Cell 3’ Reagents Kit v3 Library protocol (10x Genomics) according to manufacturer’s guidelines at the CurieCoreTech Next Generation Sequencing (ICGex, Paris, France). After individual qualification and quantification, the libraries were then equimolarly pooled and quantified using a qPCR method (KAPA library quantification kit, Roche).
The sequencing was carried out on an Illumina Novaseq 6000 instrument, using paired-end 28x91bp as sequencing mode, at the Curie Genomic Platform (Paris, France). The sequencing configuration was set to reach an average of 50,000 reads per cell.

value: pancreatic islets

value: 12 weeks

value: chow


title: Mel92.1_ UNC0642(1uM) Treated Replicate 3

description:
MEL-6
UNC0642 (1uM) treated, 48 hours

value: UNC0642 (1uM), 48 hours


title: WD+oil_1

value: serum


title: DRG, Male, 5W, CL, rep 1

description:
DRG_M_5W_CL_R1
CCI_5W_L4_CL_R1
Raw_count_table_1.csv

value: male

value: 5 weeks

value: rep 1


title: ND+oil_1

value: 40 weeks


title: NKX_5_lungs

city: Baltimore

first: Sabrina

last: Kline

state: Maryland

address: 1550 N Orleans St Suite 216

department: Dermatology

institute: Johns Hopkins Medicine

description:
Library name: NKX_5
Column name in gene_expression.xls: fpkm_NKX_5, tpm_NKX_5, read_count_NKX_5

data_processing:
The raw sequencing reads were filtered by SOPAnuke software to remove low quality reads and reads containing adaptor sequences
HISAT2 was used to align the reads to the reference genome GCF_000001635.27_GRCm39
Clean reads were aligned to reference genes with Bowtie2
Read counts were generated by software RSEM software
Assembly: GRCm39
Supplementary files format and content: Excel file includes FPKM, TPM, and read counts values for each sample

source_name: Lung

growth_protocol: S. aureus USA300 LAC4303 bacteria were streaked onto a tryptic soy agar (TSA) plate (tryptic soy broth [TSB] plus 1.5% bacto agar; BD Biosciences) and grown overnight at 37°C. Single colonies were picked and cultured in TSB at 37°C in a shaking incubator (240 rpm) overnight (18 hours), followed by a 1:50 subculture at 37°C for 2 hours to obtain mid-logarithmic growth phase bacteria. Bacteria were then pelleted, washed and resuspended in sterile PBS and the absorbance at 600 nm (A600) was measured to estimate the CFU (1×108 CFU/100 μL), which was verified by overnight culture on TSA plates.

extract_protocol:
Total RNA was extracted from about 60 mg of tissue per sample with Trizol (Invitrogen) according to the user manual instructions.
RNA libraries for RNA-seq were prepared using the DNBSEQ-G400 platform with a sequence length of PE100. Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China)

treatment_protocol: Dorsal fur of mice was shaved and depilated, followed by epicutaneous S. aureus (1e8 CFU) and cockroach antigen exposure using  for 7 days. On day 10, 11 and 12, cockroach antigen was applied intratracheally. On day 13, the lungs were perfused and excised. RNA was extracted and sent for RNA  sequencing.

value: Lung

value: S. aureus epicutaneous exposure


title: Mel92.1_ UNC0642(1uM) Treated Replicate 1

description:
MEL-4
UNC0642 (1uM) treated, 48 hours


title: NKX_4_lungs

description:
Library name: NKX_4
Column name in gene_expression.xls: fpkm_NKX_4, tpm_NKX_4, read_count_NKX_4


title: Pancreatic islets, chow diet, rep1

value: 1 week


title: WD+CCl4_1


title: Mel92.1_DMSO Treated Replicate 3

description:
MEL-3
DMSO treated

value: DMSO


title: KO2 BMDMs IL-4 stimulatio for 24 h

city: Indianapolis

first: Kai

last: Yang

state: IN

address: 1044 West Walnut Street

department: Department of Pediatrics

institute: Indiana University School of Medicine

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.7.2b) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to GENCODE M22 genes using featureCounts (from subread v1.6.5) with the following parameters: “-s0 –p –Q 10”.
Raw count were subject to differential expression analysis using EdgeR
Supplementary files format and content: mm10
Supplementary files format and content: count and differentail expression

source_name: BM

extract_protocol: Used QIAGEN Rneasy Micro kit to isolate RNA

value: BM

value: BMDMs

value: LysMCre Stk11 fl/fl


title: DRG, Male, 5W, CL, rep 3

description:
DRG_M_5W_CL_R3
CCI_5W_L4_CL_R3
Raw_count_table_1.csv

value: dorsal root ganglion (DRG)

value: Chronic Constriction Injury (CCI), contalateral side

value: rep 3


title: NKX_3_lungs

description:
Library name: NKX_3
Column name in gene_expression.xls: fpkm_NKX_3, tpm_NKX_3, read_count_NKX_3


title: KO1 BMDMs IL-4 stimulatio for 24 h


title: ExVivoPlasma_exosome_L_rep3

city: Harbin

first: Zhongting

last: Mei

state: Heilongjiang

address: Baojian Road 157

institute: Harbin Medical University

description: Small RNA expression of plasma exosomes in lung cancer mice

hyb_protocol: Cy3 labeled small RNAs were hybridized to Arraystar Mouse Small RNA Arrays in Agilent Hybridization Oven.

scan_protocol: After washing, the slides were scanned with Agilent Scanner G2505C

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using GeneSpring GX v12.1 software package (Agilent Technologies). After normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 6 samples were retained. Multiple probes from the same small RNA (miRNA/TsRNA (tRF&tiRNA)/pre-miRNA/tRNA/snoRNA) were combined into one RNA level. Differentially expressed small RNAs between two comparison groups were identified by fold change (FC) and statistical significance (p-value) thresholds. Hierarchical Clustering heatmaps, scatter plots and volcano plots were plotted to display small RNAs expression pattern among samples by R software.

source_name: Peripheral Blood, Plasma, exosome,lung,replicate 3

label_protocol: For each sample, 100 ng total RNA was firstly dephosphorylated to form the 3-OH end. The 3-OH ended RNA was then denatured by DMSO and enzymatically labeled with Cy3. The labeled RNA was hybridized onto Arraystar Mouse small RNA Microarray (8x15K, Arraystar) and the array was scanned by an Agilent Scanner G2505C.

growth_protocol: Mice were fed in a facility with 12 h light / 12 h dark cycle at 23 ± 3℃ and 30-70% humidity.

extract_protocol: The RNA samples were QC’d for quantity by NanoDrop ND-1000 spectrophotometer and RNA integrity by Bioanalyzer 2100 or gel electrophoresis.

treatment_protocol: Freshly drawn peripheral blood from healthy volunteers was irradiated, plasma obtained from blood samples was centrifuged at 2,000 g at 4℃ for 20 min, then centrifuged at 10,000 g at 4℃ for 10 min to remove cells and platelets. The isolation of exosomes was performed by ultracentrifugation. Briefly, the plasma was filtered (0.22 μm filter) and ultracentrifuged at 100,000 g at 4℃ for 70 min. Pellets were washed twice by PBS at 100,000 g ultracentrifugation, and finally resuspended in PBS for the subsequent studies.

value: Plasma

tag: disease

value: lung cancer

value: exosome


title: NKX_2_lungs

description:
Library name: NKX_2
Column name in gene_expression.xls: fpkm_NKX_2, tpm_NKX_2, read_count_NKX_2


title: Mel92.1_DMSO Treated Replicate 1

description:
MEL-1
DMSO treated


title: WT3 BMDMs IL-4 stimulatio for 24 h

value: WT


title: Mel92.1_ UNC0642(1uM) Treated Replicate 2

description:
MEL-5
UNC0642 (1uM) treated, 48 hours

value: UNC0642 (1uM), 48 hours


title: NKX_1_lungs

description:
Library name: NKX_1
Column name in gene_expression.xls: fpkm_NKX_1, tpm_NKX_1, read_count_NKX_1

value: S. aureus+Cockroach epicutaneous exposure; Cockroach IT exposure


title: MP41_A366(1uM) Treated Replicate 3

description:
MP-9
A366 (1uM) treated, 48 hours

source_name: MP-41 cell line


title: ExVivoPlasma_exosome_L_rep2

source_name: Peripheral Blood, Plasma, exosome,lung,replicate 2


title: K14_5_lungs

description:
Library name: K14_5
Column name in gene_expression.xls: fpkm_K14_5, tpm_K14_5, read_count_K14_5


title: WT1 BMDMs IL-4 stimulatio for 24 h


title: HCT116 oxpl-R E1A + oxaliplatin, biol rep 3

city: Saint-Petersburg

first: Alisa

last: Morshneva

state: Saint-Petersburg

address: Tihoretsky prospect, 4

department: Department of molecular and cellular interactions

country: Russia

institute: Institute of Cytology, RAS

description:
Library name: Unknown_CG769-002U0052
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0052

data_processing:
Trimming with Trimmomatic (Bolger et al., 2014) (HEADCROP:10 SLIDINGWINDOW:4:15 LEADING:3 TRAILING:3 MINLEN:36)
Transcript quantification via lightweight mapping using Salmon (Patro et al., 2017) (version 1.6.0). Selective alignment mode through a two-stage process: reference index construction and read mapping. Decoy sequences representing genomic regions with high sequence similarity to annotated transcripts were generated based on the human reference genome GRCh38 Gencode (release 47). "Decoy-aware" reference index was built based on a gentrome (concatenated genome and transcriptome sequences from GRCh38 Gencode release 47). Read mapping was performed with additional arguments: --validateMappings --numBootstraps 30 --seqBias --gcBias.
To enable assessment of the transcription level of adenoviral E1A, which is not part of the human reference transcriptome, the E1A sequence was manually added to the "decoy-aware" reference index prior to alignment.
Transcript-level quantifications obtained with Salmon imported and summarized to the gene level using the tximport  R package
Assembly: GRCh38 Gencode release 47
Supplementary files format and content: tab-delimited text file includes raw counts for all samples
Supplementary files format and content: csv file includes TPM values for all samples

source_name: HCT116 oxpl-R

growth_protocol: Parental HCT116 and oxaliplatin-resistant HCT116 oxpl-R cells were cultured in DMEM supplemented with 10% fetal bovine serum and gentamicin at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted from HCT116 and HCT116 oxpl-R cells using the Lira reagent (Biolabmix, Russia) according to the manufacturer’s protocol.
Library construction kit: Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen), model:13533ES96. Product purification magnetic beads: HieffNGS DNA selection Beads (Superior Ampure XP alternative) (Yeasen), model:12601ES56. The librarys were sequenced on the Illumina Novaseq X platform (Illumina, SanDiego, CA). PE150 sequencing reagent: NovaSeq X S4 Reagent Kit (San Diego).

treatment_protocol: HCT116 and HCT116 oxpl-R cells were seeded at 1.6 million cells per 5-cm culture dish. On the next day, doxycycline at 0.5 µg/mL was added to some experimental points 3 hours prior to oxaliplatin treatment to induce E1A expression. Oxaliplatin was then added to the experimental dishes at a concentration of 25 µM for 24 hours.

value: HCT116 oxpl-R

value: Human colorectal adenocarcinoma epithelial cancer cells

value: HCT116 oxpl-R TetOn-E1A

value: doxycycline (E1A induction) + oxaliplatin 25 uM, 24h


title: WT2 BMDMs IL-4 stimulatio for 24 h


title: HCT116 oxpl-R E1A + oxaliplatin, biol rep 2

description:
Library name: Unknown_CG769-002U0051
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0051


title: MP41_A366(1uM) Treated Replicate 2

description:
MP-8
A366 (1uM) treated, 48 hours


title: K14_4_lungs

description:
Library name: K14_4
Column name in gene_expression.xls: fpkm_K14_4, tpm_K14_4, read_count_K14_4

value: Lung

value: S. aureus epicutaneous exposure


title: KO3 BMDMs IL-4 stimulatio for 24 h

value: BM

value: BMDMs


title: ExVivoPlasma_exosome_L_rep1

source_name: Peripheral Blood, Plasma, exosome,lung,replicate 1


title: ExVivoPlasma_exosome_C_rep3

description: Small RNA expression of plasma exosomes in control mice

source_name: Peripheral Blood, Plasma, exosome, control,replicate 3

value: control


title: ExVivoPlasma_exosome_C_rep2

source_name: Peripheral Blood, Plasma, exosome, control,replicate 2


title: KO3 BMDMs mock

value: LysMCre Stk11 fl/fl

value: Mock


title: MP41_A366(1uM) Treated Replicate 1

description:
MP-7
A366 (1uM) treated, 48 hours


title: ExVivoPlasma_exosome_C_rep1

source_name: Peripheral Blood, Plasma, exosome, control,replicate 1

value: Plasma


title: HCT116 oxpl-R E1A + oxaliplatin, biol rep 1

description:
Library name: Unknown_CG769-002U0050
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0050


title: Mel92.1_DMSO Treated Replicate 2

description:
MEL-2
DMSO treated

value: DMSO


title: K14_3_lungs

description:
Library name: K14_3
Column name in gene_expression.xls: fpkm_K14_3, tpm_K14_3, read_count_K14_3


title: KO2 BMDMs mock


title: K14_2_lungs

description:
Library name: K14_2
Column name in gene_expression.xls: fpkm_K14_2, tpm_K14_2, read_count_K14_2


title: HCT116 oxpl-R oxaliplatin, biol rep 3

description:
Library name: Unknown_CG769-002U0049
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0049

value: oxaliplatin 25 uM, 24h


title: KO1 BMDMs mock


title: MP41_UNC0642(1uM) Treated Replicate 3

description:
MP-6
UNC0642 (1uM) treated, 48 hours


title: MP41_UNC0642(1uM) Treated Replicate 2

description:
MP-5
UNC0642 (1uM) treated, 48 hours


title: HCT116 oxpl-R oxaliplatin, biol rep 2

description:
Library name: Unknown_CG769-002U0048
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0048


title: MP41_UNC0642(1uM) Treated Replicate 1

description:
MP-4
UNC0642 (1uM) treated, 48 hours


title: WT3 BMDMs mock

value: WT


title: K14_1_lungs

description:
Library name: K14_1
Column name in gene_expression.xls: fpkm_K14_1, tpm_K14_1, read_count_K14_1


title: WT2 BMDMs mock


title: d13_5_lungs

description:
Library name: d13_5
Column name in gene_expression.xls: fpkm_d13_5, tpm_d13_5, read_count_d13_5


title: HCT116 oxpl-R oxaliplatin, biol rep 1

description:
Library name: Unknown_CG769-002U0047
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0047


title: HCT116 oxpl-R E1A, biol rep 3

description:
Library name: Unknown_CG769-002U0046
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0046

value: doxycycline (E1A induction)


title: d13_4_lungs

description:
Library name: d13_4
Column name in gene_expression.xls: fpkm_d13_4, tpm_d13_4, read_count_d13_4


title: MP41_DMSO Treated Replicate 2

description:
MP-2
DMSO treated


title: MP41_DMSO Treated Replicate 3

description:
MP-3
DMSO treated


title: d13_3_lungs

description:
Library name: d13_3
Column name in gene_expression.xls: fpkm_d13_3, tpm_d13_3, read_count_d13_3


title: WT1 BMDMs mock


title: MP41_DMSO Treated Replicate 1

description:
MP-1
DMSO treated


title: HCT116 oxpl-R E1A, biol rep 2

description:
Library name: Unknown_CG769-002U0045
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0045


title: IR_siSIRT7

city: Guangzhou City

first: Jin

last: Yi

address: Shatai South Road

department: department of toxicology

institute: Southern Medical University

data_processing:
After obtaining the raw sequencing data (Raw Data), you first need to filter the data, remove the adapter sequence, and process low-quality reads, and then evaluate the sequencing quality to obtain high-quality data (Clean Data). And compare the Clean Data with the reference genome to get the BAM file.
Use the HISAT2 software to compare the sequencing data with the reference genome, and make a comprehensive evaluation of the coverage area and coverage depth of the sequencing data. HISAT2 is the successor of TopHat2/Bowtie2. It uses an improved BWT algorithm (FM index). HISAT uses a large number of FM indexes to cover the entire genome, and combines several comparison strategies to achieve an efficient and faster comparison of RNA-seq data.
In RNA sequencing, RPKM (expected number of Reads Per Kilobase of transcript sequence per Millions basepairs sequenced) is the number of reads from a gene per kilobase length per million reads, which also considers the sequence depth and gene length pair The influence of read count is currently the most commonly used method for estimating gene expression levels. Map the bam file obtained by sequencing to the gtf file of the reference species to obtain the gene expression level, and perform regional statistics on the gene expression level of the genome according to the statistical method to reflect the overall expression level of the sample.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts and TPM values for each Sample.

source_name: skin

growth_protocol: HaCaT were cultured in Dulbecco’s modified Eagle medium supplemented with 12% fetal bovine serum and maintained at 37°C with 5% CO2 in a humidified atmosphere.

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment. Then 1 ug of total RNA for the construction was used as sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HaCaT cells were transfected with siControl or siRNA targeting SIRT7. After transfection, cells were exposed to 8 Gy X-ray treatment.

value: skin

value: HaCaT

value: Keratinocytes

value: SIRT7 knockdown

value: IR


title: IR_siControl


title: HCT116 oxpl-R E1A, biol rep 1

description:
Library name: Unknown_CG769-002U0044
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0044

value: HCT116 oxpl-R

value: Human colorectal adenocarcinoma epithelial cancer cells

value: HCT116 oxpl-R TetOn-E1A


title: HCT116 oxpl-R, biol rep 3

description:
Library name: Unknown_CG769-002U0043
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0043

value: untreated


title: d13_1_lungs

description:
Library name: d13_1
Column name in gene_expression.xls: fpkm_d13_1, tpm_d13_1, read_count_d13_1

value: Lung

value: S. aureus+Cockroach epicutaneous exposure; Cockroach IT exposure


title: Non-IR_siSIRT7

value: Non-IR


title: Lung, PLSCR1-/--IAV-7dpi

city: PROVIDENCE

first: Alina

middle: Xiaoyu

state: RI

address: 171 Meeting Street, Room 624

department: Molecular Microbiology and Immunology

institute: Brown University

description: Library name: AY6

data_processing:
CLC Genomics Workbench
Assembly: Mus musculus GRCm38
Supplementary files format and content: Differential gene expression results presented between different groups. Using DESeq2, a comparison of gene expression between groups of samples was performed. The Wald test was used to generate p-values and log2 fold changes.

extract_protocol:
Harvested right lungs were immediately snap-frozen in liquid nitrogen and stored at -80°C afterwards. Frozen lungs were homogenized in TRIzol Reagent (Invitrogen). RNA isolation was performed with RNeasy Mini Kit (Qiagen).
SMARTER mRNA-Seq Library Prep Kit

treatment_protocol: 10-12-week-old mice were intranasally infected once with 300PFU of IAV (WSN) in 30 μL of sterile PBS (Gibco). Thirty μL of sterile PBS was administrated in control mice. Only males were used in infections. Littermates were randomly assigned to experimental and control groups.

value: IAV


title: Lung, WT-IAV-7dpi

description: Library name: AY5


title: HCT116 oxpl-R, biol rep 2

description:
Library name: Unknown_CG769-002U0042
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0042


title: Lung, PLSCR1-/--IAV-3dpi

description: Library name: AY4


title: Non-IR_siControl


title: HCT116 oxpl-R, biol rep 1

description:
Library name: Unknown_CG769-002U0041
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0041


title: Ilimaquenone-treated_3

city: Gwangju

first: Yunju

last: Jo

address: 123, Cheomdangwagi-ro

institute: Gwangju Institute of Science and Technology

description: Library name: C-3

data_processing:
bcl2fastq v2.20.0 was used for base-calling. The cleaned reads were aligned to the Caenorhabditis elegans (WBcel235) using HISAT v2.1.0 (KIM et al, 2015).
Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9.
Assembly: Caenorhabditis elegans_WBcel235 (GCF_000002985.6)
Supplementary files format and content: The Excel file contains Read Count, FPKM and TPM data for each sample.

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans were maintained in M9 buffer at 20°C until the L4 stage.

extract_protocol:
Total RNAs were extracted by Quant-IT RiboGreen assay (Invitrogen, #R11490)
A library was independently prepared with 1 µg of total RNA for each sample using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #20020595)

treatment_protocol: At the L4 stage, they were treated with complete S-Basal buffer containing 200 µM FUDR and 100 µg/mL ampicillin for 11 days. IQ samples were added at a concentration of 100 µM

value: whole animal

value: wild type

value: complete S-basal(FUDR, Ampicillin, IQ)


title: d10_4_lungs

description:
Library name: d10_4
Column name in gene_expression.xls: fpkm_d10_4, tpm_d10_4, read_count_d10_4

value: S. aureus+Cockroach epicutaneous exposure


title: Lung, PLSCR1-/--PBS

description: Library name: AY2

value: PBS


title: Lung, WT-IAV-3dpi

description: Library name: AY3

value: WT


title: Ilimaquenone-treated_2

description: Library name: C-2


title: HCT116 E1A + oxaliplatin, biol rep 3

description:
Library name: Unknown_CG769-002U0040
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0040

value: HCT116 TetOn-E1A

value: doxycycline (E1A induction) + oxaliplatin 25 uM, 24h


title: d10_2_lungs

description:
Library name: d10_2
Column name in gene_expression.xls: fpkm_d10_2, tpm_d10_2, read_count_d10_2


title: d10_3_lungs

description:
Library name: d10_3
Column name in gene_expression.xls: fpkm_d10_3, tpm_d10_3, read_count_d10_3


title: HCT116 E1A + oxaliplatin, biol rep 2

description:
Library name: Unknown_CG769-002U0039
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0039


title: Lung, WT-PBS

description: Library name: AY1


title: d10_1_lungs

description:
Library name: d10_1
Column name in gene_expression.xls: fpkm_d10_1, tpm_d10_1, read_count_d10_1


title: HCT116 E1A + oxaliplatin, biol rep 1

description:
Library name: Unknown_CG769-002U0038
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0038


title: d13_2_lungs

description:
Library name: d13_2
Column name in gene_expression.xls: fpkm_d13_2, tpm_d13_2, read_count_d13_2

value: S. aureus epicutaneous exposure


title: Vehicle-treated_3

description: Library name: A-3

value: complete S-basal(FUDR, Ampicillin)


title: HCT116 oxaliplatin, biol rep 3

description:
Library name: Unknown_CG769-002U0037
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0037

value: Human colorectal adenocarcinoma epithelial cancer cells

value: oxaliplatin 25 uM, 24h


title: Naïve_5_lungs

description:
Library name: Naïve_5
Column name in gene_expression.xls: fpkm_Naive_5, tpm_Naive_5, read_count_Naive_5


title: DC012-6-16-16-CD45-2-CD103pos

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description: Library name: DC012-6-16-16-CD45-2-CD103pos

data_processing:
Adapter content was removed from fastq files using Skewer v0.2.2 and data aligned with STAR v2.5.3a to the ENSEMBLE C57BL/6J GCA_000001635.9 reference mouse genome and transcriptome. PCR duplicate reads were flagged using PICARD MarkDupilicates v1.127, gene counts for each sample were computed using GenomicRanges v1.34.0, and reads per kilobase per million (RPKM) normalized in R 3.5.2.
Genes with at least 3 reads per million (RPM) in all samples of either the WT and/or Cxcr5-/- cDC groups were considered expressed.
Assembly: mm39
Supplementary files format and content: txt file with rpkm normalized expression counts for each expressed gene

source_name: mesenteric lymph node

extract_protocol:
RNA was isolated using the RNeasy micro column with TRIzol (Qiagen)
PolyA RNA was enriched with oligo-dT beads and RNA-seq libraries constructed using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) by GeneWiz LLC

treatment_protocol: For RNA-seq, chimeras were generated from B6 Pepboy CD45.1+ mice irradiated and reconstituted with 50% B6 Pepboy CD45.1+ BM and 50% Cxcr5-/- CD45.2+ BM (1:1 B6:Cxcr5-/-). 8 days post-infection (p.i.) with 200 Heligmosomoides polygyrus (Hp) L3 larvae, msLN were digested with 0.6 mg/mL collagenase A (Sigma) and 30 g/mL DNase I (Sigma) in RPMI-1640 medium (GIBCO) for 30 min, then mechanically disrupted with glass slides. DC were positively enriched with anti-CD11c microbeads (Miltenyi) in the presence of Fc blocking antibody (anti- CD16/32; 2.4G2 BioXCell), then stained with fluorochrome-conjugated antibodies to MHC II, CD11c, CD45.1, CD45.2, CD19, CCR7, CXCR5, CD11b, and CD103. CD11c bead-enriched cells were sorted on a BD Aria into viable CD11c+MHCIIhiCD19- cells, then sorted by CD45 congenic marker into cDC2 (CD11b+CD103-) and cDC1 (CD11b-CD103+) subpopulations. Sorted DC subsets cells were pelleted and lysed in TRIzol reagent (ThermoFisher), then stored at -80 degrees C.

value: mesenteric lymph node

tag: sorting markers

tag: cd45 status


title: Vehicle-treated_2

description: Library name: A-2

tag: tissue


title: DC011-6-16-16-CD45-2-CD11bpos

description: Library name: DC011-6-16-16-CD45-2-CD11bpos

tag: cell type

tag: genotype


title: HCT116 oxaliplatin, biol rep 2

description:
Library name: Unknown_CG769-002U0036
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0036

tag: treatment


title: Vehicle-treated_1

description: Library name: A-1


title: Naïve_4_lungs

description:
Library name: Naïve_4
Column name in gene_expression.xls: fpkm_Naive_4, tpm_Naive_4, read_count_Naive_4

value: Lung


title: d10_5_lungs

description:
Library name: d10_5
Column name in gene_expression.xls: fpkm_d10_5, tpm_d10_5, read_count_d10_5


title: DC010-6-16-16-CD45-1-CD103pos

description: Library name: DC010-6-16-16-CD45-1-CD103pos

value: wt


title: HCT116 oxaliplatin, biol rep 1

description:
Library name: Unknown_CG769-002U0035
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0035

tag: cell line


title: Naïve_3_lungs

description:
Library name: Naïve_3
Column name in gene_expression.xls: fpkm_Naive_3, tpm_Naive_3, read_count_Naive_3


title: DC009-6-16-16-CD45-1-CD11bpos

description: Library name: DC009-6-16-16-CD45-1-CD11bpos


title: SAM_50_F3_3

city: Zunyi

first: yan

last: Zhang

state: Guizhou

address: Honghuagang

department: College of Basic Medicine

institute: Zunyi Medical University

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations
Data were fltered using the following specifications
peaks were called using PeaksFind version 2.2 with the following setting: RNA threshold (0 .2), Enrichment Fold (2 .5), Rescue Fold (3).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: whole

extract_protocol:
Total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification.
The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.

treatment_protocol: Using 50 μM' S-adenosylmethionine induces the Caenorhabditis elegans in the L1 stage until the nematodes grow into the young adult. Then collects the nematodes and extracts RNA.

value: whole

value: Not Applicable


title: HCT116 E1A, biol rep 3

description:
Library name: Unknown_CG769-002U0034
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0034

value: doxycycline (E1A induction)


title: Naïve_2_lungs

description:
Library name: Naïve_2
Column name in gene_expression.xls: fpkm_Naive_2, tpm_Naive_2, read_count_Naive_2


title: SAM_50_F3_2


title: Ilimaquenone-treated_1

description: Library name: C-1

value: whole animal

value: wild type


title: HCT116 E1A, biol rep 2

description:
Library name: Unknown_CG769-002U0033
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0033


title: SAM_50_F3_1


title: DC008-6-7-16-CD45-2-CD103pos

description: Library name: DC008-6-7-16-CD45-2-CD103pos


title: Naïve_1_lungs

description:
Library name: Naïve_1
Column name in gene_expression.xls: fpkm_Naive_1, tpm_Naive_1, read_count_Naive_1


title: HCT116 E1A, biol rep 1

description:
Library name: Unknown_CG769-002U0032
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0032


title: DC007-6-7-16-CD45-2-CD11bpos

description: Library name: DC007-6-7-16-CD45-2-CD11bpos


title: miR-26bKO3

city: Edinburgh

first: Andrea

last: Caporali

state: Scotland

address: 47, Little France Crescent Edinburgh

country: United Kingdom

institute: University of Edinburgh

description: RNA-seq  performed on DNBSEQ platform with PE100 (read length, 30M)

data_processing:
Firstly, reads mapped to rRNAs are removed to obtain raw data
Then low quality reads (low quality read are defined as the percentage of base which quality is lesser than 20 is greater than 40% in a read), reads with adaptors and reads in which unknown bases(N) are more than 0.1% were filtered to obtain clean reads.
The SOAPnuke software(version:v1.5.2) was used to filter reads with parameters: -n 0.001 -l 20 -q 0.4 -A 0.25 -Q 2
Filtering done using SOAPnuke software, with parameters: "-n 0.001 -l 20 -q 0.4 --adaMR 0.25 --polyX 50 --minReadLen 100"
After reads filtering, clean reads were mapped onto reference genome (mm10_UCSC_20180903) using Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT2) Version: v2.0.4, Parameters: --phred33 --sensitive --no-discordant --no-mixed -I 1 -X 1000 Parameters: --phred33 --sensitive --no-discordant --no-mixed -I 1 -X 1000
Genome mapping was followed with novel gene prediction, SNP & INDEL calling and gene splicing detection.
Novel gene prediction was performed using StringTie to reconstruct transcripts (Version: v1.0.4,
Parameters: -f 0.3 -j 3 -c 5 -g 100 -s 10000 -p 8), and  Cuffcompare(Cufflinks tools) used to compare reconstructed transcripts to reference annotation (Version: v2.2.1
Parameters: -p 12), after that,  'u','i','o','j' class code types were selected as novel transcripts. CPC (Version: v0.9-r2
Parameters: Default) was then used to predict coding potential of novel transcripts. Coding novel transcripts were then merged with reference transcripts to get a complete reference. Downstream analysis was based on this reference.
GATK was used to call SNP and INDEL variant for each sample
rMATS (Version: v4.0.2, Parameters: -t paired --nthread 8 --tstat 4) was used to detect differential alternative splicing events from the RNA-Seq data, it calculates the inclusion isoform and skipping isofrom
Clean reads were mapped to reference using Bowtie2 (Version: v2.2.5 Parameters: -q --phred33 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no- mixed--no-discordant -p1-k200
Gene expression level calculated with RSEM  (Version: v1.2.12, Parameters: default)
DEseq2 algorithms was used to detect the Differentiallyexpression genes (DEGs) (Parameters: Fold Change >= 2.00 and Adjusted Pvalue <= 0.05), followed with clustering analysis and functional annotations.
Visualisation of bioinformatics analysis was conducted with the online platform Dr. Tom (BGI Company).
Assembly: mm10_UCSC_20180903
Supplementary files format and content: The processed data files are raw_counts.fpkm.txt

source_name: Aorta

growth_protocol: The whole mouse aorta was harvested from 6-month-old wild-type and miR-26bKO mice. The aortae were dissected from surrounding tissue, and the perivascular fat was removed.

extract_protocol:
Total RNA was isolated  using Qiazol reagent and miRNeasy mini Kit (217004, QIAGEN, Germany). Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) was used to do the total RNA sample QC: RNA concentration, RIN value,28S/18S and the fragment length distribution.
The first step in the workflow involved purifying the poly-A containing mRNA molecules using poly-T oligo- attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. The PCR yield was then quantified  by Qubit and samples pooled together to make a single strand DNA circle (ssDNA circle), which gives the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq platform for  following data analysis study.  The DNBseq platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

value: Aorta

value: male

value: miR-26b knockout


title: DC006-6-7-16-CD45-1-CD103pos

description: Library name: DC006-6-7-16-CD45-1-CD103pos


title: miR-26bKO2


title: miR-26bKO1


title: SAM_50_P0_1


title: SAM_50_P0_2


title: DC005-6-7-16-CD45-1-CD11bpos

description: Library name: DC005-6-7-16-CD45-1-CD11bpos


title: SAM_50_P0_3


title: HCT116 control, biol rep 3

description:
Library name: Unknown_CG769-002U0031
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0031

value: HCT116 TetOn-E1A

value: untreated


title: WT3

value: wildtype


title: SAM_CON_P0_3


title: DC003-5-26-16-CD45-2-CD11bpos

description: Library name: DC003-5-26-16-CD45-2-CD11bpos


title: HCT116 control, biol rep 2

description:
Library name: Unknown_CG769-002U0030
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0030


title: Hd-scRNA-S

city: Wuhan

first: Gaojie

address: Donghu Southroad 7

institute: Institute of Hydrobiology, Chinese Academy of Sciences

description: Library name: library S

data_processing:
Single-cell suspensions were loaded onto prepared microfluidic chips to generate Gel Bead-In-Emulsions (GEMs), where cellular mRNA hybridized with barcoded oligonucleotides on gel beads. Reverse transcription generated cDNA with unique cell barcodes (CellBarcode) and unique molecular identifiers (UMI)
Assembly: PRJNA872356
Supplementary files format and content: barcodes files include values of which cell each read origined from each Sample
Supplementary files format and content: features files include  values of which gene each read corresponds to each Sample
Supplementary files format and content: matrix files include values which contains the raw counts of reads per gene per cell from each Sample

organism: Hygrophila difformis

source_name: shoot

extract_protocol:
Live protoplasts were immediately loaded into the 10X Genomics Chromium Single Cell 3' Platform
Libraries were constructed following the Chromium Single Cell 3' Reagent Kits v3.1 protocol and sequenced on an Illumina NovaSeq 6000 platform.

value: shoot

value: submerged


title: SAM_CON_P0_2


title: DC002-5-26-16-CD45-1-CD103pos

description: Library name: DC002-5-26-16-CD45-1-CD103pos


title: Hd-scRNA-T

description: Library name: library T

value: terrestrial


title: DC001-5-26-16-CD45-1-CD11bpos

description: Library name: DC001-5-26-16-CD45-1-CD11bpos

value: mesenteric lymph node


title: CNS_204_RGNT

status: Public on Nov 13 2025

type: genomic

city: Campinas

first: Felipe

last: Silva

address: R. Márcia Mendes, 506

country: Brazil

institute: Boldrini

hyb_protocol: bisulfite converted with Zymo EZ DNA methylation kit (Zymo Research, Irvine, CA, USA; cat. ID: D5002) and then hybridized on the 850K Infinium HD EPIC Methylation Array Bead Chip version 1 (Illumina, San Diego, CA, USA). Beadchip arrays were scanned on the NextSeq550 (Illumina, San Diego, CA, USA), which generated IDAT files

data_processing: IDAT files were checked for general quality measures by Illumina Bead Array Controls Reporter (v1.1) and minfi QCreport function. raw fluorescence intensity values were generated using preprocessRaw(), getMeth() and detectionP() minfi functions. chromosomal probes and bad quality probes were removed and remaining probes were normalized using preprocessFunnorm() function.

label: Cy3 and Cy5

source_name: Tumour tissue

label_protocol: Satandard Illumina Protocol

extract_protocol: GenElute™ Mammalian Genomic DNA Miniprep Kit (Sigma-Aldrich Co. LLC, St Louis, MO, USA; cat. ID: G1N70-1KT)

value: Tumour tissue


title: CNS_205_DNET

scan_protocol: bisulfite converted with Zymo EZ DNA methylation kit (Zymo Research, Irvine, CA, USA; cat. ID: D5002) and then hybridized on the 850K Infinium HD EPIC Methylation Array Bead Chip version 1 (Illumina, San Diego, CA, USA). Beadchip arrays were scanned on the NextSeq550 (Illumina, San Diego, CA, USA), which generated IDAT files


title: CNS_202_DGONC


title: CNS_201_EPN_PFA_1C


title: CNS_200_DIG_DIA


title: CNS_198_PA_INF


title: CNS_199_PA_INF


title: CNS_195_ATRT_MYC


title: CNS_193_PA_MID


title: CNS_190_EPN_PFA_1A


title: CNS_189_PA_INF


title: HCT116 control, biol rep 1

description:
Library name: Unknown_CG769-002U0029
Column name in raw_counts_all_samples.txt: Unknown_CG769-002U0029

value: Human colorectal adenocarcinoma epithelial cancer cells


title: CNS_186_PA_INF


title: CNS_187_AG_MYB


title: CNS_185_MB_WNT


title: CNS_183_PB_GRP2


title: CNS_179_PA_CORT


title: CNS_182_GCT_YOLKSAC


title: CNS_180_PA_INF


title: SAM_CON_P0_1

value: whole


title: CNS_184_SEGA


title: WT1


title: CNS_178_PA_INF


title: CNS_177_PA_MID


title: CNS_203_CTRL_REACTIVE


title: CNS_176_SCHW


title: CNS_175_EPN_PFB_4


title: CNS_192_GCT_TERA


title: CNS_174_PA_INF


title: CNS_171_MPNST_ATYP


title: CNS_188_MNG_BEN_3


title: CNS_169_MB_SHH_4


title: CNS_163_DNET


title: CNS_161_MB_G34_II


title: CNS_160_PB_GRP1A


title: CNS_159_PXA


title: CNS_158_PA_CORT


title: CNS_167_ATRT_SHH


title: CNS_156_PA_INF


title: CNS_155_PA_INF


title: CNS_157_GCT_GERM_KIT


title: CNS_149_CPC_PED


title: CNS_162_MB_SHH_3


title: CNS_150_DMG_K27


title: CNS_153_EPN_SPINE_SE_A


title: CNS_152_CTRL_CORPCAL


title: CNS_148_EPN_PFA_1C


title: CNS_173_EPN_PFA_1B


title: CNS_145_MB_G34_VIII


title: CNS_143_EPN_PFA_1C


title: CNS_141_PB_GRP1A


title: CNS_144_EPN_ST_ZFTA_RELA_A


title: CNS_142_PA_MID


title: CNS_170_PA_INF


title: CNS_140_PA_INF


title: CNS_166_PA_MID


title: CNS_139_MB_G34_VIII


title: CNS_138_MB_WNT


title: CNS_137_NET_PLAGL1_FUS


title: CNS_135_PA_INF


title: CNS_136_PA_INF


title: CNS_133_PA_INF


title: CNS_151_pedHGG_MYCN


title: CNS_132_PA_MID


title: CNS_154_EPN_YAP


title: CNS_131_MB_G34_III


title: CNS_124_GG


title: CNS_126_MB_G34_VII


title: CNS_127_ATRT_SHH


title: CNS_128_GBM_MES_TYP


title: CNS_119_CPC_PED


title: CNS_120_HGG_E


title: CNS_118_PA_CORT


title: CNS_116_GNT_A


title: CNS_113_GG


title: CNS_114_CPH_ADM


title: CNS_110_MB_SHH_3


title: CNS_111_PA_CORT


title: CNS_122_DNET


title: CNS_108_CPC_PED


title: CNS_115_PA_INF


title: CNS_117_PA_MID


title: CNS_134_DNET


title: CNS_106_LCH


title: CNS_107_PA_INF


title: CNS_104_EPN_ST_ZFTA_RELA_A


title: CNS_102_PA_INF


title: CNS_103_MNG_BEN_3


title: CNS_101_SEGA


title: CNS_125_PA_INF


title: CNS_123_EPN_ST_ZFTA_RELA_A


title: CNS_100_MB_SHH_4


title: CNS_099_MB_G34_VIII


title: CNS_096_PA_INF


title: CNS_098_MB_G34_II


title: CNS_094_DNET


title: CNS_095_MB_SHH_2


title: CNS_112_MNG_BEN_3


title: CNS_093_DMG_K27


title: CNS_097_CPP_PED


title: CNS_092_MB_G34_III


title: CNS_091_GCT_GERM_A


title: CNS_109_PA_MID


title: CNS_088_MB_G34_III


title: CNS_086_LGG_MYB_B


title: CNS_089_PA_INF


title: CNS_084_MB_SHH_2


title: CNS_085_DIG_DIA


title: CNS_082_CPH_PAP


title: CNS_079_CTRL_REACTIVE


title: CNS_081_SCHW


title: CNS_078_EPN_PFA_1F


title: CNS_075_PA_INF


title: CNS_074_PA_MID


title: CNS_073_PA_INF


title: CNS_072_PA_INF


title: CNS_071_MB_G34_VII


title: CNS_090_DNET


title: CNS_066_MB_G34_VIII


title: CNS_070_EPN_PFA_1B


title: CNS_068_MB_SHH_3


title: CNS_065_EPN_PFA_1D


title: CNS_063_MB_WNT


title: CNS_062_DMG_K27


title: CNS_064_MB_WNT


title: CNS_061_EPN_PFA_2A


title: CNS_060_MB_SHH_1


title: CNS_058_PA_INF


title: CNS_059_CPC_PED


title: CNS_057_PXA


title: CNS_056_PA_INF


title: CNS_054_CTRL_HEMI


title: CNS_053_MB_WNT


title: CNS_077_PA_INF


title: CNS_076_ATRT_SHH


title: CNS_050_PXA


title: CNS_052_MB_G34_III


title: CNS_051_PA_INF


title: CNS_049_MNG_BEN_1


title: CNS_047_MB_SHH_2


title: CNS_048_PA_MID


title: CNS_046_MB_G34_V


title: CNS_045_MB_G34_I


title: CNS_069_CTRL_HEMI


title: CNS_044_MB_G34_VII


title: CNS_041_PA_INF_FGFR


title: CNS_042_MB_G34_V


title: CNS_037_PA_INF


title: CNS_039_MB_SHH_2


title: CNS_040_MB_SHH_2


title: CNS_036_CPH_ADM


title: CNS_038_EPN_PFA_1C


title: CNS_035_INFLAM_ENV


title: CNS_034_CPP_PED


title: CNS_033_CPC_PED


title: CNS_031_PA_MID


title: CNS_055_PA_INF


title: CNS_030_PA_INF


title: CNS_028_PA_INF


title: CNS_025_CTRL_REACTIVE


title: CNS_027_MB_G34_IV


title: CNS_024_CTRL_CBM


title: CNS_020_GG


title: CNS_021_CTRL_HEMI


title: CNS_023_CNS_NB_FOXR2


title: CNS_019_PB_FOXR2


title: CNS_018_SCHW


title: CNS_017_GCT_TERA


title: CNS_015_RGNT


title: CNS_043_MB_WNT


title: CNS_016_CPH_PAP


title: CNS_014_EPN_PFA_2B


title: CNS_012_PA_MID


title: CNS_007_ET_PLAG


title: CNS_009_DIG_DIA


title: CNS_008_ATRT_SHH


title: CNS_010_PA_INF


title: DC004-5-26-16-CD45-2-CD103pos

description: Library name: DC004-5-26-16-CD45-2-CD103pos


title: CNS_006_ATRT_TYR


title: WT2


title: CNS_005_MET_MEL


title: CNS_003_ATRT_MYC


title: CNS_004_CPC_PED


title: CNS_001_DMG_EGFR


title: CNS_022_LGG_MYB_D


title: CNS_002_CTRL_REACTIVE


title: RNA-seq of c-Jun-OE B7H3-CAR T cells from healthy human donor 3, no TGFb

city: Stanford

first: Yiyun

last: Chen

state: California

address: 265 Campus Dr Room G2105

department: Stanford Cancer Institute

institute: Stanford University

description: Library name: B7H3Jun_noTGFb_Donor3

data_processing:
Bulk RNAseq was performed by Novogene using the NovaSeq platform. The raw RNA sequencing data was mapped to human reference genome hg38 using the STAR aligner, and genes annotated in Gencode v36 was quantified using featurecounts in the subread package.
Assembly: hg38
Supplementary files format and content: count and TPM matrices

source_name: T cells

extract_protocol:
CAR T cells were derived from the plate-bound stimulation assay described above and collected after ~20 hours of incubation. Cells were counted to ensure a maximum number of 500000 per sample.
Next, cell pellets were obtained after centrifugation and processed using the Qiagen RNeasy Micro kit and following the manufacturer’s protocol.

value: T cells

value: B7H3-CAR + c-JUN

value: no TGFb


title: RNA-seq of c-Jun-OE B7H3-CAR T cells from healthy human donor 3, TGFb-treated

description: Library name: B7H3Jun_TGFb_Donor3

value: TGFb


title: RNA-seq of B7H3-CAR T cells from healthy human donor 3, TGFb-treated

description: Library name: B7H3_TGFb_Donor3


title: RNA-seq of c-Jun-OE B7H3-CAR T cells from healthy human donor 2, TGFb-treated

description: Library name: B7H3Jun_TGFb_Donor2


title: RNA-seq of B7H3-CAR T cells from healthy human donor 2, TGFb-treated

description: Library name: B7H3_TGFb_Donor2


title: RNA-seq of B7H3-CAR T cells from healthy human donor 2, no TGFb

description: Library name: B7H3_noTGFb_Donor2


title: RNA-seq of c-Jun-OE B7H3-CAR T cells from healthy human donor 2, no TGFb

description: Library name: B7H3Jun_noTGFb_Donor2


title: RNA-seq of B7H3-CAR T cells from healthy human donor 1, TGFb-treated

description: Library name: B7H3_TGFb_Donor1


title: RNA-seq of c-Jun-OE B7H3-CAR T cells from healthy human donor 1, TGFb-treated

description: Library name: B7H3Jun_TGFb_Donor1


title: RNA-seq of c-Jun-OE B7H3-CAR T cells from healthy human donor 1, no TGFb

description: Library name: B7H3Jun_noTGFb_Donor1


title: RNA-seq of B7H3-CAR T cells from healthy human donor 1, no TGFb

description: Library name: B7H3_noTGFb_Donor1


title: CNS_013_HGG_E


title: NAD11

first: Yifei

last: Wang

address: Baofeng street

institute: Huazhong University of Science and Technology

description: Library name: SAMPLE 19

data_processing:
The libraries were sequenced on an Illumina Novaseq 6000  platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
Assembly: the reference genome  using HISAT2
Supplementary files format and content: FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count

source_name: blood

extract_protocol:
Total RNA was extracted using the TRIzol reagent  (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: blood

value: mononuclear cell

tag: condition

value: NAD


title: NAD12

description: Library name: SAMPLE 20


title: NAD10

description: Library name: SAMPLE 18


title: NAD9

description: Library name: SAMPLE 17


title: NAD8

description: Library name: SAMPLE 16


title: NAD5

description: Library name: SAMPLE 13


title: NAD2

description: Library name: SAMPLE 10


title: NAD6

description: Library name: SAMPLE 14


title: NAD1

description: Library name: SAMPLE 9


title: DAD8

description: Library name: SAMPLE 8

value: DAD


title: NAD7

description: Library name: SAMPLE 15


title: DAD5

description: Library name: SAMPLE 5


title: DAD4

description: Library name: SAMPLE 4


title: DAD6

description: Library name: SAMPLE 6


title: DAD3

description: Library name: SAMPLE 3


title: NAD4

description: Library name: SAMPLE 12


title: DAD2

description: Library name: SAMPLE 2