title: Lung macrophages from MMTV-HER2 early lung

city: The Bronx

first: Michael

last: Papanicolaou

address: 1300 Morris Park Avenue

department: Cell Biology

institute: Albert Einstein College of Medicine

data_processing:
Data processed with cellranger-5.0.1
Assembly: mm10-2020-A
Supplementary files format and content: comma separated values file containing average UMI values

source_name: MMTV-HER2 early lung

growth_protocol: Mice were maintained at specified pathogen free health status in individually ventilated cages at 21-22?C and 39-50% humidity. All animal procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of Icahn School of Medicine at Mount Sinai and Albert Einstein College of Medicine. 16-week-old female mice were used as early (‘early lesion’) stage mice and 32-week-old  females with palpable tumor(s) were used as late stage of cancer progression. Female littermates were randomly assigned to experimental groups.

extract_protocol:
Cells loaded onto 10x Genomics NextGen 3’ v.1.2 assay.
10x Genomics NextGen 3’ v.1.2 assay, as per manufacturer’s instructions

treatment_protocol: Single cell suspensions were obtained from lungs by digestion with 0.15% Collagenase 1A (SIGMA, C-9891) 2.5% bovine serum al- bumin (BSA) at 37?C with agitation for 30 min followed by passing through a 70mm cell strainer and RBC lysis (RBC lysis buffer, BioLegend) for 5 min at room temperature. For flow cytometry or fluorescence-activated cell sorting (FACS), cells were stained in FACS buffer (PBS supplemented with 10% BSA and 2mM EDTA) with BD Brilliant Stain Buffer Plus and rat monoclonal antibodies  (see Dalla et al. for detailed list of antibodies used).

value: Lung

value: Primary cells

value: Primary lung macrophages

value: wild type and MMTV-HER2


title: aNSC_control_WGS_2

status: Public on Oct 05 2024

type: SRA

city: New York

first: Andrea

last: Ventura

state: NY

department: Cancer Biology and Genetics

country: USA

institute: Memorial Sloan Kettering Cancer Center

description: shallow whole genome sequencing for copy number normalization

library_source: genomic

data_processing:
Fastq files from ATAC-seq and Whole Genome Sequencing (WGS) were aligned to the mouse genome (mm10) using Bowtie2.  Then CNVkit (Version 0.9.10) was applied to WGS bam files to identify copy number variations (CNVs) and ecDNA amplicon regions. To compare ATAC-seq signals between ecDNA Myc (Mycec) amplicon in p53fl/fl;Mycec/+ and corresponding chromosomal region in p53fl/fl, bamCoverage in deeptools (Version=3.5.3) was used for calculating the read counts with 10kb bin size and MACS (Version= 3.0.0b1) was used for peak calling. Read counts and peak numbers were normalized by segment length (10kb), sequencing depth, and copy number.
Assembly: mm10
Supplementary files format and content: bedgraph for ATACseq and bigwig for shallow WGS
Library strategy: shallow whole genome sequencing

molecule: genomic DNA

organism: Mus musculus

source_name: adult neuronal stem cells

growth_protocol: aNSCs from p53fl/fl and p53fl/; Myc-ec/+ animals were infected with AdCre and maintained in neurocult medium for approximately 5 weeks before generating ATACseq and sWGS libraries

extract_protocol:
Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge.
Profiling of chromatin was performed by ATAC-Seq as described by Buenrostro, et al. Briefly, 50,000 fresh aNSCwere washed in cold PBS and lysed. The transposition reaction containing TDE1 Tagment DNA Enzyme (Illumina catalog # 20034198) was incubated at 37°C for 30 minutes. The DNA was cleaned with the MinElute PCR Purification Kit (QIAGEN catalog # 28004) and material was amplified for 5 cycles using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs catalog # M0541L). After evaluation by real-time PCR, 4 to 5 additional PCR cycles were done. The final product was cleaned by aMPure XP beads (Beckman Coulter catalog # A63882) at a 1X ratio, and size selection was performed at a 1.5X ratio. Libraries were sequenced on a NovaSeq 6000 in a PE100 run, using NovaSeq 6000 S4 Reagent Kit v1.5 (200 Cycles) (Illumina). An average of 50 million paired reads were generated per sample.

tag: cell type

value: adult neuronal stem cells

tag: genotype

tag: treatment

value: AdCre infection


title: MCF7, 2KR, 3h, Rep 1 [2R3A_S34]

city: Boston

first: Dan

last: Lu

state: MA

address: 210 Longwood Avenue

department: Department of Systems Biology

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
Raw RNA-sequencing data was processed using the bcbio-nextgen toolkit (https://bcbio-nextgen). The bcbio-nextgen pipeline includes aligning reads to the human reference genome hg38 with STAR58 and quantifying transcripts with Salmon59. Genes with a mean average count < 10 across all samples or those with 0 counts in >90% of samples were removed from downstream analysis. For the remaining occasional missing values, a pseudocount was added and then the counts were normalized using DESeq260.
Assembly: hg38
Supplementary files format and content: tab-deliminated text file includes salmon_raw_counts for each Sample
Supplementary files format and content: tab-deliminated text file includes salmon_tpm values for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: RPMI, 10% FBS, 5% CO2, 37 degrees Celsius

extract_protocol:
Qiagen RNAeasy Kit (manufacturer's protocol) 500ng RNA were used for library preparation
Libraries were prepared using a SciClone G3 NGSx workstation (Perkin Elmer) using the Kapa mRNA HyperPrep kit (Roche Applied Science). Polyadenylated mRNAs were captured using oligo-dT-conjugated magnetic beads (Kapa mRNA HyperPrep kit, Roche Sequencing, KR1352 – v4.17) from 500 ng of total RNA on a Perkin Elmer SciClone G3 NGSx automated workstation. Poly-adenylated mRNA samples were immediately fragmented to 300-400bp using heat and magnesium. First-strand synthesis was completed using random priming followed by second-strand synthesis and A-tailing. dUTP was incorporated into the second strand to allow strand-specific sequencing of the library. Libraries were enriched and indexed using 9 cycles of amplification (Kapa mRNA HyperPrep kit, Roche Sequencing) with PCR primers, which included dual 8bp index sequences to allow for multiplexing (IDT for Illumina unique dual 8bp indexes). Excess PCR reagents were removed through magnetic bead-based cleanup using Kapa Pure magnetic beads on a SciClone G3 NGSx workstation (Perkin Elmer). The resulting libraries were assessed using a 4200 TapeStation (Agilent Technologies) and quantified by QPCR (Roche Sequencing). Libraries were pooled and sequenced on one lane of an Illumina NovaSeq S4 flow cell using paired-end, 100bp reads.

treatment_protocol: 10 Gy X-ray irradiation

tag: cell line

value: breast carcinoma

value: 10Gy X-ray Irradiation


title: Lung macrophages from wildtype early lung

state: New York

library_source: transcriptomic single cell

source_name: Wildtype early lung

tag: tissue

tag: strain

tag: age


title: aNSC_control_WGS_1


title: MCF7, 2KR, 1h, Rep 1 [2R1A_S32]


title: aNSC_ecMyc_WGS_2


title: MCF7, 2KR, 0h, Rep 1 [2R0A_S31]

value: Untreated


title: MCF7, WT, 9h, Rep 1 [WT9A_S10]

value: WT


title: MCF7, WT, 8h, Rep 1 [WT8A_S9]


title: aNSC_ecMyc_WGS_1


title: aNSC_control_ATAC_2

data_processing:
Fastq files from ATAC-seq and Whole Genome Sequencing (WGS) were aligned to the mouse genome (mm10) using Bowtie2.  Then CNVkit (Version 0.9.10) was applied to WGS bam files to identify copy number variations (CNVs) and ecDNA amplicon regions. To compare ATAC-seq signals between ecDNA Myc (Mycec) amplicon in p53fl/fl;Mycec/+ and corresponding chromosomal region in p53fl/fl, bamCoverage in deeptools (Version=3.5.3) was used for calculating the read counts with 10kb bin size and MACS (Version= 3.0.0b1) was used for peak calling. Read counts and peak numbers were normalized by segment length (10kb), sequencing depth, and copy number.
Assembly: mm10
Supplementary files format and content: bedgraph for ATACseq and bigwig for shallow WGS


title: MCF7, WT, 7h, Rep 1 [WT7A_S8]


title: aNSC_ecMyc_ATAC_2


title: aNSC_control_ATAC_1


title: CKO-AA, scRNA-seq

city: Shanghai

first: Yi

last: Li

address: 320 Yueyang Road

country: China

institute: Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences

description: 10x Genomics

data_processing:
Each scRNA-seq data set was processed by CellRanger (v6.1.1) pipeline to perform the alignment against the modified mouse reference genome mm10, filter the alignment and count barcodes and UMIs.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files contain barcodes, features and matrix.

source_name: aortic arch

extract_protocol:
The mice were perfused with 4℃ PBS, and then the tissues were collected, dissected in PBS to remove excess hair and blood. Then the aorta were finely minced and transferred to 5ml digestion mix (HBSS, 2U/µl Collagenase type I (17100017, Gibco), 2U/µl Collagenase type II (LS004177, Worthington)). The digestion mix included tissue were incubated at 37℃ for 15 minutes. The cell suspension was filtered through 40μm cell strainer and then pelleted by centrifugation at 500g for 5 minutes. Next the cells were incubated in red-blood-cell lysis buffer (1ml, eBioscience, 00-4333-57) at room temperature for 1 min. Add ten times the volume of cold PBS, centrifuged and resuspended with cold PBS. At last, the cells were pelleted by centrifugation at 300g for 5 minutes and resuspended with 100 µl cold PBS.
The cell suspense was loaded in 10x Chromium controller to generate GEMs, which were further processed into single cell 5ʹ gene expression libraries using Chromium Single Cell 5ʹ Library Kit (v2 Chemistry).

value: aortic arch

value: aortic cells

value: 16-20 weeks


title: MCF7, WT, 6h, Rep 1 [WT6A_S7]


title: aNSC_ecMyc_ATAC_1


title: Lung macrophages from wildtype late lung

source_name: Wildtype late lung


title: MCF7, WT, 5h, Rep 1 [WT5A_S6]


title: Lung macrophages from MMTV-HER2 late lung

source_name: MMTV-HER2 late lung


title: mouse_1_liver_tumor_2

data_processing:
Reads were mapped to mm10 or hg19 using the Bowtie2 aligner. To calculate genome coverage and copy number changes we used the QDNAseq R package with 15kb bins.
Assembly: hg19 and mm10
Supplementary files format and content: bedgraph files with normalized coverage

growth_protocol: HCT116 cells were infected with AdCre, expanded and sorted baased on GFP expression.

extract_protocol:
Cells were lysed in a buffer containing 0.1M NaCl, 0.038M TrisHCl, 0.01M EDTA and 0.175M SDS. DNA was extracted using the phenol-chloroform method  followed by ethanol precipitation.
After PicoGreen quantification, 42-100 ng of genomic DNA were used for library construction using the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) with 8 cycles of PCR.
Barcoded libraries were sequenced on the NovaSeq 6000, using the NovaSeq 6000 S2 or S4 Reagent Kit (200 or 300 Cycles) (Illumina) for PE100 reads. An average of 26M reads were generated per sample, corresponding to 0.7X coverage of the genome.

value: HDTI-MYC


title: MCF7, WT, 4h, Rep 1 [WT4A_S5]


title: mouse_1_liver_tumor_1


title: mouse_3_liver_tumor_3


title: MCF7, 2KR, 6h, Rep 1 [2R6A_S37]


title: MCF7, 2KR, 2h, Rep 1 [2R2A_S33]


title: MCF7, WT, 2h, Rep 1 [WT2A_S3]


title: MCF7, WT, 1h, Rep 1 [WT1A_S2]


title: MCF7, WT, 0h, Rep 1 [WT0A_S1]


title: mouse_2_liver_tumor_3


title: mouse_3_liver_tumor_2


title: CSR [GSM2012133]

city: Changsha, Hunan

first: Bing

last: Wang

address: Renminzhong Road

department: Department of Spine Surgery

institute: The Second Xiangya Hospital, Central South University

data_processing:
The raw data was handled by Skewer and data quality was checked by FastQC v0.11.2.
Clean reads were aligned to the Human genome hg38 using STAR.StringTie.
The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using Perl.
Differentially expression transcripts (DETs) were determined using the MA-plot-based method with Random Sampling (MARS) model in the DEGseq package between different groups (CSR vs. CON, DCM vs. CON, DCM vs. CSR) .
Then DETs were chosen for function and signaling pathway enrichment analysis using GO and KEGG database.
Assembly: the Human genome hg38
Supplementary files format and content: include counts values for each Sample
Supplementary files format and content: include FPKM values for each Sample

source_name: peripheral blood

extract_protocol:
Cells were harvested and total RNA was extracted by using RNAmini kit ( Qiagen, Germany). Enrichment of mRNA, fragmentation, reverse transcription, library construction, Illumina Novaseq 6000 and data analysis were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China).
Total RNA was isolated from each thymic sample using the RNAmini kit (Qiagen, Germany). RNA quality was examined by gel electrophoresis and with Qubit (Thermo, Waltham, MA, USA). For RNA sequencing, RNA samples from different groups were separated into three independent pools, each comprised of two or three distinct samples, at equal amounts. Strand-specific libraries were constructed using the TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA), and sequencing was carried out using the Illumina Novaseq 6000 instrument by the commercial service of Genergy Biotechnology Co. Ltd. (Shanghai, China).

value: peripheral blood

value: male

tag: disease

value: CSR


title: mouse_2_liver_tumor_1


title: CON [GSM2012118]

value: CON


title: CON [GSM2012124]


title: CON [GSM2012115]


title: RK783R_R1.fastq.gz

source_name: MEFs

value: MEFs


title: CON [GSM2012109]


title: CON [GSM2012103]


title: 2_3_MZ_IGO_14426_B_3_S257_L004_R1_001.fastq.gz

value: AdCre


title: RK782R_R1.fastq.gz


title: 2_3_Ras_MZ_IGO_14426_B_4_S258_L004_R1_001.fastq.gz


title: DCM [GSM2012094_]

value: DCM


title: CSR [GSM2012097]


title: 2_3_KC_IGO_14426_B_10_S251_L004_R1_001.fastq.gz


title: NSC_ecMyc_no_Cre

value: adult neuronal stem cells

value: Myc-ec/+


title: CON [GSM2012106]


title: mouse_3_liver_tumor_1


title: CSR [GSM2012088]


title: CSR [GSM2012082]


title: NSC_ecMyc_5_week


title: CSR [GSM2012079]


title: mouse_2_liver_tumor_2


title: NSC_ecMyc_3_week


title: MCF7, WT, 3h, Rep 1 [WT3A_S4]

value: breast carcinoma


title: DCM [GSM2012073]


title: CSR [GSM2012075]

value: female


title: RK784L_R1.fastq.gz


title: NSC_ecMyc_4_week


title: NSC_ecMyc_2_week


title: DCM [GSM2012071]


title: NSC_ecMyc_1_week


title: Cardiomyocytes4, palmitoylglycine 1μM, 24h

city: Beijing

first: Hongxuan

last: Xu

address: No.8 Xishiku Street

department: Cardiology

institute: Peking university first hospital

data_processing:
Low-quality regions at both ends of the sequences were trimmed using Trimmomatic, with a quality threshold set at 30. Adapter sequences were removed. Sequences containing ambiguous bases (N) were eliminated. Sequences shorter than 60 bp were discarded.
Assembly: mRatBN7.2
Supplementary files format and content: text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: Neonatal rat cardiomyocytes

extract_protocol:
RNA was harbested using Dynabeads Oligo (dT)25-61002 (ThermoFisher).
Fragmentation buffer was added to break the mRNA into short segments. Using the mRNA as a template, first-strand cDNA was synthesized with random hexamer primers. Following this, a buffer, dNTPs, DNA polymerase I, and RNase H were added to synthesize double-stranded cDNA, which was then purified using AMPure XP beads.  The purified double-stranded cDNA underwent end repair, A-tailing, and ligation of sequencing adapters, followed by size selection using AMPure XP beads. PCR amplification was then performed, and the PCR products were purified with AMPure XP beads to obtain the final library. Once the library construction was complete, preliminary quantification was conducted using a Qubit 2.0, and the library was diluted to 1.5 ng/µL. The insert size of the library was assessed using an Agilent 2100. After confirming that the insert size met expectations, accurate quantification of the library’s effective concentration was performed using Q-PCR (with effective concentration > 2 nM) to ensure library quality.

value: Neonatal rat cardiomyocytes


title: Cardiomyocytes3, palmitoylglycine 1μM, 24h


title: Cardiomyocytes5, palmitoylglycine 1μM, 24h


title: MEFs_p53_3

description: Total RNA extracted five weeks post AdCre infection

data_processing:
Reads were mapped to mm10 using the STAR aligner software
Assembly: mm10
Supplementary files format and content: STAR output Reads per gene

extract_protocol:
Samples were lysed and extracted using the Trizol reagent
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 8.4-9.9 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR.
Samples were barcoded and run on NovaSeq 6000 in a PE100 run, using the NovaSeq 6000 S2 Reagent Kit (200 Cycles) (Illumina). An average of 33 million paired reads was generated per sample. Ribosomal reads represented 0.4-1.7% of the total reads generated and the percent of mRNA bases averaged 91%.

value: AdCre-infection and HRASG12 transduction


title: Cardiomyocytes2, palmitoylglycine 1μM, 24h


title: DCM [GSM2012067]


title: DCM [GSM2012069]


title: B16-BL6 cells, sgNDUFS4, rep3

first: Tevis

last: Vitale

state: Massachusetts

address: 50 Industrial Drive, LC6201

institute: Dana-Farber Cancer Institute

data_processing:
Reads were mapped to GRCm38.84 using HiSat2.1
Reads were quantitated using SeqMonk v48.1 on the cDNA level
Counts were then normalized from FKPM to CPM
Assembly: GRCm38.84
Supplementary files format and content: comma separated file includes CPM for each sample

molecule: polyA RNA

growth_protocol: B16-BL6 melanoma cells were maintained in DMEM supplemented with 10% FBS, 1mM sodium pyruvate, and 1% pen-strep

extract_protocol:
RNA samples were prepared with TRIzol® Reagent. Briefly, cells in 60 mm dish with ~70% confluent cells were incubated with 1 ml TRIzol® Reagent for 5 minutes and then transferred into a 1.5 ml tube and mixed with 0.2 ml chloroform. After vigorously shaking for 15 seconds, samples were centrifuged at 12000 g for 15 minutes at 4 °C. The aqueous phage was collected and mixed with an equal volume of 100% isopropanol. The mixture was then centrifuged at 12000 g for 15 minutes at 4 °C to obtain RNA pellet. The supernatant was removed, and the obtained RNA pellet was washed with 75% ethanol 3 times. RNA pellet was dry and resuspended into RNase free water. The concentration of RNA was measured with a nanodrop spectrophotometer, and the quality of RNA was determined by agarose gel electrophoresis.
Samples were processed by Genewiz in accordance with their internal protocols for paired end strand independent sequencing

value: melanoma


title: MEFs_p53_2


title: Cardiomyocytes1, palmitoylglycine 1μM, 24h


title: MEFs_p53_1


title: B16-BL6 cells, sgNDUFS4, rep1


title: DCM [GSM2012065]


title: B16-BL6 cells, sgControl, rep3

value: sgControl


title: Cardiomyocytes5, DMSO, 24h


title: DCM [GSM2012063]


title: CSR [GSM2012061]


title: Cardiomyocytes4, DMSO, 24h


title: B16-BL6 cells, sgControl, rep2


title: B16-BL6 cells, sgNDUFS4, rep2


title: B16-BL6 cells, sgControl, rep1


title: CSR [GSM2012057]


title: Cardiomyocytes3, DMSO, 24h


title: DCM [GSM2012059]


title: MCF7, 2KR, 2h, Rep 2 [2R2B_S48]

value: 10Gy X-ray Irradiation


title: MEFsecMdm2_1


title: MEFsecMdm2_2


title: RK783L_R1.fastq.gz


title: NSC_p53_RNAseq_3

source_name: adult neuronal stem cell

value: adult neuronal stem cell

value: Myc-+/+;l p53fl/fl

value: AdCre-infection


title: CSR [GSM2012055]

value: peripheral blood

value: CSR


title: NSC_p53_RNAseq_2


title: Cardiomyocytes1, DMSO, 24h


title: DCM [GSM2012051]


title: Mus,BAT,Oil,rep12

city: Davis

first: Michele

middle: Andrea

last: La Merrill

state: CA

address: One Shields Ave

department: Environmental Toxicology

institute: University of California Davis

data_processing:
Sequenced single-end reads of 50 bp were trimmed using Scythe 0.993 and Sickle 1.33 was used to trim bases with a Phred quality threshold below 30, while  reads less than 30 bp were discarded.
Quality control was performed using FastQC
Alignment to the GRCm38 reference genome was done with Bismark version 0.15.0 and Bowtie 2 as the underlining aligner using -D 20 and -R 3 parameters to increase the chance for finding an alignment
The differential methylation analysis was carried out using software DMAP
Assembly: GRCm38
Supplementary files format and content: .txt, differential DNA methylation at each CpG site

source_name: Brown adipose tissue

extract_protocol:
Mice were euthanized and brown adipose tissue was excised and cut in half, with one half flash-frozen in liquid nitrogen. Flash-frozen brown adipose tissue were later pulverized and DNA was extracted using the AllPrep DNA/RNA/Protein Mini Kit (Qiagen).
DNA quality, quantity, and purity (260/280 absorbance ratios) were assessed using a Fragment Analyzer, a Qubit fluorometer, and a Nanoquant plate using an Infinite 200 PRO absorbance reader, respectively. DNA was diluted to a normalized concentration (0.222 ng/uL) and sequenced.

value: Brown adipose tissue

tag: Sex

value: Female

tag: perinatal treatment

value: OIL


title: db/db-GABP-KD 3

city: Xuzhou

first: Yinfei

state: Jiangsu

address: No. 209 Tongshan Road, Xuzhou City

institute: Xuzhou Medical University

data_processing:
We use HTSeq to statistically compare the Read Count value on each gene as the original expression level of the gene.
In order to ensure comparability of gene expression levels between different genes and samples, we standardized the expression levels using FPKM (Nosrmalization).
Assembly: GRCm39
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text files include  fpkm for each Sample

source_name: Kidney

growth_protocol: The mice were housed in the SPF animal room , and kept under adequate food, water and constant temperature and humidity.

extract_protocol:
Each group selected 6 different mouse kidney tissues, and 3 tissues were mixed together for extraction.Total RNA was extracted from each tissue sample using the Trizol method.
This project enriches mRNA with polyA structure in total RNA using Oligo (dT) magnetic beads, and breaks the RNA into fragments with a length of about 300bp using ion breaking. Select a segment with a length of 300bp because the joint length is fixed. If the broken segment has a shorter length, it will result in a higher proportion of joint sequences, thereby reducing the proportion of valid data; If the length of the interrupted fragment is longer, it is not conducive to cluster generation during the online sequencing process. Using RNA as a template, the first strand of cDNA was synthesized using 6-base random primers and reverse transcriptase, and the second strand of cDNA was synthesized using the first strand of cDNA as a template. After the library construction is completed, PCR amplification is used to enrich the library fragments, and then the library is selected based on the fragment size, with a library size of 450bp. Next, the library was inspected using Agilent 2100 Bioanalyzer, and the total concentration and effective concentration of the library were tested. Then, based on the effective concentration of the library and the amount of data required for the library, the library containing different Index sequences (each sample is added with a different Index, and finally the offline data of each sample is distinguished based on the Index) is mixed proportionally. The mixed library was uniformly diluted to 2nM and subjected to alkaline denaturation to form a single stranded library. After RNA extraction, purification, and library construction, the samples were subjected to next-generation sequencing (NGS) using the Illumina sequencing platform to perform paired end (PE) sequencing on these libraries.

value: Kidney

value: GABP-KD


title: Mus,BAT,DDT,rep11

value: DDT


title: DCM [GSM2012049]

value: female

value: DCM


title: db/db-GABP-KD 2


title: NSC_ecMyc_RNAseq_3

value: Myc-ec/+;l p53fl/fl


title: Mus,BAT,Oil,rep11


title: DCM [GSM2012047]

value: male


title: db/db-GABP-KD 1


title: Mus,BAT,DDT,rep10


title: DCM [GSM2012045]


title: NSC_ecMyc_RNAseq_2


title: db/m-GABP-OE 2

value: GABP-OE


title: Mus,BAT,Oil,rep10


title: DCM [GSM2012039]


title: Mus,BAT,Oil,rep9


title: DCM [GSM2012037]


title: Cardiomyocytes2, DMSO, 24h

value: Neonatal rat cardiomyocytes


title: db/m-GABP-OE 3


title: db/m-GABP-OE 1


title: Mus,BAT,DDT,rep12


title: NSC_p53_RNAseq_1

value: adult neuronal stem cell


title: Control Femur

city: Zurich

first: Neashan

last: Mathavan

address: GLC H 21.1, Gloriastrasse 37 / 39

department: Institute for Biomechanics

country: Switzerland

institute: ETH Zurich

description: FFPE spatial transcriptomics sequencing.

data_processing:
Demultiplexing and manual alignment of the sequencing data to the histological image were performed using the SpaceRanger analysis pipeline (10x Genomics, version 2.0.0) and Loupe Browser (10x Genomics, version 6.2.0) respectively. Further downstream data analyses and visualization were performed in R (version 4.3.1) using Seurat (77) (version 4.4.0).
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz  : list of spatial barcodes
Supplementary files format and content: features.tsv.gz : list of gene IDs
Supplementary files format and content: matrix.mtx.gz : gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg : aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg : image of tissue and spots
Supplementary files format and content: scalefactors_json.json : scale factors in json format
Supplementary files format and content: tissue_hires_image.png : hi-res image of tissue
Supplementary files format and content: tissue_lowres_image_png : low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.: list of spatial barcodes and the coordinates specifying spots

source_name: Femur

growth_protocol: 12 week old bone cell reporter (BCR) mice (https://www.ssrn.com/abstract=4476675) received femoral osteotomies. Euthanized at 17 weeks of age.

extract_protocol:
FFPE (manufacturer's protocol), 10X Visium Spatial Gene Expression (manufacturer's protocol)
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagents kit according to manufacturer’s construction.

treatment_protocol: Protocol available at https://doi.org/10.1016/j.xpro.2024.102986

value: Femur

value: Control


title: db/db-veh 3

value: veh


title: Mus,BAT,DDT,rep9


title: Mus,BAT,Oil,rep8


title: MEFsecMdm2_3

value: MEFs

value: AdCre-infection and HRASG12 transduction


title: DCM [GSM2012031]

value: peripheral blood


title: db/db-veh 2


title: Mus,BAT,Oil,rep7

value: Brown adipose tissue

value: Female

value: OIL


title: DCM [GSM2012021]


title: Mus,BAT,DDT,rep8

value: DDT


title: VPR (HSPB8) 48hpf rep2

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

data_processing:
The sequencing reads were aligned to the human GRCh38 genome using STAR, and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package.
Assembly: GRCh38
Supplementary files format and content: comma-delimited csv files included read counts  of each sample and each gene.
Supplementary files format and content: comma-delimited csv files included read counts  of each sample and each gene.

source_name: 293T cells

growth_protocol: 293T cells  were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with high glucose (HAKATA) in the presence of 10% FBS (HAKATA) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
Total RNAs were extracted using MolPure® Cell/Tissue Total RNA Kit (YEASEN) following the manufacturer’s instruction.
RNA libraries were prepared for sequencing using bgiseq500 protocols.

treatment_protocol: 293T cells were seeded into 12-well plates. The next day, 1.2 μg CRISPRa component and 2.4 μg sgRNA was transfected into cells.

value: 293T cells

value: 48 hpf


title: control VPR (HSPB8) 48hpf rep2


title: VPR (HSPB8) 48hpf rep1


title: DCM [GSM2012019]

value: DCM


title: NSC_ecMyc_RNAseq_1

value: Myc-ec/+;l p53fl/fl

value: AdCre-infection


title: db/m-veh 3

value: Kidney


title: control VPR (HSPB8) 48hpf rep1


title: DCM [GSM2012035]

value: male


title: Mus,BAT,DDT,rep7


title: db/m-veh 2


title: DCM [GSM2012015]


title: Mus,BAT,DDT,rep6


title: DCM [GSM2012013]

value: female


title: control VPRF (HSPB8) 48hpf rep2


title: control VPRF (HSPB8) 48hpf rep1


title: Mus,BAT,Oil,rep6


title: DCM [GSM2012012]


title: Loaded Femur

value: Femur

value: Loaded


title: Mus,BAT,Oil,rep5


title: Sirt55

city: Guangzhou

first: Li

last: Ma

state: Guangdong

address: Sun-Yat university

department: Heart Center

institute: Guangzhou Women and Children's Medical Center, Guangzhou Medical University

data_processing:
RNA sequencing libraries were constructed using Illumina TruSeq RNA Preparation kit and Illumina Ribo-Zero GoldrRNA Removal Kit according to the manufacturer’s instructions, and subsequently sequencing was performed via Illumina NextSeq 500 with the 300bp paired-end reads. The
The filtered RNA reads alignment and map on reference genome (GRCm38) via HISAT2 software (http://ccb.jhu.edu/software/hisat2/index.shtml). Consequently, the raw read counts were quantified by HTSeq software (https://htseq.readthedocs.io,version 0.6.1) based on BAM files.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Mus_musculus. GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Sirt5 knockout

extract_protocol:
Ribosomal RNA (rRNA) was removed from Total RNA using QIAseq FastSelect RNA Removal Kit (Qiagen, Venlo, The Netherlands) according to the manufacturer’s instructions. The enriched mRNAs and non-coding RNAs were fragmented into short fragments (approximately 300 bp) using a fragmentation buffer and reverse-transcribed to cDNA with random primers, and this first-strand cDNA was used as the template for second-strand cDNA synthesis. Then, the cDNA fragments were end-repaired and ligated to Illumina sequencing adapters. The second-strand cDNA was digested using Uracil-DNA Glycosylase (UDG). The digested products were size selected (approximately 450 bp), PCR amplified, and quality assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). After cDNA library construction, a paired-end sequencing was performed using Illumina Hiseq 4000 systems (Illumina, San Diego, CA, USA). The raw data were filtered, and the clean data were mapped to the reference genome Mus_musculus. GRCm38.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: left ventricular tissue

tag: time

value: Six weeks after TAC surgery

value: Sirt5 knockout


title: VPRF (HSPB8) 48hpf rep2


title: Sirt54


title: db/db-veh 1

value: veh


title: Mus,BAT,DDT,rep5

value: Brown adipose tissue

value: Female


title: VPRF (HSPB8) 48hpf rep1


title: Sirt53


title: DCM [GSM2012009]

value: peripheral blood


title: db/m-veh 1


title: 3XVPR (HSPB8) 48hpf rep2

value: 293T cells


title: 3XVPR (HSPB8) 48hpf rep1

value: 48 hpf


title: Sirt52


title: Mus,BAT,DDT,rep4

value: DDT


title: DCM [GSM2012007]

value: DCM


title: WT7

source_name: wild-type

value: wild type


title: control 3XVPR (HSPB8) 48hpf rep2


title: DCM [GSM2012006]


title: Mus,BAT,Oil,rep4

value: OIL


title: control 3XVPR (HSPB8) 48hpf rep1


title: WT6


title: Mus,BAT,DDT,rep2


title: Mus,BAT,DDT,rep1


title: WT5


title: DCM [GSM2012004]


title: DCM [GSM2012010]

value: male


title: WT4


title: Mus,BAT,Oil,rep3


title: DCM [GSM2012003]


title: WT3


title: 3XVPRF (HSPB8) 48hpf rep2


title: DCM [GSM2012002]


title: WT1


title: Mus,BAT,DDT,rep3


title: DCM [GSM2012008]


title: 3XVPRF (HSPB8) 48hpf rep1


title: Mus,BAT,Oil,rep2


title: Mus,BAT,Oil,rep1


title: DCM [GSM2012005]


title: control 3XVPRF (HSPB8) 48hpf rep1


title: 017Day42

status: Public on Oct 04 2024

type: RNA

city: Urbana

first: Timothy

middle: M.

last: Fan

state: Illinois

address: 1008 West Hazelwood Drive

department: Veterinary Clinical Medicine

institute: University of Illinois Urbana Champaign

description: Nanostring Canine IO nCounter panel (XT-CIO-12)

hyb_protocol: Hybridization of RNA to the Canine IO nCounter panel probe set (Nanostring) was performed according to manufacturer's instructions for 23 hours at 65C. Hybridized RNA was loaded into the analysis cartridge using Nanostring PrepStation.

scan_protocol: Scanning of analysis cartridge was performed on Nanostring Digital Analyzer under maximum resolution.

data_processing: Nanostring nSolver software was used to process count data. Background thresholding was performed using the mean of 8 negative control probes.

organism: Canis lupus familiaris

source_name: Tumor

growth_protocol: n/a - client-owned dogs with malignant melanoma

extract_protocol: RNA was extracted from FFPE tissue scrolls (10um) using Qiagen FFPE RNEasy kit following manufacturer's protocol. Samples were QC'd for concentration and fragment analysis on Bioanalyzer (Agilent) prior to hybridization to the nCounter panel probe set.

treatment_protocol: Pet dogs with melanoma  were enrolled into four cohorts of 1, 3,10, and 20 µg/kg administered by local injection of aluminum hydroxide-tethered interleukin-12 (JEN-101) every three weeks for four cycles. For dogs without disease progression or clinically significant toxicity, another four cycles of JEN-101 every three weeks were allowable. Dogs were followed for up to one year following completion of treatment. Baseline tumor biopsy was required in all dogs and post-treatment biopsies were collected when clinically feasibility or at the time of death.

tag: melanoma

value: Oral malignant melanoma

value: 10 years

tag: weight

value: 25 kg

value: Intratumoral JEN-101

tag: dose

value: 20 µg/kg


title: 017Pre-tx


title: 017Day21


title: CON [GSM2011000]

value: female

value: CON


title: 010Day21

value: 11 years

value: 10 µg/kg


title: 010Day105


title: 010Day42


title: 010Day63


title: 010Pre-tx


title: 003Day63

value: 27 kg

value: 1 µg/kg


title: 003Pre-tx


title: 008Pre-tx

value: 5 years


title: MelJuso, Rocaglamide A, replicate 1

city: Brno

first: Core Facility

last: Bioinformatics

address: Kamenice 5

country: Czech Republic

institute: CEITEC - Masaryk University

data_processing:
Sequence reads were trimmed for low-quality sequence using Trimmomatic (parameter LEADING: 3 TRAILING: 3 SLIDINGWINDOW: 4:5)
Trimmed sequence reads were mapped to Homo sapiens genome (GRCh38-p10) using STAR
Read count extraction was done using featureCount and normalization were performed using the R package DESeq2
Assembly: GRCh38-p10
Supplementary files format and content: TAB-delimited file with the read counts from featureCount.

source_name: MEL-JUSO

growth_protocol: A375 and MelJuso human melanoma cell lines were cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum (FBS), 1 % penicillin/streptomycin, and 2 mM L-glutamine in humified atmosphere with 5 % CO2 at 37C.

extract_protocol:
Melanoma cells were seeded in 12-well cell culture plates and treated with Rocaglamide A or DMSO 24 hours later. Total RNA was isolated 20 h post-treatment using RNAeasy Mini Kit (QIAGEN). Cells were lysed directly in the plates.
RNA libraries for RNA-seq were prepared using Lexogen QuantSeq FWD kit, 75bp Directional RNA Library Prep Kit for Illumina and polyA selection. Sequencing was performed at the CEITEC Core Facility Genomics (Brno, Czech Republic)

treatment_protocol: Melanoma cells were treated for 20 hours with 100 nM Rocaglamide A (RocA). Controls were treated with a corresponding volume of the vehicle (DMSO).

value: MEL-JUSO

value: Melanoma

value: Rocaglamide A


title: MelJuso, Rocaglamide A, replicate 3


title: 001Mass5

value: Cutaneous melanoma

value: 12 years


title: 001Mass6


title: 001Mass4


title: A375, Rocaglamide A, replicate 3


title: control 3XVPRF (HSPB8) 48hpf rep2

value: 293T cells

value: 48 hpf


title: BAB3141

type: genomic

city: Seattle

first: Jesse

last: Bengtsson

state: WA

address: 720 Broadway

institute: Pacific Northwest Research Institute

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed following the manufacturer’s protocol.

scan_protocol: Scanned on an Agilent G2600D scanner. Images were quantified using Agilent Feature Extraction Software (version 12.1.1.1)

data_processing: Agilent Feature Extraction Software (version 12.1.1.1) was used for background subtraction and normalization.

source_name: Whole Blood Extracted Genomic DNA from BAB3114

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C, 65°C for 20 minutes. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP,

extract_protocol: DNA was isolated from either peripheral blood or LCLs with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

value: Male

tag: test

source_name: Genomic DNA extracted from Male LCL NA15510

tag: reference

value: Reference Sample


title: MelJuso, Rocaglamide A, replicate 2


title: 001Mass2

value: Intratumoral JEN-101


title: 001Mass1


title: 001Mass1.2


title: A375, Rocaglamide A, replicate 2


title: 010Day84

value: Oral malignant melanoma


title: A375, Rocaglamide A, replicate 1


title: MelJuso, control, replicate 3

value: DMSO


title: 010Day119

source_name: Lung metastasis

value: 11 years


title: MelJuso, control, replicate 2


title: A375, control, replicate 1


title: A375, control, replicate 2


title: WT whole brain AGO2 Input, replicate 1

first: Stephanie

last: Ceman

address: 506 S Mathews Ave

department: Cell and Developmental Biology

institute: University of Illinois Urbana-Champaign

data_processing:
UMIs were removed using umi_tools (v1.1.1)
3' adapters were trimmed using cutadapt (v3.2)
Reads were mapped to mm10 using STAR (v2.7.7a).
PCR duplicates were removed using umi_tools (v1.1.1). Peaks were called using CLIPper(v2.0.1). IP-Input fold enrichment and p-value were calculated for each peak.
miRNAs from miRBase (v22.1) were "reverse mapped" to any reads that did not map to repetitive elements or the genome using bowtie (v1.2.3). The miRNA portion of each read was then trimmed, and the remainder of the read was mapped to the genome using STAR (v2.7.7a). PCR duplicates were resolved using umi_tools (v1.1.1), and miRNA target clusters were identified using CLIPper (v2.0.1).
Assembly: mm10
Supplementary files format and content: Browser extensible data with AGO2 input-normalized clusters for each sample.
Supplementary files format and content: Browser extensible data with miRNA input-normalized for each sample.

source_name: whole brain

extract_protocol:
Cryopreserved whole brains of WT and Mov10 Deletion P0 pups were ground and UV-crossinliked before lysis using eCLIP lysis mix and sonication. After this AGO2 was immunoprecipitated dephosphorylated with alkaline phosphatase (FastAP, Thermo Fisher) and T4 PNK (NEB) and an RNA adapter was ligated to the 3’ ends.
RNA adapter ligation, IP-western, reverse transcription, DNA adapter ligation, and PCR amplification were performed as described [PMID27018577].

value: whole brain

value: WT


title: RA-FLS, MTX, biol rep 2

city: Gothenburg

first: Anna-Karin

middle: Hultgård

last: Ekwall

address: Guldhedsgatan 10A

department: Rheumatology and Inflammation Research

country: Sweden

institute: University of Gothenburg

data_processing:
Data quality assessment was performed using FastQC (0.11.2) and filtering using PRINSEQ (0.20.3).
Reads were mapped to the human reference genome (hg19, UCSC assembly, Feb 2009) using STAR (2.5.2b).
The alignment was sorted and indexed with SAM tools (1.3.1).
Read counts were calculated using HTSeq (0.6.1p1).
Normalization of read counts was performed using DESeq2 size factor method.
Assembly: hg19
Supplementary files format and content: XLSX file includes normalized counts by size factor.

growth_protocol: Primary rheumatoid arthritis fibroblast-like synoviocytes  were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in a humidified 5% CO2 atmosphere at 37C.

extract_protocol:
RNA was isolated using RNeasy Micro Kit (Qiagen).
Libraries were prepared using TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold (Illumina).

treatment_protocol: Cells were pre-treated for 24 h with 1 uM methotrexate or 2,5 uM tofacitinib or vehicle. They were then stimulated with 2 ng/mL interleukin-1b + 20 ng/mL platelet-derived growth factor in fresh 1% FBS medium with or without the drug for 48 h.

value: methotrexate


title: RA-FLS, TOFA, biol rep 2

source_name: rheumatoid arthritis fibroblast-like synoviocytes

value: tofacitinib


title: Mov10 Deletion whole brain AGO2 Input, replicate 1

value: Mov10 Deletion


title: RA-FLS, MTX, biol rep 1

value: rheumatoid arthritis fibroblast-like synoviocytes


title: RA-FLS, TOFA, biol rep 3


title: RA-FLS, TOFA, biol rep 1


title: 001Mass3

value: 1 µg/kg


title: RA-FLS, control, biol rep 2

value: untreated


title: Mov10 Deletion whole brain AGO2 Input, replicate 2


title: WT whole brain AGO2 IP, replicate 1


title: Mov10 Deletion whole brain AGO2 IP, replicate 1


title: RA-FLS, control, biol rep 1


title: A375, control, replicate 3

value: Melanoma


title: Mouse LZ GFP-cMYCneg short-read rep2

city: Cambridge

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

country: United Kingdom

institute: The Babraham Institute

data_processing:
Quality of sequencing data was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). This indicated that mouse LZ GFP-cMYCneg rep3, and LZ GFP-cMYCpos rep 1 and rep 2 (for which library preparation initially failed and was therefore repeated) were substantial outliers when their GC content was compared to the remaining samples; they were thus excluded from downstream analysis.
Reads were trimmed for adapters and low quality base calls using Trim Galore, with default parameters (v0.6.6; https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Reads were then mapped to the GRCm39 mouse reference genome using Hisat2 (v2.1.0; Kim et al., 2019).
BAM files were imported into Seqmonk (v1.47.1; http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/), excluding those with mapping quality < 30, and reads were quantified over merged mRNA isoforms from the gencode vM28 annotation, using the RNA-seq quantitation pipeline.
TPM/FPKM for each sample (excluding those that failed QC) were calculated using Stringtie, only considering annotated transcript isoforms from the gencode vM28 annotation
Assembly: GRCm39
Supplementary files format and content: Mouse_short-read_gene_counts.txt: tab-delimited text file containing gene names and ensembl IDs, together with raw read counts in each sample, generated using Seqmonk
Supplementary files format and content: Mouse_short-read_TPM.txt: tab-delimited text file containing gene names and ensembl IDs, together with gene-level TPM in each sample (excluding those that were excluded from downstream analysis), generated using Stringtie

source_name: Spleen

extract_protocol:
For germinal centre B cell populations, cell lysates from were kept in 22.5 μl RLT plus buffer at -80 °C. These were thawed on ice, and where necessary to provide sufficient cells, pooled. The RNA was then purified using a ratio of 0.6x Agencourt RNAClean XP (Beckman Coulter- A63987); RNA was eluted in 4 μl nuclease-free H2O. 0.5 μl was used to assess RNA quality using the Agilent 2100 Bioanalyzer, with RIN > 7.5 used as a threshold for inclusion in library generation. The remaining RNA was split equally between short- and long-read library generation.
See Samples section
cDNA was generated using the SMARTseq v4 ultra low input RNA kit for sequencing; 0.03 pg SIRV/ERCC spike-in RNA (https://www.lexogen.com/store/sirv-set4/) was added into the reverse transcription reaction for each sample. Libraries were then prepared from the cDNA using the Nextera XT DNA library preparation kit. Note that for three samples (Mouse LZ GFP-cMYCneg rep3; LZ GFP-cMYCpos rep1 and LZ GFP-cMYCpos rep2), initial library preparation failed. Nuclease-free water was therefore added to the tubes in order to retrieve all remaining RNA, and library preparation repeated, resulting in measurable libraries

treatment_protocol:
Mice aged 8-16 weeks were immunised with 2 x 10^8 Sheep Red Blood Cells (SRBCs) intraperitoneally. Single cell suspensions of splenocytes were prepared on day 8 following immunisation, and red blood cells lysed with ACK buffer. Cells were then sorted by flow cytometry based on the indicated markers.
See Samples section

value: Spleen

value: Light zone GC B cells

value: c-MYCGFP/GFP

value: Female

tag: number of_mice_pooled

tag: flow markers


title: Mouse LZ GFP-cMYCpos short-read rep1

tag: cell type

tag: genotype


title: Mouse LZ GFP-cMYCpos short-read rep2


title: Mouse LZ GFP-cMYCneg short-read rep3


title: Mouse LZ GFP-cMYCpos short-read rep3


title: MelJuso, control, replicate 1

tag: cell line

value: MEL-JUSO

tag: treatment


title: Mouse LZ GFP-cMYCpos short-read rep4

tag: strain

tag: tissue


title: Mouse LZ GFP-cMYCneg short-read rep1


title: RA-FLS, control, biol rep 3


title: Mouse LZ GFP-cMYCpos short-read rep5


title: Mouse DZ short-read rep2

value: Dark zone GC B cells


title: Mouse DZ short-read rep4


title: Mouse DZ short-read rep3


title: Mouse naïve short-read rep4

extract_protocol:
1x10^5 naive B cells isolated by FACS were directly sorted into an Eppendorf tube containing 350 μl RLT plus buffer (Qiagen-1053393). Cells were homogenized with gentle pipetting and 1 volume ratio of 80% ethanol was added. The rest of RNA isolation was conducted according to the protocol of RNeasy Plus Micro Kit (Qiagen-74034). RNA was eluted in 11 μl nuclease-free H2O. 1 μl was used to assess RNA quality using the Agilent 2100 Bioanalyzer, with RIN > 7.5 used as a threshold for inclusion in library generation. 1.5 μl RNA was then used for short-read library generation, with a further 1.5 μl used to generate corresponding long-read libraries.
See Samples section
cDNA was generated using the SMARTseq v4 ultra low input RNA kit for sequencing; 0.03 pg SIRV/ERCC spike-in RNA (https://www.lexogen.com/store/sirv-set4/) was added into the reverse transcription reaction for each sample. Libraries were then prepared from the cDNA using the Nextera XT DNA library preparation kit. Note that for three samples (Mouse LZ GFP-cMYCneg rep3; LZ GFP-cMYCpos rep1 and LZ GFP-cMYCpos rep2), initial library preparation failed. Nuclease-free water was therefore added to the tubes in order to retrieve all remaining RNA, and library preparation repeated, resulting in measurable libraries

treatment_protocol:
Single cell suspensions of splenocytes were prepared from mice aged 8-16 weeks, and red blood cells lysed with ACK buffer. Cells were then sorted by flow cytometry based on the indicated markers.
See Samples section

value: Naive B cells


title: Mouse DZ short-read rep1


title: Mouse DZ short-read rep5


title: Mouse naïve short-read rep1


title: Mouse naïve short-read rep2


title: Mov10 Deletion whole brain AGO2 IP, replicate 2


title: Smartseq2_PA_299

first: Tiago

last: Castro

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
For 10x genomics sequencing, fastq files were aligned to the mouse genome (mm39) using the Cell Ranger pipeline (v. 7.0.1).
Data was processed using the Seurat package in R, with cells containing more than 5% mitochondrial reads excluded.
Normalization was performed using the SCTransform function.
Differential expression was analyzed using Wilcoxon-Rank-Test with Bonferroni correction.
For Smartseq2, reads were aligned to the mouse genome (GRCm38.p6) using STAR aligner.
Quantification matrices were generated using RSEM, processed in the Seurat pipeline, and filtered based on mitochondrial content.
Cells were clustered and visualized in t-SNE space using Seurat.
Assembly: mm39
Supplementary files format and content: Tab-separated matrix files for gene counts, normalized data.

growth_protocol: All tumor cell lines were grown in DMEM supplemented with 1% L-Glutamine and 1% Penicillin/Streptomycin.

extract_protocol:
Freshly collected tumor-draining lymph nodes (tdLNs) and tumors were processed for single-cell isolation. Tumors were digested with collagenase D and DNase I, and lymph nodes were digested with collagenase D. Single-cell suspensions were then prepared, stained, and sorted by FACS based on surface markers, as detailed in the Methods section.
Single-cell RNA-seq libraries were constructed using the Chromium platform (10x Genomics) following the manufacturer’s instructions. The RNA from sorted cells was processed for library construction, aiming for specific read lengths for each segment of sequencing. Libraries for bulk RNA-seq were prepared using the Smart-Seq2 method.

treatment_protocol: Mice were injected with various tumor cell lines as described. Antibody treatments (e.g., anti-IL-27, anti-CD40L, anti-CTLA-4, anti-PD-1, or anti-MHC-II) were administered at specified doses and time points. LIPSTIC substrate biotin–LPETG was injected as described for labeling intratumoral APC-T cell interactions.

tag: mouse name

tag: timepoint

value: late

tag: plate date


title: Smartseq2_PA_298


title: 10xGenomics_Gex


title: Smartseq2_PA_297

value: early


title: Mouse naïve short-read rep3

value: WT

tag: Sex


title: Smartseq2_PA_293


title: Smartseq2_PA_292


title: Smartseq2_PA_291


title: Smartseq2_PA_294


title: Smartseq2_PA_290


title: RA-FLS, MTX, biol rep 3

value: methotrexate


title: Mouse LZ GFP-cMYCneg short-read rep4


title: Mouse LZ GFP-cMYCneg short-read rep5


title: Smartseq2_PA_295


title: Smartseq2_PA_289


title: Smartseq2_PA_287


title: 10xGenomics_Hto


title: Smartseq2_PA_286


title: Smartseq2_PA_285


title: Smartseq2_PA_288


title: Mouse naïve short-read rep5


title: Smartseq2_PA_284


title: Smartseq2_PA_282


title: Smartseq2_PA_280


title: Smartseq2_PA_278


title: Smartseq2_PA_279


title: Smartseq2_PA_281


title: Smartseq2_PA_283


title: Smartseq2_PA_273


title: Smartseq2_PA_274


title: Smartseq2_PA_275


title: Smartseq2_PA_271


title: Smartseq2_PA_266


title: Smartseq2_PA_276


title: Smartseq2_PA_265


title: Smartseq2_PA_264


title: Smartseq2_PA_272


title: Smartseq2_PA_263


title: Smartseq2_PA_269


title: Smartseq2_PA_262


title: Smartseq2_PA_259


title: Smartseq2_PA_258


title: Smartseq2_PA_261


title: Smartseq2_PA_257


title: Smartseq2_PA_256


title: Smartseq2_PA_255


title: Smartseq2_PA_270


title: Smartseq2_PA_254


title: Smartseq2_PA_253


title: Smartseq2_PA_260


title: Smartseq2_PA_252


title: Smartseq2_PA_251


title: Smartseq2_PA_249


title: Smartseq2_PA_248


title: Smartseq2_PA_267


title: Smartseq2_PA_247


title: Smartseq2_PA_268


title: Smartseq2_PA_246


title: Smartseq2_PA_243


title: Smartseq2_PA_245


title: Smartseq2_PA_242


title: Smartseq2_PA_238


title: Smartseq2_PA_237


title: Smartseq2_PA_234


title: Smartseq2_PA_239


title: Smartseq2_PA_232


title: Smartseq2_PA_231


title: Smartseq2_PA_296


title: Smartseq2_PA_236


title: Smartseq2_PA_235


title: Smartseq2_PA_250


title: Smartseq2_PA_233


title: Smartseq2_PA_227


title: Smartseq2_PA_229


title: Smartseq2_PA_225


title: Smartseq2_PA_223


title: Smartseq2_PA_226


title: 008Day168

tag: melanoma

value: Oral malignant melanoma

tag: age

value: 5 years

value: Intratumoral JEN-101

value: 10 µg/kg


title: Smartseq2_PA_277


title: Smartseq2_PA_228


title: Smartseq2_PA_241


title: Smartseq2_PA_244


title: Smartseq2_PA_218


title: Smartseq2_PA_221


title: Smartseq2_PA_217


title: Smartseq2_PA_224


title: Smartseq2_PA_216


title: Smartseq2_PA_215


title: Smartseq2_PA_214


title: Smartseq2_PA_209


title: Smartseq2_PA_210


title: Smartseq2_PA_208


title: Smartseq2_PA_213


title: Smartseq2_PA_230


title: Smartseq2_PA_207


title: Smartseq2_PA_205


title: Smartseq2_PA_222


title: Smartseq2_PA_240


title: Smartseq2_PA_204


title: Smartseq2_PA_206


title: Smartseq2_PA_201


title: Smartseq2_PA_200


title: Smartseq2_PA_202


title: Smartseq2_PA_220


title: Smartseq2_PA_199


title: Smartseq2_PA_196


title: Smartseq2_PA_198


title: Smartseq2_PA_195


title: Smartseq2_PA_194


title: Smartseq2_PA_192


title: Smartseq2_PA_193


title: Smartseq2_PA_190


title: Smartseq2_PA_219


title: Smartseq2_PA_191


title: Smartseq2_PA_187


title: Smartseq2_PA_203


title: Smartseq2_PA_186


title: Smartseq2_PA_185


title: Smartseq2_PA_212


title: Smartseq2_PA_188


title: Smartseq2_PA_183


title: Smartseq2_PA_182


title: Smartseq2_PA_189


title: Smartseq2_PA_179


title: Smartseq2_PA_178


title: Smartseq2_PA_197


title: Smartseq2_PA_181


title: Smartseq2_PA_177


title: Smartseq2_PA_175


title: Smartseq2_PA_184


title: Smartseq2_PA_176


title: Smartseq2_PA_174


title: Smartseq2_PA_173


title: Smartseq2_PA_169


title: Smartseq2_PA_172


title: Smartseq2_PA_170


title: Smartseq2_PA_168


title: Smartseq2_PA_167


title: Smartseq2_PA_164


title: Smartseq2_PA_180


title: Smartseq2_PA_165


title: Smartseq2_PA_162


title: Smartseq2_PA_159


title: Smartseq2_PA_160


title: Smartseq2_PA_157


title: Smartseq2_PA_156


title: Smartseq2_PA_171


title: Smartseq2_PA_152


title: Smartseq2_PA_154


title: Smartseq2_PA_151


title: Smartseq2_PA_155


title: Smartseq2_PA_148


title: Smartseq2_PA_149


title: Smartseq2_PA_161


title: Smartseq2_PA_153


title: Smartseq2_PA_143


title: Smartseq2_PA_147


title: Smartseq2_PA_142


title: Smartseq2_PA_145


title: Smartseq2_PA_146


title: Smartseq2_PA_163


title: Smartseq2_PA_140


title: Smartseq2_PA_144


title: Smartseq2_PA_141


title: Smartseq2_PA_166


title: Smartseq2_PA_139


title: Smartseq2_PA_138


title: Smartseq2_PA_135


title: Smartseq2_PA_134


title: Smartseq2_PA_133


title: Smartseq2_PA_150


title: Smartseq2_PA_132


title: Smartseq2_PA_136


title: Smartseq2_PA_137


title: Smartseq2_PA_131


title: Smartseq2_PA_130


title: Smartseq2_PA_126


title: Smartseq2_PA_127


title: Smartseq2_PA_122


title: Smartseq2_PA_129


title: Smartseq2_PA_128


title: Smartseq2_PA_125


title: Smartseq2_PA_121


title: Smartseq2_PA_119


title: Smartseq2_PA_117


title: Smartseq2_PA_113


title: Smartseq2_PA_116


title: Smartseq2_PA_118


title: Smartseq2_PA_115


title: Smartseq2_PA_114


title: Smartseq2_PA_111


title: Smartseq2_PA_110


title: Smartseq2_PA_112


title: Smartseq2_PA_108


title: Smartseq2_PA_104


title: Smartseq2_PA_158


title: Smartseq2_PA_103


title: Smartseq2_PA_107


title: Smartseq2_PA_105


title: Smartseq2_PA_109


title: Smartseq2_PA_123


title: Smartseq2_PA_102


title: Smartseq2_PA_98


title: Smartseq2_PA_120


title: Smartseq2_PA_101


title: Smartseq2_PA_100


title: Smartseq2_PA_124


title: Smartseq2_PA_97


title: Smartseq2_PA_96


title: Smartseq2_PA_94


title: Smartseq2_PA_92


title: Smartseq2_PA_90


title: Smartseq2_PA_93


title: Smartseq2_PA_91


title: Smartseq2_PA_89


title: Smartseq2_PA_88


title: Smartseq2_PA_87


title: Smartseq2_PA_84


title: Smartseq2_PA_106


title: Smartseq2_PA_86


title: Smartseq2_PA_85


title: Smartseq2_PA_79


title: Smartseq2_PA_83


title: Smartseq2_PA_77


title: Smartseq2_PA_82


title: Smartseq2_PA_80


title: Smartseq2_PA_99


title: Smartseq2_PA_76


title: Smartseq2_PA_95


title: Smartseq2_PA_74


title: Smartseq2_PA_72


title: Smartseq2_PA_70


title: Smartseq2_PA_68


title: Smartseq2_PA_71


title: Smartseq2_PA_66


title: Smartseq2_PA_73


title: Smartseq2_PA_65


title: Smartseq2_PA_69


title: Smartseq2_PA_62


title: Smartseq2_PA_67


title: Smartseq2_PA_63


title: Smartseq2_PA_61


title: Smartseq2_PA_60


title: Smartseq2_PA_81


title: Smartseq2_PA_78


title: Smartseq2_PA_58


title: Smartseq2_PA_59


title: Smartseq2_PA_211


title: Smartseq2_PA_55


title: Smartseq2_PA_54


title: Smartseq2_PA_53


title: Smartseq2_PA_57


title: Smartseq2_PA_51


title: Smartseq2_PA_52


title: Smartseq2_PA_56


title: Smartseq2_PA_48


title: Smartseq2_PA_50


title: Smartseq2_PA_49


title: Smartseq2_PA_64


title: Smartseq2_PA_47


title: Smartseq2_PA_46


title: Smartseq2_PA_45


title: Smartseq2_PA_43


title: Smartseq2_PA_41


title: Smartseq2_PA_40


title: Smartseq2_PA_42


title: Smartseq2_PA_38


title: Smartseq2_PA_44


title: Smartseq2_PA_37


title: Smartseq2_PA_36


title: Smartseq2_PA_33


title: Smartseq2_PA_34


title: Smartseq2_PA_32


title: Smartseq2_PA_35


title: Smartseq2_PA_28


title: Smartseq2_PA_27


title: Smartseq2_PA_30


title: Smartseq2_PA_25


title: Smartseq2_PA_23


title: Smartseq2_PA_21


title: Smartseq2_PA_24


title: Smartseq2_PA_20


title: Smartseq2_PA_75


title: Smartseq2_PA_22


title: Smartseq2_PA_19


title: Smartseq2_PA_39


title: Smartseq2_PA_18


title: Smartseq2_PA_15


title: Smartseq2_PA_17


title: Smartseq2_PA_14


title: Smartseq2_PA_12


title: Smartseq2_PA_16


title: Smartseq2_PA_10


title: Smartseq2_PA_11


title: Smartseq2_PA_13


title: Smartseq2_PA_8


title: Smartseq2_PA_31


title: Smartseq2_PA_9


title: Smartseq2_PA_7


title: Smartseq2_PA_6


title: Smartseq2_PA_26


title: Smartseq2_PA_5


title: Smartseq2_PA_4


title: Smartseq2_PA_2


title: Smartseq2_PA_3


title: Smartseq2_PA_29


title: Smartseq2_PA_1


title: Smartseq2_Lipstic_TdLN_556

value: Tumor


title: Smartseq2_Lipstic_TdLN_555


title: Smartseq2_Lipstic_TdLN_553

source_name: Biotin+

value: Biotin+


title: Smartseq2_Lipstic_TdLN_550


title: Smartseq2_Lipstic_TdLN_551


title: Smartseq2_Lipstic_TdLN_552


title: Smartseq2_Lipstic_TdLN_554


title: Smartseq2_Lipstic_TdLN_549


title: Smartseq2_Lipstic_TdLN_548


title: Smartseq2_Lipstic_TdLN_542


title: Smartseq2_Lipstic_TdLN_545


title: Smartseq2_Lipstic_TdLN_546


title: Smartseq2_Lipstic_TdLN_543


title: Smartseq2_Lipstic_TdLN_544


title: Smartseq2_Lipstic_TdLN_539


title: Smartseq2_Lipstic_TdLN_541


title: Smartseq2_Lipstic_TdLN_538


title: Smartseq2_Lipstic_TdLN_536


title: Smartseq2_Lipstic_TdLN_540


title: Smartseq2_Lipstic_TdLN_535


title: Smartseq2_Lipstic_TdLN_534


title: Smartseq2_Lipstic_TdLN_537


title: Smartseq2_Lipstic_TdLN_533


title: Smartseq2_Lipstic_TdLN_532


title: Smartseq2_Lipstic_TdLN_529


title: Smartseq2_Lipstic_TdLN_531


title: Smartseq2_Lipstic_TdLN_527


title: Smartseq2_Lipstic_TdLN_528


title: Smartseq2_Lipstic_TdLN_525


title: Smartseq2_Lipstic_TdLN_524


title: Smartseq2_Lipstic_TdLN_526


title: Smartseq2_Lipstic_TdLN_547


title: Smartseq2_Lipstic_TdLN_523


title: Smartseq2_Lipstic_TdLN_521


title: Smartseq2_Lipstic_TdLN_520


title: Smartseq2_Lipstic_TdLN_522


title: Smartseq2_Lipstic_TdLN_518


title: Smartseq2_Lipstic_TdLN_516


title: Smartseq2_Lipstic_TdLN_514


title: Smartseq2_Lipstic_TdLN_515


title: Smartseq2_Lipstic_TdLN_519


title: Smartseq2_Lipstic_TdLN_513


title: Smartseq2_Lipstic_TdLN_517


title: Smartseq2_Lipstic_TdLN_507


title: Smartseq2_Lipstic_TdLN_530


title: Smartseq2_Lipstic_TdLN_510


title: Smartseq2_Lipstic_TdLN_504


title: Smartseq2_Lipstic_TdLN_506


title: Smartseq2_Lipstic_TdLN_505


title: Smartseq2_Lipstic_TdLN_508


title: Smartseq2_Lipstic_TdLN_503


title: Smartseq2_Lipstic_TdLN_500


title: Smartseq2_Lipstic_TdLN_499


title: Smartseq2_Lipstic_TdLN_497


title: Smartseq2_Lipstic_TdLN_496


title: Smartseq2_Lipstic_TdLN_498


title: Smartseq2_Lipstic_TdLN_494


title: Smartseq2_Lipstic_TdLN_493


title: Smartseq2_Lipstic_TdLN_502


title: Smartseq2_Lipstic_TdLN_495


title: Smartseq2_Lipstic_TdLN_491


title: Smartseq2_Lipstic_TdLN_492


title: Smartseq2_Lipstic_TdLN_511


title: Smartseq2_Lipstic_TdLN_488


title: Smartseq2_Lipstic_TdLN_512


title: Smartseq2_Lipstic_TdLN_490


title: Smartseq2_Lipstic_TdLN_485


title: Smartseq2_Lipstic_TdLN_509


title: Smartseq2_Lipstic_TdLN_489


title: Smartseq2_Lipstic_TdLN_487


title: Smartseq2_Lipstic_TdLN_483


title: Smartseq2_Lipstic_TdLN_486


title: Smartseq2_Lipstic_TdLN_482


title: Smartseq2_Lipstic_TdLN_481


title: Smartseq2_Lipstic_TdLN_480


title: Smartseq2_Lipstic_TdLN_479


title: Smartseq2_Lipstic_TdLN_501


title: Smartseq2_Lipstic_TdLN_477


title: Smartseq2_Lipstic_TdLN_474


title: Smartseq2_Lipstic_TdLN_476


title: Smartseq2_Lipstic_TdLN_478


title: Smartseq2_Lipstic_TdLN_475


title: Smartseq2_Lipstic_TdLN_473


title: Smartseq2_Lipstic_TdLN_471


title: Smartseq2_Lipstic_TdLN_466


title: Smartseq2_Lipstic_TdLN_467


title: Smartseq2_Lipstic_TdLN_469


title: Smartseq2_Lipstic_TdLN_468


title: Smartseq2_Lipstic_TdLN_484


title: Smartseq2_Lipstic_TdLN_464


title: Smartseq2_Lipstic_TdLN_470


title: Smartseq2_Lipstic_TdLN_465


title: Smartseq2_Lipstic_TdLN_462


title: Smartseq2_Lipstic_TdLN_461


title: Smartseq2_Lipstic_TdLN_456


title: Smartseq2_Lipstic_TdLN_459


title: Smartseq2_Lipstic_TdLN_455


title: Smartseq2_Lipstic_TdLN_460


title: Smartseq2_Lipstic_TdLN_453


title: Smartseq2_Lipstic_TdLN_454


title: Smartseq2_Lipstic_TdLN_451


title: Smartseq2_Lipstic_TdLN_449


title: Smartseq2_Lipstic_TdLN_450


title: Smartseq2_Lipstic_TdLN_452


title: Smartseq2_Lipstic_TdLN_448


title: Smartseq2_Lipstic_TdLN_445


title: Smartseq2_Lipstic_TdLN_472


title: Smartseq2_Lipstic_TdLN_463


title: Smartseq2_Lipstic_TdLN_446


title: Smartseq2_Lipstic_TdLN_442


title: Smartseq2_Lipstic_TdLN_441


title: Smartseq2_Lipstic_TdLN_438


title: Smartseq2_Lipstic_TdLN_439


title: Smartseq2_Lipstic_TdLN_436


title: Smartseq2_Lipstic_TdLN_444


title: Smartseq2_Lipstic_TdLN_440


title: Smartseq2_Lipstic_TdLN_458


title: Smartseq2_Lipstic_TdLN_437


title: Smartseq2_Lipstic_TdLN_457


title: Smartseq2_Lipstic_TdLN_433


title: Smartseq2_Lipstic_TdLN_434


title: Smartseq2_Lipstic_TdLN_429


title: Smartseq2_Lipstic_TdLN_431


title: Smartseq2_Lipstic_TdLN_430


title: Smartseq2_Lipstic_TdLN_432


title: Smartseq2_Lipstic_TdLN_427


title: Smartseq2_Lipstic_TdLN_426


title: Smartseq2_Lipstic_TdLN_447


title: Smartseq2_Lipstic_TdLN_424


title: Smartseq2_Lipstic_TdLN_443


title: Smartseq2_Lipstic_TdLN_422


title: Smartseq2_Lipstic_TdLN_423


title: Smartseq2_Lipstic_TdLN_425


title: Smartseq2_Lipstic_TdLN_420


title: Smartseq2_Lipstic_TdLN_418


title: Smartseq2_Lipstic_TdLN_435


title: Smartseq2_Lipstic_TdLN_415


title: Smartseq2_Lipstic_TdLN_416


title: Smartseq2_Lipstic_TdLN_413


title: Smartseq2_Lipstic_TdLN_417


title: Smartseq2_Lipstic_TdLN_412


title: Smartseq2_Lipstic_TdLN_411


title: Smartseq2_Lipstic_TdLN_428


title: Smartseq2_Lipstic_TdLN_410


title: Smartseq2_Lipstic_TdLN_414


title: Smartseq2_Lipstic_TdLN_409


title: Smartseq2_Lipstic_TdLN_408


title: Smartseq2_Lipstic_TdLN_406


title: Smartseq2_Lipstic_TdLN_404


title: Smartseq2_Lipstic_TdLN_403


title: Smartseq2_Lipstic_TdLN_407


title: Smartseq2_Lipstic_TdLN_402


title: Smartseq2_Lipstic_TdLN_401


title: Smartseq2_Lipstic_TdLN_400


title: Smartseq2_Lipstic_TdLN_398


title: Smartseq2_Lipstic_TdLN_399


title: Smartseq2_Lipstic_TdLN_421


title: Smartseq2_Lipstic_TdLN_395


title: Smartseq2_Lipstic_TdLN_397


title: Smartseq2_Lipstic_TdLN_396


title: Smartseq2_Lipstic_TdLN_393


title: Smartseq2_Lipstic_TdLN_419


title: Smartseq2_Lipstic_TdLN_392


title: Smartseq2_Lipstic_TdLN_391


title: Smartseq2_Lipstic_TdLN_390


title: Smartseq2_Lipstic_TdLN_389


title: Smartseq2_Lipstic_TdLN_387


title: Smartseq2_Lipstic_TdLN_388


title: Smartseq2_Lipstic_TdLN_385


title: Smartseq2_Lipstic_TdLN_383


title: Smartseq2_Lipstic_TdLN_384


title: Smartseq2_Lipstic_TdLN_381


title: Smartseq2_Lipstic_TdLN_405


title: Smartseq2_Lipstic_TdLN_380


title: Smartseq2_Lipstic_TdLN_382


title: Smartseq2_Lipstic_TdLN_379


title: Smartseq2_Lipstic_TdLN_378


title: Smartseq2_Lipstic_TdLN_376


title: Smartseq2_Lipstic_TdLN_375


title: Smartseq2_Lipstic_TdLN_377


title: Smartseq2_Lipstic_TdLN_374


title: Smartseq2_Lipstic_TdLN_394


title: Smartseq2_Lipstic_TdLN_371


title: Smartseq2_Lipstic_TdLN_372


title: Smartseq2_Lipstic_TdLN_373


title: Smartseq2_Lipstic_TdLN_369


title: brown adipocytes, WT 4

city: Daejeon

first: Ju Hee

last: Lee

address: Munhwa-ro 266

country: South Korea

institute: Chungnam National University

data_processing:
The libraries were used for 100 nt paired-end sequencing by an Illumina HiSeq4000 (Illumina).
After removing the low-quality and adapter sequences using Trimmomatic, the reads were aligned with the Mus musculus genome (mm10) using HISAT (ver. 2.0.5)
Two types of indexes were used for alignment (a global, whole-genome index and tens of thousands of small local indexes), which were downloaded from the UCSC table browser (http://genome.uscs.edu)
StringTie (ver. 2.1.3b) was used to assemble the transcript, and provided the relative abundance estimates as fragments per kilobase of exon per million fragments mapped (FPKM) values of the transcript or gene.
After excluding the genes with one more than zero FPKM values, the signal value (FPKM+1) was transformed to a base 2 logarithm and normalized by quantile normalization methods to reduce the systematic bias.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes read counts and FPKM values for each Sample

source_name: brown adipose tissue

extract_protocol:
RNA was isolated using TRIzolTM Reagent (Life Technologies, Thermo Fisher Scientific, Cat. 15596018). 1.0 ug of total RNA was used for the construction of sequencing libraries.
1 μg RNA and a TruSeq RNA Library Prep Kit v2 (Illumina, San Diego, CA, USA, Cat. RS-122-2001) were used

value: brown adipose tissue

tag: disease state

value: control


title: Smartseq2_Lipstic_TdLN_370


title: brown adipocytes, WT 3


title: brown adipocytes, WT 2


title: Smartseq2_Lipstic_TdLN_368


title: Smartseq2_Lipstic_TdLN_386


title: Smartseq2_Lipstic_TdLN_366


title: brown adipocytes, KO 4

value: brown adipocytes-specific Crif1 KO

value: model of mitochondrial dysfunction


title: brown adipocytes, KO 3


title: Smartseq2_Lipstic_TdLN_367


title: brown adipocytes, KO 2


title: Smartseq2_Lipstic_TdLN_364


title: brown adipocytes, KO 1


title: Smartseq2_Lipstic_TdLN_362


title: Male rep3

city: Zhengzhou

first: Zhaoran

last: Ti an

state: Henan

address: No.100 Science Avenue

institute: Zhengzhou University

data_processing:
Trim Smart-seq2 public primer sequence from the Reads
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: stamens

extract_protocol:
Leaf and immature floral buds were collectedand,and RNA was harvested using Trizol reagent.5–10 μg total RNA was used as the template for constructing RNA-seq libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: stamens

tag: Stage

value: Flower Bud Differentiation


title: Male rep1


title: Smartseq2_Lipstic_TdLN_361

city: New York


title: Smartseq2_Lipstic_TdLN_363


title: Smartseq2_Lipstic_TdLN_359


title: Smartseq2_Lipstic_TdLN_360


title: Leaf rep2

source_name: leaf

value: leaf


title: Leaf rep1


title: Smartseq2_Lipstic_TdLN_358


title: Female rep3

source_name: gynoecium

value: gynoecium


title: Smartseq2_Lipstic_TdLN_356


title: Leaf rep3


title: Female rep2


title: Female rep1


title: Smartseq2_Lipstic_TdLN_357


title: Smartseq2_Lipstic_TdLN_355


title: Smartseq2_Lipstic_TdLN_354


title: Smartseq2_Lipstic_TdLN_353


title: Smartseq2_Lipstic_TdLN_365


title: OA_PBS_cartilage_1

city: shanghai

first: shu

middle: I

last: zhao

address: Road siping 1239

institute: Tongji University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Rattus norvegicus. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files includes raw counts for each samples
Supplementary files format and content: tab-delimited text files includes FPKM for each samples

source_name: cartilage

extract_protocol:
The tibia and femur were both removed, and total RNA from the cartilages was  extracted as described above.
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: 8-week old SD rats undergoing DMM+ACLT operations allocated into two distinct categories: OA + PBS group; OA + PBS-EVsM1 group.

value: cartilage

value: Sprague Dawley

value: OA surgery and PBS injection


title: Smartseq2_Lipstic_TdLN_352


title: OA_M1 EV_cartilage_2

value: WT

value: OA surgery and EVsM1 injection


title: OA_PBS_cartilage_2


title: brown adipocytes, WT 1


title: Male rep2


title: Smartseq2_Lipstic_TdLN_351


title: Smartseq2_Lipstic_TdLN_350


title: Smartseq2_Lipstic_TdLN_349


title: Smartseq2_Lipstic_TdLN_347


title: Smartseq2_Lipstic_TdLN_348


title: Smartseq2_Lipstic_TdLN_346


title: 24 hours post injury, Experiment 1,Replicate 2

city: Baltimore

first: Yang

last: Jin

state: MARYLAND

address: 1800 Orleans St

institute: Johns Hopkins University

data_processing:
All snRNA-seq samples were analyzed using R package Seurat v4.1.4 (Hao et al, 2021). Ambient RNA contaminations were estimated and removed using R package DecountX (Yang et al., 2020). Low-quality cells were removed based on the following criteria: total RNA counts < 1000 or > 25000, total gene counts < 200 or > 10000, percentage of mitochondria RNA expression > 30 %. Cell doublets were identified using R package DoubletFinder (McGinnis et al., 2019).
Assembly: GRCz11
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

organism: Danio rerio

source_name: Experiment 1, Replicate 2

growth_protocol: Adult wild-type AB, Tg[gfap:nGFP]mi2004, TgBAC[nes:EGFP]tud100 and Tg[olig2:eGFP]vu12 transgenic lines, and albinob4 mutant lines of zebrafish (Danio rerio) were maintained in the Center for Zebrafish Research at the University of Notre Dame Freimann Life Sciences Center. Fish used for experimentation were between 6 and 12 months old (3.5-4.5 cm in length) and maintained in standard conditions, 26.5 °C and 30% humidity, with a 14-h light, 10-h dark cycle (Westerfield, 2007). Approximately equal numbers of male and female zebrafish were used in each experiment.  Prior to and following any experiments, the fish were either anesthetized or euthanized using either 1:1000 or 1:500 2-phenoxyethanol (2-PE, Sigma-Aldrich, St. Louis, MO, USA), respectively.

extract_protocol:
Telencephalons of undamaged and severe bfTBI damaged fish at 5, 12, 18, 24, 48, 72, 96, 120, 144, and 168 hpi were dissected as described above. Six telencephalons per group were placed in a Low-Bind Tube (Eppendorf) and snap frozen using liquid nitrogen. Nuclei were extracted using the Frankenstein Protocol as previously described (Martelotto et al. 2020) with some modification. Briefly 500 µL of Lysis buffer (1% Tris-HCl/0.2% NaCl/0.3%MgCl/0.1% NP40 in nuclease-free water) was added to brains. Brains were homogenized using a dounce homogenizer (10-20 times). Homogenate was passed through a 70 µm mesh strainer (Miltenyi Biotech, Auburn, CA, USA) and spun down at 500 xg at 4˚C for 5 minutes. Supernatant was discarded and the nuclear pellet was resuspended in Nuclei Wash Buffer (1% BSA in PBS with 0.2U/µL RNase inhibitors (Roche)). Nuclei were washed and resuspended 2 additional times as described above, and cells were resuspended to a concentration of ~1,000-1,500 nuclei/µL. Nuclei samples were passed through a 35 µm mesh strainer (Miltenyi Biotech).
Cell suspension concentration and percent viability were determined by staining with Trypan Blue Stain (0.4%) (Thermo-Fisher Scientific) and Countess II Automated Cell Countess. Nuclei were loaded into Chromium Next GEM Chip G (10X Genomics, Pleasanton, CA, USA) with a targeted recovery of 10,000 nuclei per well and processed with Chromium Controller or Chromium iX (10X Genomics). Single-nuclei RNA-Seq libraries were prepared with Chromium Single Cell 3' Reagent Kit (v3.1 - Dual Index; 10X Genomics PN-1000269 | PN-1000215) at the Genomics and Bioinformatics Core Facility at the University of Notre Dame, following the standard throughput manual workflow and pooled at equal molar ratios. Libraries were sequenced on NovaSeq 6000 System at Center for Medical Genomics at Indiana University.

treatment_protocol: bfTBI was induced as previously described (Hentig et al. 2021), with the only modification being the injury site. Briefly, fish were anesthetized in 1:1000 2-phenoxyethanol (2-PE, Sigma-Aldrich) until unreactive to a startle stimulus. Fish were laid in a clay mold and a steel disk was placed on their head at the juncture of the telencephalon and optic tectum. Fish were then given either a sham, mild, moderate, or severe bfTBI (Hentig et al. 2021) by dropping a ball bearing through a tube onto the steel disk (Fig. 1a). Sham injuries were induced by dropping the ball bearing onto the clay mold next to the zebrafish and are referred to as undamaged. Undamaged and injured fish were then placed into an aerated recovery tank prior to further experimentation.

value: telencephalon

value: 24 hours post injury


title: 24 hours post injury, Experiment 2,Replicate 1

source_name: Experiment 1, Replicate 1


title: 168 hours post injury, Experiment 2,Replicate 1

source_name: Experiment 2, Replicate 1

value: 168 hours post injury


title: 168 hours post injury, Experiment 2,Replicate 2

source_name: Experiment 2, Replicate 2


title: 24 hours post injury, Experiment 1,Replicate 1


title: 144 hours post injury, Experiment 2,Replicate 2

value: 144 hours post injury


title: 144 hours post injury, Experiment 2,Replicate 1


title: Smartseq2_Lipstic_TdLN_345

value: Biotin+

value: Tumor


title: 24 hours post injury, Experiment 2,Replicate 2


title: Smartseq2_Lipstic_TdLN_341


title: 120 hours post injury, Experiment 2,Replicate 2

value: 120 hours post injury


title: 120 hours post injury, Experiment 2,Replicate 1


title: Smartseq2_Lipstic_TdLN_342


title: Smartseq2_Lipstic_TdLN_340


title: OA_M1 EV_cartilage_1


title: 96 hours post injury, Experiment 2,Replicate 2

value: 96 hours post injury


title: 96 hours post injury, Experiment 2,Replicate 1


title: Smartseq2_Lipstic_TdLN_339


title: 72 hours post injury, Experiment 2,Replicate 2

value: 72 hours post injury


title: Smartseq2_Lipstic_TdLN_337


title: 72 hours post injury, Experiment 2,Replicate 1


title: Smartseq2_Lipstic_TdLN_336


title: Smartseq2_Lipstic_TdLN_338


title: Smartseq2_Lipstic_TdLN_335


title: Undamaged, Experiment 2, Replicate 2

value: Undamaged


title: Undamaged, Experiment 2, Replicate 1


title: Smartseq2_Lipstic_TdLN_344


title: Smartseq2_Lipstic_TdLN_343


title: 72 hours post injury, Experiment 1,Replicate 2


title: Smartseq2_Lipstic_TdLN_332


title: Smartseq2_Lipstic_TdLN_333


title: 72 hours post injury, Experiment 1,Replicate 1


title: Smartseq2_Lipstic_TdLN_334


title: 48 hours post injury, Experiment 1,Replicate 1

value: 48 hours post injury


title: Smartseq2_Lipstic_TdLN_330


title: 48 hours post injury, Experiment 1,Replicate 2


title: 18 hours post injury, Experiment 1,Replicate 2

value: 18 hours post injury


title: 12 hours post injury, Experiment 1,Replicate 2

value: 12 hours post injury


title: 18 hours post injury, Experiment 1,Replicate 1


title: Smartseq2_Lipstic_TdLN_328


title: Smartseq2_Lipstic_TdLN_327


title: Smartseq2_Lipstic_TdLN_329


title: 12 hours post injury, Experiment 1,Replicate 1


title: Smartseq2_Lipstic_TdLN_326


title: Smartseq2_Lipstic_TdLN_324


title: Smartseq2_Lipstic_TdLN_323


title: Smartseq2_Lipstic_TdLN_325


title: 5 hours post injury, Experiment 1,Replicate 2

value: 5 hours post injury


title: 5 hours post injury, Experiment 1,Replicate 1


title: Undamaged, Experiment 1, Replicate 2


title: Undamaged, Experiment 1, Replicate 1


title: Smartseq2_Lipstic_TdLN_321


title: Smartseq2_Lipstic_TdLN_331


title: Smartseq2_Lipstic_TdLN_320


title: Smartseq2_Lipstic_TdLN_318


title: Smartseq2_Lipstic_TdLN_317


title: mo27_fish3_rep2

city: Salt Lake City

first: Andrea

middle: Lynn

last: Sposato

state: UT

address: 1390 President's Circle

department: Biology

institute: University of Utah

description: 10X Genomics

data_processing:
Single-cell RNA seq reads were processed with Cellranger from 10X Genomics with the default settings, using GRCz11 v4.3.2 reference (Lawson et al., 2020) for zebrafish read alignments.
Assembly: GRCz11
Supplementary files format and content: Tab separated values files and matrix files

source_name: Testis

growth_protocol: Wild-type Tübingen zebrafish were used for all experiments. Ages of animals are noted in sample title and age metadata. All zebrafish work was performed at University of Utah’s CBRZ zebrafish facility. This study was conducted under the approval of the Office of Institutional Animal Care and Use Committee (IACUC no. 20-07013) of the University of Utah’s animal care and use program.

extract_protocol:
After euthanasia by immersion in ice-cold water, testes were dissected from fish and immediately placed in a dissociation solution of 440 µL 1X Hank’s Balanced Salt Solution (HBSS), 50 µL 10% pluronic F-68, and 10 µL 0.26U/mL liberase TM. Tissue was incubated at 37°C for approximately 45 minutes while rotating at 750 rpm in an Eppendorf Thermomixer. The dissociation reaction was stopped by adding 1% bovine serum albumin (BSA) in 500 µL cold HBSS. The cell suspensions were filtered through a 40 µm cell strainer. Cells were pelleted in a 4°C centrifuge at 200g for 5 minutes, washed with 0.5% BSA in 500 µL cold HBSS, pelleted again and resuspended in 0.5% BSA in 500 µL cold HBSS. Single-cell RNA sequencing libraries were prepared by the University of Utah High-Throughput Genomics Shared Resource using the 10X Genomics Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI. Libraries were sequenced with the NovaSeq Reagent Kit v1.5 150x150 bp Sequencing.
Libraries were constructed according to the manufacturer's protocol (10X chromium controller)

value: Testis

value: 27 months


title: mo27_fish3_rep1

description: 10X Genomics


title: mo27_fish2_rep1

description: 10X Genomics


title: mo27_fish4_rep1

description: 10X Genomics


title: mo27_fish4_rep2

description: 10X Genomics


title: Smartseq2_Lipstic_TdLN_316


title: Smartseq2_Lipstic_TdLN_315


title: mo22_fish1_rep2

description: 10X Genomics

value: 22 months


title: mo22_fish1_rep1

description: 10X Genomics


title: mo20_fish1_rep2

description: 10X Genomics

value: 20 months


title: Smartseq2_Lipstic_TdLN_313


title: Smartseq2_Lipstic_TdLN_312


title: mo12_fish2_rep1

description: 10X Genomics

value: 12 months


title: Smartseq2_Lipstic_TdLN_322


title: mo20_fish1_rep1

description: 10X Genomics


title: Smartseq2_Lipstic_TdLN_311


title: Smartseq2_Lipstic_TdLN_310


title: mo12_fish1_rep1

description: 10X Genomics


title: Smartseq2_Lipstic_TdLN_309


title: Smartseq2_Lipstic_TdLN_308


title: mo5_fish2_rep2

description: 10X Genomics

value: 5 months


title: mo5_fish2_rep3

description: 10X Genomics


title: Smartseq2_Lipstic_TdLN_319


title: mo27_fish1_rep1

description: 10X Genomics


title: Smartseq2_Lipstic_TdLN_307


title: mo5_fish2_rep1

description: 10X Genomics


title: mo5_fish1_rep3

description: 10X Genomics


title: Smartseq2_Lipstic_TdLN_314


title: Smartseq2_Lipstic_TdLN_305

value: naïve


title: mo5_fish1_rep2

description: 10X Genomics


title: mo5_fish1_rep1

description: 10X Genomics


title: Smartseq2_Lipstic_TdLN_306


title: WGBS of MRV sample 4

city: Zhuhai

first: Mincong

last: Liang

address: No. 2 Daxue Road

department: School of Marine Sciences

institute: Sun Yat-sen University

data_processing:
The raw data were trimmed and filtered by Trimmomatic v0.39 (“ILLUMINACLIP:TruSeq3-PE-2:2:30:10:8:true SLIDINGWINDOW:5:20 LEADING:5 TRAILING:5 MINLEN:36
Clean data were mapped to the MRV genome, deduplicated and methylation extracted (--ignore_r2 2) using Bismark v0.24.2, Bowtie2 v2.5.2 and SAMtools v1.17.
Assembly: MG941005.3
Supplementary files format and content: The number of methylations and unmethylations counts for each cytosines in MRV genome based on the WGBS data.

organism: Mandarin fish ranavirus

source_name: Virion

extract_protocol:
The total DNA from the purified virions was extracted using the FastPure Cell/Tissue DNA Isolation Mini Kit following the manufacturer's protocol (Vazyme, China).
Libraries were prepared using kit following to the manufacturer's protocol.

value: Virion

value: inoculating Mandarin fish fry (MFF-1) cells with MRV


title: Smartseq2_Lipstic_TdLN_303


title: Smartseq2_Lipstic_TdLN_304


title: WGBS of MRV sample 3


title: plasma_HNSCC_tumour free [C45F1]

city: Sao Paulo

first: Patricia

last: Severino

state: Sao Paulo

address: Rua Comendador Elias Jafet, 755

department: Albert Einstein Research and Education Institute

country: Brazil

institute: Hospital Israelita Albert Einstein

hyb_protocol: The hybridization to probes were performed at 65°C for 24 hours following the manufacturer’s protocol.

scan_protocol: The hybridized probes were purified on nCounter Prep Station and counted on Digital Analyzer.

data_processing: Data was analyzed by nSolver 4.0 software. Data was normalized using 5 miRNA more stable following normFinder analysis

label: Biotin label and molecular barcode

source_name: plasma tumour free

label_protocol: From ~ 30-100ng (or 3ul) of each RNA sample was added to the miRNA-tag ligation reaction for annealing, followed by ligation and purification.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from plasma patients before any treatment and when considered tumour free using Plasma slurry kit (Norgen)

treatment_protocol: not applicable

tag: condition

value: tumour free

tag: histology

tag: tnm

value: Male


title: plasma_HNSCC_tumour free [C40F1]


title: plasma_HNSCC_tumour free [C44F1]


title: WGBS of MRV sample 2


title: Smartseq2_Lipstic_TdLN_302


title: Smartseq2_Lipstic_TdLN_301


title: Smartseq2_Lipstic_TdLN_300


title: DNA from Kazakh individual 296

city: Astana

first: Ulykbek

last: Kairov

address: Kabanbay batyr ave.53

department: Center for Life Sciences

country: Kazakhstan

institute: National Laboratory Astana, Nazarbayev University

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 296

hyb_protocol: DNA was loaded onto BeadChips arrays

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Normalized signal intensity and genotype were computed using Illumina's GenomeStudio v.2 software. GSA MG v2 was used for genotyping
Genotype: AA,AB,BB,or NC (no call)

label: biotin

source_name: blood

label_protocol: 200 ng of Genomic DNA was amplified overnight at 37 degrees.  DNA was fragmented via FMS and precipitated with 2-propanol and PM1. Then DNA is resuspended

extract_protocol: DNA isolation from frozen blood was performed with Gentra Purgene Blood kit (Qiagen)

tag: health status

value: Healthy

value: blood


title: plasma_HNSCC_tumour presence [C40F0]

source_name: plasma in tumour presence

value: tumour presence


title: plasma_HNSCC_tumour presence [C44F0]


title: plasma_HNSCC_tumour presence [C38F0]


title: plasma_HNSCC_tumour presence [C45F0]


title: plasma_HNSCC_tumour free [C38F1]


title: Smartseq2_Lipstic_TdLN_299

tag: cell line


title: DNA from Kazakh individual 294

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 294


title: plasma_HNSCC_tumour free [C37F1]


title: plasma_HNSCC_tumour presence [C36F0]

value: Female


title: DNA from Kazakh individual 292

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 292


title: plasma_HNSCC_tumour free [C33F1]


title: Smartseq2_Lipstic_TdLN_298

tag: treatment


title: DNA from Kazakh individual 290

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 290


title: DNA from Kazakh individual 288

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 288


title: Smartseq2_Lipstic_TdLN_297


title: plasma_HNSCC_tumour free [C32F1]


title: plasma_HNSCC_tumour presence [C33F0]


title: DNA from Kazakh individual 287

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 287


title: Smartseq2_Lipstic_TdLN_296


title: plasma_HNSCC_tumour presence [C37F0]


title: plasma_HNSCC_tumour presence [C32F0]


title: DNA from Kazakh individual 286

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 286


title: plasma_HNSCC_tumour presence [C30F0]


title: plasma_HNSCC_tumour free [C36F1]


title: Smartseq2_Lipstic_TdLN_294


title: plasma_HNSCC_tumour presence [C29F0]


title: plasma_HNSCC_tumour free [C29F1]


title: DNA from Kazakh individual 285

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 285


title: DNA from Kazakh individual 283

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 283


title: plasma_HNSCC_tumour free [C28F1]


title: Smartseq2_Lipstic_TdLN_295


title: plasma_HNSCC_tumour presence [C28F0]


title: Smartseq2_Lipstic_TdLN_293


title: plasma_HNSCC_tumour free [C26F1]


title: plasma_HNSCC_tumour free [C27F1]


title: plasma_HNSCC_tumour presence [C27F0]


title: plasma_HNSCC_tumour presence [C26F0]


title: Smartseq2_Lipstic_TdLN_292


title: plasma_HNSCC_tumour free [C30F1]


title: plasma_HNSCC_tumour free [C23F1]


title: DNA from Kazakh individual 281

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 281


title: Smartseq2_Lipstic_TdLN_291


title: plasma_HNSCC_tumour presence [C23F0]


title: Smartseq2_Lipstic_TdLN_290


title: DNA from Kazakh individual 280

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 280


title: Smartseq2_Lipstic_TdLN_289


title: plasma_HNSCC_tumour free [C19F1]


title: plasma_HNSCC_tumour presence [C19F0]


title: Smartseq2_Lipstic_TdLN_288


title: DNA from Kazakh individual 277

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 277


title: DNA from Kazakh individual 282

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 282


title: Smartseq2_Lipstic_TdLN_287


title: plasma_HNSCC_tumour presence [C18F0]


title: DNA from Kazakh individual 278

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 278


title: DNA from Kazakh individual 275

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 275


title: plasma_HNSCC_tumour free [C17F1]


title: DNA from Kazakh individual 273

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 273


title: plasma_HNSCC_tumour presence [C17F0]


title: Smartseq2_Lipstic_TdLN_286


title: plasma_HNSCC_tumour presence [C16F0]


title: plasma_HNSCC_tumour free [C13F1]


title: Smartseq2_Lipstic_TdLN_285


title: Smartseq2_Lipstic_TdLN_284


title: plasma_HNSCC_tumour presence [C13F0]


title: plasma_HNSCC_tumour free [C21F1]


title: DNA from Kazakh individual 272

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 272


title: plasma_HNSCC_tumour presence [C21F0]


title: plasma_HNSCC_tumour presence [C11F0]


title: plasma_HNSCC_tumour free [C11F1]


title: DNA from Kazakh individual 271

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 271


title: plasma_HNSCC_tumour free [C10F1]


title: plasma_HNSCC_tumour free [C18F1]


title: plasma_HNSCC_tumour presence [C10F0]


title: Smartseq2_Lipstic_TdLN_283


title: plasma_HNSCC_tumour free [C16F1]


title: plasma_HNSCC_tumour free [C6F1]


title: DNA from Kazakh individual 268

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 268


title: DNA from Kazakh individual 269

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 269


title: Smartseq2_Lipstic_TdLN_282


title: Smartseq2_Lipstic_TdLN_281


title: plasma_HNSCC_tumour presence [C6F0]


title: plasma_HNSCC_tumour free [C5F1]


title: plasma_HNSCC_tumour presence [C5F0]


title: Smartseq2_Lipstic_TdLN_280


title: Smartseq2_Lipstic_TdLN_279


title: plasma_HNSCC_tumour free [C2F1]


title: DNA from Kazakh individual 267

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 267


title: plasma_HNSCC_tumour free [C1F1]


title: plasma_HNSCC_tumour presence [C1F0]


title: DNA from Kazakh individual 266

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 266


title: plasma_HNSCC_tumour presence [C2F0]


title: Smartseq2_Lipstic_TdLN_278


title: DNA from Kazakh individual 265

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 265


title: plasma_NSCLC_tumour presence [P31F0]

value: Lung adenocarcinoma


title: DNA from Kazakh individual 264

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 264


title: DNA from Kazakh individual 270

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 270


title: plasma_NSCLC_tumour presence [P30F0]


title: plasma_NSCLC_tumour presence [P28F0]


title: plasma_NSCLC_tumour free [P27F1]


title: plasma_NSCLC_tumour free [P30F1]


title: plasma_NSCLC_tumour free [P28F1]


title: DNA from Kazakh individual 263

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 263


title: plasma_NSCLC_tumour presence [P27F0]


title: DNA from Kazakh individual 262

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 262


title: Smartseq2_Lipstic_TdLN_275


title: plasma_NSCLC_tumour free [P31F1]


title: DNA from Kazakh individual 261

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 261


title: Smartseq2_Lipstic_TdLN_273


title: DNA from Kazakh individual 260

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 260


title: DNA from Kazakh individual 259

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 259


title: Smartseq2_Lipstic_TdLN_277


title: plasma_NSCLC_tumour presence [P26F0]


title: plasma_NSCLC_tumour free [P24F1]


title: Smartseq2_Lipstic_TdLN_276


title: plasma_NSCLC_tumour presence [P24F0]


title: plasma_NSCLC_tumour free [P21F1]


title: plasma_NSCLC_tumour presence [P20F0]

value: Lung squamous cell carcinoma


title: plasma_NSCLC_tumour free [P20F1]


title: plasma_NSCLC_tumour presence [P21F0]

value: no informtation


title: plasma_NSCLC_tumour presence [P19F0]

value: no information


title: DNA from Kazakh individual 257

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 257


title: DNA from Kazakh individual 258

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 258


title: plasma_NSCLC_tumour free [P18F1]


title: Smartseq2_Lipstic_TdLN_270


title: Smartseq2_Lipstic_TdLN_271


title: plasma_NSCLC_tumour presence [P18F0]


title: Smartseq2_Lipstic_TdLN_269


title: plasma_NSCLC_tumour free [P15F1]


title: plasma_NSCLC_tumour free [P26F1]


title: DNA from Kazakh individual 256

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 256


title: Smartseq2_Lipstic_TdLN_274


title: plasma_NSCLC_tumour presence [P15F0]


title: Smartseq2_Lipstic_TdLN_268


title: Smartseq2_Lipstic_TdLN_272


title: plasma_NSCLC_tumour presence [P14F0]


title: Smartseq2_Lipstic_TdLN_267


title: plasma_NSCLC_tumour free [P14F1]


title: DNA from Kazakh individual 253

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 253


title: Smartseq2_Lipstic_TdLN_266


title: DNA from Kazakh individual 252

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 252


title: plasma_NSCLC_tumour presence [P13F0]


title: plasma_NSCLC_tumour free [P9F1]


title: DNA from Kazakh individual 251

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 251


title: Smartseq2_Lipstic_TdLN_265


title: Smartseq2_Lipstic_TdLN_264


title: plasma_NSCLC_tumour presence [P9F0]


title: plasma_NSCLC_tumour free [P8F1]


title: plasma_NSCLC_tumour presence [P8F0]


title: plasma_NSCLC_tumour free [P7F1]


title: Smartseq2_Lipstic_TdLN_263


title: Smartseq2_Lipstic_TdLN_262


title: DNA from Kazakh individual 249

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 249


title: DNA from Kazakh individual 255

description:
Genomic DNA from Kazakh population with 766221 SNPs were genotyped by GSA MG v2
SAMPLE 255


title: plasma_NSCLC_tumour presence [P7F0]


title: Smartseq2_Lipstic_TdLN_261