title: Melanocytes with wild type BRAF in shDsg1 CM #3

value: melanocytes

value: Melanocytes were transduced with wild type BRAF and treated with CM from keratinocytes expressing shDsg1


title: endometrium, LH3_2, rep2

status: Public on Nov 18 2024

type: SRA

city: Shenzhen

first: zhu

last: kongfu

address: NanShan

country: China

institute: The Hong Kong University - Shenzhen Hospital

library_source: transcriptomic single cell

data_processing:
The raw sequencing data was separately processed using CellRanger pipeline (v.7.0.0) with default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

organism: Homo sapiens

source_name: endometrium

extract_protocol:
A one-step dissociation protocol was used to disperse fresh endometrium tissue. Before dissociation, the tissue was rinsed with cold Phosphate Buffered Saline (PBS, Gibco) on a Petri dish to remove blood and mucus. Excess PBS was removed after rinsing. The tissue was then minced into small pieces using surgical blade with a small amount of benchtop medium (1% FBS + 1% Penicillin-Streptomycin + 1% Glutamine) or PBS to prevent tissue from drying out. Tissue digestion was then immediately performed using DMEM-F12 (Gibco) reconstituted DNase I (4mg/ml, Worthington) and Collagenase III (2.5mg/ml, Worthington) in a 50-ml Falcon tube, which was horizontally incubated at 37 °C water bath with constant shaking for 1 hour. After digestion, the cell suspension were filtered through 40μm sieves (BD Bioscience) and then loaded onto Ficoll-Paque (GE Healthcare) density gradient for red blood cell removal. Further removal of red blood cells was conducted using red blood lysis solution (Meitianni) for 5 minutes at room temperature. Dead cells were removed using the MACS dead cell removal kit (130-090-101, Miltenyi) following the manufacturer’s protocol. The cell viability and concentration of final resulted single-cell suspension was assessed for subsequent scRNA-seq experiments.
The qualified endometrial single-cell suspensions of were placed in a cold box (4 °C), and appropriate number of cells were loaded onto the Chromium Controller platform within 2 hours. Single-cell encapsulation, barcoding, reverse transcription, cDNA generation and library construction were performed following the manufacturer’s protocol (Single Cell 3' reagent kit v3.1, 10X Genomics). Single-cell libraries of each donor were sequenced with a pair-end mode (150bp) on a DNBSEQ-T7 instrument (GenePlus Technology) with a minimum sequencing depth of 50,000 reads/ per cell.

tag: tissue

value: endometrium

tag: Sex

value: female

tag: group


title: N96L (A066)

city: Bar Harbor

first: Chih-Hao

last: Chang

state: ME

address: 600 Main Street

country: USA

institute: The Jackson Laboratory

library_source: transcriptomic

data_processing:
Bulk RNA of the 9 excised tissues (heart, hippocampus, hypothalamus, kidney, liver, prefrontal cortex, skeletal muscle, small intestine, and spleen) (4 samples per treatment and time combination) was isolated with the QIAGEN miRNeasy mini extraction kit (QIAGEN) and cDNA was synthesized with the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems). RNA quality was assessed with a Bioanalyzer 2100 (Agilent Technologies). Poly(A)-selected RNA-seq libraries were generated using the Illumina TruSeq RNA Sample preparation kit v2. RNA-seq was performed in a 150-bp paired-end format with a minimum of 40 million reads per sample on the Illumina HiSeq platform according to the manufacturer’s instructions. RNA-seq reads were filtered and trimmed for quality scores >30 using a custom python script. The filtered reads were aligned to Mus musculus GRCm38 using RSEM (v1.2.12) (58) with Bowtie2 (v2.2.0)(21) (command: rsem-calculate-expression -p 12--phred33-quals --seed-length 25 --forward-prob 0 --time --output-genome-bam -- bowtie2).RSEM calculates expected counts and transcript per million (TPM). The expected counts from RSEM were used in the Bioconductor edgeR 3.20.9 package(22-24) to determine differentially expressed genes.
Assembly: Mus musculus GRCm38
Supplementary files format and content: .Rdata contains FPKM counts
Supplementary files format and content: tab-delimited text file contains expected count, TPM, and FPKM

organism: Mus musculus

source_name: Liver

extract_protocol:
Bulk RNA of the 9 excised tissues (heart, hippocampus, hypothalamus, kidney, liver, prefrontal cortex, skeletal muscle, small intestine, and spleen) (4 samples per treatment and time combination) was isolated with the QIAGEN miRNeasy mini extraction kit (QIAGEN) and cDNA was synthesized with the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems).
Poly(A)-selected RNA-seq libraries were generated using the Illumina TruSeq RNA Sample preparation kit v2.

treatment_protocol: mice were treated with 2DG (6g/L) through water or just water for 96 hours or 4 weeks

value: Liver

tag: strain

tag: genotype

value: WT

tag: treatment

value: Control

tag: timepoint

value: 96 hours

value: male


title: N96K (A065)

source_name: Kidney

value: Kidney


title: endometrium, LH11_1, rep1


title: Melanocytes with wild type BRAF in shDsg1 CM #2

city: Chicago

first: Ziyou

last: Ren

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

data_processing:
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library
library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data ( clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end cleanreads were aligned to the reference genome using Hisat2 v2.0.5.
Assembly: hg38
Supplementary files format and content: gene count value

source_name: skin

growth_protocol: Keratinocytes and melanocytes were isolated from neonatal foreskin provided by the Northwestern University Skin Biology and Diseases Research-Based Center as previously described (Roth-Carter et al., 2022). Keratinocytes were grown in M154 medium (Thermo Fisher Scientific) supplemented with human keratinocyte growth supplement (Thermo Fisher Scientific), 1,000 x gentamycin/amphotericin B solution (ThermoFisher Scientific), and 0.07mM CaCl2. Melanocytes were cultured in OptiMEM (Thermo Fisher Scientific) containing 5% fetal bovine serum (MilliporeSigma), 10 ng/ml bFGF (ConnStem), 1 ng/ml heparin (MilliporeSigma), 0.1 mM N6, 2’-O-dibutyryladenosine 3:5-cyclic monophosphate (MilliporeSigma), 0.1 mM 3-isobutyl-1-methyl xanthine (MilliporeSigma), and 1% penicillin/streptomycin (Corning). All cells were maintained at 37 °C with 5% CO2.

extract_protocol:
RNA was harvested using Quick-RNA miniprep kit (Zymo).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP

treatment_protocol: Conditioned media (CM) from keratinocytes were prepared by following previously published procedure (Arnette et al., 2020). Melanocytes were transduced with wild type BRAF or mutant BRAFV600E, then treated with CM from keratinocytes expressing shCTL or shDsg1 for 3 days.

value: skin

tag: cell line

value: human melanocytes

tag: cell type


title: Melanocytes with wild type BRAF in shDsg1 CM #1


title: endometrium, LH11_2, rep2


title: endometrium, LH9_3, rep3


title: N96HC (A062)

source_name: Hippocampus

value: Hippocampus


title: Melanocytes with wild type BRAF in shCTL CM #3

value: Melanocytes were transduced with wild type BRAF and treated with CM from keratinocytes expressing shCTL


title: N96PC (A063)

source_name: Prefrontal cortex

value: Prefrontal cortex


title: N96HT (A061)

source_name: Hypothalamus

value: Hypothalamus


title: N96SI (A060)

source_name: Ilium

value: Ilium


title: N96H (A058)

source_name: Heart

value: Heart


title: endometrium, LH5_3, rep3


title: Melanocytes with wild type BRAF in shCTL CM #2

value: melanocytes


title: Melanocytes with wild type BRAF in shCTL CM #1


title: endometrium, LH9_2, rep2

value: endometrium


title: N96K (A056)


title: endometrium, RIF_3, rep3

value: female

value: RIF


title: N96L (A057)

value: Liver

value: WT


title: Control melanocytes in shDsg1 CM #3

value: Conditioned media from keratinocytes expressing shDsg1


title: Control melanocytes in shDsg1 CM #2


title: N96S (A055)

source_name: Spleen

value: Spleen

value: Control

value: 96 hours

value: male


title: N96H (A067)


title: endometrium, LH9_1, rep1


title: N96S (A064)


title: N4wPC (A054)

value: 4 weeks


title: N4wHT (A052)


title: Control melanocytes in shDsg1 CM #1

value: skin

value: human melanocytes


title: N4wHC (A053)

value: Hippocampus


title: endometrium, LH7_3, rep3


title: N4wSI (A051)

value: Ilium


title: N96SM (A059)

source_name: Skeletal muscle

value: Skeletal muscle


title: endometrium, LH5_2, rep2


title: N4wH (A049)

value: Heart


title: N4wS (A046)


title: N4wHC (A044)


title: N4wSM (A050)


title: endometrium, LH7_2, rep2

value: endometrium


title: N4wL (A048)


title: Control melanocytes in shCTL CM #3

value: melanocytes

value: Conditioned media from keratinocytes expressing shCTL


title: Control melanocytes in shCTL CM #2


title: N4wHT (A043)

value: Hypothalamus


title: endometrium, LH7_PGT_3, rep3

value: female


title: N4wPC (A045)

value: Prefrontal cortex

value: WT


title: N4wK (A047)

value: Kidney

value: Control


title: NsO-HRVC+CYT387-2

city: Hong Kong

first: Jie

last: Zhou

address: 102 Pokfulam Road, Pokfulam, Hong Kong

department: Microbiology

country: Hong Kong

institute: The University of Hong Kong

description: Nasal organoid

data_processing:
Quality control of raw fastq data was carried out by FastQC v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and fastp [PMID: 30423086].
Clean reads were aligned to the UCSC GRCh38 reference and the Rhinovirus C3 strain genome (GenBank: OK161378.1) using Hisat2 v2.2.1 [PMID: 31375807].
HTSeq v0.6.1 [PMID: 25260700] was used to generate raw read count for each gene.
Differential expression analysis was performed using DESeq2 [PMID: 25516281]. Genes with log2|fold change| > 1 and adjusted p-value < 0.05 were considered significantly different.
Volcano plot was generated using EnhancedVolcano R package (https://github.com/kevinblighe/EnhancedVolcano). Heatmaps of gene expression levels were constructing using the pheatmap R package (https://cran.r-project.org/web/packages/pheatmap/index.html). Gene set enrichment analysis (GSEA) was performed using fgsea R package (https://github.com/ctlab/fgsea).
Assembly: UCSC GRCh38
Supplementary files format and content: Text files of raw counts.

source_name: differentiated nasal organoid

extract_protocol:
Samples were harvested for RNA extraction using RNeasy Mini Kit (Qiagen, Cas.74106).
cDNA libraries were prepared by KAPA mRNA HyperPrep Kit according to the manufacturer's protocol.

value: differentiated nasal organoid

value: ciliated cell, goblet cell, club cell, basal cell, etc


title: Control melanocytes in shCTL CM #1

value: skin


title: endometrium, LH7_1, rep1


title: NsO-HRVC-1

description: Nasal organoid

value: HRV-C


title: N4wK (A038)

value: 4 weeks

value: male


title: NsO-HRVC+CYT387-1

description: Nasal organoid


title: N4wSI (A042)

value: Ilium


title: endometrium, LH7_PGT_2, rep2


title: T4wPC (A036)


title: N4wSM (A041)

value: Skeletal muscle


title: NsO-Mock-2

description: Nasal organoid

value: Mock-treated


title: T4wHC (A035)

value: Hippocampus


title: endometrium, LH7_PGT_1, rep1

value: endometrium


title: endometrium, LH5_1, rep1


title: endometrium, RIF_2, rep2

value: RIF


title: T4wHT (A034)

value: Hypothalamus


title: N4wL (A039)

value: Liver


title: NsO-HRVC-2

description: Nasal organoid


title: endometrium, RIF_6, rep6

value: female


title: T4wSM (A032)

value: WT


title: endometrium, RIF_7, rep7


title: T4wHT (A031)

value: Heart


title: T4wL (A030)


title: N4wS (A037)

value: Spleen

value: Control


title: AwO-HRVC+CYT387-1

description: Airway organoid

source_name: differentiated airway organoid

value: differentiated airway organoid

value: ciliated cell, goblet cell, club cell, basal cell, etc


title: T4wSI (A033)

value: 4 weeks


title: NsO-Mock-1

description: Nasal organoid

value: differentiated nasal organoid


title: Skeletal muscle, inactive, replicate 7

city: Downers Grove

first: Erin

middle: J

last: Stephenson

address: 555 31st street

institute: Midwestern University

data_processing:
Raw files were imported to Galaxy and trimmed using fastp
Trimmed files were aligned to genome assembly GRCm39 using RNA STAR in Galaxy
Reads were mapped in Galaxy using featureCounts
Count normalization was completed using the DESeq2 package in R
Assembly: GRCm39
Supplementary files format and content: csv file includes raw counts for each sample
Supplementary files format and content: csv file includes normalized counts for each sample

source_name: Skeletal muscle (gastrocnemius, medial belly)

extract_protocol:
The gastrocnemius muscle was freeze clamped immediately upon harvest. The entire medial belly was bead homogenized in trizol and RNA was extracted using chloroform methanol extraction. RNA was then column purified using a Purelink RNA kit.
RNA was sent to Azenta for PolyA cDNA library preparation and sequencing

value: Inactive 6 weeks


title: AwO-HRVC+CYT387-2

description: Airway organoid


title: T4wPC (A027)

value: Prefrontal cortex

value: male


title: N4wH (A040)


title: T4wK (A029)

value: Kidney


title: T4wHC (A026)

value: Hippocampus


title: endometrium, RIF_1, rep1

value: endometrium

value: RIF


title: T4wSI (A024)

value: Ilium


title: T4wS (A028)


title: AwO-Mock-2

description: Airway organoid

value: Mock-treated


title: AwO-HRVC-2

description: Airway organoid

value: HRV-C


title: Skeletal muscle, inactive, replicate 6

value: Skeletal muscle (gastrocnemius, medial belly)


title: Skeletal muscle, activity reduction, replicate 6

value: Treadmill trained 4 weeks, inactive 2 weeks


title: T4wSM (A023)

value: Skeletal muscle

value: WT


title: N4wHC (A089)

value: Control


title: T4wH (A022)

value: Heart

value: 4 weeks


title: AwO-HRVC-1

description: Airway organoid

value: differentiated airway organoid

value: ciliated cell, goblet cell, club cell, basal cell, etc


title: T4wHT (A025)

value: Hypothalamus

value: male


title: Skeletal muscle, activity reduction, replicate 7


title: T4wL (A021)

value: Liver


title: AwO-Mock-1

description: Airway organoid


title: T4wK (A020)

value: Kidney


title: Skeletal muscle, activity reduction, replicate 5


title: 182_recurrent_GFAP_short_TalaSlide1Again_039

city: Basel

first: Sabrina

middle: Annie

last: Hogan

address: Hebelstrasse 20

country: Switzerland

institute: University of Basel

description: GFAP

data_processing:
GeoMx DSP data were evaluated and prepared for downstream analysis following the GeoMx-NGS gene expression analysis workflow until the filtering step. Segments with less than 4% of the genes detected were removed and the cut-off for gene detection was set at 2%. Reads from duplicated samples were summed using the aggregateAcrossCells function from the scuttle package. One outlier sample was excluded (DSP-1001660005533-A-C08). The package limma was used to perform between-samples cyclic loess normalization
Assembly: GeoMx NGS bioinformatic processing Pipeline. In the first step, the raw reads (raw sequencing FASTQ files) are compiled with the configuration file, which specifies the processing parameters. Next, the raw reads are processed by computationally removing the adapter sequences (resulting in trimmed reads), and merging the overlapping paired-end reads (resulting in stitched reads). In the third step, the stitched reads are aligned to the RTS- ID barcodes in the reference assay, creating aligned reads and assigning raw counts to biological target names. Then, PCR duplicates are removed using the Unique Molecular Identifier in each read, resulting in deduplicated reads. The DCC files are created and presented as a .zip file in a folder which you designate and can then be uploaded into the DSP Control Center for study creation in the DSP Data Analysis Suite, or loaded into R for data processing with the GeomxTools open software package.
Supplementary files format and content: SpatialTranscriptomics_normalized_log2_cpm.xlsx: normalised log2 counts per million
Library strategy: Spatial Transcriptomics

source_name: GBM

extract_protocol:
Slide-mounted FFPE TMA was processed for antigen retrieval using a heat induced epitope retrieval protocol for 20 minutes followed by a 5-min wash with 1μg/mL proteinase K solution. TMA was next incubated overnight with GeoMx RNA detection probes containing-photocleavable oligos
Sequencing libraries were generated by PCR from the oligos and sequenced using Illumina NovaSeq according to the manufacturer’s protocol

value: GBM

tag: primary recurrent

value: recurrent

tag: relapse time

value: short

tag: patient id

tag: panel

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: folder name


title: T4wS (A019)

value: Spleen


title: Skeletal muscle, trained, replicate 7

value: Skeletal muscle (gastrocnemius, medial belly)

value: Treadmill trained 6 weeks


title: T96HC (A017)

value: Hippocampus

value: WT

value: 96 hours


title: T96PC (A018)

value: Prefrontal cortex


title: Skeletal muscle, activity reduction, replicate 4

value: Treadmill trained 4 weeks, inactive 2 weeks


title: 608_primary_GFAP_long_TalaSlide1Again_038

description: GFAP

value: primary

value: long

tag: ref id


title: T96SI (A015)

value: Ilium

value: male


title: T96HT (A016)

value: Hypothalamus


title: 608_primary_GFAP_long_TalaSlide1Again_037

description: GFAP

value: GBM


title: 599_recurrent_CD64_short_TalaSlide1Again_036

value: recurrent


title: T96K (A011)

value: Kidney


title: T96L (A012)

value: Liver


title: T96SM (A014)

value: Skeletal muscle


title: N4wPC (A009)

value: Control

value: 4 weeks


title: T96H (A013)

value: Heart


title: Skeletal muscle, inactive, replicate 4

value: Skeletal muscle (gastrocnemius, medial belly)

value: Inactive 6 weeks


title: 599_recurrent_GFAP_short_TalaSlide1Again_035

description: GFAP

value: short

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: Skeletal muscle, inactive, replicate 3


title: T96S (A010)

value: Spleen

value: WT

value: 96 hours


title: Skeletal muscle, activity reduction, replicate 3

value: Treadmill trained 4 weeks, inactive 2 weeks


title: 291_primary_GFAP_long_TalaSlide1Again_034

description: GFAP

value: primary

value: long


title: 599_recurrent_CD64_short_TalaSlide1Again_033

value: GBM

value: recurrent


title: Skeletal muscle, trained, replicate 6

value: Treadmill trained 6 weeks


title: Skeletal muscle, inactive, replicate 5


title: N4wL (A003)

value: Liver

value: male


title: N4wH (A004)

value: Control

value: 4 weeks


title: N4wHC (A008)

value: Hippocampus


title: Skeletal muscle, inactive, replicate 1

value: Skeletal muscle (gastrocnemius, medial belly)

value: Inactive 6 weeks


title: endometrium, LH3_1, rep1

value: endometrium

value: female


title: MCAO_Ctrl_A

city: Vestec

first: Lukas

last: Valihrach

address: Prumyslova 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science

data_processing:
Adaptor sequences and low-quality reads were removed using TrimmomaticSE v0.36. Reads mapping to mtDNA and rRNA were filtered out using SortMeRNA v2.1 with default parameters. The remaining reads were aligned to GRCm38 and ERCC reference using STAR v2.5.2b with default parameters81. Mapped reads were counted over Gencode vM8 gene annotation using htseq-count with union mode for handling of overlapping reads.
We filtered the data for genes with >10 reads and normalized them by varianceStabilizingTransformation function. We applied the DESeq model using DESeq function with type of fit parameter set to ‘local’.
Assembly: mm10/GRCm38
Supplementary files format and content: tab-delimited text file containing DESeq normalized expression matrix.

molecule: polyA RNA

source_name: brain

extract_protocol:
Samples were collected from the injured cortical region (including affected as well as non-affected brain tissue) and homogenized using the TissueLyser (QIAGEN). Total RNA was extracted with TRI Reagent (Sigma-Aldrich) according to the manufacturer’s protocol and treated with TURBO DNA-free kit (Thermo Fisher). RNA quantity and purity was assessed using the NanoDrop 2000 spectrophotometer (Thermo Fisher) and RNA integrity was assessed using the Fragment Analyzer (Agilent). All samples had RQN > 8.
Libraries were prepared from 400 ng total RNA with QuantSeq 30 Library Prep Kit FWD (Lexogen) according to manufacturer’s protocol. 1 µl of ERCC spike-in (c = 0.01x; Thermo Fisher) per library was included. Libraries were quantified on the Qubit 2 fluorometer (Thermo Fisher) and Fragment Analyzer (Agilent), and sequenced on the NextSeq 500 high-output (Illumina) with 85 bp single-end reads. 11.5 – 38 million reads were obtained per library with a median of 16 million reads

treatment_protocol: Prior to the induction of MCAO, mice were anaesthetized with 3% isoflurane (Aerrane, Baxter) and amaintained in 2% isoflurane using a vaporizer (Tec-3, Cyprane Ltd.). A skin incision between the orbit and the external auditory meatus was made, and a 1-2 mm hole was drilled through the frontal bone 1 mm rostral to the fusion of the zygoma and the squamosal bone, about 3.5 mm ventrally to the dorsal surface of the brain. The middle cerebral artery (MCA) was exposed after the dura was opened and removed. The MCA was occluded by short coagulation with bipolar tweezers (SMT) at a proximal location, followed by transection of the vessel to ensure permanent occlusion. During the surgery, body temperature was maintained at 37 ± 1C using a heating pad. This MCAO model yields small infarct lesions in the parietal cortical region. Intact cortical tissue from 3 months old mice was used as control.

value: brain

tag: condition

value: Ctrl

tag: replicate

value: A


title: N4wSI (A006)

tag: tissue

value: Ilium

value: WT


title: MCAO_7D_SH_D

value: Sham

value: 7 days

value: D


title: N4wSM (A005)

value: Skeletal muscle

tag: Sex


title: 599_recurrent_GFAP_short_TalaSlide1Again_033

description: GFAP

value: GBM

value: recurrent

value: short

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: MCAO_7D_E

value: MCAO

value: E


title: 38_recurrent_GFAP_long_TalaSlide1Again_028

description: GFAP

value: long


title: MCAO_7D_C

value: C


title: MCAO_Ctrl_D

value: brain

value: Control


title: 94_recurrent_GFAP_long_TalaSlide1Again_032

description: GFAP


title: N4wS (A001)

value: Spleen

value: 4 weeks

value: male


title: 599_recurrent_GFAP_short_TalaSlide1Again_036

description: GFAP


title: MCAO_7D_SH_C

value: Sham


title: MCAO_Ctrl_C

value: Ctrl


title: MCAO_Ctrl_B

value: B


title: Skeletal muscle, trained, replicate 2

value: Skeletal muscle (gastrocnemius, medial belly)

value: Treadmill trained 6 weeks


title: 94_recurrent_CD64_long_TalaSlide1Again_031

value: GBM

value: recurrent


title: Skeletal muscle, inactive, replicate 2

value: Inactive 6 weeks


title: Skeletal muscle, trained, replicate 5


title: 38_primary_GFAP_long_TalaSlide1Again_026

description: GFAP

value: primary

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: 94_primary_GFAP_long_TalaSlide1Again_030

description: GFAP

value: long


title: Skeletal muscle, activity reduction, replicate 2

value: Treadmill trained 4 weeks, inactive 2 weeks


title: 38_recurrent_GFAP_long_TalaSlide1Again_027

description: GFAP


title: MCAO_7D_SH_B

value: brain

value: 7 days


title: 38_primary_GFAP_long_TalaSlide1Again_025

description: GFAP


title: MCAO_3h_SH_B

value: 3 hours


title: Skeletal muscle, activity reduction, replicate 1


title: 94_primary_GFAP_long_TalaSlide1Again_029

description: GFAP


title: MCAO_3h_SH_A

value: A


title: MCAO_7D_SH_A


title: Skeletal muscle, trained, replicate 4


title: MCAO_3h_D

value: MCAO

value: D


title: TEPA, replicate 1

city: Kensington

first: Orazio

last: Vittorio

address: High St

department: School of Biomedical Sciences, Faculty of Medicine

country: Australia

institute: UNSW Sydney

data_processing:
Raw sequencing data was converted into gene expression profiles for individual cells using the BD Rhapsody WTA Analysis Pipeline provided on the Seven Bridges Platform (Seven Bridges Genomics).
Assembly: mm10
Supplementary files format and content: Comma-separated values

source_name: Th-MYCN Tumor

growth_protocol: Th-MYCN transgenic animals were recruited for treatment when a small tumor (3-4mm diameter) was manually palpated.

extract_protocol:
Th-MYCN tumor sections were dissociated into single cell suspensions followed non-specific IgG antibody binding using Mouse BD Fc CD16/CD32 Block (BD Pharmingen). Cells were then surface stained with CD3ε-FITC (clone 145-2C11, 1:100, Thermo Fisher Scientific), NK1.1-PE (clone PK136, 1:200, Thermo Fisher Scientific) and CD11b-BV421 (clone M1/70, 1:200, BioLegend). Tumor cells were selected for using previously optimised gating strategy using the absence of described markers. Flow sorting was performed using a BD FACSAria III (BD Biosciences).
Whole transcriptome libraries were constructed following the BD Rhapsody single-cell whole-transcriptome amplification workflow according to the manufacturer’s instructions. Libraries were quantified using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2200 and the Qubit High Sensitivity double-stranded DNA Assay Kit (Thermo Fisher Scientific). Resulting DNA libraries were sequenced on an Illumina NovaSeq 6000 S4 2×150 bp kit to yield an average of 80,000 reads per cell.

treatment_protocol: Recruited Th-MYCN animals were treated with saline control or TEPA (400mg/kg) for seven days before tumor collection.

value: Th-MYCN Tumor

value: Flow-sorted cells (tumor, lymphocyte, myeloid)

tag: disease

value: Neuroblastoma

value: TEPA

value: Female

tag: time


title: MCAO_7D_D


title: Skeletal muscle, trained, replicate 3

value: Skeletal muscle (gastrocnemius, medial belly)

tag: genotype

value: Treadmill trained 6 weeks


title: MCAO_3h_B

value: B


title: Control, replicate 1

tag: treatment

value: Control


title: 417_recurrent_CD64_short_TalaSlide1Again_021

value: GBM

value: recurrent

value: short

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: MCAO_3D_SH_B

value: brain

value: Sham

tag: timepoint

value: 3 days


title: Biol rep 4, infected + 4u8c

city: Worcester

first: Christopher

last: Sassetti

state: Massachusetts

address: 55 Lake Avenue North

institute: University of Massachusetts Chan Medical School

description: Processed data column: 30

data_processing:
Sequencing file quality was verified using FastQC version 0.11.5. Reads were trimmed using Cutadapt version 4.1, then mapped to the mouse Ensembl GRCm38 genome using STAR version 2.5.2b.
Transcripts were quantified using RSEM version 1.3.3. Subsequent analysis was completed in R version 4.1.2.
Files were imported using the Bioconductor package tximport version 1.22.0. Genes with a TPM greater than or equal to 0.5 in atleast 15 libraries were included.
Assembly: GRCm38  mm10
Supplementary files format and content: Comma seperated values file including normalized counts for all samples

source_name: Bone marrow derived

growth_protocol: BMDMs were differentiated from marrow harvested from  8-12 week old C57BL/6J mice (ordered from Jackson Laboratory) for 8 days in DMEM + 10% FBS, 20% conditioned L929 supernatant, HEPES, and sodium pyruvate. 3 days both initial harvest, additional media was added, and 5 days post harvest, media was removed and replaced with fresh media. 8 days post initial plating, cells were harvested and re-plated in DMEM, 10% FBS, HEPES and sodium pyruvate.

extract_protocol:
Following infection, cells were lysed in triZOL. Samples were then mixed 5:1 with chloroform and shaken. Samples were then spun to separate layers and aqueous layer containing RNA collected. RNA isolation/purification was then performed using Direct-zol RNA MiniPrep kit.
Libraries were prepared by Azenta using the NEBNext Ultra II RNA Library Prep Kit with polyA selection per manufacturer's instructions

treatment_protocol: For infections: H37Rv was grown to mid-log phase in 7h9 for day of infection. Single cell suspensions of bacteria were prepared using a soft spin (700 RPM for 10 min, no brake) and then approximate MOI calculated via OD600. Bacteria was added in culture media to cells at a ratio of 1:9 (cells:bacteria) and plates were spun at 500xg for 10 min. Plates were then returned to the incubator for 4 h, before media was removed, and wells were washed with media, and then fresh media containing inhibitors as appropriate was added. Cells were then incubated until time of extraction. Inhibitor treatments: Inhibitors were added to cells at 1.5x concentration 2 hours prior to infection. Concentration was brought to 1x upon addition of bacteria. Uninhibited wells received vehicle control (DMSO). 4 hours post infection, wells were washed and fresh media containing inhibitors added to cells.

value: Bone marrow derived

tag: cell line

value: Primary cell

value: Bone marrow derived macrophage

value: H37Rv MOI 9 + 4u8c


title: Skeletal muscle, trained, replicate 1


title: MCAO_7D_A

value: MCAO

value: 7 days

value: A


title: MCAO_3h_SH_D

value: 3 hours

value: D


title: MCAO_7D_B

value: B


title: MCAO_3h_SH_C

value: C


title: TEPA, replicate 2

value: Th-MYCN Tumor

tag: cell type

value: Flow-sorted cells (myeloid)

value: Neuroblastoma

value: TEPA

value: Female


title: 417_primary_GFAP_short_TalaSlide1Again_019

description: GFAP

value: GBM

tag: primary recurrent

value: primary

value: short

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: MCAO_3h_C

value: brain


title: 38_primary_GFAP_long_TalaSlide1Again_024

description: GFAP

tag: relapse time

value: long


title: Biol rep 4, infected + Ceapin-A7

description: Processed data column: 28

value: Bone marrow derived

value: Primary cell

value: Bone marrow derived macrophage

value: H37Rv MOI 9 + Ceapin-A7


title: MCAO_3h_E

value: MCAO

value: 3 hours

value: E


title: 417_primary_GFAP_short_TalaSlide1Again_018

description: GFAP

tag: patient id


title: MCAO_3h_A

value: A


title: 417_recurrent_CD64_short_TalaSlide1Again_023

value: recurrent

tag: panel


title: 417_recurrent_GFAP_short_TalaSlide1Again_022

description: GFAP

tag: folder name


title: MCAO_3D_SH_C

value: Sham

value: 3 days

value: C


title: MCAO_3D_SH_D

value: D


title: Control, replicate 2

value: Th-MYCN Tumor

value: Flow-sorted cells (myeloid)

value: Neuroblastoma

value: Control

value: Female


title: MCAO_24h_SH_D

value: brain

value: 24 hours


title: 417_recurrent_CD64_short_TalaSlide1Again_020

value: GBM

value: short

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA

tag: ref id


title: MCAO_3D_SH_A

tag: condition


title: Biol rep 4, infected + GSK2606414

description: Processed data column: 29

value: Bone marrow derived

value: Primary cell

value: Bone marrow derived macrophage


title: Biol rep 3, infected + 4u8c

description: Processed data column: 22

value: H37Rv MOI 9 + 4u8c


title: MCAO_3D_E

value: MCAO

value: 3 days

tag: replicate

value: E


title: MCAO_24h_SH_A

tag: tissue

value: Sham

value: A


title: MCAO_3D_D

value: D


title: MCAO_24h_D


title: MCAO_3D_C

value: C


title: MCAO_24h_C


title: MCAO_3D_B

value: B


title: MCAO_24h_B

value: brain


title: Biol rep 4, infected unhibited

description: Processed data column: 26

value: H37Rv MOI 9


title: Biol rep 3, infected + Ceapin-A7

description: Processed data column: 20

value: H37Rv MOI 9 + Ceapin-A7


title: Biol rep 3, infected unhibited

description: Processed data column: 18


title: MCAO_12h_SH_C

value: 12 hours


title: MCAO_3D_A


title: MCAO_24h_SH_C

value: 24 hours


title: 185_recurrent_GFAP_short_TalaSlide1Again_016

description: GFAP

value: GBM

value: recurrent

value: short

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: Biol rep 3, infected + GSK2606414

description: Processed data column: 21

value: Bone marrow derived

value: Primary cell

value: Bone marrow derived macrophage


title: Biol rep 3, uninfected

description: Processed data column: 17


title: MCAO_24h_A

value: MCAO


title: 185_primary_GFAP_short_TalaSlide1Again_014

description: GFAP

value: primary


title: Biol rep 4, uninfected

description: Processed data column: 25


title: MCAO_12h_SH_D

value: Sham

value: D


title: 185_recurrent_GFAP_short_TalaSlide1Again_017

description: GFAP


title: MCAO_12h_E

value: E


title: 282_primary_GFAP_long_TalaSlide1Again_011

description: GFAP

value: long


title: MCAO_12h_SH_A

value: brain

value: A


title: MCAO_12h_D

value: 12 hours


title: MCAO_12h_C

value: C


title: MCAO_12h_B

value: B


title: 282_primary_GFAP_long_TalaSlide1Again_0010

description: GFAP

value: GBM


title: MCAO_24h_SH_B

value: 24 hours


title: Biol rep 2, infected + GSK2606414

description: Processed data column: 13


title: 182_primary_GFAP_short_TalaSlide1Again_013

description: GFAP

value: short

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: 356_primary_GFAP_short_TalaSlide1Again_009

description: GFAP


title: 182_primary_GFAP_short_TalaSlide1Again_012

description: GFAP


title: Biol rep 2, infected + Ceapin-A7

description: Processed data column: 12

value: Bone marrow derived

value: Primary cell

value: H37Rv MOI 9 + Ceapin-A7


title: atac, adf_re, 3

city: Rehovot

first: Ido

last: Goldstein

address: POB 12

department: Institute of Biochemistry, Food Science and Nutrition

country: Israel

institute: The Hebrew University of Jerusalem

library_source: genomic

data_processing:
Binary Base Call (BCL) output files from a Nextseq 500 machine were converted to FASTQ format, using BCL to FASTQ (bcl2fastq v2.20.0.422 Copyright (c) 2007-2017 Illumina, Inc.).
Fastq files were mapped to the mm10 mouse genome assembly using Bowtie2
Assembly: mm10
Supplementary files format and content: bedGraph

molecule: genomic DNA

source_name: liver tissue

growth_protocol: Female, 6 weeks-old mice (C57BL/6JOlaHsd) were randomly assigned to either the URF or ADF groups (12 mice per group). The experiment started after 1 week of acclimation. The URF group had ad libitum access to food (Teklad TD2018) and water for 30 days. The ADF group had ad libitum access to food and water for 24 h followed by ad libitum access to only water for 24 h.

extract_protocol:
RNA-seq: Total RNA was isolated from liver pieces (30 mg) using NucleoSpin kit (Macherey-Nagel cat# 740955.25) according to the manufacturer’s protocol. ATAC-seq: To isolate nuclei, liver samples (10 mg) were homogenized in hypotonic sucrose buffer (250 mM sucrose, 10 mM Tris-Hcl pH 7.8, 0.1% Igepal, 3mM MgCl2, 10mM KCl, 0.2 mM Dithiothreitol, 0.5 mM spermidine, protease inhibitor cocktail) in a dounce homogenizer. Homogenate was filtered through a 20 µM filter, spun and washed (10 mM Tris-Hcl pH 7.5, 3 mM MgCl2, 10 mM NaCl, 0.1% tween-20). 50,000 nuclei were included for next steps as described (Corces et al., 2017). Each sample was sequenced at a depth of at least 50X106 reads (paired-end).
For quality control of RNA yield and library synthesis products, the RNA ScreenTape and D1000 ScreenTape kits (both from Agilent Technologies), Qubit® RNA HS Assay kit, and Qubit® DNA HS Assay kit (both from Invitrogen) were used for each specific step. mRNA libraries were prepared from 1 µg RNA using the KAPA Stranded mRNA-Seq Kit, with mRNA Capture Beads (KAPA biosystems, cat# KK8421). ATAC DNA libraries were prepared using the KAPA HyperPrep Kit (KAPA biosystems, cat# KR0961).

treatment_protocol: Mice were subjected to either a 4-week alternate day fasting (ADF) regimen or unrestricted feeding (URF). At the end of the experiment mice were divided to two groups: the first group was euthanized after a 24 h fasting period (ADF_f or URF_f). The second group fasted for 24 h followed by ad libitum refeeding for 24 h at the end of which they were euthanized (ADF_re or URF_re). The control for each fasting state is the re-feeding group. Each group has 3 replicates.

value: liver

tag: strain


title: 185_primary_GFAP_short_TalaSlide1Again_015

description: GFAP

value: primary


title: 356_primary_GFAP_short_TalaSlide1Again_007

description: GFAP


title: Biol rep 2, uninfected

description: Processed data column: 9

value: Bone marrow derived macrophage


title: Biol rep 2, infected + 4u8c

description: Processed data column: 14

value: H37Rv MOI 9 + 4u8c


title: atac, adf_f, 2


title: MCAO_12h_A

value: MCAO


title: MCAO_12h_SH_B

value: brain

value: Sham


title: 356_primary_CD64_short_TalaSlide1Again_008


title: atac, urf_re, 2


title: atac, urf_re, 3


title: Biol rep 1, infected + Ceapin-A7

description: Processed data column: 4


title: Biol rep 2, infected unhibited

description: Processed data column: 10

value: H37Rv MOI 9


title: 195_primary_GFAP_long_TalaSlide1Again_003

description: GFAP

value: long


title: atac, urf_f, 2


title: atac, adf_re, 2


title: atac, adf_re, 1


title: 195_primary_GFAP_long_TalaSlide1Again_002

description: GFAP


title: 356_primary_CD64_short_TalaSlide1Again_006


title: atac, adf_f, 1


title: atac, adf_f, 3


title: Biol rep 1, infected + 4u8c

description: Processed data column: 6


title: rna, adf_f, 3


title: 195_recurrent_GFAP_long_TalaSlide1Again_005

description: GFAP

value: recurrent


title: 195_recurrent_CD64_long_TalaSlide1Again_004

value: GBM


title: atac, urf_f, 3


title: Biol rep 1, infected + GSK2606414

description: Processed data column: 5


title: rna, adf_re, 2


title: atac, urf_f, 1


title: HSK, scRNAseq

city: Tianjin

first: yandong

last: pei

address: 94 Weijin Rd.,

institute: Nankai University

description: GEXSCOPE

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (version 1.9.0) (https://github.com/singleron-RD/CeleScope) pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt (version 1.17) to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR (version 2.6.1a) to map reads to the reference genome GRCm38 (ensemble version 92 annotation). UMI counts and gene counts of each cell were acquired with featureCounts (version 2.0.1) software, and used to generate expression matrix files for subsequent analysis.
The UMI counts matrices of four HSK, HSW, NK and NW samples were merged for downstream analysis. Pre-processing, quality control and normalization were performed using Scanpy. We removed the cells that had greater than 10% expression originating from mitochondrial genes as well as expressed less than 200 genes or greater than 6,000 genes to filter out low-quality cells and doublets. We also filtered genes that expressed in less than 3 cells. After quality control, we got 25947 cells and 25144 genes in total. Then the filtered UMI counts were normalized by scanpy.pp.normalize_total function with default parameters and log-transformed by scanpy.pp.log1p function. Top 2000 highly variable genes were identified using scanpy.pp.highly_variable_genes function.
Clustering was performed using a deep learning-based clustering method DESC. DESC first pretrained an autoencoder and initialized the clustering using Louvain, then iteratively fine-tuned the encoder and cluster layer to produce the final cluster assignment in a self-supervised manner. We used two hidden layers in the encoder, and 2000 highly variable genes as the input of DESC, yielded 11 clusters. The cell types were identified based on the expression of well-known marker genes.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
The fresh lung tissues were stored in the sCelLiveTM Tissue Preservation Solution (Singleron) on ice after the surgery within 30 mins. The specimens were washed with Hanks Balanced Salt Solution (HBSS) for three times, minced into small pieces, and then digested with 3 mL sCelLiveTM Tissue Dissociation Solution (Singleron) by Singleron PythoN™ Tissue Dissociation System at 37 °C for 15 minutes. The cell suspension was collected and filtered through a 40-micron sterile strainer. Afterwards, the GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron) was added, and the mixture [Cell: RCLB = 1:2 (volume ratio)] was incubated at room temperature for 5-8 minutes to remove red blood cells. The mixture was then centrifuged at 300 × g 4°C for 5 minutes to remove supernatant and suspended softly with PBS. For each experimental group, cells from 5 mice were pooled into one sample for single cell capture and cDNA library construction.
Single-cell suspensions (2×10^5 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron)13. Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: lung

value: HySu-FUNDC1-KO (HSK)

tag: age

value: 11 weeks old


title: atac, urf_re, 1


title: rna, urf_re, 3


title: rna, adf_re, 3


title: Copntrol_2

source_name: control

value: control

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: 182_recurrent_GFAP_short_Tala_025

description: GFAP

value: short


title: Biol rep 1, uninfected

description: Processed data column: 1

value: Bone marrow derived

value: Primary cell


title: rna, adf_re, 1

value: liver


title: rna, urf_f, 3


title: 195_primary_GFAP_long_TalaSlide1Again_001

description: GFAP

value: primary


title: rna, adf_f, 2


title: rna, adf_f, 1


title: PAECs,EC-KO3

data_processing:
STAR (version 2.7.10b) was used to align reads to the reference genome
Expression counts quantification was performed using featureCounts (v2.0.3)
Assembly: mm10
Supplementary files format and content: Tab-delimited text files includes raw counts for all sample

source_name: primary endothelial cells

growth_protocol: Primary endothelial cells were maintained in ECM supplemented with 10% fetal bovine serum (FBS) , ECGS, and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
The mRNA was purified from 1ug total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Primary endothelial cells were isolated from mouse lungs by the magnet-beads method as described above. Dead cells were excluded by the Dead Cell Removal kit.
Total RNA was isolated and purified using the Transzol Up Plus RNA kit (TransGen Biotech, ER501) following the manufacturer's procedure.

value: primary endothelial cells


title: HSW, scRNAseq

description: GEXSCOPE

value: HySu-WT (HSW)


title: NK, scRNAseq

description: GEXSCOPE

value: Normoxia-FUNDC1-KO (NK)


title: rna, urf_re, 1


title: rna, urf_re, 2


title: PAECs,EC-KO2


title: NW, scRNAseq

description: GEXSCOPE

value: Normoxia-WT (NW)


title: Biol rep 1, infected unhibited

description: Processed data column: 2

value: Bone marrow derived macrophage

value: H37Rv MOI 9


title: PAECs,EC-KO1


title: rna, urf_f, 2


title: 599_recurrent_GFAP_short_Tala_022

description: GFAP

value: GBM

value: recurrent


title: MCF7, NR4A1_KO, rep1

city: Fuzhou

first: Sunwang

last: Xu

address: Chazhong Road 20th

institute: The First Affiliated Hospital of Fujian Medical University

data_processing:
The clean reads were mapped to the human genome (GRCh38) using HISAT2. FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq-count. Differential expression analysis was performed using the DESeq (2012) R package.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Breast

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

value: Breast

value: Breast cancer cell


title: MCF7, NR4A1_KO, rep3


title: 608_primary_GFAP_long_Tala_024

description: GFAP

value: long


title: 10X_Genomic_RNA-seq of Homo sapeins: nonmalignant narsopharyngeal biopsy of patient N68

city: Beijing

first: ruoyan

last: Li

address: Yiheyuan street

institute: Peking University

description:
NPC_10X_barcodes.tsv
NPC_10X_cell-barcode-process.txt
NPC_10X_genes.tsv
NPC_10X_matrix.mtx

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hybrid reference  genome containing human (UCSC hg19) and EBV (NCBI NC_00705.1) reference sequence using Bowtie 2 with default parameters.
Reads mapped to human reference were used to quantify gene expression levels of host genes. We initially used RSEM to calculate the TPM value of each gene and then transformed TPM into log2(TPM+1).
We defined genes with TPM>1 as expressed genes and filtered cells with expressed gene < 2000. Meanwhile, we calculated a house keeping gene score (HKGS) for each cell based on previously defined gene list and filtered cells with HKGS <3.5.For the remining cells, we calculated the aggregate expression Ea of each gene where Ea=log2(average(TMP1...k)+1) and excluded genes with Ea <4. Finally, we calculaed the relative expression value Er of each gene in the form of Eri,j=Ei,j-average[Ei,1...n].
Reads mapped to human reference were used to quantify gene expression levels of host genes. We initially used RSEM to calculate the TPM value of each gene and then transformed TPM into log2(TPM+1).
Reads mapped to EBV genome were retrieved to quantify gene expression levels of virus using Cufflinks. And we used gene coding sequence (CDS) regions to define transcripts of EBV genes in this study.
For 10X genomics, scRNA data generated from 10X Genomics platform was processed using CelllRanger (Version 2.1.0). Firstly,  "CellRanger mkfastq" was used to de-multiplexes raw base call (BCL) files into FASTQ files. Second, "CellRanger count" was used to perform alignment and quantify  gene expression level of single cells through barcode recognizing and UMI counting. For merging cells from different tumors, we used "CellRanger aggr" pipeline and normalized by equalizing the read depth of different libraries. The output was converted to a Seurat object using R Seurat package (version 2.1.0) for further analyses.
For bulk RNA-seq samples, 18 NPC tissues were obtained. Total RNA were isolated by the commercial RNA/DNA extracted kit (Omega,USA) , the cDNA library preparation and sequencing  as reported previously (Lijuan Hu, 2016, Front. Med.). Combining with reported data (Lijuan Hu, 2016, Front. Med.; Li zhang, Mol. Cancer Res.,2018), in total, 140 cases RNA-seq data were for downstream processing. Firstly, paired-end reads from the 140 bulk RNA-seq data were mapped to he human-EBV hybrid genome using TopHat (version 2.1.1) with default parameters. Cufflinks (version 2.2.1) tool suite was then used to quantify gene expression levels. Briefly, we applied Cuffquant to the BAM file of each sample to calculate gene and transcript expression. Then, the results of all the samples were combined and normalized using Cuffnorm, generating the final expression matrix. This expression matrix was used for further analyses.
We adopted a previous reported sliding-average stragy (Itay etc. 2016, Science) to normalize specific gene expression patterns and infer CNVs.
To infer CNV based on low-pass whole genome sequencing,  paired end reads from low-pass whole sequencing was mapped to hg19 (UCSC) using BWA with default parameters. We removed PCR duplicates using "Samtools rmdup" followed by calculating the coverage depth at each covered base using "Samtools depth". We segmentaed the genome into small windows with 0.5Mb in size and calculated total depth in each window. The total depth of each window was further normalized by the sequencing data volume. Using the Loess normalization, we corrected bias from genomic GC content and calculated depth ratios across he whole genome of tumor samples using total depth of white blood cell samples as controls. Circular binary segmentation (CBS) algorithm documented in R DNA Copy package was used to merge windows with similar depth ratios into genomic segments. The adjacent segments were further joined using MergeLevels.
Genome_build: hg19,NC_007605.1
Supplementary_files_format_and_content: Sparse matrices file includes gene expression matrixs for  single cell host and virus of 22 samples with 10x Genomics Chemistry:NPC_10X_matrix.mtx
Supplementary_files_format_and_content: Tab -seqarated values (TSV) file includes barcode sequences correspond to column indices for 22 samples with 10x Genomics Chemistry:NPC_10X_barcodes.tsv
Supplementary_files_format_and_content: Tab -seqarated values (TSV) file includes gene names correspond to raw indices for 22 samples with 10x Genomics Chemistry:NPC_10X_genes.tsv
Supplementary_files_format_and_content: Tab-delimited text file includes each cell barcode processed corresponding to sample type and name:NPC_10X_cell-barcode-process.txt

source_name: Nonmalignant narsopharyngeal cells

extract_protocol:
Fresh tumors were transported in RPMI-1640 immediately on ice after resection. Rising the NPC biopsies with PBS(pH7.4), tumor tissues were minced into tiny cubes about 1-2mm3. Enzymatically dissociated the pieces of tissues into single-cell suspension. Then the cells were used for staining and FACS. The targeting (EpCAM-positive or negative) single cell was sorted into a  96-well plate for smart-seq2.  For the droplet-based scRNA-seq, EpCAM-positive/negative cells (with a ratio from 1:10 to 1:1) were enrichment in PCR tubes containing 5μL 1%FBS-PBS, which were then stored on ice. Before proceeding to the 10X Genomics GemCode platform, cell number and viability were measured using the Neubauer improved cell counter plate (WATSON).
The Smart-seq2 protocol was performed on single sorted cells as described (Picelli et al., 2014) with some modifications. In brief, full-length cDNA was synthesized through the template-switching reaction using the Superscript II reverse transcriptase (Invitrogen). cDNA was amplified using KAPA HiFi HotStartReadyMix. The cDNA libraries were barcoded and constructed using the TruePre DNA Library Prep Kit V2 kit. For 3’ droplet-based single-cell library construction, we loaded an expected number of cells into the chip to generate the Gel Beads-in-emulsion (GEMs). After post GEM-RT cleanup and cDNA amplification, 3’ droplet-based single-cell libraries were constructed according to the Single Cell 3’ Reagent Kit V2 User Guide.

value: Isolated single cell

value: nasopharynx

tag: tumor stage

tag: facs antibody


title: rna, urf_f, 1

tag: treatment


title: MCF7, Ctrl, rep3


title: 608_primary_CD64_long_Tala_024

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: MCF7, Ctrl, rep2


title: PAECs,FL2

tag: genotype


title: 599_primary_GFAP_short_Tala_023

description: GFAP

value: short


title: PAECs,FL3


title: 599_recurrent_CD64_short_Tala_022


title: 599_primary_CD64_short_Tala_023


title: 10X_Genomic_RNA-seq of Homo sapeins: nonmalignant narsopharyngeal biopsy of patient N61


title: PAECs,FL1


title: 10X_Genomic_RNA-seq of Homo sapeins: nonmalignant narsopharyngeal biopsy of patient N57


title: 10X_Genomic_RNA-seq of Homo sapeins: nonmalignant narsopharyngeal biopsy of patient N54


title: MCF7, Ctrl, rep1

tag: cell line


title: 10X_Genomic_RNA-seq of Homo sapeins: nonmalignant narsopharyngeal biopsy of patient N52


title: 10X_Genomic_RNA-seq of Homo sapeins:primar tumor of NPC patient 69

source_name: NPC cells

value: NPC-isolated single cell

value: T3N2M0 III


title: 291_primary_GFAP_long_Tala_021

description: GFAP

value: primary


title: 10X_Genomic_RNA-seq of Homo sapeins: nonmalignant narsopharyngeal biopsy of patient N53


title: 10X_Genomic_RNA-seq of Homo sapeins: nonmalignant narsopharyngeal biopsy of patient N55


title: MCF7, NR4A1_KO, rep2

tag: cell type


title: 94_recurrent_CD64_long_Tala_020

tag: primary recurrent


title: 10X_Genomic_RNA-seq of Homo sapeins:primar tumor of NPC patient 64

value: T2N1M0 II


title: 10X_Genomic_RNA-seq of Homo sapeins:primar tumor of NPC patient 63

value: T2N2M0 III


title: MLL4+/- Mouse Replicate3

city: Gwanak-gu

first: Chong-Su

last: Kim

state: --- Select One ---

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Dongduk Women's University

data_processing:
Preprocessing for raw reads was performed to remove low-quality reads and artifacts such as adapter sequences, contaminant DNA, and PCR duplicates.
Assembly: mm10
Supplementary files format and content: xlsx file that contains FPKM values for each sample

source_name: liver

extract_protocol:
All RNA from liver tissue was isolated using TRIzol (Thermo Fisher Scientific) and RNA samples were treated with DNase (Invitrogen) and then purified using RNeasy mini kit (Qiagen).
RNA-seq libraries were generated according to the TruSeq Stranded mRNA Sample Preparation Guide (Part # 15031047 Rev. E). RNA-seq libraries were validated by bioanalyzer and real-time RT-PCR.

value: liver


title: MLL4+/- Mouse Replicate1


title: MLL4+/- Mouse Replicate2


title: 94_primary_GFAP_long_Tala_019

description: GFAP

tag: relapse time


title: 10X_Genomic_RNA-seq of Homo sapeins:primar tumor of NPC patient 62


title: 94_primary_CD64_long_Tala_019

tag: patient id


title: 10X_Genomic_RNA-seq of Homo sapeins:primar tumor of NPC patient 66

value: T2N3M0 IVb


title: 10X_Genomic_RNA-seq of Homo sapeins:primar tumor of NPC patient 58

value: T3N0M0 III


title: 38_recurrent_GFAP_long_Tala_018

description: GFAP

value: GBM

tag: panel


title: 10X_Genomic_RNA-seq of Homo sapeins:primar tumor of NPC patient 59


title: WT Mouse Replicate3

value: WT


title: 10X_Genomic_RNA-seq of Homo sapeins:primar tumor of NPC patient 51

value: T3N3M0 Ivb


title: WT Mouse Replicate4


title: 94_recurrent_GFAP_long_Tala_020

description: GFAP

value: recurrent

tag: folder name


title: WT Mouse Replicate2


title: 10X_Genomic_RNA-seq of Homo sapeins:primar tumor of NPC patient 50

value: T2N0M0 II


title: WT Mouse Replicate1


title: 38_recurrent_CD64_long_Tala_018

value: long

tag: ref id


title: 10X_Genomic_RNA-seq of Homo sapeins:primar tumor of NPC patient 65

value: nasopharynx

value: T1N3M0 IVb


title: 38_primary_GFAP_long_Tala_017

description: GFAP

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: 10X_Genomic_RNA-seq of Homo sapeins:primar tumor of NPC patient 60

value: NPC-isolated single cell

value: T3N3M0 IVb


title: 10X_Genomic_RNA-seq of Homo sapiens:primar tumor of NPC patient 46

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hybrid reference  genome containing human (UCSC hg19) and EBV (NCBI NC_00705.1) reference sequence using Bowtie 2 with default parameters.
Reads mapped to human reference were used to quantify gene expression levels of host genes. We initially used RSEM to calculate the TPM value of each gene and then transformed TPM into log2(TPM+1).
We defined genes with TPM>1 as expressed genes and filtered cells with expressed gene < 2000. Meanwhile, we calculated a house keeping gene score (HKGS) for each cell based on previously defined gene list and filtered cells with HKGS <3.5.For the remining cells, we calculated the aggregate expression Ea of each gene where Ea=log2(average(TMP1...k)+1) and excluded genes with Ea <4. Finally, we calculaed the relative expression value Er of each gene in the form of Eri,j=Ei,j-average[Ei,1...n].
Reads mapped to human reference were used to quantify gene expression levels of host genes. We initially used RSEM to calculate the TPM value of each gene and then transformed TPM into log2(TPM+1).
Reads mapped to EBV genome were retrieved to quantify gene expression levels of virus using Cufflinks. And we used gene coding sequence (CDS) regions to define transcripts of EBV genes in this study.
For 10X genomics, scRNA data generated from 10X Genomics platform was processed using CelllRanger (Version 2.1.0). Firstly,  "CellRanger mkfastq" was used to de-multiplexes raw base call (BCL) files into FASTQ files. Second, "CellRanger count" was used to perform alignment and quantify  gene expression level of single cells through barcode recognizing and UMI counting. For merging cells from different tumors, we used "CellRanger aggr" pipeline and normalized by equalizing the read depth of different libraries. The output was converted to a Seurat object using R Seurat package (version 2.1.0) for further analyses.
For bulk RNA-seq samples, 18 NPC tissues were obtained. Total RNA were isolated by the commercial RNA/DNA extracted kit (Omega,USA) , the cDNA library preparation and sequencing  as reported previously (Lijuan Hu, 2016, Front. Med.). Combining with reported data (Lijuan Hu, 2016, Front. Med.; Li zhang, Mol. Cancer Res.,2018), in total, 141 cases RNA-seq data were for downstream processing. Firstly, paired-end reads from the 141 bulk RNA-seq data were mapped to he human-EBV hybrid genome using TopHat (version 2.1.1) with default parameters. Cufflinks (version 2.2.1) tool suite was then used to quantify gene expression levels [].Briefly, we applied Cuffquant to the BAM file of each sample to calculate gene and transcript expression. Then, the results of all the samples were combined and normalized using Cuffnorm, generating the final expression matrix. This expression matrix was used for further analyses.
We adopted a previous reported sliding-average stragy (Itay etc. 2016, Science) to normalize specific gene expression patterns and infer CNVs.
To infer CNV based on low-pass whole genome sequencing,  paired end reads from low-pass whole sequencing was mapped to hg19 (UCSC) using BWA with default parameters. We removed PCR duplicates using "Samtools rmdup" followed by calculating the coverage depth at each covered base using "Samtools depth". We segmentaed the genome into small windows with 0.5Mb in size and calculated total depth in each window. The total depth of each window was further normalized by the sequencing data volume. Using the Loess normalization, we corrected bias from genomic GC content and calculated depth ratios across he whole genome of tumor samples using total depth of white blood cell samples as controls. Circular binary segmentation (CBS) algorithm documented in R DNA Copy package was used to merge windows with similar depth ratios into genomic segments. The adjacent segments were further joined using MergeLevels.
Genome_build: hg19,NC_007605.1
Supplementary_files_format_and_content: tab-delimited text files include TPM values for host genes of NPC16,NPC17 and NPC36 with full-length method Smart-seq2:NPC16-17-36.list.matrix
Supplementary_files_format_and_content: tab-delimited text files include TPM values for viru genes NPC16,NPC17 and NPC36 with full-length method Smart-seq2:NPC16-17-36.EBV.list.matrix
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  single cell host and virus of NPC33 with 10x Genomics Chemistry:NPC33-10X-matrix.txt
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  single cell host and virus of NPC36 with 10x Genomics Chemistry:NPC36-10X-matrix.txt
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  single cell host and virus of NPC46 with 10x Genomics Chemistry:NPC46-10X-matrix.txt
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  single cell host and virus of NPC47 with 10x Genomics Chemistry:NPC47-10X-matrix.txt
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  single cell host and virus of NPC49 with 10x Genomics Chemistry:NPC49-10X-matrix.txt
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  all the NPC cases of bulk RNA-seq including 18 new patients:Bulk_RNA-seq_genes.fpkm_table.txt

extract_protocol:
Fresh tumors were transported in RPMI-1640 immediately on ice after resection. Rising the NPC biopsies with PBS(pH7.4), tumor tissues were minced into tiny cubes about 1-2mm3. Enzymatically dissociated the pieces of tissues into single-cell suspension. Then the cells were used for staining and FACS. The targeting single cell was sorted into a  96-well plate which containing lysis buffer including oligo dT30 primer, dNTP mix, 0.1% Triton-100 and RNase inhibitor.
The full-length cDNA is synthesized through the template-switching oligo and SS II reverse transcriptase (Invitrogen). cDNA is amplified using KAPA HiFi HotStartReadyMix (KAPA Biosysytems). Full length cDNA libraries were barcoded using the TruePreTM DNA Library Prep Kit V2 protocol (Vazyme Biotech Co.). For 10x gemomic experiments, we followed the 10X genomics chemistry.

value: T3N2M0 III


title: 10X_Genomic_RNA-seq of Homo sapiens:primar tumor of NPC patient 36


title: 10X_Genomic_RNA-seq of Homo sapiens:primar tumor of NPC patient 47

value: T4N3M1 IVc


title: 10X_Genomic_RNA-seq of Homo sapiens:primar tumor of NPC patient 49


title: NRAS/AKT Tumor, Isotype, scRNA-seq

first: Nickolas

last: Teo

address: 1/F, Laboratory Block, 21 Sassoon Road

department: SBMS

institute: HKU

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were perfomed using Cell Ranger v6.0.0
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: HCC tumor

extract_protocol:
2g of tumor tissue were extracted from cancerous livers, cut into small pieces, and dissociated into cell suspensions using gentleMACS Dissociator (Miltenyi Biotec) in dissociation buffer containing 0.5mg/ml of Collagenase IV (Gibco) and 100μg/ml of DNase I (Goldbio) at 37℃. Single cell suspensions were collected after filtering through a 70μm cell strainer, and stained with fluorescent conjugated antibodies specific to CD45 (clone 30-F11, Biolegend) and TER-119 (Biolegend) for 20 min at 4°C. Live, single, tumour (CD45-TER119-) cells were then sort-purified with BD Influx into FBS-containing tubes, and were kept on ice until the cells were further processed for scRNAseq.
Single cell encapsulation and cDNA libraries were prepared with Chromium Next GEM Single Cell 5’ Reagent Kit v2 (Dual Index) and Chromium Next GEM Chip K Single Cell Kit, following manufacturer's instructions

treatment_protocol: NRAS/AKT-driven HCC was induced in B6 mice via HTVI. Mice were culled at 4 weeks after tumor induction for profiling of tumor cells

value: HCC tumor

value: Tumor


title: NRAS/AKT Tumor, anti-Ly6G, scRNA-seq

description: 10x Genomics


title: 38_primary_CD64_long_Tala_017

value: primary


title: Single_cell_RNA-seq(Smart-seq2) of Homo sapiens: lympho node metastatic tumor of NPC patient 17

description:
NPC16-17-36.EBV.list.matrix
NPC16-17-36.list.matrix

value: head neck lymph node

value: T3N3M1 IVc


title: BM neutrophil with GM-CSF,  LA, and 10058-F4

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore.
Trimed reads were mapped to UCSC mouse genome mm10 using STAR
Gene counts were quantified by featureCounts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: Neutrophil

extract_protocol:
High-quality total RNA was extracted using RNeasy Mini Kit (Qiagen)
PolyA enrichment RNA-seq

treatment_protocol: Neutrophils purified from bone marrow were cultured in complete RPMI (RPMI 1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin) with or without the addition of GM-CSF, linoleic acid, or 10058-F4.

value: Neutrophil


title: 182_recurrent_CD64_short_Tala_025

value: GBM

value: short


title: Single_cell_RNA-seq(Smart-seq2) of Homo sapiens: lympho node metastatic tumor of NPC patient 16


title: 10X_Genomic_RNA-seq of Homo sapiens:primar tumor of NPC patient 33

value: T3N2M1 IVc


title: 417_recurrent_CD64_short_Tala_015

value: recurrent


title: Single_cell_RNA-seq(Smart-seq2) of Homo sapiens: lympho node metastatic tumor of NPC patient 36

value: T2N3M0 IVb


title: 417_recurrent_GFAP_short_Tala_016

description: GFAP


title: BM neutrophil with GM-CSF and LA

value: GM-CSF + LA


title: Single_cell_RNA-seq(Smart-seq2) of Homo sapiens: primary tumor of NPC patient 17

value: nasopharynx


title: 417_primary_GFAP_short_Tala_014

description: GFAP

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: BM neutrophil with GM-CSF

value: GM-CSF


title: BM neutrophil with LA

value: Linoleic acid


title: Single_cell_RNA-seq(Smart-seq2) of Homo sapiens: primary tumor of NPC patient 36

value: NPC-isolated single cell


title: Single_cell_RNA-seq(Smart-seq2) of Homo sapiens: primary tumor of NPC patient 16

value: T4N3M1 IVc


title: Basal cells from normal donor 5

city: Duarte

first: Crystal

middle: N

last: Marconett

email: cmarcone@usc.edu, cmarconett@coh.org

state: CA

address: 1500 E Duarte Rd

department: Integrative Translational Sciences

institute: City of Hope

data_processing:
Raw FASTQ files underwent quality control analysis using FASTQC. Adapter sequences were then trimmed from raw FASTQ reads using AdapterTrimmer. Reads were then filtered to remove those of low quality. Retained reads had a quality score of >30 per base for at least 90% of the read.
Reads were then aligned to the Hg38 genome with STAR aligner (PMC3530905) using the Ensembl v110 (July 2023 release) transcriptome build.
Counts per gene per sample were then used for calculating differential expression analysis in DeSeq2 (PMID: 25516281) in R
Preprocessing of raw ATACseq data to generate clean read files was performed as was done for the RNA samples. Cleaned ATACseq reads were aligned to the hg38 genome using bwa aligner (PMID: 19451168).
Peak enrichment was subsequently calculated using the GenRich peak caller (Gaspar, John M. "Genrich: detecting sites of genomic enrichment."GitHub repository. GitHub(2018)) using the intrinsic background of the sample. Peaks were then annotated to nearest-neighbor genes using the annotatepeaks.pl function in HOMER (PMID: 20513432), which also binned peaks into categories relative to the genomic structures they occurred in (eg; promoter, enhancer, etc).
Assembly: Hg38
Supplementary files format and content: Bulk RNAseq table of counts in .CSV format
Supplementary files format and content: GenRich narrowpeak genomic files

source_name: Lung Basal cells

growth_protocol: Remnant human transplant lungs were obtained in compliance with Institutional Review Board-approved protocols for the use of human source material in research (HS-07-00660) and processed within 3 days of death

extract_protocol:
Lung parenchyma was macrodissected to a depth of > 2mm in order to isolate alveolar tissue. The visceral pleura was removed using forceps, and alveolar tissue was then minced to fine pieces with scissors. Tissue was then washed in 50:50 DMEM/F12 media, which is a 50:50 mixture of DME-F12 (#D64421, Sigma) and DMEM High Glucose (#21063, GIBCO) supplemented with 1% penicillin/streptomycin (), 0.1% Gentamycin (#G1272, Sigma), and 1% Fungizone (A2411, Sigma). Following overnight incubation, the tissue was again minced briefly using a razor blade and resuspended in HBSS media without Ca2+ or Mg2+ supplemented with 13U/mL of elastase (#LS002280, Worthington) for 30min at 37C. Cells were filtered through a gauze mesh and then through a 100um filter, then pelleted and resuspended in 50:50 DMEM/F12 media and applied to a Percoll density gradient centrifugation, followed by IgG panning (#I4506, Sigma). Magnetic-activated sorting with Epcam+ beads (Miltenyi Biotec #130-061-101) and FcR blocking (Biotec #130-059-901) was then performed, followed by separation using LS columns (Miltenyi Biotec #130-042-401). Following separation, Cells were counted using trypan blue to measure viability. After counting, cells were fixed in 4% paraformaldehyde (PFA) for 10 minutes, washed with Phosphate Buffered Saline (1xPBS), resuspended in PBS for each cytospin. Cytospins were prepared using EZ single cytofunnels (#1439045, Thermo Fisher Scientific) and a Shandon CytoSpin III cytocentrifuge (GMI, Ramsey, Minnesota). Cytospin slides were stored at -20°C until use.
For RNA, 6 million AT2 or basal cells were frozen into a pellet and stored at -80C. RNA was extracted using the Aurum Total RNA Mini kit (# 7326820, BioRad, Hercules CA) according to manufacturer guidelines. 2 ug of total RNA then underwent bulk RNA library preparation with PolyA selection performed by Genewiz (now Azenta, Burlington MA). Samples were barcoded using Illumina adapters to allow for multiplexed sequencing. For ATAC, between 5-50 K of freshly isolated AT2 cells were placed in 0.1 to 0.25 mL of ATAC lysis buffer (AM1) and immediately processed for ATAC library generation using the Active Motif ATACseq kit (#53150, Carlsbad CA) according to manufacturer guidelines. Nextera i7 dual indexing primers were used for library construction as listed in Table 1. Integration of indexing primers was performed with the Tn5 enzymes listed in Table 1. The Benchmark Scientific H5000-H MultiTherm shaker was used to ensure uniformity in library construction. The Agilent 4200 Tape Station system was used for assessment of ATAC fragment quality throughout library construction
Bulk RNA paired end sequencing and bulk AT2 ATAC paired end sequencing was performed at Genewiz, using an Illumina HiSeq at 2x150 bp. RNAseq was performed using single index chemistry, whereas ATACseq was performed using dual-index chemistry.

value: Lung Basal cells

tag: disease state

value: Normal

value: Basal


title: 417_primary_CD64_short_Tala_013

value: primary


title: 417_primary_CD64_short_Tala_012


title: BM neutrophil only

value: Neutrophil

value: Complete media


title: Alveolar Epithelial Type 2 cells from normal donor 2, ATAC-seq

source_name: Lung AT2 cells

extract_protocol:
Lung parenchyma was macrodissected to a depth of > 2mm in order to isolate alveolar tissue. The visceral pleura was removed using forceps, and alveolar tissue was then minced to fine pieces with scissors. Tissue was then washed in 50:50 DMEM/F12 media, which is a 50:50 mixture of DME-F12 (#D64421, Sigma) and DMEM High Glucose (#21063, GIBCO) supplemented with 1% penicillin/streptomycin (), 0.1% Gentamycin (#G1272, Sigma), and 1% Fungizone (A2411, Sigma). Following overnight incubation, the tissue was again minced briefly using a razor blade and resuspended in HBSS media without Ca2+ or Mg2+ supplemented with 13U/mL of elastase (#LS002280, Worthington) for 30min at 37C. Cells were filtered through a gauze mesh and then through a 100um filter, then pelleted and resuspended in 50:50 DMEM/F12 media and applied to a Percoll density gradient centrifugation, followed by IgG panning (#I4506, Sigma). Magnetic-activated sorting with Epcam+ beads (Miltenyi Biotec #130-061-101) and FcR blocking (Biotec #130-059-901) was then performed, followed by separation using LS columns (Miltenyi Biotec #130-042-401). Following separation, Cells were counted using trypan blue to measure viability. After counting, cells were fixed in 4% paraformaldehyde (PFA) for 10 minutes, washed with Phosphate Buffered Saline (1xPBS), resuspended in PBS for each cytospin. Cytospins were prepared using EZ single cytofunnels (#1439045, Thermo Fisher Scientific) and a Shandon CytoSpin III cytocentrifuge (GMI, Ramsey, Minnesota). Cytospin slides were stored at -20°C until use.
For RNA, 6 million AT2 cells were frozen into a pellet and stored at -80C. RNA was extracted using the Aurum Total RNA Mini kit (# 7326820, BioRad, Hercules CA) according to manufacturer guidelines. 2 ug of total RNA then underwent bulk RNA library preparation with PolyA selection performed by Genewiz (now Azenta, Burlington MA). Samples were barcoded using Illumina adapters to allow for multiplexed sequencing. For ATAC, between 5-50 K of freshly isolated AT2 cells were placed in 0.1 to 0.25 mL of ATAC lysis buffer (AM1) and immediately processed for ATAC library generation using the Active Motif ATACseq kit (#53150, Carlsbad CA) according to manufacturer guidelines. Nextera i7 dual indexing primers were used for library construction as listed in Table 1. Integration of indexing primers was performed with the Tn5 enzymes listed in Table 1. The Benchmark Scientific H5000-H MultiTherm shaker was used to ensure uniformity in library construction. The Agilent 4200 Tape Station system was used for assessment of ATAC fragment quality throughout library construction
Bulk RNA paired end sequencing and bulk AT2 ATAC paired end sequencing was performed at Genewiz, using an Illumina HiSeq at 2x150 bp. RNAseq was performed using single index chemistry, whereas ATACseq was performed using dual-index chemistry.

value: Lung AT2 cells


title: Alveolar Epithelial Type 2 cells from normal donor 3, ATAC-seq


title: 185_recurrent_GFAP_short_Tala_011

description: GFAP

value: GBM

value: short


title: Alveolar Epithelial Type 2 cells from normal donor 1, ATAC-seq


title: 7d

city: Shanghai

first: Heng

last: Chen

address: 639 Zhizaoju Road

institute: Shanghai Jiao Tong University

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria: Ø MT% < 30%;  Ø Cell Gene Number < Median Gene Number * 2; Ø Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mm10
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Jaw

extract_protocol:
Each sample was placed in a sterile Petri dish on ice. Fat, fibrous and necrotic areas were removed, and the tissue was subsequently minced to smaller pieces of less than 3 mm. Samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase Ⅱ (Worthington) for 60 min at 37°C, with agitation. Subsequently, the sample was filtered using a 70-mm nylon mesh (Miltenyi #130-095-823). 10 ml of this cell suspension was counted by Trypan Blue to determine the concentration of live cells. The sample was then centrifuged at 300g and 4℃ for 5 min, and the supernatant was discarded. The cell pellet was resuspended in 1 ml freezing media (Gibco) for long term cryopreservation in liquid nitrogen. Throughout the dissociation procedure, cells were maintained on ice whenever possible, and the entire procedure was completed in less than 1 hr.
Cryopreserved single-cell suspensions were promptly thawed and prepared as outlined by the 10x Genomics Single Cell 3 v3.1 Reagent Kit user guide.

value: Jaw

value: wild-type

value: Irradiation


title: 185_recurrent_GFAP_short_Tala_010

description: GFAP

source_name: GBM

value: recurrent

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: Alveolar Epithelial Type 2 cells from IPF donor 1, ATAC-seq

value: IPF


title: 1d


title: Alveolar Epithelial Type 2 cells from IPF donor 2, ATAC-seq


title: Alveolar Epithelial Type 2 cells from normal donor 3, RNA-seq

description:
NORMAL_AT2_rep3
AT2_IPF_v_NORMAL_bulkRNAseq_tableofcounts_FINAL-1.csv


title: Ctrl


title: Alveolar Epithelial Type 2 cells from normal donor 1, RNA-seq

description:
NORMAL_AT2_rep1
AT2_IPF_v_NORMAL_bulkRNAseq_tableofcounts_FINAL-1.csv


title: Basal cells from normal donor 4


title: 185_primary_CD64_short_Tala_009


title: 182_primary_GFAP_short_Tala_008

description: GFAP


title: Alveolar Epithelial Type 2 cells from IPF donor 2, RNA-seq

description:
IPF.AT2.rep2
AT2_IPF_v_NORMAL_bulkRNAseq_tableofcounts_FINAL-1.csv


title: vdj

city: Newark

first: Arthur

middle: James

last: VanValkenburg

state: NJ

address: 185 S Orange Ave

institute: Rutgers New Jersey Medical School

description: 10x Genomics

data_processing:
Germinal center (GC) B cells were sorted from the spleens of 3 B6.SLE1.yaa mice for each timepoint of 2 months (pre-disease), 4 months (disease onset), and 6 months (disease onset).
6000 GC B cells from each mouse were barcoded with hashtag antibodies, pooled, processed through the 10X RNA/V(D)J kit, and sequenced with the 10x Genomics Noavaseq 6000.
Data was aligned to mm10 reference genome with cellranger ver.XXX.
Output scRNA-seq FASTQ files were processed using Immcantations pipelines from Kleinstein Lab pREST0 and Change-O for BCR alignment and V(D)J alignment respectively.
Seurat (v.5.0.1) was used to analyze gene expression data to determine differences in GC B cell gene expression, V(D)J sequences, and BCR repertoire at different stages of the onset of lupus
Assembly: mm10
Supplementary files format and content: tab separated, comma separated, and matrix files

source_name: Germinal Center B cells

extract_protocol:
3 B6.SLE1.yaa mice at 2 months of age (pre-disease), 4 months of age (disease onset), and 6 months of age (disease onset) were sacrificed. Each mouse was barcoded using hashtag antibodies[cat#?]. 40,000 GC B cells were sorted from each mouse using the NJMS Flow Core FACS Aria. 6,000 cells from each sample were pooled and processed through the 10X RNA/V(D)J kit and sequenced Novaseq 6000; Illumina
library was construtcted according to the manufacturer's recommendations.

value: Germinal Center B cells


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_66

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hybrid reference  genome containing human (UCSC hg19) and EBV (NCBI NC_00705.1) reference sequence using Bowtie 2 with default parameters.
Reads mapped to human reference were used to quantify gene expression levels of host genes. We initially used RSEM to calculate the TPM value of each gene and then transformed TPM into log2(TPM+1).
We defined genes with TPM>1 as expressed genes and filtered cells with expressed gene < 2000. Meanwhile, we calculated a house keeping gene score (HKGS) for each cell based on previously defined gene list and filtered cells with HKGS <3.5.For the remining cells, we calculated the aggregate expression Ea of each gene where Ea=log2(average(TMP1...k)+1) and excluded genes with Ea <4. Finally, we calculaed the relative expression value Er of each gene in the form of Eri,j=Ei,j-average[Ei,1...n].
Reads mapped to human reference were used to quantify gene expression levels of host genes. We initially used RSEM to calculate the TPM value of each gene and then transformed TPM into log2(TPM+1).
Reads mapped to EBV genome were retrieved to quantify gene expression levels of virus using Cufflinks. And we used gene coding sequence (CDS) regions to define transcripts of EBV genes in this study.
For 10X genomics, scRNA data generated from 10X Genomics platform was processed using CelllRanger (Version 2.1.0). Firstly,  "CellRanger mkfastq" was used to de-multiplexes raw base call (BCL) files into FASTQ files. Second, "CellRanger count" was used to perform alignment and quantify  gene expression level of single cells through barcode recognizing and UMI counting. For merging cells from different tumors, we used "CellRanger aggr" pipeline and normalized by equalizing the read depth of different libraries. The output was converted to a Seurat object using R Seurat package (version 2.1.0) for further analyses.
For bulk RNA-seq samples, 18 NPC tissues were obtained. Total RNA were isolated by the commercial RNA/DNA extracted kit (Omega,USA) , the cDNA library preparation and sequencing  as reported previously (Lijuan Hu, 2016, Front. Med.). Combining with reported data (Lijuan Hu, 2016, Front. Med.; Li zhang, Mol. Cancer Res.,2018), in total, 140 cases RNA-seq data were for downstream processing. Firstly, paired-end reads from the 140 bulk RNA-seq data were mapped to he human-EBV hybrid genome using TopHat (version 2.1.1) with default parameters. Cufflinks (version 2.2.1) tool suite was then used to quantify gene expression levels. Briefly, we applied Cuffquant to the BAM file of each sample to calculate gene and transcript expression. Then, the results of all the samples were combined and normalized using Cuffnorm, generating the final expression matrix. This expression matrix was used for further analyses.
We adopted a previous reported sliding-average stragy (Itay etc. 2016, Science) to normalize specific gene expression patterns and infer CNVs.
To infer CNV based on low-pass whole genome sequencing,  paired end reads from low-pass whole sequencing was mapped to hg19 (UCSC) using BWA with default parameters. We removed PCR duplicates using "Samtools rmdup" followed by calculating the coverage depth at each covered base using "Samtools depth". We segmentaed the genome into small windows with 0.5Mb in size and calculated total depth in each window. The total depth of each window was further normalized by the sequencing data volume. Using the Loess normalization, we corrected bias from genomic GC content and calculated depth ratios across he whole genome of tumor samples using total depth of white blood cell samples as controls. Circular binary segmentation (CBS) algorithm documented in R DNA Copy package was used to merge windows with similar depth ratios into genomic segments. The adjacent segments were further joined using MergeLevels.
Genome_build: hg19,NC_007605.1
Supplementary_files_format_and_content: tab-delimited text files include TPM values for host genes of NPC16,NPC17 and NPC36 with full-length method Smart-seq2:NPC16-17-36.list.matrix
Supplementary_files_format_and_content: tab-delimited text files include TPM values for viru genes NPC16,NPC17 and NPC36 with full-length method Smart-seq2:NPC16-17-36.EBV.list.matrix
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  single cell host and virus of NPC33 with 10x Genomics Chemistry:NPC33-10X-matrix.txt
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  single cell host and virus of NPC36 with 10x Genomics Chemistry:NPC36-10X-matrix.txt
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  single cell host and virus of NPC46 with 10x Genomics Chemistry:NPC46-10X-matrix.txt
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  single cell host and virus of NPC47 with 10x Genomics Chemistry:NPC47-10X-matrix.txt
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  single cell host and virus of NPC49 with 10x Genomics Chemistry:NPC49-10X-matrix.txt
Supplementary_files_format_and_content: tab-delimited text files include TPM values for  all the NPC cases of bulk RNA-seq including 18 new patients:Bulk_RNA-seq_genes.fpkm_table.txt

source_name: NPC tissue

value: NPC primary tumor

value: nasopharynx


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_64


title: Alveolar Epithelial Type 2 cells from IPF donor 1, RNA-seq

description:
IPF.AT2.rep1
AT2_IPF_v_NORMAL_bulkRNAseq_tableofcounts_FINAL-1.csv


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_62


title: 282_primary_GFAP_long_Tala_006

description: GFAP

data_processing:
GeoMx DSP data were evaluated and prepared for downstream analysis following the GeoMx-NGS gene expression analysis workflow until the filtering step. Segments with less than 4% of the genes detected were removed and the cut-off for gene detection was set at 2%. Reads from duplicated samples were summed using the aggregateAcrossCells function from the scuttle package. One outlier sample was excluded (DSP-1001660005533-A-C08). The package limma was used to perform between-samples cyclic loess normalization
Assembly: GeoMx NGS bioinformatic processing Pipeline. In the first step, the raw reads (raw sequencing FASTQ files) are compiled with the configuration file, which specifies the processing parameters. Next, the raw reads are processed by computationally removing the adapter sequences (resulting in trimmed reads), and merging the overlapping paired-end reads (resulting in stitched reads). In the third step, the stitched reads are aligned to the RTS- ID barcodes in the reference assay, creating aligned reads and assigning raw counts to biological target names. Then, PCR duplicates are removed using the Unique Molecular Identifier in each read, resulting in deduplicated reads. The DCC files are created and presented as a .zip file in a folder which you designate and can then be uploaded into the DSP Control Center for study creation in the DSP Data Analysis Suite, or loaded into R for data processing with the GeomxTools open software package.
Supplementary files format and content: SpatialTranscriptomics_normalized_log2_cpm.xlsx: normalised log2 counts per million
Library strategy: Spatial Transcriptomics

extract_protocol:
Slide-mounted FFPE TMA was processed for antigen retrieval using a heat induced epitope retrieval protocol for 20 minutes followed by a 5-min wash with 1μg/mL proteinase K solution. TMA was next incubated overnight with GeoMx RNA detection probes containing-photocleavable oligos
Sequencing libraries were generated by PCR from the oligos and sequenced using Illumina NovaSeq according to the manufacturer’s protocol

value: long


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_60


title: Alveolar Epithelial Type 2 cells from normal donor 2, RNA-seq

description:
Normal.AT2rep2
AT2_IPF_v_NORMAL_bulkRNAseq_tableofcounts_FINAL-1.csv

value: Normal


title: Alveolar Epithelial Type 2 cells from IPF donor 3, ATAC-seq


title: Gene Expression

description: 10x Genomics


title: Aorta 9, high fat diet and iron-overload

city: Harbin

first: Xiang

last: Peng

address: Baojian Street

institute: The Second Affiliated Hospital of Harbin Medical University

data_processing:
CLC Genomic Workbench
HISAT2 software
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

source_name: Aorta

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNEXT Ultra TM RNA Library Prep Kit for Illumina.

value: Aorta

value: Apoe-/-

value: high fat diet and intraperitoneal injection of ammonium iron(III) citrate


title: 282_primary_CD64_long_Tala_006

value: primary


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_53


title: Aorta 8, high fat diet and iron-overload


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_52


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_54


title: Aorta 7, high fat diet and iron-overload


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_51


title: 185_recurrent_CD64_short_Tala_010

value: GBM


title: 356_primary_CD64_short_Tala_005

value: short


title: antibody capture

description: 10x Genomics


title: Aorta 6, high fat diet

value: high fat diet


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 737


title: HR-3-Input

city: nanjing

first: yongfei

last: li

address: No.155 Hanzhong Road

department: Department of Mastopathy

institute: The Affiliated Hospital of Nanjing University of Chinese Medicine (Jiangsu Province Hospital of TCM)

data_processing:
library strategy: meRIP-seq
Agilent 2100 Bioanalyzer was used to detect library quality
The library concentration was diluted to 8 pM and the hiseq300/4000 PE Cluster Kit (# pe-410-1001, Illumina) was used to generate clusters in Illumina cBot
Illumina HiSeq 4000 was used for sequencing
 statistic analysis; HISAT2
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: peaks_mRNA.xlsx

source_name: breast cancer cell

growth_protocol: The breast cancer cell line BT474 and BT474.TtzmR were cultured routinely in DMEM (Gibco-Invitrogen, Carlsbad, CA, USA), with 10% Fetal Bovine Serum (FBS), with Penicillin Streptomycin (Gibco) at 37C in an atmosphere of 5% CO2 in air.

extract_protocol:
Enrichment of RNA fragments containing m6A methylation sites by immunoprecipitation with anti-n6-methyadenosine (m 6A) antibodies
The sequencing libraries of post-m6a mRNA and input mRNA were constructed respectively with KAPA Stranded mrna-seq Kit

tag: cell line background

value: resistant cells


title: Aorta 5, high fat diet

tag: tissue


title: 195_recurrent_GFAP_long_Tala_004

description: GFAP


title: HS-3-Input

value: sensitive cells


title: 182_primary_CD64_short_Tala_007


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 664


title: 195_recurrent_CD64_long_Tala_003

value: recurrent


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient C_57


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 581


title: HS-3-IP

tag: antibody

value: anti-m6A antibody


title: Aorta 4, high fat diet


title: 195_primary_GFAP_long_Tala_002

description: GFAP

value: (v1.0) Human NGS Whole Transcriptome Atlas RNA


title: HR-3-IP


title: HS-2-Input


title: 356_primary_GFAP_short_Tala_005

description: GFAP


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 527

tag: age


title: 195_primary_CD64_long_Tala_001


title: Aorta 2, chow diet

value: chow diet


title: Aorta 3, chow diet


title: Aorta 1, chow diet


title: HR-2-Input


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 456

value: NPC primary tumor

tag: tumor stage


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 480

value: nasopharynx


title: HS-2-IP


title: CD8+ NRT cells, scTCR-seq analysis, tcr repertoire

city: Nanjing

first: Yuncheng

last: Bei

state: Jiangsu

address: Zhongshan Road No.321

department: Oncology

institute: Nanjing Drum Tower Hospital

data_processing:
Illumina NovaSeq 6000 reads were trimmed and clipped for quality control in Trimmomatic v0.27
read quality was checked for each sample using FastQC.
High-quality reads were then imported into TopHat v2.0.8 for alignment into BAM files.
BAM files were imported into the RNA-Seq pipeline of Partek Genomics Suite, version 6.6 (Copyright 2009, Partek Inc., St. Louis, MO, USA), and RPKM counts were calculated (RefSeq release 2013-5-10). Exclusions included a minimum RPKM value of 1.0 in at least two of the 16 samples (potentially duplicates of one sample group). RPKM values were log2-transformed with an offset value of 1.0.
Assembly: Genome_build: Alignment was initially to the transcriptome (hg19, GRCh37.72), and then to the genome (hg19, GRCh37).
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scTCR-seq

source_name: PBMC

growth_protocol: All cells were cultured in AIM-V medium with 10% human AB serum (Valley biomedical, Cat no. HP1022), 50 ng/ml OKT-3 (eBioscience, Cat no. 14-0037-82), 20 IU/ml rhIL-2 (Genscript, Cat no. Z00368-50), 12.5 ng/ml rhIL-7, and 12.5 ng/ml rhIL-15 (Genscript, Cat no. Z00377-50). All cells were incubated at 37oC in 5% CO2.

extract_protocol:
A pool of ~750,000 barcodes are sampled separately to index each cell’s transcriptome. It is done by partitioning cell harvested after neoantigen-specific stimulation into nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated cDNAs share a common 10x Barcode. GEMs are generated by combining barcoded Single Cell 5’ Gel Beads, a Master Mix with cells, and Partitioning Oil on Chromium Next GEM Chip G. To achieve single cell resolution, cells are delivered at a limiting dilution, such that the majority (~90 – 99%) of generated GEMs contains no cell, while the remainder largely contain a single cell. Immediately following GEM generation, the Gel Bead is dissolved and any co-partitioned cell is lysed. Oligonucleotides containing an Illumina R1 sequence (read 1 sequencing primer), a 16 nt 10x Barcode, a 10 nt unique molecular identifier (UMI), and  13 nt template switch oligo (TSO) are released and mixed with the cell lysate and a Master Mix containing reverse transcription (RT) reagents and poly(dT) RT primers. Incubation of the GEMs produces 10x Barcoded, full-length cDNA from polyadenylated mRNA.
Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size prior to 5’ Gene Expression library construction. primers, a sample index, and Illumina R2 sequence (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and Sample Index PCR. The final libraries contain the primers priming sites used in Illumina sequencers
10X5'+VDJ and single-cell RNA-Seq

treatment_protocol: PBMC were isolated from healthy donors, and unfractionated PBMC were firstly exposed to GM-CSF plus IFN- 2A for DC differentiation, and LPS and TLR7/8 ligand R848 (Resiquimod) for DC maturation. Subsequently candidate neopeptides were added. Antigen-pulsed DC facilitated T-cells activation. Finally, exogenous IL-7 was used for sustained expansion of CD4+ and CD8+ antigen-responsive T-cells.

value: PBMC

value: CD8+ T cell

value: neoantigen-specific activation


title: Control_1

source_name: control

value: control


title: NRAS/AKT TIL, anti-Ly6G, scRNA-seq

city: Hong Kong

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were perfomed using Cell Ranger v6.0.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
2g of tumor tissue were extracted from cancerous livers, cut into small pieces, and dissociated into cell suspensions using gentleMACS Dissociator (Miltenyi Biotec) in dissociation buffer containing 0.5mg/ml of Collagenase IV (Gibco) and 100μg/ml of DNase I (Goldbio) at 37℃. Single cell suspensions were collected after filtering through a 70μm cell strainer. Immune cells were enriched via a density-gradient centrifugation approach using Percoll (Cytiva), and red blood cells were removed using a Red Blood Cell Lysing Buffer (Sigma). The tumor infiltrating leukocytes were then stained with a fluorescent conjugated antibody specific to CD45 (clone 30-F11, Biolegend) for 20 min at 4°C. Live, single, immune (CD45+) cells were then sort-purified with BD Influx into FBS-containing tubes, and were kept on ice until the cells were further processed for scRNAseq.
Single cell encapsulation and cDNA libraries were prepared with  Chromium Next GEM Single Cell 5’ Reagent Kit v2 (Dual Index) and Chromium Next GEM Chip K Single Cell Kit, following manufacturer's instructions

treatment_protocol: NRAS/AKT-driven HCC was induced in B6 mice via HTVI. Mice were culled at 4 weeks after tumor induction for profiling of tumor infiltrating leukocytes

value: HCC tumor

value: Tumor infiltrating leukocytes

tag: sorted cells

value: immune (CD45+) cells

value: NRAS/AKT HCC-bearing mice


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 437


title: HS-1-Input


title: Bulk RNA-seq of Homo sapiens: primary tumor of NPC patient 371


title: HR-2-IP