title: 16071_0016

city: Bochum

first: Michael

last: Sand

state: NRW

address: Gudrunstr. 56

department: Depatment of Dermatology, Venereology and Allergology

institute: Ruhr-University Bochum

description:
genomic DNA and total RNA
BCC 16

data_processing:
Library strategy: DNA-seq
Furthermore, annotations were added in order to identify known pathogenic variants or explore novel variants that are predicted to have a deleterious effect by virtue of a change in amino acid, disruption of a regulatory motif, or the disease- or pathway-association of the affected gene. Therefore, the databases HGMD (Human Gene Mutation Database), EVS (Exome Variant Server) and ClinVar (public archive of relationships among sequence variation and human phenotype) were accessed. The initially generated quality filtered variant lists were finally filtered in order to reduce the number of reported variants to those with possible clinical relevant or pathological effects. In addition, we conducted a second variant analysis of all 16 samples starting from the aligned BAM-files. Variants were called using the FreeBayes algorithm (14). Called were both SNPs and InDel variants reaching as low as a minimal detection rate of 1%. Resulting variant candidates have been PHRED-quality filtered in order to remove sites with a high chance of being polymorphic.
Genome_build: hg19
Supplementary_files_format_and_content: excel file showing all Dicer mutations . Variants were called using the FreeBayes algorithm. Called were both SNPs and InDel variants reaching as low as a minimal detection rate of 1%. Resulting variant candidates have been PHRED-quality filtered in order to remove sites with a high chance of being polymorphic.

source_name: epithelial skin tumor

extract_protocol:
Genomic DNA (gDNA) and total RNA were isolated in parallel from the same sample using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. An on-column DNase digestion step was included in the RNA isolation protocol. The final volume of the eluate was 50 μl for gDNA and 30 μl for total RNA. The total RNA samples were isolated for RNA and miRNA sequencing analysis. An aliquot of each total RNA sample was used to determine RNA concentration and purity on the NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). All samples were analyzed on the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) using RNA 6000 Nano LabChip Kits (Agilent Technologies, Santa Clara, USA) and RNA integrity number (RIN) was determined.   An aliquot of each gDNA sample was used to determine purity and approximate DNA concentration on the NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). The TruSeq Custom Amplicon Low Input (TSCA) library preparation protocol was followed. The gDNA samples were additionally quantified using the highly sensitive fluorescent dye-based Qubit® dsDNA HS Assay Kit (ThermoFisherScientific, Karlsruhe, Germany).
The microRNA maturing enzyme Dicer 1 (ribonuclease III, Gene ID 23405 on Chromosome 14) was defined as the target gene. The online tool Illumina Design Studio (http://designstudio.illumina.com/) was used to design an amplicon-based enrichment panel (TruSeq Custom Amplicon Low Input) that targets the DICER1 gene. The design strategy was based on human reference genome hg19 including the coding sequence of DICER1 with a targeted amplicon size of 175 bp (13).
Library preparation was performed with the TruSeq Custom Amplicon Low Input Library Kit (Illumina, San Diego, USA) using a dual pool approach according to the manufacturer´s protocol (1).
Hybridization of oligos to genomic DNA was performed in a 96-well plate, followed by extension and ligation to form DNA templates consisting of the regions of interest flanked by universal primer sequences. Using indexed primers, DNA templates were amplified by PCR and elongated with barcodes and sequencing adapters. In addition to the 16 gDNA samples, resulting in 32 DNA-oligo-pool samples, a control DNA (2800M) and a non-template control (NTC) were processed in parallel in order to control the complete library preparation process. Identification of each sample was ensured by an unique index sequence combination allowing identification of each sample. The DNA 1000 and High Sensitivity LabChip Kit (Agilent Technologies, Santa Clara, USA) were used on the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) to analyze the quality and fragment distribution of the generated libraries. The expected PCR product size including adapter sequences was ~ 280 bp for the targeted amplicon size of 175 bp.
bidirectional sequencing was performed, starting first at the end of the sense strand (read 1) and subsequently at the end of the complementary strand (read 2). Both reads had a length of 150 bases, finally producing 300 bases of sequence information in 2 x 150 bp paired-end (PE) reads.

value: basal cell carcinoma

value: BCC 16

tag: tumor type

value: sclerodermiform

value: epidermal skin tumor


title: 16071_0015

status: Public on Oct 25 2019

type: SRA

country: Germany

description:
genomic DNA and total RNA
BCC 15

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: diagnosis

tag: patient id

value: BCC 15

tag: cell type


title: 16071_0014

description:
genomic DNA and total RNA
BCC 14

value: BCC 14


title: 16071_0013

description:
genomic DNA and total RNA
BCC 13

value: BCC 13


title: Sulf2-TTR Gli1 WT replicate 1

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

country: USA

institute: Mayo Clinic

description:
1759-liver_tumor
processed data file: GeneCount.tsv

library_source: transcriptomic

data_processing:
Base calling was performed with the Illumina bcl2fastq.
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/).
The paired end reads were aligned by TopHat 2.0.6.
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: GeneCount.tsv: Tab-delimited text file includes raw counts and RPKM values for each gene per sample.

molecule: total RNA

organism: Mus musculus

source_name: Liver tumor

extract_protocol:
Standard Trizol-based extraction protocol.
cDNA libraries were generated in accord with the Illumina RNA-Seq preparation protocol.

tag: genotype/variation

value: SULF2 overexpression with WT Gli1

tag: tissue

value: Liver tumor


title: 16071_0012

description:
genomic DNA and total RNA
BCC 12

value: BCC 12


title: 16071_0009

description:
genomic DNA and total RNA
BCC 9

value: BCC 9


title: 16071_0010

description:
genomic DNA and total RNA
BCC 10

value: BCC 10


title: 16071_0011

description:
genomic DNA and total RNA
BCC 11

value: BCC 11


title: 16071_0007

description:
genomic DNA and total RNA
BCC 7

value: BCC 7

value: nodular


title: 16071_0006

description:
genomic DNA and total RNA
BCC 6

value: BCC 6


title: WT_3

city: Dundee

first: Mahima

last: Swamy

state: Angus

address: Dow Street

department: MRC Protein Phosphorylation and Ubiquitylation Unit

country: United Kingdom

institute: University of Dundee

description: small intestinal epithelial organoids derived from Wild type (WT) C57BL6/J mice

data_processing:
The read alignment was performed in two stades; first, the reads were aligned against the reference genome mm10 (from Illumina iGenomes website) using STAR version 2.5.2b. Then the reads were assocated with known genes and the number of reads associated with each gene was counted using subreads package (v1.5.1) Gene annotation was based on RefSeq
Only uniquley aligned reads were used for downstream analyses. In all samples, >18 million reads alligned uniquely, equivalent to 76% or greater of all mapped reads
The gene-wise read counts were normalised using the TMM normalisation method of the edgeR R/Bioconductor package.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing Normalized expression values for all samples and genes with annotations

source_name: Small intestine

extract_protocol: The samples were prepared for the sequencing using Illumina TruSeq Stranded mRNA Sample Preparation Kit and they were sequenced with the HiSeq 2500 instrument using single-end sequencing chemistry and 50bp read length. Total of 12 samples were run on two sequencing lanes.

tag: background strain

value: small intestinal epithelial organoids

tag: treatment

value: Untreated

tag: genotype

value: Wild type

tag: pairs


title: WT-IL22_2

value: IL-22 (2ng/ml) for 3 hours)


title: WT_2


title: 16071_0005

description:
genomic DNA and total RNA
BCC 5

value: basal cell carcinoma

value: BCC 5

value: epidermal skin tumor


title: Cord_Blood_ASD_female_7

type: RNA

city: Davis

first: Charles

middle: E

last: Mordaunt

state: CA

address: 3318 Tupper Hall, One Shields Ave

department: Medical Microbiology and Immunology

institute: University of California, Davis

hyb_protocol: Biotin-labeled cRNA was hybridized to Human Gene 2.0 array (Affymetrix) at the John's Hopkins Sequencing and Microarray core using the manufacturer's protocol

scan_protocol: Hybridized arrays were scanned at the John's Hopkins Sequencing and Microarray core. EARLI and MARBLES samples were measured separately and in multiple batches within each study. The manufacturer’s protocol was followed for all washing, staining and scanning procedures.

data_processing: The raw fluorescence data (in Affymetrix CEL file format) with one perfect match and one mismatched probe in each set were analyzed using oligo package in R. Within each study, signal distribution was first assessed in perfect-match probe intensity and Robust multi-Chip Average (RMA) normalized data. During the quality control step, we identified outliers, overly noisy experiments and experimental design problems using the arrayQualityMetrics and oligo R packages. Outliers were excluded based on loading in principle component 1, the Kolmogorov-Smirnov test, median normalized unscaled standard error, and the sum of the distances to all other arrays. For the MARBLES study, 3 outliers were identified and excluded, then 162 samples were normalized using RMA. For the EARLI study, 6 outliers were identified and excluded, then 109 samples were normalized using RMA. We used surrogate variable analysis (SVA) to control for unmeasured environmental, demographic and technical factors that may have substantial effects on gene expression using the SVA R package. Differential expression was determined using the limma package in R with diagnosis and surrogate variables included in the linear model. Expression was compared between ASD and TD subjects, and also Non-TD and TD subjects. Fold change and standard error from each study were input into the METAL command-line tool for meta-analysis. Shared data was limited to those subjects who gave consent.

label: biotin

source_name: Umbilical cord blood from ASD female subject

label_protocol: Total RNA with RIN > 7 was converted cDNA and in vitro transcribed to biotin-labeled cRNA at the John's Hopkins Sequencing and Microarray core using the manufacturer's protocol (Affymetrix)

extract_protocol: Umbilical cord blood was collected at the time of birth in PAXgene Blood RNA Tubes with the RNA stabilization reagent (BD Biosciences) and stored at -80C. RNA isolation was performed with the PAXgene Blood RNA Kit (Qiagen) following the manufacturer’s protocol.

value: ASD

tag: Sex

value: female

tag: study

value: MARBLES

tag: array batch


title: Cord_Blood_ASD_female_2


title: Cord_Blood_ASD_female_4


title: 16071_0004

description:
genomic DNA and total RNA
BCC 4

value: BCC 4


title: Cord_Blood_ASD_female_3


title: WT-IL22_3


title: Cord_Blood_ASD_female_5


title: Patient 14, skin melanocytic neoplasm, MST14

city: Maastricht

first: Lisa

middle: Maria

last: Hillen

state: Limburg

address: P. Debyelaan 25

department: Department of Pathology

country: Netherlands

institute: Maastricht University Medical Center

description:
MST14
9329/05
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

hyb_protocol: Samples were hybridized to NanoString PanCancer Pathway Panel probes according to manufacturer's instructions

scan_protocol: Samples were scanned on the nCounter System according to manufacturer's instructions.

data_processing:
Gene expression counts were normalized based on total library size (total number of counts per sample, see Supplemental Material, Table 1S). As such, both the housekeeping and endogenous genes were used for normalization. This method is commonly used when many genes are analyzed simultaneously (NanoString recommends >300). The studied samples showed a mean library size of 307914 counts (median 292412; range 789054 (sample AST4) to 19042 (sample MST4)). All analyses were performed using R and Bioconductor packages.
Marker Discovery and Validation of differentially expressed genes from the nCounter data was done using the limma and voom method in R (Green, Wilkins et al. 2016). Three conditions were studied: (i) SN vs. MST, (ii) SN vs. AST, and (iii) AST vs. MST. The limma procedure borrows information across all genes, which makes the analysis robust even when the sample size is small (Ritchie, Phipson et al. 2015). The voom procedure was applied to non-parametrically estimate the mean-variance relationship of the log-transformed gene counts, which is important when dealing with expression count data (Law, Chen et al. 2014).

source_name: skin melanocytic neoplasm

label_protocol: NanoString capture and reporter probe mix, Nat Biotechnol 2008;26:317-25.

growth_protocol: not relevant

extract_protocol: Serial sections, 5µm thick, were cut from FFPE tissue blocks using a microtome. One section per sample was mounted onto a glass slide and stained with Hematoxylin and Eosin (H&E), which served as corresponding reference section to obtain at least 70% tumor purity. For RNA and DNA isolation FFPE sections were collected in Eppendorf tubes, deparaffinized with xylol washing steps (1-4 times) and rehydrated in a graded alcohol series, starting at 100%, proceeding with 96% and completing with 70% ethanol. Each time tubes were washed with xylol/ethanol for 5 min in a centrifugation step for 5 min at 13000g. Subsequently the pellets were dried for 1 h at 56°C. RNA and DNA were isolated by AllPrep DNA/RNA FFPE kit (Qiagen, Hildesheim, Germany) according to the manufacturer's instructions. Purified RNA was measured in a spectrophotometer (Nanodrop, 2000; Thermo Scientific). Finally, another section was cut from the rest of FFPE block and stained with H&E, and the inclusion criteria were evaluated again on this section.

treatment_protocol: not relevant

tag: individual

value: Patient 14

value: Malignant Spitz Tumor (MST)


title: Patient 13, skin melanocytic neoplasm, MST13

description:
MST13
1266/06
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 13


title: 16071_0003

description:
genomic DNA and total RNA
BCC 3

value: BCC 3


title: Cord_Blood_ASD_female_1


title: 16071_0008

description:
genomic DNA and total RNA
BCC 8

value: BCC 8

value: nodular


title: WT_1

value: small intestinal epithelial organoids


title: Patient 12, skin melanocytic neoplasm, MST12

description:
MST12
11135/06
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 12


title: 16071_0001

description:
genomic DNA and total RNA
BCC 1

value: BCC 1


title: WT-IL22_1

value: IL-22 (2ng/ml) for 3 hours)

value: Wild type


title: sham biological rep 2

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from lymphatic endothelium in the cervical lymph node of animals that underwent a sham operation.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

source_name: Lymphatic endothelium of the cervical lymph node

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: C57BL/6 mice were maintained until 12-14 weeks of age.

extract_protocol: TRIzol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice were subjected to middle cerebral artery occlusion or sham operation. CLNs were isolated from mice at 3 hours post reperfusion after a 1 hour transient focal ischemia (3H) and from sham controls (n=3 per experimental group, each sample representing pooled CLNs from 4 animals). LYVE-1 positive cells were isolated from each pool.

value: sham operation


title: 3H biological rep 2

description: Gene expression data from lymphatic endothelium in the cervical lymph node of animals 3 hours post reperfusion after a 1-hour transient focal ischemia.

value: focal cerebral ischemia/reperfusion


title: 3H biological rep 1


title: Patient 11, skin melanocytic neoplasm, MST11

description:
MST11
5885/10
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 11


title: sham biological rep 3


title: 3H biological rep 3


title: APC-IL22_3

description: small intestinal epithelial organoids derived from Apc (Min, multiple intestinal neoplasia) mice

value: Apc Min/Min


title: APC_3

value: Untreated


title: sham biological rep 1


title: Patient 10, skin melanocytic neoplasm, MST10

description:
MST10
10.931/05
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 10


title: APC-IL22_2


title: Patient 9, skin melanocytic neoplasm, MST9

description:
MST9
25.867/10
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 9


title: Patient 8, skin melanocytic neoplasm, MST8

description:
MST8
5734/10
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 8

value: Malignant Spitz Tumor (MST)


title: APC_1


title: Patient 7, skin melanocytic neoplasm, MST7

description:
MST7
15389/09
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 7


title: APC-IL22_1


title: 50-ver-35day-3rd

city: Daejeon

first: Haemyeong

last: Jung

address: 125 Gwahak-ro, Yuseong-gu

department: Plant Systems Engineering Research Center

country: South Korea

institute: KRIBB

description:
PolyA RNA
D35_50_3
processed data file: Whole_gene_expression.xlsx

data_processing:
Raw sequencing data were filtered using standard RNA-seq parameters (Illumina pipeline).
Adapter contamination, low-quality regions, and N-base reads were trimmed from the raw reads, and then reads with a Phred quality score of 31 (Q ≥ 20) or 25 base pairs (bp) were filtered out.
The cleaned datasets were pooled and mapped to the Chinese cabbage reference gene set. To obtain assembly results, reference-guided assembly was performed using 36,285 genes from the coding sequence regions of the reference genome.
Genome_build: Brapa_sequence_v1.5_CDS
Supplementary_files_format_and_content: Whole_gene_expression.xlsx: Excel file includes processed data.

organism: Brassica rapa subsp. pekinensis

extract_protocol:
Total RNA was prepared from Chinese cabbage leaf tissue using Trizol (TaKaRa, Tyoko, Japan).
mRNA collected from leaf tissues of the two inbred lines was fragmented and used as a template for synthesis of first-strand cDNA using random hexamers and reverse transcriptase. Second-strand cDNA was synthesized using DNA polymerase I (New England BioLabs, Ipswich, MA, USA) amd RNase H (Invitrogen, Carlsbad, CA, USA). The resultant cDNA fragments were purified, end-repaired, polyA-tailed, and ligated to index adapters following the Illumina protocol.

tag: line

value: Leaf

tag: developmental stage

value: Vegetative growth

tag: time point

value: Day 35


title: 50-ver-35day-2nd

description:
PolyA RNA
D35_50_2
processed data file: Whole_gene_expression.xlsx


title: APC_2

value: small intestinal epithelial organoids


title: PG_E12_mesenchyme 3 (Bulk RNA-seq)

city: Bethesda

first: Rei

last: Sekiguchi

state: MD

address: 30 Convent Drive

institute: National Institute of Dental and Craniofacial Research

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCm38.p3 mouse genome using STAR v2.5.2a in  single-pass mode. With the following parameters:  --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.25 --outFilterScoreMinOverLread 0.25 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Genome_build: Custom mm10/GRCm38.vM11+ERCCs
Supplementary_files_format_and_content: Tab delimited files include a raw counts and TMM-normalized expression matrices.

source_name: E12 parotid mesenchyme

extract_protocol:
Submandibular salivary glands at embryonic day (E) 11.5 and parotid glands at E12 were harvested. At least three independent biological replicates were collected. The TRIzol RNA isolation method was used (Invitrogen). RNA quantity and integrity were assessed using a 2100 Bioanalyzer (Agilent Technologies). All samples for sequencing had RNA integrity (RIN) values > 8.7.
Total RNA per sample was reverse transcribed, and full-length cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio USA). Libraries for Illumina sequencing were prepared using the Nextera XT kit (Illumina), pooled, and analyzed on four lanes of a HiSeq 1500 (Illumina).

tag: age

value: PG

value: mesenchyme

tag: strain

value: ICR


title: PG_E12_mesenchyme 4 (Bulk RNA-seq)


title: UCB_G-CSF_Inno_6

city: La Plata

first: Martin

middle: Carlos

last: Abba

state: Buenos Aires

country: Argentina

institute: School of Medical Sciences - UNLP

hyb_protocol: The hybridization steps were carried out according to the Agilent protocol and images were scanned using a Genepix 4000B microarray scanner (Axon Instruments, Foster City, CA, USA)

scan_protocol: Image analysis and initial quality control were performed using Agilent Feature Extraction Software v10.2.

data_processing: We used the Limma Bioconductor package for background adjustment (normexp method), within (Loess algorithm) and between (quantiles method) arrays normalization

source_name: Mononuclear cells derived of umbilical cord blood

label_protocol: For microarray gene expression analysis, 2 μg of RNA from ADSCs with and G-CSF treatment labeled with Cy3 were individually hybridized on Agilent Whole Human Genome 4X44K microarrays to analyze ~40000 transcripts (Agilent Technologies, Palo Alto, CA, USA) using the RNA derived from the corresponding ADSC without G-CSF treatment (labeled with Cy5) as reference.

growth_protocol: ADSC were cultured in 3 biological replicates for 6 hours in LG-DMEM containing 10% FBS, 1% PS and G-CSF (200 ng / ml).

extract_protocol: Total RNA was extracted from pelleted cells and purified using a Quick-RNA™ MiniPrep (Zymo research) according to the manufacturer’s protocol. RNA quality and concentration was determined with the Nanodrop (Thermo Scientific).

treatment_protocol: The individual wells were harvested simultaneously after 6 h of G-CSF exposure for RNA extraction.

tag: biosource

value: Umbilical Cord Blood

value: innovative G-CSF

tag: treatement

value: untreated


title: Patient 4, skin melanocytic neoplasm, MST4

description:
MST4
Sp16
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 4


title: Patient 5, skin melanocytic neoplasm, MST5

description:
MST5
24381/07
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 5


title: UCB_G-CSF_Inno_3


title: UCB_G-CSF_Bios_6

value: biosimilar G-CSF


title: UCB_G-CSF_Inno_5


title: UCB_G-CSF_Inno_4


title: PG_E12_mesenchyme 2 (Bulk RNA-seq)

tag: cell type


title: Patient 3, skin melanocytic neoplasm, MST3

description:
MST3
Sp14
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 3

tag: tissue


title: UCB_G-CSF_Bios_4


title: UCB_G-CSF_Inno_1


title: UCB_G-CSF_Bios_3


title: UCB_G-CSF_Bios_2


title: Patient 6, skin melanocytic neoplasm, MST6

description:
MST6
14264/08
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 6


title: UCB_G-CSF_Inno_2


title: UCB_G-CSF_Bios_1


title: PG_E12_mesenchyme 1 (Bulk RNA-seq)


title: AMSC_G-CSF_Inno_5

source_name: Adipose derived mesenchymal stem cells

value: adipose tissues


title: AMSC_G-CSF_Inno_4


title: 50-ver-35day-1st

description:
PolyA RNA
D35_50
processed data file: Whole_gene_expression.xlsx


title: UCB_G-CSF_Bios_5


title: AMSC_G-CSF_Inno_6


title: PG_E12_epithelium 3 (Bulk RNA-seq)

source_name: E12 parotid epithelium

value: epithelium


title: 50-ver-0day-2nd

description:
PolyA RNA
D0_50_2
processed data file: Whole_gene_expression.xlsx

value: Leaf

value: Day 0


title: PG_E12_epithelium 2 (Bulk RNA-seq)


title: Patient 2, skin melanocytic neoplasm, MST2

description:
MST2
Sp10
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 2

value: Malignant Spitz Tumor (MST)


title: 50-ver-0day-1st

description:
PolyA RNA
D0_50
processed data file: Whole_gene_expression.xlsx

value: Vegetative growth


title: SMG_E11.5_mesenchyme 4 (Bulk RNA-seq)

source_name: E11.5 submandibular mesenchyme

value: SMG

value: mesenchyme


title: PG_E12_epithelium 1 (Bulk RNA-seq)

value: PG

value: ICR


title: 4004-ver-0day-3rd

description:
PolyA RNA
D0_4004_3
processed data file: Whole_gene_expression.xlsx


title: Patient 1, skin melanocytic neoplasm, MST1

description:
MST1
Sp9
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 1


title: 50-ver-0day-3rd

description:
PolyA RNA
D0_50_3
processed data file: Whole_gene_expression.xlsx


title: Patient 10, skin melanocytic neoplasm, AST10

description:
AST10
STad3
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 10

value: Atypical Spitz Tumor (AST)


title: SMG_E11.5_mesenchyme 3 (Bulk RNA-seq)


title: 4004-ver-35day-3rd

description:
PolyA RNA
D35_4004_3
processed data file: Whole_gene_expression.xlsx

value: Day 35


title: Patient 8, skin melanocytic neoplasm, AST8

description:
AST8
STad1
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 8


title: Patient 7, skin melanocytic neoplasm, AST7

description:
AST7
St6
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 7


title: Patient 9, skin melanocytic neoplasm, AST9

description:
AST9
STad2
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 9


title: SMG_E11.5_mesenchyme 1 (Bulk RNA-seq)


title: SMG_E11.5_mesenchyme 2 (Bulk RNA-seq)


title: Patient 5, skin melanocytic neoplasm, AST5

description:
AST5
St4
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 5


title: Patient 6, skin melanocytic neoplasm, AST6

description:
AST6
St5
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 6


title: 16071_0049_small RNA

description:
BCC 14
small RNA

data_processing:
Sequencing of all libraries was performed at a final concentration of 1.8 pM and with a 1% PhiX v3 control library spike-in on the NextSeq500 sequencing system (Illumina, San Diego, USA). For cluster generation and sequencing of all samples, three high output (HO) single-end 75 cycles (1x75bp SE) runs were performed for the small RNA libraries. Sequencing was operated under the control of the NextSeq Control Software V2.1.0 (Illumina, San Diego, USA). The resulting mRNA and totalRNA reads were quality controlled and mapped against the human reference genome. The resulting small RNA reads were quality controlled, mapped against miRBase 21 and the human GRCh38 non-coding RNAs. In sum, the achieved quality values of the NextSeq500 sequencing runs met the manufacturers given specifications (Illumina, San Diego, USA). All data could be used for in depth data analysis.
The CLC Genomics Workbench 9.5.3 (CLC bio, a Qiagen company) was used for in-depth analysis of differential gene expression. Excel 2010 was used for filtering of differentially expressed transcripts and small RNAs. During bioinformatics analysis, the CLC Genomics Workbench adds annotation information to the data, based on the selected reference genome.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with RPKM

extract_protocol:
Genomic DNA (gDNA) and total RNA were isolated in parallel from the same sample using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. An on-column DNase digestion step was included in the RNA isolation protocol. The final volume of the eluate was 50 μl for gDNA and 30 μl for total RNA. The total RNA samples were isolated for RNA and miRNA sequencing analysis. An aliquot of each total RNA sample was used to determine RNA concentration and purity on the NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). All samples were analyzed on the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) using RNA 6000 Nano LabChip Kits (Agilent Technologies, Santa Clara, USA) and RNA integrity number (RIN) was determined.   An aliquot of each gDNA sample was used to determine purity and approximate DNA concentration on the NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). The TruSeq Custom Amplicon Low Input (TSCA) library preparation protocol was followed. The gDNA samples were additionally quantified using the highly sensitive fluorescent dye-based Qubit® dsDNA HS Assay Kit (ThermoFisherScientific, Karlsruhe, Germany).   Genomic DNA (gDNA) and total RNA were isolated in parallel from the same sample using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. An on-column DNase digestion step was included in the RNA isolation protocol. The final volume of the eluate was 50 μl for gDNA and 30 μl for total RNA. The total RNA samples were isolated for RNA and miRNA sequencing analysis. An aliquot of each total RNA sample was used to determine RNA concentration and purity on the NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). All samples were analyzed on the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) using RNA 6000 Nano LabChip Kits (Agilent Technologies, Santa Clara, USA) and RNA integrity number (RIN) was determined.   An aliquot of each gDNA sample was used to determine purity and approximate DNA concentration on the NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). The TruSeq Custom Amplicon Low Input (TSCA) library preparation protocol was followed. The gDNA samples were additionally quantified using the highly sensitive fluorescent dye-based Qubit® dsDNA HS Assay Kit (ThermoFisherScientific, Karlsruhe, Germany).
For small RNA sequencing, one small RNA sequencing library was prepared from five total RNA samples derived from FFPE tissue samples (sBCC samples 10-14) using the NEBNext® Small RNA Library Prep Kit for Illumina. The kit targets microRNAs and other small RNAs that have a 3' hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes.
Library preparation for the smallRNA samples isolated from FFPE tissue was performed with the TruSeq® Stranded Total RNA incl. Ribo-Zero Gold technology (Illumina, San Diego, USA), according to the manufacturer´s protocol.

tag: diagnosis

value: basal cell carcinoma

tag: patient id

value: BCC 14

tag: tumor type

value: sclerodermiform

value: epithelial skin tumor


title: 16071_0047_small RNA

description:
BCC 12
small RNA

value: BCC 12


title: 16071_0048_small RNA

description:
BCC 13
small RNA

value: BCC 13


title: SMG_E11.5_epithelium 4 (Bulk RNA-seq)

source_name: E11.5 submandibular epithelium

value: SMG

value: epithelium


title: Patient 4, skin melanocytic neoplasm, AST4

description:
AST4
St3
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 4


title: AMSC_G-CSF_Inno_1

value: adipose tissues

tag: treatment

value: innovative G-CSF

value: untreated


title: AMSC_G-CSF_Inno_2


title: AMSC_G-CSF_Bios_6

value: biosimilar G-CSF


title: AMSC_G-CSF_Bios_4


title: AMSC_G-CSF_Bios_5


title: AMSC_G-CSF_Inno_3


title: 16071_0046_small RNA

description:
BCC 11
small RNA

value: BCC 11


title: AMSC_G-CSF_Bios_3


title: AMSC_G-CSF_Bios_2


title: AMSC_G-CSF_Bios_1


title: 16071_0014_RNA-seq

description: BCC 14

data_processing:
Sequencing was operated under the control of the NextSeq Control Software V2.1.0 (NCS). After image and signal processing as well as de-multiplexing, for each sequencing run separate *.fastq-files per read and lane (L001- L004) were generated for each sample. Hence, four *.fastq-files per sample were generated. Primary image processing was performed on the NextSeq500 instrument using Real Time Analysis 2.4.11 Software (RTA). Primary data analysis was performed using the bcl2fastq 2.15.0.4 software package. The Illumina Sequence Analysis Viewer (SAV) v1.9.1 and v2.1.8 was used for imaging and evaluation of the sequencing run performance.
The CLC Genomics Workbench 9.5.3 (CLC bio, a Qiagen company) was used for in-depth analysis of differential gene expression. Excel 2010 was used for filtering of differentially expressed transcripts and small RNAs. During bioinformatics analysis, the CLC Genomics Workbench adds annotation information to the data, based on the selected reference genome.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with expression values for each sample.

extract_protocol:
Genomic DNA (gDNA) and total RNA were isolated in parallel from the same sample using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. An on-column DNase digestion step was included in the RNA isolation protocol. The final volume of the eluate was 50 μl for gDNA and 30 μl for total RNA. The total RNA samples were isolated for RNA and miRNA sequencing analysis. An aliquot of each total RNA sample was used to determine RNA concentration and purity on the NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). All samples were analyzed on the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, USA) using RNA 6000 Nano LabChip Kits (Agilent Technologies, Santa Clara, USA) and RNA integrity number (RIN) was determined.   An aliquot of each gDNA sample was used to determine purity and approximate DNA concentration on the NanoDrop ND-1000 spectral photometer (Peqlab, Erlangen, Germany). The TruSeq Custom Amplicon Low Input (TSCA) library preparation protocol was followed. The gDNA samples were additionally quantified using the highly sensitive fluorescent dye-based Qubit® dsDNA HS Assay Kit (ThermoFisherScientific, Karlsruhe, Germany).
For mRNA sequencing analysis, one RNA sequencing library was prepared from five total RNA samples (sBCC samples 10-14) from fresh frozen tissue with the Illumina TruSeq® Stranded mRNA HT technology. Library preparation for the total RNA samples isolated from fresh frozen tissue was performed with the TruSeq® Stranded mRNA HT technology (Illumina, San Diego, USA), according to the manufacturer´s protocol. For small RNA sequencing, one small RNA sequencing library was prepared from five total RNA samples derived from FFPE tissue samples (sBCC samples 10-14) using the NEBNext® Small RNA Library Prep Kit for Illumina. The kit targets microRNAs and other small RNAs that have a 3' hydroxyl group resulting from enzymatic cleavage by Dicer or other RNA processing enzymes.
Sequencing of all libraries was performed at a final concentration of 1.8 pM and with a 1% PhiX v3 control library spike-in on the NextSeq500 sequencing system (Illumina, San Diego, USA). For cluster generation and sequencing of all samples, three high output (HO) single-end 75 cycles (1x75bp SE) runs were performed for the total RNA and mRNA  libraries. Sequencing was operated under the control of the NextSeq Control Software V2.1.0 (Illumina, San Diego, USA). The resulting mRNA and totalRNA reads were quality controlled and mapped against the human reference genome. In sum, the achieved quality values of the NextSeq500 sequencing runs met the manufacturers given specifications (Illumina, San Diego, USA). All data could be used for in depth data analysis.


title: SMG_E11.5_epithelium 3 (Bulk RNA-seq)

value: ICR


title: 16071_0045_small RNA

description:
BCC 10
small RNA

value: BCC 10


title: 16071_0013_RNA-seq

description: BCC 13


title: 16071_0012_RNA-seq

description: BCC 12


title: 16071_0011_RNA-seq

description: BCC 11


title: Patient 1, skin melanocytic neoplasm, AST1

description:
AST1
Sp4
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 1

value: Atypical Spitz Tumor (AST)


title: Patient 27, skin melanocytic neoplasm, SN27

description:
SN27
KSPad
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 27

value: Spitz nevi (SN)


title: Patient 2, skin melanocytic neoplasm, AST2

description:
AST2
St1
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 2


title: 16071_0010_RNA-seq

description: BCC 10

value: basal cell carcinoma

value: sclerodermiform

value: epithelial skin tumor


title: Patient 3, skin melanocytic neoplasm, AST3

description:
AST3
St2
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 3


title: SMG_E11.5_epithelium 2 (Bulk RNA-seq)

value: SMG

value: epithelium


title: Tbx21CreRFPneg

city: New York

first: Herman

last: Gudjonson

state: NY

address: 417 E 68th St

department: Computational and Systems Biology Program, SKI

institute: Memorial Sloan Kettering Cancer Center

description:
mouse_spleen_counts_normalized_4464x11755.tsv
mouse_spleen_cell_metadata_4464x9.tsv

data_processing:
Single-cell RNA seq samples were individually processed using the SEQC v0.2.1 pipeline (Azizi et al., 2018) using the package provided mm38 mouse genome reference or hg38 human genome reference and default parameters for the 10X platform. The SEQC pipeline performs read alignment, multi-mapping read resolution, as well as cell barcode and UMI correction to generate a (cells x genes) count matrix. The pipeline filters empty droplets from true cells based on total molecule counts, filters cells with >20% mitochondrial molecule fraction and filters cells with low library complexity. For each sample, an additional library size filter was used to remove any remaining low quality cell libraries. Genes that were expressed in more than 10 cells were retained for further analysis.
The filtered count matrix was normalized for library size. This normalized matrix was then multiplied by the median of the total molecule count across all cells for numerical stability and log2 transformed with a pseudocount of 0.1 for downstream analysis.
Phenograph was used to cluster PCA reduced expression data for cell type identification. Putative cell doublets were identified using DoubletDetection (gitub.com/JonathanShor/DoubletDetection) and removed from further analysis.
Genome_build: mm38 or hg38
Supplementary_files_format_and_content: tab-delimited text files containing raw counts generated by the SEQC pipeline for each sample, library-size normalized log2-transformed counts for each experiment and associated cell metadata containing per-cell annotations as presented in the publication.  The file cell_barcodes.tsv.gz (available on the series record) includes the cell barcode for each cell ID.

molecule: polyA RNA

source_name: spleen

extract_protocol:
Spleens were digested in collagenase in RPMI1640 supplemented with 5% fetal calf serum, 1% L-glutamine, 1% penicillin–streptomycin, 10 mM HEPES, 1 mg/ml collagenase A (Sigma, 11088793001) and 1U/mL DNase I (Sigma, 10104159001) for 45 min at 37°C, 250 rpm. Samples were washed and incubated in digest solution for 30 min. Digested samples were filtered through 100-μm strainers and centrifuged to remove collagenase solution. Mouse DC subsets were enriched from a pool of two spleens with Dynabeads™ Mouse DC Enrichment Kit (Invitrogen). Lin(CD3, CD19, CD90)–CD64–Ly6C–CD11c+MHCII+ cells were then purified using an Aria II cell sorter (BD Bioscience) into two populations (RFP+ and RFP– cells). Cells were sorted into cRPMI, before being pelleted and resuspended in RPMI-2% FBS for single-cell RNA seq.
The scRNA-seq libraries were prepared following the user guide manual (CG00052 Rev E) provided by the 10X Genomics and Chromium™ Single Cell 3' Reagent Kit (v2). Briefly, samples were encapsulated in microfluidic droplets at a dilution of ~70 cells/µl (doublet rate ~3.9%.). Encapsulated cells were subjected to reverse transcription (RT) reaction at 53ºC for 60 min. After RT step, the emulsion droplets were broken and barcoded-cDNA was purified with DynaBeads, followed by 14-cycles of PCR-amplification (98 °C for 180 s; [98 °C for 15 s, 67 °C for 20 s, 72 °C for 60 s] x 12-cycles; 72 °C for 60 s). 50 ng of PCR-amplified barcoded-cDNA was fragmented with the reagents provided in the kit and purified with SPRI beads to obtain an average fragment size of 600 bp. Next, the DNA library was ligated to the sequencing adapter followed by indexing PCR (98 °C for 45 s; [98 °C for 20 s, 54 °C for 30 s, 72 °C for 20 s] x 10 cycles; 72 °C for 60 s). The resulting DNA library was double-size purified (0.6-0.8X) with SPRI beads and sequenced on an Illumina NovaSeq platform  (R1 – 26 cycles, i7 – 8 cycles, R2 – 96 cycles) resulting in 184.5-186.1 million reads per sample (average reads per single-cell being 42,000 and average reads per transcript 4.40-7.14).

value: spleen

tag: purification


title: U2AF1-Mut iCLIP

city: Stanford

first: Mohammad

last: Shahrokh Esfahani

state: California

address: 265 Campus Drive

institute: Stanford University

data_processing:
Library strategy: iCLIP-seq
Sequencing reads were trimmed of 3' adaptors, collapsed for PCR duplicates, stripped of the 5' barcode, and mapped to the human (hg38) genome using bowtie2
RT stop identificaiton, gene assignment, and peak calling was performed as in FAST-iCLIP (PMID: 25411354)
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig

source_name: HCC78-derived cell line

growth_protocol: XX cells were grown in DMEM with 10% FBS and 1% penicillin-streptomycin.

extract_protocol:
Lysates were sonicated, and U2AF1 complexes were isolated with an anti-FLAG-M2 agarose (Sigma) antibody.
Libraries were prepared according to the FAST-iCLIP protocol (PMID: 25411354)

treatment_protocol: Tagged U2AF1 was induced with XX dox for XX time. Cells were then UV crosslinked at 254nm for 0.3J/cm^2 to in vivo fix RNA-RBP interactions.

tag: cell line

value: HCC78-derived cell line

tag: genotype/variation


title: RL_control_ADRC

city: Glasgow

first: Rashida

last: Lathan

address: 126 University Avenue

department: Institute of Cardiovascular and Medical Sciences

institute: University of Glasgow

data_processing:
Cell Ranger normalization/demultiplexing
STAR alignment
R Seurat read and transcript cutoff quality control
R Seurat analysis
Genome_build: Rnor_6.0.97
Supplementary_files_format_and_content: cloupe

organism: Rattus norvegicus

source_name: adipose-derived regenerative cells

extract_protocol:
Fat harvested and enzymatically processed per Cytori protocol to isolate a stromal based fraction of cells, frozen, thawed, DAPI excluded to select live cells
RNA isolation based on Chromium Next GEM Single Cell 3’ v3 kit, standard Illumina PolyA selection library prep before NextSeq500 sequencing

value: inguinal fat


title: Patient 26, skin melanocytic neoplasm, SN26

description:
SN26
SPad7
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

tag: individual

value: Patient 26


title: SMG_E11.5_epithelium 1 (Bulk RNA-seq)

value: ICR


title: Sz2_1TB

first: Jonathan

middle: Leigh

last: Messerschmidt

address: 149 13th Street

department: Center for Cancer Immunology, Cutaneous Biology Research Center, Center for Cancer Research

institute: Massachusetts General Hospital

description: MmuPV1 infection

data_processing:
Novogene: Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Novogene: "The Sequenced Reads/raw reads often contain low quality reads or reads with adaptors. In order to avoid this, it's necessary to filter the raw reads under conditions to get the clean reads. Raw reads filtering conditions are as follows: (1) Remove reads containing adaptors; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) The Qscore (Quality value) of over 50% bases of the read is <= 5."
Novogene: "Mapping the clean reads to the reference genome or the transcriptome is the basis for the next following analysis. Novogene use STAR to accomplish the mapping. In order to avoid losing a lot of effective junction reads, Novogene use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely."
Novogene: "For the samples with biological replicates, differential expression analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2010). It provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. So, if the readcount of the i-th gene in j-th sample is Kij, there is: Kij ～ NB(μij,σij2). And the resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate."
Novogene: "Volcano diagram can visually show the whole distribution of differential expression genes. For the samples with biological replicates, the threshold of differential expression genes is: padj < 0.05. For the samples without biological replicates, the threshold of differential expression genes is: |log2(FoldChange)| > 1 and qvalue < 0.005."
Novogene: "Cluster Analysis of differential expression genes was used to estimate expression pattern of differential expression genes under different experimental conditions. Through clustering genes in similar expression pattern, unknown functions of transcripts were recognized, with the reason that same kind of transcripts have similar functions or participate in the same metabolic processes or cellular pathways. Hierarchical clustering analysis was carried out with the log10(FPKM+1) of union differential expression genes of all comparison groups under different experimental conditions."
Genome_build: mm10
Supplementary_files_format_and_content: readcount_genename.txt - contains read counts for all genes across all samples. Used for subsequent analysis performed by Novogene.

source_name: SKH-1 Mouse

extract_protocol:
Tissue was extacted using the Qiagen RNeasy Mini Kit (50) Cat no. 74104
Novogene: "Briefly, mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA is first fragmented randomly by addition of fragmentation buffer. Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization(1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads."

treatment_protocol: Mice were either infected with MmuPV1 or sham infected then completed a 25 week DMBA-UV skin cancer induction protocol. Three weeks following infection, mice were treated on their back skin with 50 ug of DMBA, rested for one week, then subjected to 3 doses of 100 mJ/cm^2 per week for 25 weeks.

tag: infection status

value: Infected

value: Skin Wart


title: U2AF1-WT iCLIP


title: Patient 25, skin melanocytic neoplasm, SN25

description:
SN25
SPad6
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 25


title: Patient 24, skin melanocytic neoplasm, SN24

description:
SN24
SPad5
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 24


title: Sz4_2B

description: MmuPV1 infection

value: Skin


title: Sz4_2TB

description: MmuPV1 infection


title: Sy9_1TB

description: MmuPV1 infection, completed 25 wk DMBA-UV Protocol

value: Skin Tumor


title: Sz2_1B

description: MmuPV1 infection


title: Tbx21CreRFPpos


title: mouse 26

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

data_processing:
The Raw sequencing data was processed to remove any adaptor, PCR primers and low quality transcripts using FASTQC and Trimomatic softwares.
tophat2 and bowtie2
HTSEQ count was used for read counting
Data was voom normalised and Limma was used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: Counts

source_name: skin

extract_protocol:
Wounds from the back skin of mice were removed, flash frozen in liquid nitrogen, and RNA was harvested using QIAGEN miRNeasy kit (Cat No: 217004). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: skin wound


title: mouse 23


title: Patient 22, skin melanocytic neoplasm, SN22

description:
SN22
SPad3
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 22

value: Spitz nevi (SN)


title: Patient 23, skin melanocytic neoplasm, SN23

description:
SN23
SPad4
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 23


title: mouse 21


title: Sy9_1B


title: Sy20_1TB

description: MmuPV1 infection


title: Patient 21, skin melanocytic neoplasm, SN21

description:
SN21
SPad2
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 21


title: mouse 19

value: blank


title: Patient 19, skin melanocytic neoplasm, SN19

description:
SN19
Sp18
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 19


title: Patient 20, skin melanocytic neoplasm, SN20

description:
SN20
SPad1
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 20


title: Sy20_1B

description: MmuPV1 infection


title: mouse 18


title: Sy19_1TB


title: mouse 16


title: SynH_v3.8_T4_rep3

city: Madison

first: Robert

last: Landick

state: WI

address: 1550 Linden Dr

institute: University of Wisconsin

data_processing:
Reads were filtered for low quality and adapter readthrough using trimmomatic version 0.30 using the following parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:22:10 SLIDINGWINDOW:4:28 MINLEN:75.
Reads were aligned to 2032 GenBank chromosome and plasmid sequences CP023677, CP023678, CP023679, CP023680, and CP023681 using RSEM version 1.2.3 and Bowtie version 1.0.0 (ref) using the following parameters:  --paired-end --calc-ci --estimate-rspd --forward-prob 0 --phred33-quals.
RSEM expected counts were used for downstream differential expression analysis. Pearson correlation between vectors of counts that belong to biological replicates was employed to detect outlier libraries. All the retained libraries had inter-replicate Pearson correlation of at least 0.95. Features representing rRNA and tRNA, and genes with count sums less 5000 across all remaining samples were removed from the matrix before differential expression analysis.
Gene count normalization and differential expression testing was performed using DESeq2 version 1.14.1 run on R version 3.3.0
Genome_build: Genebank Accessions CP023677, CP023678, CP023679, CP023680, and CP023681
Supplementary_files_format_and_content: Raw expected counts matrix from RSEM and final DESeq2 results matrix

organism: Zymomonas mobilis subsp. mobilis

source_name: bacterial cell culture

extract_protocol:
Cells for RNA isolation were collected using ice-cold ethanol/phenol stop solution and RNA was extracted using hot phenol method. RNA was then DNase treated.  rRNA subtraction was performed using either Ribo-Zero rRNA Removal Kits from Illumina
Illumina TruSeq Paired-end RNA-seq kit

tag: timepoint

tag: media condition

value: (-) LDI

value: bacterial cell culture


title: mouse 12

value: DSCG


title: Sy19_1B

value: Infected


title: SynH_v3.8_T4_rep2


title: Sy13_4TB

description: MmuPV1 infection

value: Skin Wart


title: SynH_v3.8_T4_rep1


title: mouse 10


title: Patient 15, skin melanocytic neoplasm, SN15

description:
SN15
Sp11
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 15


title: Patient 16, skin melanocytic neoplasm, SN16

description:
SN16
Sp12
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 16


title: Patient 18, skin melanocytic neoplasm, SN18

description:
SN18
Sp15
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 18


title: Patient 17, skin melanocytic neoplasm, SN17

description:
SN17
Sp13
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 17


title: mouse 9

value: skin wound


title: SynH_v3.8_T3_rep3


title: Sy12_1TB

value: Skin Tumor


title: SynH_v3.8_T3_rep2


title: Sy13_4B

description: MmuPV1 infection

value: Skin


title: Patient 13, skin melanocytic neoplasm, SN13

description:
SN13
Sp7
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 13

value: Spitz nevi (SN)


title: Patient 14, skin melanocytic neoplasm, SN14

description:
SN14
Sp8
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 14


title: Sy12_1B


title: mouse 4


title: mouse 3


title: SynH_v3.8_T2_rep3


title: SynH_v3.8_T3_rep1


title: Patient 12, skin melanocytic neoplasm, SN12

description:
SN12
NV1
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 12


title: mouse 6


title: Patient 11, skin melanocytic neoplasm, SN11

description:
SN11
Sp5
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 11


title: Patient 10, skin melanocytic neoplasm, SN10

description:
SN10
Sp3
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 10


title: Sy11_1TB


title: Btheta_colon_4

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: DR-BT.counts.tsv.gz

data_processing:
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing (custom script)
mapping with tophat2 on the mm10 transcriptome
filtering out low alignment score reads and multiple mapping reads (samtools)
duplication filtering using unique molecular identifiers (custom scripts). UMI sequence is at the 4rth position in the read ID (separation by ":")
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: colon lamina propria

growth_protocol: Live cells were sorted by flow cytometry from the mouse colon.

extract_protocol:
Colons were were digested with collagenase/dispase to single cell suspensions. T cells were sorted by flow cytometry as CD45+ TCRb+ CD4+ cells. Single cells were then encapsulated in nanodroplets according to the InDrops protocol.
mRNA was reverse transcribed using adapters containing oligo dT in each droplet. The emulsion was then broken and linear amplification was performed by in vitro transcription. Illumina adapters were added by reverse transcription and PCR. Library were sequenced using a NextSeq500.

tag: library name

tag: Sex

value: male

tag: age (weeks)


title: SynH_v3.8_T2_rep2

tag: strain

value: (-) LDI

value: bacterial cell culture


title: genomic DNA from total WBC of acute phase AE patient 5

type: genomic

city: Kaohsiung

first: Sung-Chou

last: Li

state: Kaohsiung

address: No.386, Dazhong 1st Rd

department: Department of Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: We had 8 DNA samples examined with EPIC chips, including 3 HC, 5 AE at acute phase. For each sample, the Grn.idat and Red.idat raw files were provided. In addition, the beta matrix table is also available. We included only the CpG markers with cg accession number, e.g. cg00000029, for analysis in our study.

label: Cy5 and Cy3

source_name: acute phase AE patient 5

label_protocol: Standard Illumina Protocol

growth_protocol: Whole blood samples were collected from the subjects, followed by red blood cell (RBC) lysis with RBC lysis buffer to enrich total white blood cells (WBCs).

extract_protocol: We used QIAamp® DNA Blood Mini Kit (QIAGEN, CA, USA) to extract DNA following the manufacturer’s protocols.

treatment_protocol: The extracted DNA samples were bisulfite modified with EZ DNA Methylation-Lightning TM Kit (Zymo Research, Irvine, USA). Briefly, 0.5g of DNA was mixed with lightning conversion reagent, followed by the thermal-cycling condition: 98℃ for 8 min, 54℃ for 60 min and held at 4℃. Next, the DNA samples were loaded into spin column and mixed with M-binding buffer. After centrifuge, spin column was incubated with L-desulphonation buffer at room temperature. Finally, bisulfite modified DNA was eluted using M-elution buffer and stock at -80℃.

tag: disease state

value: Autoimmune encephalitis

tag: gender

value: Male


title: Btheta_colon_3

description: DR-BT.counts.tsv.gz


title: SynH_v3.8_T2_rep1

tag: tissue


title: Sy11_1B

value: Infected


title: Sx9_1B

description: Sham infection, completed 25 wk DMBA-UV Protocol

value: Uninfected


title: SynH_v3.8_T1_rep3


title: Btheta_colon_2

description: DR-BT.counts.tsv.gz


title: genomic DNA from total WBC of acute phase AE patient 1

source_name: acute phase AE patient 1

value: Female


title: Sx9_1TB


title: Sx8_1TB


title: Patient 9, skin melanocytic neoplasm, SN9

description:
SN9
Sp2
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

source_name: skin melanocytic neoplasm

value: Patient 9


title: Btheta_colon_1

description: DR-BT.counts.tsv.gz


title: Patient 7, skin melanocytic neoplasm, SN7

description:
SN7
Ksp7
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 7


title: Patient 8, skin melanocytic neoplasm, SN8

description:
SN8
Sp1
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 8


title: genomic DNA from total WBC of healthy control 1

description: genomic DNA from total WBC of healthy control subject

source_name: healthy control 1

value: healthy control


title: genomic DNA from total WBC of acute phase AE patient 3

source_name: acute phase AE patient 3


title: genomic DNA from total WBC of healthy control 3

source_name: healthy control 3


title: genomic DNA from total WBC of acute phase AE patient 2

source_name: acute phase AE patient 2


title: Patient 6, skin melanocytic neoplasm, SN6

description:
SN6
Ksp6
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 6

value: Spitz nevi (SN)


title: Young_Tconv#3

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: pooled lymph nodes

extract_protocol:
1,000 cells were double-sorted by Moflo Astrios cell sorter into 5ul Buffer TCL (Qiagen) with 1% 2-Mercaptoethanol (Sigma).Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter)
Polyadenylated mRNA was selected using an anchored oligo(dT) primer and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR-amplified using barcoded primers such that each sample carried a specific combination of illumine P5 and P7 barcodes, and were pooled prior to sequencing. Sequencing was performed on an illumina NextSeq500 using 2X25bp reads.

tag: cell type

value: CD4+ T cells

value: Foxp3-GFP (C57BL/6)

value: pooled lymph nodes

tag: age

value: 10 days


title: Sx8_1B

value: Skin


title: genomic DNA from total WBC of acute phase AE patient 4

source_name: acute phase AE patient 4


title: SynH_v3.8_T1_rep1

value: (-) LDI

value: bacterial cell culture


title: Young_Tconv#2


title: SynH_v3.8_T1_rep2


title: SynH_v3.11_T4_rep3

value: (+) LDI


title: Patient 5, skin melanocytic neoplasm, SN5

description:
SN5
Ksp5
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 5


title: SynH_v3.11_T4_rep2


title: BCC 14 DNA methylation

first: Michael

last: Sand

institute: Ruhr-University Bochum

hyb_protocol: After hybridization and washing of the microarrays, the primers on the BeadChips were extended complementary to the binding DNA sample. This reaction incorporates labelled nucleotides. Incorporation of a G corresponds to the methylated state, A to the unmethylated state on the complementary strand.

scan_protocol: Fluorescent signal intensities of the labelled and stained nucleotides on the BeadChips were detected with a dual color channel approach and the Illumina iScan™ System (Illumina, San Diego, USA).

data_processing:
Intensity files were generated by the iScan System for the green and the red channel (Illumina, San Diego, USA). The software tool GenomeStudio V2011.1 (Illumina, San Diego, USA) was used for quality control and visualization of the performance of microarray analysis as well as for methylation analysis. Raw microarray data were imported into GenomeStudio V2011.1 and analyzed. For the Infinium Methylation Assay, the β value was calculated as: β = Max (Signal B, 0) / Max (Signal A, 0) + Max (Signal B, 0) + 100. For Infinium I assays, signal A and signal B were produced by two different bead types and reported in the same color.
The file Methylation_Profiling_Supplementary_Material_II.xlsx includes both signal intensity and average Beta values.

label: Cy3 and Cy5

source_name: BCC

label_protocol: Allele-specific single base extension of the primer incorporates a biotin nucleotide or a dinitrophenyl labelled nucleotide (C and G nucleotides are biotin labelled, A and T nucleotides are dinitrophenyl labelled). Hybridized DNA was then removed and the labelled extended primers were stained and dried.

extract_protocol:
In order to detect and quantify DNA methylation in sBCC samples 10-14, Infinium MethylationEPIC BeadChips (Illumina, San Diego, USA) with over 850’000 methylation sites were used in combination with bisulfite conversion of DNA samples and the Infinium HD Assay for Methylation.
First, gDNA was modified by bisulfite conversion. Using the EZ DNA MethylationTM Kit (Zymo Research, Irvine, USA), 500 ng of methylated DNA was treated with bisulfite according to manufacturer’s instructions, thereby converting unmethylated cytosine into uracil. After the on-column desulphonation step, bisulfite converted DNA samples were then further processed using the Illumina Infinium HD Assay for Methylation (Illumina, San Diego, USA) according to manufacturer’s instructions: First, bisulfite converted DNA was denatured and neutralized. Second, the DNA was amplified by three orders of magnitude in a whole-genome amplification step. After enzymatic fragmentation, the amplified DNA was precipitated using isopropanol. After resuspension, the DNA was hybridized onto the microarrays.
The microarray hybridization was performed according to the Infinium HD Assay Methylation Protocol Guide (Illumina, San Diego, USA). The bisulfite-converted DNA samples were hybridized at 48°C for 16 hrs on separate Illumina Infinium MethylationEPIC Arrays. DNA fragments anneal to locus-specific 50 nucleotide oligomers which are covalently linked to different bead types.

tag: diagnosis

value: basal cell carcinoma

tag: patient id

value: BCC 14

value: epidermal skin tumor

tag: tumor type

value: sclerodermiform


title: Sx6_1TB

value: Uninfected

value: Skin Tumor


title: Young_Tconv#1


title: Adult_Tconv#3

value: 7 weeks


title: genomic DNA from total WBC of healthy control 2

source_name: healthy control 2

value: healthy control

value: Male


title: SynH_v3.11_T4_rep1


title: Patient 3, skin melanocytic neoplasm, SN3

description:
SN3
Ksp3
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

data_processing:
Gene expression counts were normalized based on total library size (total number of counts per sample, see Supplemental Material, Table 1S). As such, both the housekeeping and endogenous genes were used for normalization. This method is commonly used when many genes are analyzed simultaneously (NanoString recommends >300). The studied samples showed a mean library size of 307914 counts (median 292412; range 789054 (sample AST4) to 19042 (sample MST4)). All analyses were performed using R and Bioconductor packages.
Marker Discovery and Validation of differentially expressed genes from the nCounter data was done using the limma and voom method in R (Green, Wilkins et al. 2016). Three conditions were studied: (i) SN vs. MST, (ii) SN vs. AST, and (iii) AST vs. MST. The limma procedure borrows information across all genes, which makes the analysis robust even when the sample size is small (Ritchie, Phipson et al. 2015). The voom procedure was applied to non-parametrically estimate the mean-variance relationship of the log-transformed gene counts, which is important when dealing with expression count data (Law, Chen et al. 2014).

extract_protocol: Serial sections, 5µm thick, were cut from FFPE tissue blocks using a microtome. One section per sample was mounted onto a glass slide and stained with Hematoxylin and Eosin (H&E), which served as corresponding reference section to obtain at least 70% tumor purity. For RNA and DNA isolation FFPE sections were collected in Eppendorf tubes, deparaffinized with xylol washing steps (1-4 times) and rehydrated in a graded alcohol series, starting at 100%, proceeding with 96% and completing with 70% ethanol. Each time tubes were washed with xylol/ethanol for 5 min in a centrifugation step for 5 min at 13000g. Subsequently the pellets were dried for 1 h at 56°C. RNA and DNA were isolated by AllPrep DNA/RNA FFPE kit (Qiagen, Hildesheim, Germany) according to the manufacturer's instructions. Purified RNA was measured in a spectrophotometer (Nanodrop, 2000; Thermo Scientific). Finally, another section was cut from the rest of FFPE block and stained with H&E, and the inclusion criteria were evaluated again on this section.

value: Patient 3

value: Spitz nevi (SN)


title: Sx6_1B


title: BCC 13 DNA methylation

value: BCC 13

value: Female


title: Adult_Tconv#2

value: CD4+ T cells

value: Foxp3-GFP (C57BL/6)

value: pooled lymph nodes


title: Patient 4, skin melanocytic neoplasm, SN4

description:
SN4
Ksp4
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 4


title: Patient 2, skin melanocytic neoplasm, SN2

description:
SN2
Ksp2
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

value: Patient 2


title: Sx10_1B

value: Skin


title: Sx10_1TB


title: SynH_v3.11_T3_rep2

value: (+) LDI

value: bacterial cell culture


title: SynH_v3.11_T3_rep3


title: BCC 11 DNA methylation

value: basal cell carcinoma

value: BCC 11

value: epidermal skin tumor

value: sclerodermiform


title: CP_SUH_2_Rep1

city: Urbana

first: Dessiree

middle: Patricia

last: Zerpa Catanho

state: Illinois

address: 1201 W. Gregory Dr, 279 ERML

institute: University of Illinois at Urbana-Champaign

description: Hermaphrodite post-meiosis replicate 1

data_processing:
FastQC (Version 0.11.5) for raw read quality evaluation
Trimmomatic (Version 0.36) for adapters and low-quality reads removal (ILLUMINACLIP:Adapters.fa:2:30:10 LEADING:28 TRAILING:28 MINLEN:30)
Hisat2 (Version 2.0.5) for alignment
SAM files to BAM files converted with samtools (Version 1.3.1)
Aligned reads were counted using featureCounts (Version 1.5.2) and summarized per gene ID
Genome_build: ASGPBv0.4
Supplementary_files_format_and_content: Processed data files (Text document) contain raw read counts (not normalized) for each "Geneid". Processed FASTA file contains the sequences for each "Geneid" identifier used in the processed data files (Text document)

organism: Carica papaya

source_name: Flower buds

growth_protocol: Papaya plants grown at the Kunia Research Station of Hawaii Agriculture Research Center (HARC)

extract_protocol:
TRIzol Reagent (Ambion USA)
TruSeq Stranded mRNA LT kit (Illumina USA) using Low Sample Protocol

treatment_protocol: No treatment

value: Hermaphrodite

tag: cultivar

value: SunUp

value: flower bud

tag: size

tag: Stage

value: post-meiosis


title: BCC 12 DNA methylation

address: Gudrunstr. 56

value: BCC 12

value: Female


title: 534-LPS-D5

city: Copenhagen

first: Xiaoyu

last: Pan

address: Dyrlægevej 68

country: Denmark

institute: University of Copenhagen

data_processing:
Quality and adapter trimming of raw reads were performed using TrimGalore (Babraham Binoinformatics).
The remaining clean reads were aligned to the porcine genome (Sscrofa11.1) using Tophat.
The annotated gene information of porcine genome was downloaded from Ensembl.
The script htseq-count was used to generate gene count matrix.
The gene count was normalized using DESeq2.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: A matrix table of normalized gene count from DESeq2.

organism: Sus scrofa

source_name: Distal small intestine

extract_protocol:
Total RNA from the distal small intestines was isolated with RNeasy Micro Kit (Qiagen).
Sequencing libraries were constructed using NEBNext Ultra RNA library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations. RNA libraries were sequenced on the Illumina HiSeq 4000 platform with paired-end 150-bp reads production.

tag: group

tag: litter

value: F


title: CP_SUH_1_Rep1

description: Hermaphrodite pre-meiosis replicate 1

value: pre-meiosis


title: Patient 1, skin melanocytic neoplasm, SN1

description:
SN1
Ksp1
770 genes (including 40 housekeeping genes) PanCancer Pathways Panel: https://www.nanostring.com/products/gene-expression-panels/hallmarks-cancer-gene-expression-panel-collection/pancancer-pathways-panel).

tag: individual

value: Patient 1

value: Spitz nevi (SN)


title: SynH_v3.11_T3_rep1

tag: timepoint

tag: media condition


title: 533-LPS-D5

tag: Sex

value: M


title: Submandibular Gland E12 mesenchyme (Single cell RNA-seq)

data_processing:
*R1_001.fastq.gz: contain cell barcode (first 16 nt) and UMI (next 10 nt)
*R2_001.fastq.gz: contains the 98 bp RNA sequence.
*I1_001.fastq.gz: contains the 8 bp sample index.
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger v2.1.1 pipeline using default settings.
Secondary analysis was performed using the Seurat2 and Monocle2 R packages.
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger v2.1.1 gene counts matrices.

source_name: E12 submandibular mesenchyme

extract_protocol:
Submandibular and parotid glands at E12, approximately 10 of each, were harvested from mouse embryos in cold DMEM/F12 (Life Technologies). To separate the epithelium from the mesenchyme, salivary glands were treated with Dispase II (Thermo Fisher Scientific) at 37 ºC with 5% CO2 for 10 minutes. To dissociate these separated tissues into single cells, salivary epithelium and mesenchyme were separately digested in 1.5-ml tubes containing cold protease solution: 10 mg/ml Bacillus Licheniformis protease (Creative Enzymes NATE0633)(Adam et al. 2017), 40 μl Accutase, and 40 μl Accumax (Innovative Cell Technologies). The protease digestion was inhibited by the addition of 1 ml of cold DMEM/F12 with 10% fetal bovine serum (FBS) to the protease solution. The cells were filtered through a 40-μm strainer (Bel-Art Productions). The dissociated cells were pelleted in a swinging bucket centrifuge . The supernatant was aspirated until only 20-30 μl remained. After adding 1 ml of cold DMEM/F12 containing 1% FBS for a second wash, the cells were again pelleted. The supernatant was aspirated, and the cells were resuspended and placed on ice until single-cell capture. Cell viability and concentration were evaluated using acridine orange dye and a Cellometer Auto 2000 (Nexcelom Bioscience). Cell viability of >95% was observed in all samples.
Library preparation was performed according to the manufacturer’s instructions for the 10× Chromium single-cell kit (10x Genomics). The libraries were then pooled and sequenced on four lanes on a NextSeq500 sequencer (Illumina).

value: SMG

value: mesenchyme

tag: strain

value: ICR


title: BCC 10 DNA methylation

value: basal cell carcinoma

value: BCC 10


title: Submandibular Gland E12 epithelium (Single cell RNA-seq)

source_name: E12 submandibular epithelium

value: epithelium


title: CP_AU9M_2_Rep1

description: Male post-meiosis replicate 1

value: Male


title: Adult_Tconv#1

value: CD4+ T cells

value: Foxp3-GFP (C57BL/6)

value: pooled lymph nodes

value: 7 weeks


title: Parotid Gland E12 mesenchyme (Single cell RNA-seq)

source_name: E12 parotid mesenchyme

value: PG


title: 531-LPS-D5


title: 538-LPS-D5


title: SynH_v3.11_T2_rep2

source_name: bacterial cell culture

value: (+) LDI

value: bacterial cell culture


title: SynH_v3.11_T2_rep3


title: CP_AU9M_1_Rep1

description: Male pre-meiosis replicate 1

value: flower bud

value: pre-meiosis


title: 517-LPS-D5

value: M


title: Parotid Gland E12 epithelium (Single cell RNA-seq)

source_name: E12 parotid epithelium


title: SynH_v3.11_T2_rep1


title: 512-LPS-D5


title: Neonate

city: Vancouver

first: Maryam

last: Ghaedi

state: BC

address: 675 West 10th Avenue

department: Terry Fox Laboratory

country: Canada

institute: BC Cancer Agency

data_processing:
The obtained libraries were sequenced on NextSeq 500 (Illumina). Cell Ranger software (v2.0.1; 10X Genomics) was used to perform demultiplexing, alignment, counting as well as initial clustering, and differential gene expression analysis. The reads were aligned to the mm10 genome, with the genome re-annotated to include YFP, TCR and immunoglobulin genes. ScRNA-seq analysis was performed using Seurat package (Butler et al., 2018) (version 2.1.0) in R (version 3.4.2) (R core team, 2017).
Genome_build: The reads were aligned to the mm10 genome, with the genome re-annotated to include YFP, TCR and immunoglobulin genes.

source_name: Lung CD45low/+Linlow cells

extract_protocol:
To acquire lung tissue single cell suspensions, tissue was minced and fragments were digested in 5 ml DMEM containing collagenase IV (142.5 U/ml; Thermo Fisher, 17104019) and DNase I (118,050 U/ml, Sigma-Aldrich, 9003-98-9) for 25 minutes at 37°C on a shaker (150 rpm). The single cell suspension was filtered through a 70μm cell strainer and washed once with 5 ml DMEM containing 10% FBS and Penicillin-Streptomycin (10,000 U/mL). The acquired cells were enriched for leukocytes by a 36% Percoll (Sigma-Aldrich, P4937) gradient media and red blood cell lysis.   Adult or neonatal (12-day-old) RORα-YFP mouse lungs were process as described. Pooled adult or neonatal single cell suspensions were incubated with anti-mouse CD16/32 antibody (clone 2.4G2). The cells were then stained with Viability Dye (Thermo Fisher, 65-0865-18), anti-CD45 and Lin-cocktail antibodies including anti-CD3, TCRαβ, TCRγδ, NKp46, CD19, CD11b, CD11c, Ly-6C/G (Gr-1) and Ter119. Viable CD45low/+LinlowYFP− and YFP+ cells were purified at 2 to 1 ratio for adult mice samples. Neonatal sample cells were purified as CD45low/+LinlowCD8−YFP− and YFP+ cells at 2 to 1 ratio.
Purified ells were loaded on the Chromium Single Cell Controller (10X Genomics) and libraries were prepped using the Chromium Single Cell 3′ Reagents Kits (v2 chemistry; 10X Genomics), according to the manufacturer’s protocol.

tag: mouse model and strain

value: RORα-YFP (B6.RoraIRES-Cre (Chou et al., 2013) × B6.R26R-EYFP)

value: Mixed


title: CP_AU9F_1_Rep1

description: Female pre-meiosis replicate 1

value: Female

tag: tissue


title: SynH_v3.11_T1_rep3


title: SynH_v3.11_T1_rep2


title: Adult1

value: Pooled lungs from  8 mice (47-day-old), 4 mice (56-day-old), and 1 mouse (69-day-old)


title: 511-LPS-D5


title: CP_AU9F_2_Rep1

description: Female post-meiosis replicate 1

value: post-meiosis


title: 114-LPS-D5

value: F


title: SynH_v3.11_T1_rep1


title: SHZ-9

city: Shihezi

first: jin

last: li

state: Xinjiang

address: North Fourth Road

department: college of life science

country: China

institute: Shihezi university

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Cutadapt software with parameters O = 10, min_len = 35, a = adaptor sequence and Prinseq software with parameters trim_qual_left = 20, trim_qual_right = 20, trim_qual_window = 10, trim_qual_step = 1
All clean_reads were used to assembly the transcriptome sequence through the Trinity software with parameters --min_contig_length 200 --seqType fq.
The RSEM/bowtie program (version 1.2.8; Madison, WI, USA) with a cutoff defined at v =2 software was used for the mapping and the RSeQC (http://rseqc.sourceforge.net/) was used for the statistic of the mapping with default settings.
The expression level of unigenes (Fragment Per Kilo bases per Million mapped Reads, FPKM) was calculated by the RSEM/bowtie program with default settings. Since the transcriptome sequencing had no biological repetition, the analysis of differential unigene expression was conducted in reference to the Audic method (Audic and Claverie,1997).
Supplementary_files_format_and_content: FPKM

organism: Verticillium dahliae

source_name: hypha

growth_protocol: The SHZ-4, SHZ-5, and SHZ-9 strains was cultured in the Czapek liquid medium for 14 days at the conditions of 25℃, dark, and 180 rpm/min.

extract_protocol:
The spore suspension was abtained through filtering the hyphae off. The spore suspension was then centrifuged to collect the concentrated spores. The total RNA were extracted using the Fungal RNA miniprep kit (Biomiga, San Diego, USA) according to the manufacturer’s instructions. Total RNA was sent to the Sangon Biotech Cooperation (Shanghai, China) for RNA examination and sequencing. The sequencing platform was a HiSeq-2500-Pe-125 of Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hypha

tag: culture days


title: 110-LPS-D5


title: scATAC_MPAL5R_T1

first: Jeffrey

middle: Michael

last: Granja

address: 87 Hulme Ct Apt 101

department: Genetics

data_processing:
The Cell Ranger ATAC Software Suite (version 1.0.0) was used for processing sequencing information and single cell barcodes
Read pairs were aligned and deduplicated to yield fragment intervals whose ends signify accessibiltiy sites along the genome where the Tn5 transposase made cuts
Regions of enriched accessibility, i.e. peaks were identified with MACS2
Barcodes likely associated with whole cells were identified by analyzing the number of fragments (1000) mapped near TSS regions (8) and a peak-barcode matrix is defined
genome build: hg19/Grhc37
processed data files format and content: fragments-tsv files contain aligned scATAC-seq fragments

source_name: MPAL Donor Peripheral Blood

extract_protocol:
Nuclei were extracted from cells that were cryopreserved (fresh frozen in either Bambanker freezing media or 10% DMSO with 90% serum). Thawed cells were not filtered for viability prior to loading into droplets.
10X Genomics Single Cell ATAC Kit version 2

tag: disease state

value: mixed-phenotype acute leukemia (MPAL)

value: Peripheral Blood

tag: age


title: scATAC_BMMC_D6T1

data_processing:
The Cell Ranger RNA Software Suite (version 3.0.0) was used for processing sequencing information and single cell barcodes
Matrix was filtered for mitochondrial and ribosomal RNA.
Cells were filtered unique molecular identifies greater than 1000 and number of genes greater than 400.
genome build: hg19/Grhc37
processed data files format and content: scRNA-rds files are a binary R file that contain a scRNA-seq counts sparse matrix; scADT-rds files are a binary R file that contain a scADT-seq counts matrix associated with the scRNA-seq sparse matrix

source_name: Healthy Human Bone Marrow

value: Healthy

value: Bone Marrow


title: SHZ-5


title: 108-LPS-D5


title: scATAC_MPAL5_T2

source_name: MPAL Donor Bone Marrow Aspirate


title: scATAC_BMMC_D5T1


title: scATAC_MPAL5_T1


title: CITE_PBMC_D4T2

data_processing:
Library strategy: CITE-seq
The Cell Ranger RNA Software Suite (version 3.0.0) was used for processing sequencing information and single cell barcodes
Matrix was filtered for mitochondrial and ribosomal RNA.
Cells were filtered unique molecular identifies greater than 1000 and number of genes greater than 400.
genome build: hg19/Grhc37
processed data files format and content: scRNA-rds files are a binary R file that contain a scRNA-seq counts sparse matrix; scADT-rds files are a binary R file that contain a scADT-seq counts matrix associated with the scRNA-seq sparse matrix

source_name: Healthy Human Peripheral Blood

extract_protocol:
All cells used in this study were cryopreserved (fresh frozen in either Bambanker freezing media or 10% DMSO with 90% serum). Thawed cells were not filtered for viability prior to loading into droplets.
10X Genomics Single Cell RNA version 2

tag: molecule subtype

value: polyA RNA + ADT


title: CP_SUH_2_Rep2

description: Hermaphrodite post-meiosis replicate 2

value: Hermaphrodite

value: SunUp


title: CP_SUH_1_Rep2

description: Hermaphrodite pre-meiosis replicate 2

value: flower bud


title: 522-LPS-D1


title: scATAC_MPAL4_T2


title: 521-LPS-D1


title: CITE_BMMC_D1T2


title: CP_AU9M_2_Rep2

description: Male post-meiosis replicate 2

value: Male


title: scATAC_MPAL4_T1

value: M


title: 520-LPS-D1


title: CP_AU9F_2_Rep2

description: Female post-meiosis replicate 2


title: scATAC_MPAL5R_T2


title: scATAC_MPAL3_T1


title: CP_AU9M_1_Rep2

description: Male pre-meiosis replicate 2

value: pre-meiosis


title: scATAC_MPAL3_T2


title: 507-LPS-D1


title: melanoma_p2_frozen

description:
human_melanoma_counts_normalized_9315x19445.tsv
human_melanoma_cell_metadata_9315x14.tsv

data_processing:
Single-cell RNA seq samples were individually processed using the SEQC v0.2.1 pipeline (Azizi et al., 2018) using the package provided mm38 mouse genome reference or hg38 human genome reference and default parameters for the 10X platform. The SEQC pipeline performs read alignment, multi-mapping read resolution, as well as cell barcode and UMI correction to generate a (cells x genes) count matrix. The pipeline filters empty droplets from true cells based on total molecule counts, filters cells with >20% mitochondrial molecule fraction and filters cells with low library complexity. For each sample, an additional library size filter was used to remove any remaining low quality cell libraries. Genes that were expressed in more than 10 cells were retained for further analysis.
The filtered count matrix was normalized for library size. This normalized matrix was then multiplied by the median of the total molecule count across all cells for numerical stability and log2 transformed with a pseudocount of 0.1 for downstream analysis.
Phenograph was used to cluster PCA reduced expression data for cell type identification. Putative cell doublets were identified using DoubletDetection (gitub.com/JonathanShor/DoubletDetection) and removed from further analysis.
Genome_build: mm38 or hg38
Supplementary_files_format_and_content: tab-delimited text files containing raw counts generated by the SEQC pipeline for each sample, library-size normalized log2-transformed counts for each experiment and associated cell metadata containing per-cell annotations as presented in the publication.  The file cell_barcodes.tsv.gz (available on the series record) includes the cell barcode for each cell ID.

source_name: melanoma tumor

extract_protocol:
Fresh tumor tissue was dissociated by manual mincing followed by an incubation of 30 min at 37°C in RPMI with liberase (0.83mg/ml; Sigma-Aldrich), alternated with 3 rounds of dissociation with a gentleMACSTM dissociator (Miltenyi). After dissociation, cell suspensions were filtered with a 100 μm filter, and resuspended in ACK lysis buffer before washing with RPMI-5% FBS. Cells were then washed with PBS and stained with LIVE/DEAD Fixable Ghost Dye™ Red 780 followed by anti-CD45.  Viable immune cells were sorted on a FACS Aria II sorter (BD Biosciences). Human CD45+ cells from human melanoma samples were FACS-isolated and short term stored at -80C in Bambanker prior to single cell RNA-seq.
The scRNA-seq libraries were prepared following the user guide manual (CG00052 Rev E) provided by the 10X Genomics and Chromium™ Single Cell 3' Reagent Kit (v2). Briefly, samples were encapsulated in microfluidic droplets at a dilution of ~70 cells/µl (doublet rate ~3.9%.). Encapsulated cells were subjected to reverse transcription (RT) reaction at 53ºC for 60 min. After RT step, the emulsion droplets were broken and barcoded-cDNA was purified with DynaBeads, followed by 14-cycles of PCR-amplification (98 °C for 180 s; [98 °C for 15 s, 67 °C for 20 s, 72 °C for 60 s] x 12-cycles; 72 °C for 60 s). 50 ng of PCR-amplified barcoded-cDNA was fragmented with the reagents provided in the kit and purified with SPRI beads to obtain an average fragment size of 600 bp. Next, the DNA library was ligated to the sequencing adapter followed by indexing PCR (98 °C for 45 s; [98 °C for 20 s, 54 °C for 30 s, 72 °C for 20 s] x 10 cycles; 72 °C for 60 s). The resulting DNA library was double-size purified (0.6-0.8X) with SPRI beads and sequenced on an Illumina NovaSeq platform  (R1 – 26 cycles, i7 – 8 cycles, R2 – 96 cycles) resulting in 184.5-186.1 million reads per sample (average reads per single-cell being 42,000 and average reads per transcript 4.40-7.14).

value: melanoma tumor

tag: purification


title: CP_AU9F_1_Rep2

description: Female pre-meiosis replicate 2

value: Female

tag: cultivar


title: SHZ-4


title: melanoma_p2_fresh

extract_protocol:
Fresh tumor tissue was dissociated by manual mincing followed by an incubation of 30 min at 37°C in RPMI with liberase (0.83mg/ml; Sigma-Aldrich), alternated with 3 rounds of dissociation with a gentleMACSTM dissociator (Miltenyi). After dissociation, cell suspensions were filtered with a 100 μm filter, and resuspended in ACK lysis buffer before washing with RPMI-5% FBS. Cells were then washed with PBS and stained with LIVE/DEAD Fixable Ghost Dye™ Red 780 followed by anti-CD45.  Viable immune cells were sorted on a FACS Aria II sorter (BD Biosciences). Human CD45+ cells from human melanoma samples were FACS-isolated into RPMI-2% FBS for single cell RNA-seq.
The scRNA-seq libraries were prepared following the user guide manual (CG00052 Rev E) provided by the 10X Genomics and Chromium™ Single Cell 3' Reagent Kit (v2). Briefly, samples were encapsulated in microfluidic droplets at a dilution of ~70 cells/µl (doublet rate ~3.9%.). Encapsulated cells were subjected to reverse transcription (RT) reaction at 53ºC for 60 min. After RT step, the emulsion droplets were broken and barcoded-cDNA was purified with DynaBeads, followed by 14-cycles of PCR-amplification (98 °C for 180 s; [98 °C for 15 s, 67 °C for 20 s, 72 °C for 60 s] x 12-cycles; 72 °C for 60 s). 50 ng of PCR-amplified barcoded-cDNA was fragmented with the reagents provided in the kit and purified with SPRI beads to obtain an average fragment size of 600 bp. Next, the DNA library was ligated to the sequencing adapter followed by indexing PCR (98 °C for 45 s; [98 °C for 20 s, 54 °C for 30 s, 72 °C for 20 s] x 10 cycles; 72 °C for 60 s). The resulting DNA library was double-size purified (0.6-0.8X) with SPRI beads and sequenced on an Illumina NovaSeq platform  (R1 – 26 cycles, i7 – 8 cycles, R2 – 96 cycles) resulting in 184.5-186.1 million reads per sample (average reads per single-cell being 42,000 and average reads per transcript 4.40-7.14).


title: 506-LPS-D1


title: 505-LPS-D1


title: scATAC_MPAL2_T1


title: 525-LPS-D1


title: melanoma_p1


title: scATAC_MPAL1_T2


title: EC ALE-4_H2O2_2

city: San Diego

first: Amitesh

last: Anand

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from RNA-Seq were mapped onto the reference genome (NC_000913.2) using bowtie with default options to generate SAM output files
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package with strand inversion for the dUTP protocol and strict intersection mode
Estimated the dispersion of each gene using DESeq2
Transcript per Million (TPM) were calculated by DESeq2
Genome_build: E.coli genome(NC_000913.3)
Supplementary_files_format_and_content: csv file includes TPM values for each Sample

organism: Escherichia coli K-12

source_name: EC ALE-4_H2O2_mid-log phase bacteria culture

growth_protocol: Glycerol stocks of E. coli strains were inoculated into M9 minimal media with glucose as carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol: KAPA Stranded RNA-Seq Kit

tag: media

value: M9 minimal media w/ 4g/L glucose

tag: treatment

value: 2 mM Hydrogen peroxide


title: EC ALE-4_H2O2_1


title: CITE_PBMC_D4T1

value: F