title: BYDVcajal2

city: Shihezi

first: Qiang

last: Fu

state: Xinjiang

address: Bei 4 Road

institute: Shihezi University

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data). The steps are: (1) Trim Smart-seq2 public primer sequence from the Reads; (2) Remove the contaminated reads for adapters; (3) Remove the low quality reads; (4) Remove the reads whose N base more than 5% for total bases.
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample, the formula is shown as：RPKM=(106*R)/(NL/103). R is the number of reads in a certain sample that is assigned to a certain gene, N is the total number of mapped reads in the certain sample and L is the length of the certain gene.
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates. Under the assumption that the number of reads derived from a gene (or transcript isoform) follows abinomial distribution, DEGseq is proposed based on MA-plot and widely used for differential gene expression analysis. The P-value could be assigned to each gene and adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs). DESeq2 v1.6.3 was designed for differential gene expression analysis between two samples with biological replicates under the theoretical basis obeys the hypothesis of negative binomial distribution for the value of count. Differing from DESeq, DESeq2 estimates the depth parameters of samples and gene-specific, as well as uses "linear regression" for dispersion to "shrink", which was mainly considering genes of the same expression level may share the similarity deviations or own their the expression characteristics. DESeq2 estimates the expression level of each gene in per sample by the linear regression, then calculates the p-value with Wald test. Finally the p-value was corrected by the BH method. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs).
The GO (Gene Ontology, http://geneontology.org/) enrichment of DEGs was implemented by the hypergeometric test, in which p-value is calculated and adjusted as q-value, and data background is genes in the whole genome. GO terms with q<0.05 were considered to be significantly enriched. GO enrichment analysis could exhibits the biological functions of the DEGs. KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) is a database resource containing a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks. The KEGG enrichment of DEGs was implemented by the hypergeometric test, in which p-value was adjusted by multiple comparisons as q-value. KEGG terms with q<0.05 were considered to be significantly enriched.
Genome_build: Bos taurus
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Ovis aries

source_name: primary interstitial cells of Cajal

growth_protocol: The duodenum of Merino sheep (about 8 months old) used to isolate primary ICC was collected from Hualing Livestock Slaughterhouse in Urumqi, Xinjiang. The duodenum was washed with 0.1 M phosphate-buffered saline (PBS) plus 50 mg/ml of Penicillin/Streptomycin solution several times. The mucosa and submucosa of the duodenum were removed under an anatomic microscope, and strips of muscle were cut into small pieces (l–2 mm3) and digested with Hank’s balanced salt solution plus 1 mg/mL Collagenase (type II; Thermo Fisher Scientific, catalog number: 17101015) and trypsin (0.05%; Thermo Fisher Scientific, catalog number: 25200056) in a standard cell incubator for 30 min. To stop digestion, an equal volume of Medium 199 (Thermo Fisher Scientific) plus 20% FBS, 5% Penicillin/Streptomycin solution, 5 ng/mL of human stem cell factor (HEOPP-1902, Cyagen Biosciences, Guangzhou, China), and 1×MEM non-essential amino acids solution (Thermo Fisher Scientific, catalog number: 11140050) were used. The digested mixture was passed through a 200-mesh screen, and 20% Ficoll 400 (Sigma) density gradient centrifugation was performed to purify ICC as described previously (Zhang et al., 2017)

extract_protocol:
Monolayers of ICC infected with/without BVDV were harvested and lysed using TRIzol solution.
Sequencing libraries were generated using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, Beverly, MA, USA) following the manufacturer’s recommendations.

treatment_protocol: Monolayers of ICC (approximately 80% confluence) infected with or without BVDV TC (100 TCID50/0.1 ml) for 36 h

value: Duodenum

value: about 8 months old

tag: virus strain infection

value: BVDV TC strain

tag: hours of virus infection


title: BYDVcajal1

status: Public on Jun 01 2019

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: age


title: cajal3


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_H4

city: Cambridge

first: Aviv

last: Regev

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

country: USA

institute: Broad Institute

description:
Sex: Female for HEK293 and Male for NIH3T3
scRNA-seq
3'-end
mixture_hg19_mm10_count_matrix.mtx, mixture_hg19_mm10_gene.tsv, mixture_hg19_mm10_cell.tsv

data_processing:
For scRNA-seq and snRNA-seq data, scumi v0.1.0 (https://bitbucket.org/jerry00/scumi-dev/src/master/) was used to produce cell by gene sparse matrices (UMI count matrices for 3'-end methods and read count matrices for Smart-seq2). More specifically, STAR v2.6.1a was used for alignment except for Smart-seq2 and CEL-Seq2 data where HISAT v2.0.5 was used. featureCounts from the Subread package, v1.6.2 was used to tag each alignment with a gene tag. For bulk RNA-Seq data, reads were mapped to the reference genomes using Bowtie v0.12.9, and further quantified by RSEM v1.3.0 to generate transcripts per million values.
Genome_build: scRNA-seq data: a merged hg19 and mm10 geome for human and mouse mixture datasets, hg38 (GRCh38) for human PBMCs, and mm10 for mouse cortex data; bulk RNA-Seq data, hg38 (GRCh38) for human data and mm10 for mouse data
Supplementary_files_format_and_content: scRNA-seq data: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary_files_format_and_content: scRNA-seq data: cell.tsv, cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: scRNA-seq data: gene.tsv, gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: Bulk RNA-Seq data: TPM_bulk.tsv, tab-delimited text files of transcripts per million measurements of genes in each sample
Supplementary_files_format_and_content: mixture_hg19_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: mixture_hg19_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: mixture_hg19_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_count_matrix.mtx :A gene by cell count matrix in the matrix market format
Supplementary_files_format_and_content: pbmc_hg38_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: cortex_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: HEK293_PBMC_TPM_bulk.tsv :A matrix of transcripts per million measurements
Supplementary_files_format_and_content: NIH3T3_cortex_TPM_bulk.tsv :A matrix of transcripts per million measurements

organism:
Homo sapiens
Mus musculus

source_name: Mixture of human HEK293 and murine NIH3T3 cell lines

extract_protocol:
Total RNA from bulk samples was extracted using Quick-RNA Mini Prep (Zymo Research) following the vendor protocol with a DNase treatment step
For library construction methods, see SAMPLES, description: Library Construction field. For details see the Methods section in the manuscript

tag: Sex

value: Pooled male and female

tag: library construction

value: sci-RNA-seq


title: R35-28

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description: Sample collection protocol: Cryopreserved mononuclear cells were thawed and rested for 1 hour at 37℃. Cell types were pre-enriched using MagniSort® CD19 Positive Selection followed by CD4 memory T cell enrichment (eBioscience). Fc receptors on all cells were blocked using human IgG, followed by staining with panels outlined in Table 1 and separation on BD Aria Fusion sorter. A dump channel consisting of viability dye and antibodies to CD14, CD16, and either CD19 or CD3 was used to exclude unwanted cell types from cTfh cell  sorts

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
Reads were trimmed using Trim Galore v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse GRCm38 genome assembly using HISAT2 2.1.0 (no soft clipping). BAM files were imported to Seqmonk v1.43.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/).
Genome_build: GRCm38
Supplementary_files_format_and_content: A log2RPM count quantitation was carried in SeqMonk (v1.45.0) using the RNA-Seq pipeline. The file is tab delimited and contains the following columns: (1) Feature (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Ensembl-ID; (7-..) log2 RPM for each sample

organism: Homo sapiens

source_name: Blood

extract_protocol:
mRNA was isolated from sorted circulating Tfh cells (CD4+CD45RA-CXCR5+PD1+ICOS+CD38+ cells) using the SMART-SeqV4 Ultra-low input RNA kit (Takara-Clontech) and sorting 200 cells directly into lysis buffer.
cDNA libraries were subsequently generated using the Nextera XT DNA kit (Illumina).

tag: cell type

value: Blood

tag: adjuvant

value: GLA-SE


title: CD8.HC20

type: genomic

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Average Beta

label: CD8 (clone SK1, FITC-conjugated, Becton Dickinson)

molecule: genomic DNA

source_name: Healthy Control

label_protocol: standard Illumina protocol

extract_protocol: Sorting strategies listed above. DNA was prepared using QIAamp DNA Micro Kit (Qiagen)

value: CD8+ Tcells

value: F


title: R35-07


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_H3


title: CD8.HC22

value: M


title: CD8.HC16


title: cajal2


title: CD8.HC15


title: BYDVcajal3


title: CD8.HC19


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_H5


title: R35-00


title: cajal1


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_H2


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_H1


title: R34-07


title: CD8.HC6


title: Scavina 72 hai Pathogen 5

city: University Park

first: Mark

last: Guiltinan

state: Pennsylvania

address: 422 Life Sciences Bldg.

department: Plant Molecular Biology

institute: Penn State University

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S72P5

data_processing:
Low quality sequence and adapters removed using Trimmomatic (Bolger et al., 2014)
Reads mapped to reference genome using hisat2 (Kim et al., 2015)
Coverage graphs prepared using BEDtools (Quinlan and Hall, 2010)
Data initially visualized and quality manually assessed using IGV (Thorvaldsdottir et al., 2013)
Read counts for each gene calculated using featureCounts (Liao et al., 2014)
Differential expression calculated using Deseq2 (Love et al., 2014)
Genome_build: Criollo cacao genome version 2 (Argout et al., 2017)
Supplementary_files_format_and_content: Raw counts table (output from featurecounts) and Deseq2 normalized counts table used for calculating differential expression.

organism: Theobroma cacao

source_name: Scavina 6 leaf tissue

growth_protocol: Plants used for the experiment were grafts of NA32 and SCA6 shoots onto a standard rootstock. Plants were grown in a shade net house on the CNRA campus in Adiopodoume, Cote d'Ivoire.

extract_protocol:
Two leaves from different plants were pooled for each biological replicate. ~9cm^2 pieces of tissue were cut from each of the two leaves and grinded in a mortar and pestle using liquid nitrogen. RNA was extracted using Invitrogen plant RNA reagent according to instructions.
Libraries were barcoded and prepared using a Truseq Stranded mRNA Library prep kit according to manufacturer's instructions.
Equimolar pools of libraries were sequenced on a HiSeq 2500 in Rapid Mode with 100nt single reads. A total of five rapid runs were used.

treatment_protocol: On the morning of inoculation, plants in the pathogen treatment block were sprayed with zoospore suspension at 300,000 zoospores / mL. They were sprayed four times, twice from above to expose adaxial surfaces and twice from below to expose abaxial surfaces. Control plants were sprayed four times, as described, with distilled water.

tag: genotype

value: Scavina 6

tag: time point

value: 72 hai

tag: treatment

value: Phytophthora megakarya


title: CD8.HC17


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_H11


title: CD8.HC12


title: R32-28


title: CD8.HC13


title: R34-00


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_H10


title: CD8.HC8


title: CD8.HC5


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_G9


title: Scavina 72 hai Pathogen 1

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S72P1


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_H12


title: CD8.HC11


title: R32-00


title: Scavina 72 hai Pathogen 3

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S72P3


title: CD8.HC3


title: Scavina 72 hai Control 5

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S72C5

value: Water


title: CD8.SP2

source_name: Secondary-Progressive


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_G8


title: R32-07


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_H6


title: Scavina 72 hai Control 4

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S72C4


title: CD8.HC4


title: R34-28


title: CD8.RR11

source_name: Relapsing-Remitting


title: CD8.SP9


title: CD8.RR12


title: R31-07


title: R31-00


title: CD8.SP11


title: Scavina 72 hai Control 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S72C2


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_G6


title: R10-28

value: Alum


title: CD8.RR7


title: Nanay 72 hai Pathogen 5

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N72P5

source_name: Nanay 32 leaf tissue

value: Nanay 32


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_G5


title: R10-07


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_G4


title: Scavina 72 hai Control 1

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S72C1


title: CD8.RR8


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_G3


title: Nanay 72 hai Pathogen 4

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N72P4


title: CD8.SP1


title: Nanay 72 hai Pathogen 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N72P2


title: R09-28


title: R10-00


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_G2


title: Nanay 72 hai Pathogen 1

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N72P1


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_G7


title: Nanay 72 hai Control 5

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N72C5


title: R09-07


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_G12


title: R09-00


title: Nanay 72 hai Control 3

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N72C3


title: CD8.RR4


title: R08-28


title: R08-07


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_G11


title: Nanay 72 hai Control 1

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N72C1


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_G10


title: Scavina 72 hai Pathogen 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S72P2


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_G1

description:
Sex: Female for HEK293 and Male for NIH3T3
scRNA-seq
3'-end
mixture_hg19_mm10_count_matrix.mtx, mixture_hg19_mm10_gene.tsv, mixture_hg19_mm10_cell.tsv


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_F9


title: R08-00

description: Sample collection protocol: Cryopreserved mononuclear cells were thawed and rested for 1 hour at 37℃. Cell types were pre-enriched using MagniSort® CD19 Positive Selection followed by CD4 memory T cell enrichment (eBioscience). Fc receptors on all cells were blocked using human IgG, followed by staining with panels outlined in Table 1 and separation on BD Aria Fusion sorter. A dump channel consisting of viability dye and antibodies to CD14, CD16, and either CD19 or CD3 was used to exclude unwanted cell types from cTfh cell  sorts


title: Scavina 48 hai Pathogen 5

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S48P5

value: 48 hai


title: Nanay 72 hai Control 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N72C2


title: R07-07


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_F8


title: CD8.RR3


title: Scavina 48 hai Pathogen 4

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S48P4


title: Scavina 48 hai Pathogen 3

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S48P3


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_F6


title: R05-28


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_F7


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_F5


title: Nanay 48 hai Pathogen 5

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N48P5


title: CD4.HC22

label: fluorochrome-conjugated antibodies against human CD4 (clone SK3, APC-conjugated, Becton Dickinson)

value: CD4+ Tcells


title: CD8.RR1


title: R05-07


title: R05-00


title: CD4.HC21


title: CD4.HC17


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_F4


title: CD4.HC6


title: R04-28


title: R04-07


title: CD4.HC20


title: Nanay 48 hai Pathogen 4

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N48P4


title: CD4.HC7


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_F3


title: CD4.HC12


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_F2


title: R04-00


title: Nanay 48 hai Pathogen 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N48P2


title: CD4.HC2


title: CD4.HC4


title: CD8.RR2


title: Nanay 48 hai Pathogen 3

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N48P3


title: R02-28


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_F1


title: CD8.RR5


title: R02-07


title: Scavina 24 hai Pathogen 4

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S24P4

value: 24 hai


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_F12


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_F11


title: R02-00


title: Scavina 24 hai Pathogen 5

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S24P5


title: Scavina 24 hai Pathogen 3

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S24P3


title: R01-28


title: CD4.HC5


title: CD4.SP9


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_F10


title: Scavina 48 hai Pathogen 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S48P2


title: Scavina 24 hai Pathogen 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S24P2


title: CD4.HC1


title: CD4.SP13


title: R01-07


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_E9


title: Scavina 24 hai Control 4

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S24C4


title: R01-00


title: Scavina 24 hai Control 3

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S24C3


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_E8

description:
Sex: Female for HEK293 and Male for NIH3T3
scRNA-seq
3'-end
mixture_hg19_mm10_count_matrix.mtx, mixture_hg19_mm10_gene.tsv, mixture_hg19_mm10_cell.tsv


title: CD4.SP7


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_E7


title: Scavina 24 hai Control 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S24C2


title: amplicon.ET09.circJAK2

city: New York

first: Kyu-Tae

last: Kim

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
10x data was processed using Cell Ranger (version 2.1.0 or 3.0.0 according to used chemistry version) using default parameters. RNA reads were aligned to the human or mouse reference genome, or human and mouse reference concatenation for species mixing experiment.
Amplicon reads was processed following steps: 1) Identification of reads with proper priming, 2) Identification of cell barcodes (CB) that match with the whitelisted CB, 3) Replacement of CB that are not perfectly matched with the whitelist CB, 4) Deduplication of reads, and 5) Analyze reads with CB that are also observed in the 10x scRNA-seq data.
Output matrices processed from amplicon data have three columns: barcodes (BC), number of wildtype calls (num.WT.call), and number of mutant calls (num.MUT.call).
Supplementary_files_format_and_content: mutation call

source_name: ET09, amplicon, circularization

extract_protocol:
Cryopreserved patient samples approved by the Institutional Review Board of Memorial Sloan-Kettering Cancer Center were thawed and stained using standard procedures (10 min, 4°C) with the surface antibody CD34-PE-Vio770 (clone AC136, Miltenyi Biotec) and DAPI (Sigma-Aldrich). Cells were then sorted for DAPI-negative, CD34+ and CD34-negative cells using BD Influx. For the species mixing experiment, human MPL expressing Ba/F3 and UT-7 cell lines were generated by retroviral transduction, after which they were subjected to infection with CALR variant lentiviral supernatants. Wildtype UT7 cells and mutant Ba/F3 cells were mixed in equal proportions.
The standard 10x Genomics Chromium v.2 or v3 protocol was carried out according to manufacturer’s recommendations (10x Genomics, Pleasanton, CA) until after emulsion breakage and recovery of first strand cDNA. If the targeted gene of interest, e.g. SF3B1, was not robustly detected by the standard 10x procedure (i.e. if <60% of the expected cells showed expression) based on a priori knowledge in a similar dataset, a gene-specific primer was spiked into 10x primer mix at 1% of the concentration of the cDNA amplification primers for the initial cDNA PCR step. Then, during the amplification step, the 10x cDNA library underwent an extra cycle of PCR beyond the manufacturer’s recommended number of cycles. After cleanup with SPRIselect, a small portion of the cDNA library, 3 µL (~10% of total) was aliquoted for targeted genotyping, and the remaining cDNA underwent the standard 10x protocol. The cDNA set aside for GoT was amplified for 3 to 4 additional cycles using KAPA HiFi HotStart ReadyMix (KAPABiosystems) and 10x primer mix to provide sufficient material for the enrichment step. After clean-up, locus-specific reverse primers and the generic forward SI-PCR were used to amplify the site of interest of the cDNA template (Supplementary Table 3) using ~10 PCR cycles. The locus-specific reverse primers contain a partial Illumina read 2 handle, a stagger to increase the complexity of the library for optimal sequencing and a gene specific region to allow specific priming. The SI-PCR oligo (10x) anneals to the partial Illumina read 1 sequence at the 3’ end of the molecule, preserving the cell barcode (CB) and UMI. After the initial amplification and SPRI purification to remove unincorporated primers, a second PCR was performed with a generic forward PCR primer (P5_generic) to retain the CB and UMI together with an RPI-x primer (Illumina) to complete the P7 end of the library and add a sample index. The targeted amplicon library was subsequently spiked into the remainder of the 10x library to be sequenced together on a HiSeq 2500 or sequenced separately on MiSeq with v3 chemistry (Illumina). The cycle settings were as follows: 26 cycles for read 1, 98 or 130 cycles for read 2, and 8 cycles for sample index.

tag: source

value: BMMC

tag: targeted mutation

tag: vaf (targeted exon sequencing)

value: 16.4% (source:unfractionated PB)

value: Female

tag: diagnosis

value: ET

tag: wbc(k/mcl)

tag: hg(g/dl)

tag: platelets(k/mcl)

tag: pb blast count

tag: bm blast count

tag: bm fibrosis

value: Aspirin


title: CD8.RR6

value: CD8+ Tcells

tag: age

tag: Sex


title: CD4.SP5

tag: cell type

value: F


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_E6

value: Pooled male and female

tag: library construction

value: sci-RNA-seq


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_E5


title: amplicon.MF04.CALR

source_name: MF04, amplicon, straight

value: PBMC

value: CALR exon9 K385fs*47 (c.1154_1155insTTGTC)

value: 17.3% (source:CD34- cells)

value: Male

value: Post-ET MF

value: None; previously IFN


title: Nanay 24 hai Pathogen 5

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N24P5

tag: genotype

value: Nanay 32

value: Phytophthora megakarya


title: amplicon.MF03.CALR

source_name: MF03, amplicon, straight

value: 20.6% (source:CD34- cells)

value: MF


title: CD4.SP8

value: CD4+ Tcells


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_E4


title: amplicon.MF02.CALR

source_name: MF02, amplicon, straight

value: 25% (source:unfractionated PB)


title: Scavina 24 hai Control 1

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S24C1

value: Scavina 6

tag: time point

value: 24 hai

value: Water


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_E3

value: Pooled male and female


title: amplicon.ET04.CALR

source_name: ET04, amplicon, straight

value: BMMC

value: 16.7% (source:CD34- cells)

value: Female

value: ET

tag: treatment

value: Aspirin


title: CD4.SP3

value: M


title: CD4.SP2


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_E2

value: sci-RNA-seq


title: CD4.SP1


title: Nanay 24 hai Pathogen 4

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N24P4

value: Nanay 32


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_E1


title: 10x.ET09

data_processing:
10x data was processed using Cell Ranger (version 2.1.0 or 3.0.0 according to used chemistry version) using default parameters. RNA reads were aligned to the human reference genome, or human reference concatenation for species mixing experiment.
Amplicon reads was processed following steps: 1) Identification of reads with proper priming, 2) Identification of cell barcodes (CB) that match with the whitelisted CB, 3) Replacement of CB that are not perfectly matched with the whitelist CB, 4) Deduplication of reads, and 5) Analyze reads with CB that are also observed in the 10x scRNA-seq data.
Genome_build: GRCh38 or hg19
Supplementary_files_format_and_content: counts

source_name: Mixing UT7 & Ba/F3, scRNA-seq

tag: source

value: 16.4% (source:unfractionated PB)


title: Nanay 24 hai Control 5

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N24C5


title: Nanay 24 hai Pathogen 3

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N24P3

value: Phytophthora megakarya


title: Nanay 24 hai Pathogen 1

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N24P1


title: Nanay 24 hai Control 3

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N24C3


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_E12


title: CD4.RR14

value: F


title: 10x.MF04

source_name: MF04, scRNA-seq

value: PBMC

tag: targeted mutation

value: CALR exon9 K385fs*47 (c.1154_1155insTTGTC)

value: 17.3% (source:CD34- cells)

value: Male

value: Post-ET MF

value: None; previously IFN


title: CD4.RR13

value: CD4+ Tcells


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_E11

value: Pooled male and female


title: CD4.RR12


title: 10x.MF03

source_name: MF03, scRNA-seq

tag: vaf (targeted exon sequencing)

value: 20.6% (source:CD34- cells)

value: MF


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_E10


title: CD4.RR11


title: Nanay 24 hai Control 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N24C2

value: 24 hai

value: Water


title: 10x.MF02

source_name: MF02, scRNA-seq

value: 25% (source:unfractionated PB)

tag: diagnosis


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_D9

value: sci-RNA-seq


title: 10x.ET05

source_name: ET05, scRNA-seq

value: BMMC

value: 18% (source:unfractionated BM)

value: ET

tag: wbc(k/mcl)


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_D8

source_name: Mixture of human HEK293 and murine NIH3T3 cell lines


title: Scavina 6 hai Pathogen 3

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S6P3

value: Scavina 6

value: 6 hai

value: Phytophthora megakarya


title: Nanay 24 hai Control 1

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N24C1

value: Nanay 32


title: Scavina 6 hai Pathogen 5

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S6P5


title: axial stem cell line CFS5, biological replicate 2

city: Neuherberg

first: Dmitry

last: Shaposhnikov

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Center Munich

data_processing:
FASTQ generation was done automatically in Illumina BaseSpace application
Fastq files were trimmed using Trimmomatic with default parameters in Galaxy platform
Reads were aligned to hg38 human genome using HiSAT2 in Galaxy platform
counts were generated from bam files using featureCounts in Galaxy platform
Genome_build: hg38
Supplementary_files_format_and_content: csv file containing raw count table for all samples

source_name: embryonic stem cells

growth_protocol: Parental H9 cell line was grown in Matrigel-coated plates in mTESR1 medium. AxSC lines were grown in RPMI1640+B27 supplement wihtout vitamin A supplemented with 5 µM CHIR99021 only (CH5 line), 7.5 µM CHIR999021 + 10 µM SB431542 (CS7 line) or 5 µM CHIR99021 + 10 µM SB431542 + 100 ng/ml FGF2 (CFS5 line)

extract_protocol:
RNA was extracted using Qiagen RNeasy Mini kit according to manufacturer's instructions
Total RNA libraries were prepared from 1 µg of total RNA using Illumina TruSeq Stranded Total RNA LT kit according to manufacturer's instructions.

tag: passage

tag: ligands

tag: chir conc.

value: 5 µM


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_D7


title: axial stem cell line CFS5, biological replicate 1


title: axial stem cell line CS7, biological replicate 1


title: CD4.RR5

value: F


title: Scavina 6 hai Control 4

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S6C4


title: amplicon.ET05.CALR

source_name: ET05, amplicon, straight

value: Male

tag: hg(g/dl)

tag: platelets(k/mcl)

tag: pb blast count

tag: bm blast count


title: CD4.RR3

tag: cell type

value: CD4+ Tcells

tag: age

tag: Sex

value: M


title: axial stem cell line CH5, biological replicate 1

value: CHIR99021 only


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_D6

value: Pooled male and female

tag: library construction


title: CD4.RR2


title: CD4.RR1


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_D4


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_D3


title: Scavina 6 hai Pathogen 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S6P2

source_name: Scavina 6 leaf tissue

tag: genotype

tag: time point

tag: treatment


title: CD4.RR10


title: CD4.RR9


title: Scavina 6 hai Control 3

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S6C3

value: Water


title: parental hESC line H9, biological replicate 1


title: CD4.RR6


title: colorectal adenoma P6b

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

description: genomic DNA from colorectal adenoma

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan with standard recommended Illumina scanner setting

data_processing: Preprocessing was carried out by RnBeads pipeline with default settings. Raw data was later normalized using the SWAN method included in the R-conductor package minfi.

label: Cy5 and Cy3

source_name: recurrent colorectal adenoma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from colorectal adenoma samples using Qiagen Gentra Kit according to standard instructions. DNA was bisulfite converted using Zymo EZ-96 DNA methylation Kit

tag: gender

tag: sample type

value: colorectal adenoma

tag: recurrence status

value: recurrent

tag: histology

value: Tubulo-villous

tag: localization

value: Cecum


title: parental hESC line H9, biological replicate 2

tag: passage

tag: ligands

tag: chir conc.


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_D2

value: sci-RNA-seq


title: CD4.RR8

source_name: Relapsing-Remitting


title: Scavina 6 hai Control 1

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S6C1

value: Scavina 6


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_D1

description:
Sex: Female for HEK293 and Male for NIH3T3
scRNA-seq
3'-end
mixture_hg19_mm10_count_matrix.mtx, mixture_hg19_mm10_gene.tsv, mixture_hg19_mm10_cell.tsv


title: Scavina 6 hai Control 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S6C2

value: 6 hai


title: Nanay 6 hai Pathogen 5

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N6P5

source_name: Nanay 32 leaf tissue

value: Phytophthora megakarya


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_D12


title: amplicon.MF01.circCALR

data_processing:
10x data was processed using Cell Ranger 2.1.0 using default parameters. RNA reads were aligned to the human or mouse referece genome, or human and mouse reference concatenation for species mixing experiment.
Amplicon reads was processed following steps: 1) Identification of reads with proper priming, 2) Identification of cell barcodes (CB) that match with the whitelisted CB, 3) Replacement of CB that are not perfectly matched with the whitelist CB, 4) Deduplication of reads, and 5) Analyze reads with CB that are also observed in the 10x scRNA-seq data.
Output matrices processed from amplicon data have three columns: barcodes (BC), number of wildtype calls (num.WT.call), and number of mutant calls (num.MUT.call).
Genome_build: GRCh38 or hg19/mm10

source_name: MF01, amplicon, circularization

extract_protocol:
Cryopreserved patient samples approved by the Institutional Review Board of Memorial Sloan-Kettering Cancer Center were thawed and stained using standard procedures (10 min, 4°C) with the surface antibody CD34-PE-Vio770 (clone AC136, Miltenyi Biotec) and DAPI (Sigma-Aldrich). Cells were then sorted for DAPI-negative, CD34+ and CD34-negative cells using BD Influx. For the species mixing experiment, human MPL expressing Ba/F3 and UT-7 cell lines were generated by retroviral transduction, after which they were subjected to infection with CALR  variant lentiviral supernatants. Wildtype UT7 cells and mutant Ba/F3 cells were mixed in equal proportions.
The standard 10x Genomics Chromium v.2 protocol was carried out according to manufacturer’s recommendations (10x Genomics, Pleasanton, CA) until after emulsion breakage and recovery of first strand cDNA. If the targeted gene of interest, e.g. SF3B1, was not robustly detected by the standard 10x procedure (i.e. if <60% of the expected cells showed expression) based on a priori knowledge in a similar dataset, a gene-specific primer was spiked into 10x primer mix at 1% of the concentration of the cDNA amplification primers for the initial cDNA PCR step. Then, during the amplification step, the 10x cDNA library underwent an extra cycle of PCR beyond the manufacturer’s recommended number of cycles. After cleanup with SPRIselect, a small portion of the cDNA library, 3 µL (~10% of total) was aliquoted for targeted genotyping, and the remaining cDNA underwent the standard 10x protocol. The cDNA set aside for GoT was amplified for 3 to 4 additional cycles using KAPA HiFi HotStart ReadyMix (KAPABiosystems) and 10x primer mix to provide sufficient material for the enrichment step. After clean-up, locus-specific reverse primers and the generic forward SI-PCR were used to amplify the site of interest of the cDNA template (Supplementary Table 3) using ~10 PCR cycles. The locus-specific reverse primers contain a partial Illumina read 2 handle, a stagger to increase the complexity of the library for optimal sequencing and a gene specific region to allow specific priming. The SI-PCR oligo (10x) anneals to the partial Illumina read 1 sequence at the 3’ end of the molecule, preserving the cell barcode (CB) and UMI. After the initial amplification and SPRI purification to remove unincorporated primers, a second PCR was performed with a generic forward PCR primer (P5_generic) to retain the CB and UMI together with an RPI-x primer (Illumina) to complete the P7 end of the library and add a sample index. The targeted amplicon library was subsequently spiked into the remainder of the 10x library to be sequenced together on a HiSeq 2500 or sequenced separately on MiSeq with v3 chemistry (Illumina). The cycle settings were as follows: 26 cycles for read 1, 98 or 130 cycles for read 2, and 8 cycles for sample index.

tag: source

value: PBMC

tag: targeted mutation

value: CALR exon9 K385fs*47 (c.1154_1155insTTGTC)

tag: vaf (targeted exon sequencing)

value: 45% (source:unfractionated PBMCs)

value: Female

tag: diagnosis

value: Post-ET myelofibrosis

tag: wbc(k/mcl)

tag: hg(g/dl)

tag: platelets(k/mcl)

tag: pb blast count

value: Indeterminate

tag: bm fibrosis

value: None; previously anagrelide


title: colorectal adenoma P4a

description: genomic DNA from colorectal adenoma

source_name: primary colorectal adenoma with recurrence

tag: gender

value: Male

value: primary with recurrence


title: colorectal adenoma P4b

description: genomic DNA from colorectal adenoma

tag: sample type

value: colorectal adenoma


title: amplicon.TF1_HEL.circJAK2

source_name: mixing TF1 & HEL, amplicon, circularization

value: mixing study

tag: Sex

value: missing

tag: age

tag: bm blast count

tag: treatment


title: Nanay 6 hai Pathogen 4

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N6P4

tag: genotype

value: Nanay 32

tag: time point


title: colorectal adenoma P3b

description: genomic DNA from colorectal adenoma

tag: recurrence status

value: recurrent

tag: histology

value: Tubulo-villous

tag: localization

value: Sigmoid


title: amplicon.MF05.SF3B1

source_name: MF05, amplicon, straight

tag: source

tag: targeted mutation

tag: vaf (targeted exon sequencing)

value: 43.5% (source:CD34+ cells)

tag: diagnosis

value: Myelofibrotic myeloid neoplasm

value: Procrit; previously hydroxyurea and anagrelide


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_D11

value: Pooled male and female

tag: library construction

value: sci-RNA-seq


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_D5


title: Nanay 6 hai Pathogen 3

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N6P3

value: 6 hai

value: Phytophthora megakarya


title: amplicon.MF05.CALR

value: PBMC

value: CALR exon9 K385fs*47 (c.1154_1155insTTGTC)

value: 47.5% (source:CD34+ cells)

value: Female

tag: wbc(k/mcl)

tag: hg(g/dl)

tag: platelets(k/mcl)

tag: pb blast count

value: Indeterminate

tag: bm fibrosis


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_D10

tag: Sex


title: colorectal adenoma P3a

description: genomic DNA from colorectal adenoma

tag: gender

tag: sample type

value: colorectal adenoma

value: primary with recurrence


title: amplicon.MF01.CALR

source_name: MF01, amplicon, straight

value: 45% (source:unfractionated PBMCs)

tag: age

value: Post-ET myelofibrosis

tag: bm blast count

tag: treatment

value: None; previously anagrelide


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_C9


title: Nanay 6 hai Control 5

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N6C5

tag: genotype

value: Nanay 32

tag: time point

value: Water


title: colorectal adenoma P6a

description: genomic DNA from colorectal adenoma

value: Male

tag: recurrence status

tag: histology

value: Tubulo-villous

tag: localization

value: Cecum


title: Nanay 6 hai Pathogen 1

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N6P1

value: 6 hai


title: colorectal adenoma P2b

description: genomic DNA from colorectal adenoma

value: recurrent

value: Sigmoid


title: Nanay 6 hai Control 3

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N6C3


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_C8

value: Pooled male and female

tag: library construction

value: sci-RNA-seq


title: 10x.ET04

source_name: ET04, scRNA-seq

tag: source

value: BMMC

tag: targeted mutation

tag: vaf (targeted exon sequencing)

value: 16.7% (source:CD34- cells)

value: Female

tag: diagnosis

value: ET

tag: wbc(k/mcl)

value: Aspirin


title: 10x.MF05

data_processing:
10x data was processed using Cell Ranger 2.1.0 using default parameters. RNA reads were aligned to the human or mouse referece genome, or human and mouse reference concatenation for species mixing experiment.
Amplicon reads was processed following steps: 1) Identification of reads with proper priming, 2) Identification of cell barcodes (CB) that match with the whitelisted CB, 3) Replacement of CB that are not perfectly matched with the whitelist CB, 4) Deduplication of reads, and 5) Analyze reads with CB that are also observed in the 10x scRNA-seq data.
Genome_build: GRCh38 or hg19/mm10
Supplementary_files_format_and_content: counts

source_name: MF05, scRNA-seq

value: PBMC

value: CALR exon9 K385fs*47 (c.1154_1155insTTGTC)

value: 47.5% (source:CD34+ cells)

tag: Sex

value: Myelofibrotic myeloid neoplasm

tag: hg(g/dl)

tag: platelets(k/mcl)

tag: pb blast count

value: Indeterminate

tag: bm fibrosis

value: Procrit; previously hydroxyurea and anagrelide


title: colorectal adenoma P1b

description: genomic DNA from colorectal adenoma

tag: gender

tag: sample type

value: colorectal adenoma

value: Tubulo-villous

value: Rectum


title: colorectal adenoma P2a

description: genomic DNA from colorectal adenoma

value: primary with recurrence

value: Sigmoid


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_C7

value: Pooled male and female

value: sci-RNA-seq


title: Nanay 6 hai Control 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N6C2

tag: genotype

value: Nanay 32

tag: time point

value: 6 hai

tag: treatment

value: Water


title: Nanay 6 hai Control 1

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N6C1


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_C6


title: 10x.ET03

source_name: ET03, scRNA-seq

value: BMMC

value: 29% (source:CD34- cells)

value: Male

tag: age

value: ET

tag: bm blast count

value: Aspirin


title: amplicon.ET03.CALR

source_name: ET03, amplicon, straight

tag: source


title: 10x.MF01

source_name: MF01, scRNA-seq

value: PBMC

tag: targeted mutation

value: CALR exon9 K385fs*47 (c.1154_1155insTTGTC)

value: 45% (source:unfractionated PBMCs)

value: Female

value: Post-ET myelofibrosis

value: Indeterminate

value: None; previously anagrelide


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_C5

source_name: Mixture of human HEK293 and murine NIH3T3 cell lines

value: Pooled male and female

tag: library construction


title: Scavina 0 hai Pathogen 4

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S0P4

value: Scavina 6

value: 0 hai

value: Phytophthora megakarya


title: Scavina 6 hai Pathogen 1

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S6P1

value: 6 hai


title: 10x.ET02

source_name: ET02, scRNA-seq

value: BMMC

tag: vaf (targeted exon sequencing)

value: 26% (source:CD34- cells)

tag: diagnosis


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_C4

tag: Sex

value: sci-RNA-seq


title: normal colon mucosa N3

description: genomic DNA from normal colon mucosa

source_name: normal colon mucosa

value: Male

value: normal colon mucosa

tag: recurrence status

tag: histology

tag: localization

value: Transverse


title: colorectal adenoma P1a

description: genomic DNA from colorectal adenoma

value: colorectal adenoma

value: primary with recurrence

value: Tubulo-villous

value: Rectum


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_C3


title: 10x.ET01

source_name: ET01, scRNA-seq

value: 15% (source:CD34+ cells)

value: Female

value: ET

tag: wbc(k/mcl)

tag: hg(g/dl)

tag: platelets(k/mcl)

tag: pb blast count

tag: bm fibrosis

value: Aspirin; previously hydroxyurea


title: Scavina 0 hai Pathogen 3

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S0P3

source_name: Scavina 6 leaf tissue

tag: genotype

value: Scavina 6

tag: time point

value: 0 hai

tag: treatment


title: Scavina 0 hai Pathogen 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S0P2

value: Phytophthora megakarya


title: hOEplusDox_3

city: Shanghai

first: yanhua

last: du

address: 227 South Chongqing Road, Huangpu District

department: Shanghai Institute of Immunology

institute: Shanghai Jiaotong University School of Medicine

data_processing:
Sequencing reads from each sample were mapped to the human reference genome (hg38 version) by using TopHat v2.1.1
Sequencing counts at the gene level were obtained using HTSeq v 0.9.1.
R (version 3.4.0) package DESeq2 was then used to normalize gene counts and identify differential expressed genes between different conditions.
Genome_build: hg38 (human)
Supplementary_files_format_and_content: tab-delimited text file includes normalized gene counts values for each sample

source_name: MGE-like progenitor cells

growth_protocol: Human ESCs were broken up into colonies and suspended in hESCM for 4 days to form EBs. EBs were then switched to the NIM to guide the cells toward the NE fate for 2 days. During the period, SB431542 (2 µM, Stemgent) and LDN193189 (200 nM, Stemgent), inhibitors to block TGF-β and BMP signaling, were added to the EBs from Days 0 to 6. At Days 6-17, cell aggregates were adherently cultured and neuroectoderm cells were formed. For ventralization, a combination of SHH (250 ng/mL, R&D Systems) and the smoothened activator purmorphamine (0.3μM, Stemgent) were added to the neuroectoderm cells from day 10 to day 17. NPs were maintained in suspension culture as neurospheres in NIM from day 17 to day 25.

extract_protocol:
MGE cells were collected, or MGE was removed from embryo. RNA was harvested using Trizol reagent. NEBNext Ultra RNA library Prep Kit for Illumina (E7530) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the manufacturer’s protocol.

treatment_protocol: As to hOEplusDox groups, Dox (0.1μg/mL) was added into the NIM medium from day 17 to 25.

tag: cell-type/tissue

value: hESC-derived MGE-like progenitor cells

tag: cell line

tag: Stage

value: Day 25 after differentiation

value: Inducible Ctnnb1 overexpression with Dox treatment


title: Scavina 0 hai Pathogen 1

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S0P1


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_C2

value: Pooled male and female

tag: library construction

value: sci-RNA-seq


title: Scavina 0 hai Control 5

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S0C5

value: Water


title: normal colon mucosa N1

description: genomic DNA from normal colon mucosa

tag: gender

value: Male

tag: sample type

value: normal colon mucosa

value: Descending


title: colorectal adenoma A54

description: genomic DNA from colorectal adenoma

value: colorectal adenoma

tag: recurrence status

value: primary with recurrence

value: Tubulo-villous

value: Rectum


title: colorectal adenoma A54b

description: genomic DNA from colorectal adenoma

source_name: recurrent colorectal adenoma

value: Female

value: recurrent

tag: histology


title: normal colon mucosa N2

description: genomic DNA from normal colon mucosa

tag: localization

value: Transverse


title: Scavina 0 hai Control 4

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S0C4

value: Scavina 6

value: 0 hai


title: hOEplusDox_1

value: hESC-derived MGE-like progenitor cells

value: Day 25 after differentiation


title: hOEplusDox_2

value: Inducible Ctnnb1 overexpression with Dox treatment


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_C12

description:
Sex: Female for HEK293 and Male for NIH3T3
scRNA-seq
3'-end
mixture_hg19_mm10_count_matrix.mtx, mixture_hg19_mm10_gene.tsv, mixture_hg19_mm10_cell.tsv

tag: Sex

value: Pooled male and female

value: sci-RNA-seq


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_C11


title: hOE-Dox_3

value: Inducible Ctnnb1 overexpression without Dox treatment


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_C1


title: Scavina 0 hai Control 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S0C2

value: Water


title: hOE-Dox_2


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_C10


title: colorectal adenoma A53b

description: genomic DNA from colorectal adenoma

value: Cecum


title: hOE-Dox_1


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_B9


title: colorectal adenoma A53

description: genomic DNA from colorectal adenoma

value: colorectal adenoma


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_B8


title: hKO_5

value: Ctnnb1 knockout


title: Nanay 0 hai Pathogen 3

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N0P3

source_name: Nanay 32 leaf tissue

value: Nanay 32

value: Phytophthora megakarya


title: hKO_4


title: colorectal adenoma A52

description: genomic DNA from colorectal adenoma

source_name: primary colorectal adenoma with recurrence

value: Male

value: primary with recurrence

value: Tubulo-villous

value: Rectum


title: Nanay 0 hai Pathogen 5

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N0P5

value: 0 hai


title: hKO_3

value: hESC-derived MGE-like progenitor cells


title: Nanay 0 hai Pathogen 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N0P2


title: Scavina 0 hai Control 1

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
S0C1

value: Scavina 6


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_B6


title: colorectal adenoma A50

description: genomic DNA from colorectal adenoma

value: Female


title: hKO_2

value: Day 25 after differentiation


title: Nanay 0 hai Control 5

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N0C5


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_B7

value: Pooled male and female

value: sci-RNA-seq


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_B5


title: colorectal adenoma A51

description: genomic DNA from colorectal adenoma

value: Tubular


title: hWT_3

value: wild type


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_B4


title: Nanay 0 hai Control 4

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N0C4

value: Water


title: hKO_1

value: Ctnnb1 knockout


title: Nanay 0 hai Control 2

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N0C2

value: Nanay 32


title: colorectal adenoma A48

description: genomic DNA from colorectal adenoma

value: colorectal adenoma

value: Ascending


title: colorectal adenoma A45

description: genomic DNA from colorectal adenoma

source_name: colorectal adenoma without recurrence

value: Male

value: without recurrence

value: Descending


title: Nanay 0 hai Control 1

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N0C1

value: 0 hai


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_B3


title: hWT_2

value: hESC-derived MGE-like progenitor cells


title: colorectal adenoma A46

description: genomic DNA from colorectal adenoma

value: primary with recurrence

value: Tubulo-villous

value: Rectum


title: colorectal adenoma A44

description: genomic DNA from colorectal adenoma

value: Female

value: Sigmoid


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_B2

value: Pooled male and female

value: sci-RNA-seq


title: colorectal adenoma A47

description: genomic DNA from colorectal adenoma

value: Cecum


title: 7.4 GFP-

city: Cincinnati

middle: L

last: Baccei

state: OH

address: 231 Albert Sabin Way

department: Anesthesiology

institute: University of Cincinnati

description: nuclear RNA

data_processing:
Illumina Casava1.8 software was used for basecalling, demultiplex, and export to fastq format.
RNA-Seq data was processed using the TrimGalore toolkit which employs Cutadapt to trim low-quality bases and Illumina sequencing adapters from the 3’ end of the reads.  Only reads that were 20 nt or longer after trimming were kept for further analysis.  Reads were mapped to the GRCm38v73 version of the mouse genome and transcriptome using the STAR RNA-Seq alignment tool .  Reads were kept for subsequent analysis if they mapped to a single genomic location.  Gene counts were compiled using the HTSeq tool.
Normalization and differential expression was carried out using the DESeq2 Bioconductor package within the R statistical programming environment.
Genome_build: GRCm38v73
Supplementary_files_format_and_content: excel files show normalized expression for each target in each sample (output from DESeq2).  Additional statistical information relevant to differential gene analysis or change-over-time analysis is included.

organism: Mus musculus

source_name: Spinal cord dorsal horn, lumbar

extract_protocol:
Lumbar spinal cord dorsal horns (bilateral) were dissected out of mice expressing Sun1-GFP fusion protein under the control of pDyn promoter.  Tissue was homogenized and filtered to liberate intact nuclei.  Nuclei suspensions were separated by FACS to yield GFP+ sample and GFP- sample from the same animal (5,000 nuclei each sample).  RNA from each sample was purified using RNAqueous micro kit (Thermofisher) and used for downstream RNA-Seq
RNA libraries were prepared for sequencing using NuGEN SoLo RNA-Seq System v2, with 15 cycles of amplification
RNA-Seq, Illumina HiSeq 1000

tag: strain

tag: age

value: postnatal day 7

value: M

tag: population

value: unidentified non-pDyn spinal nuclei


title: hWT_1

value: Day 25 after differentiation

value: wild type


title: Nanay 0 hai Pathogen 1

description:
Stage C leaves, plants grown in shade net house in Adiopodoume, Cote d'Ivoire
N0P1

value: Nanay 32

value: Phytophthora megakarya


title: colorectal adenoma A43

description: genomic DNA from colorectal adenoma

value: colorectal adenoma

value: without recurrence


title: colorectal adenoma A49

description: genomic DNA from colorectal adenoma

value: Male

value: primary with recurrence

value: Tubular

value: Ascending


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_B1


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_B11


title: 7.4 GFP+

description: nuclear RNA

value: pDyn-lineage spinal nuclei


title: 7.3 GFP-

description: nuclear RNA


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_B10

value: Pooled male and female


title: Vehicle replicate 4, GFP+ cells from 3 mice [Kentucky assay: bourgeonal]

type: RNA

city: Lexington

first: Timothy

middle: S

last: McClintock

state: Kentucky

address: 508 Medical Science Buildi

department: Physiology

institute: University of kentucky

description: mRNA abundance data

hyb_protocol: after fragmentation cRNA was hybridized for 16 hr at 45C on Clariom S Arrays. These were washed and stained in an Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix GCS3000 7G Scanner

data_processing: The data were analyzed with Affymetrix Gene Expression Console software using default analysis settings and global scaling as normalization method.

label: biotin

source_name: Olfactory mucosa; Vehicle-stimulated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 - 100 ng of total RNA.

growth_protocol: 24 mice of both sexes, ages 7 - 12 weeks, were placed individuallly in clean air chambers for 40 hrs under air flow of 3.1L/min

extract_protocol: Mice were euthanized, olfactory mucosa were dissected, dissociated, and subjected to FACS.

treatment_protocol: After 26 hrs, half the mice were intermittently stimulated with vehicle (filtered air) or odorant for 10 sec every 20 min.

tag: tissue

value: Olfactory mucosa

tag: agent

value: Vehicle

tag: cell type

value: FACS sample, GFP-


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_B12

value: sci-RNA-seq


title: colorectal adenoma A40

description: genomic DNA from colorectal adenoma

value: Female

value: Tubulo-villous


title: 7.2 GFP-

description: nuclear RNA

value: postnatal day 7

value: F

value: unidentified non-pDyn spinal nuclei


title: 7.3 GFP+

description: nuclear RNA

value: M


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_A8


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_A7


title: Vehicle replicate 3, GFP- cells from 3 mice [Kentucky assay: bourgeonal]

description: mRNA abundance data

value: FACS sample, GFP+


title: Vehicle replicate 2, GFP+ cells from 3 mice [Kentucky assay: bourgeonal]

description: mRNA abundance data


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_A6


title: Vehicle replicate 3, GFP+ cells from 3 mice [Kentucky assay: bourgeonal]

description: mRNA abundance data


title: colorectal adenoma A39

description: genomic DNA from colorectal adenoma

value: colorectal adenoma

value: without recurrence

value: Cecum


title: colorectal adenoma A37

description: genomic DNA from colorectal adenoma

value: Male

value: Tubular

value: Rectum


title: Vehicle replicate 4, GFP- cells from 3 mice [Kentucky assay: bourgeonal]

description: mRNA abundance data

value: Olfactory mucosa


title: colorectal adenoma A41

description: genomic DNA from colorectal adenoma

value: Hepatic flexure


title: colorectal adenoma A38

description: genomic DNA from colorectal adenoma

value: Ascending


title: colorectal adenoma A36

description: genomic DNA from colorectal adenoma

value: Sigmoid


title: colorectal adenoma A42

description: genomic DNA from colorectal adenoma

value: Female


title: 7.2 GFP+

description: nuclear RNA

value: pDyn-lineage spinal nuclei


title: Vehicle replicate 2, GFP- cells from 3 mice [Kentucky assay: bourgeonal]

description: mRNA abundance data

value: Vehicle


title: colorectal adenoma A35

description: genomic DNA from colorectal adenoma


title: Vehicle replicate 1, GFP+ cells from 3 mice [Kentucky assay: bourgeonal]

description: mRNA abundance data

value: FACS sample, GFP-


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_A5

value: Pooled male and female

value: sci-RNA-seq


title: 7.1 GFP-

description: nuclear RNA

value: postnatal day 7

value: F

value: unidentified non-pDyn spinal nuclei


title: 21.3 GFP-

description: nuclear RNA

value: postnatal day 21

value: M


title: colorectal adenoma A34

description: genomic DNA from colorectal adenoma

value: Male

value: colorectal adenoma

value: without recurrence

value: Tubular


title: 7.1 GFP+

description: nuclear RNA


title: 21.3 GFP+

description: nuclear RNA


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_A4


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_A3


title: colorectal adenoma A31

description: genomic DNA from colorectal adenoma

value: Tubulo-villous

value: Rectum


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_A2


title: colorectal adenoma A32

description: genomic DNA from colorectal adenoma

value: Female

value: Transverse


title: 21.2 GFP-

description: nuclear RNA


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_A1


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_A9


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_A12


title: 21.1 GFP-

description: nuclear RNA


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_A11


title: 21.2 GFP+

description: nuclear RNA

value: pDyn-lineage spinal nuclei


title: Odor replicate 4, GFP- cells from 3 mice [Kentucky assay: bourgeonal]

description: mRNA abundance data

source_name: Olfactory mucosa; bourgeonal-stimulated

value: Olfactory mucosa

value: bourgeonal

value: FACS sample, GFP+


title: Mixture2.CBU1CANXX.103117_SciSeq-p2_A10

value: Pooled male and female

value: sci-RNA-seq


title: Odor replicate 3, GFP- cells from 3 mice [Kentucky assay: bourgeonal]

description: mRNA abundance data


title: Odor replicate 3, GFP+ cells from 3 mice [Kentucky assay: bourgeonal]

description: mRNA abundance data

value: FACS sample, GFP-


title: colorectal adenoma A30

description: genomic DNA from colorectal adenoma

value: primary with recurrence


title: Odor replicate 2, GFP- cells from 3 mice [Kentucky assay: bourgeonal]

description: mRNA abundance data


title: colorectal adenoma A33

description: genomic DNA from colorectal adenoma

value: Cecum


title: Odor replicate 4, GFP+ cells from 3 mice [Kentucky assay: bourgeonal]

description: mRNA abundance data


title: Odor replicate 2, GFP+ cells from 3 mice [Kentucky assay: bourgeonal]

description: mRNA abundance data


title: 21.1 GFP+

description: nuclear RNA

value: postnatal day 21

value: F


title: 80.4 GFP+

description: nuclear RNA

value: postnatal day 80

value: M


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_H9


title: 80.3 GFP-

description: nuclear RNA

value: unidentified non-pDyn spinal nuclei


title: colorectal adenoma A29b

description: genomic DNA from colorectal adenoma

value: Male

value: colorectal adenoma

value: recurrent

value: Tubular


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_H8


title: 80.3 GFP+

description: nuclear RNA

value: pDyn-lineage spinal nuclei


title: 80.2 GFP-

description: nuclear RNA


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_H6


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_H7


title: Vehicle replicate 1, GFP- cells from 3 mice [Kentucky assay: bourgeonal]

description: mRNA abundance data

value: Olfactory mucosa

value: Vehicle


title: Odor replicate 1, GFP- cells from 3 mice [Kentucky assay: bourgeonal]

description: mRNA abundance data

value: bourgeonal

value: FACS sample, GFP+


title: colorectal adenoma A24b

description: genomic DNA from colorectal adenoma

value: Female

value: Ascending


title: colorectal adenoma A25

description: genomic DNA from colorectal adenoma

value: primary with recurrence

value: Tubulo-villous

value: Transverse


title: 80.4 GFP-

description: nuclear RNA

value: postnatal day 80


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_H5

value: Pooled male and female

value: sci-RNA-seq


title: 80.2 GFP+

description: nuclear RNA

value: F


title: Odor replicate 1, GFP+ cells from 3 mice [Kentucky assay: bourgeonal]

description: mRNA abundance data

value: FACS sample, GFP-


title: colorectal adenoma A29

description: genomic DNA from colorectal adenoma

value: Male

value: colorectal adenoma

value: Cecum


title: Vehicle replicate 4, GFP- cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data

value: Olfactory mucosa


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_H4


title: Vehicle replicate 3, GFP- cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data

value: Vehicle


title: 80.1 GFP-

description: nuclear RNA

value: unidentified non-pDyn spinal nuclei


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_H3


title: 80.1 GFP+

description: nuclear RNA

value: pDyn-lineage spinal nuclei


title: Vehicle replicate 4, GFP+ cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data


title: colorectal adenoma A26

description: genomic DNA from colorectal adenoma

value: Female


title: colorectal adenoma A27b

description: genomic DNA from colorectal adenoma

value: recurrent

value: Rectum


title: Vehicle replicate 3, GFP+ cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data


title: knock-out pupae2 rep2 (rna-seq)

city: Irvine

first: Grace

middle: Yuh Chwen

last: Lee

state: CA

address: UCI

institute: University of California, Irvine

description: processed data files are read counts for each gene

data_processing:
raw reads were pre-processed with trim-galore to remove adatoprs and low quality bases
processed reads were mapped to reference genomes with TopHat
read counts for each gene were generated by htseq-count
Genome_build: D. melanogaster release 6 (fly base)
Supplementary_files_format_and_content: read counts for the exons of each gene

organism: Drosophila melanogaster

source_name: knock-out pupae

growth_protocol: Flies were reared on standard medium at 25C, 12hr/12hr light and dark cycle

extract_protocol:
Embryos were collected on standard apple juice plate. Before collection, pre-collection for 1hr was performed. Embryos were then collected for 4 hours and aged for 4 hours in 25C. L3 larva and mixed pupa were collected with wetted paintbursh.
Illumina TreSeq

value: whole fly

tag: developmental stage

value: pupae

tag: genotype/variation

value: CG7804 knock-out


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_H2

value: Pooled male and female


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_H1

value: sci-RNA-seq


title: knock-out pupae2 rep1 (rna-seq)


title: Vehicle replicate 2, GFP+ cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data


title: Vehicle replicate 2, GFP- cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data

value: FACS sample, GFP+


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_H12


title: colorectal adenoma A22

description: genomic DNA from colorectal adenoma

value: primary with recurrence

value: Tubulo-villous


title: Vehicle replicate 1, GFP+ cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data

value: FACS sample, GFP-


title: wildtype pupae2 (rna-seq)

source_name: wildtype pupae

value: wildtype


title: Odor replicate 4, GFP+ cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data

source_name: Olfactory mucosa; undecanal bourgeonal mixture -stimulated

value: Olfactory mucosa

value: undecanal bourgeonal mixture


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_H11


title: Odor replicate 4, GFP- cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data


title: wildtype pupae1 (rna-seq)


title: colorectal adenoma A24

description: genomic DNA from colorectal adenoma

value: colorectal adenoma

value: Ascending


title: colorectal adenoma A21

description: genomic DNA from colorectal adenoma

value: Male

value: Tubular


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_H10


title: colorectal adenoma A20

description: genomic DNA from colorectal adenoma

value: Female

value: Hepatic flexure


title: knock-out pupae1 (rna-seq)

value: whole fly

value: pupae


title: colorectal adenoma A28

description: genomic DNA from colorectal adenoma

value: Rectum


title: Vehicle replicate 1, GFP- cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data

value: Vehicle


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_G9

value: Pooled male and female

value: sci-RNA-seq


title: knock-out larvae2 rep2 (rna-seq)

source_name: knock-out larvae

value: larvae

value: CG7804 knock-out


title: knock-out larvae2 rep1 (rna-seq)


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_G8

source_name: Mixture of human HEK293 and murine NIH3T3 cell lines


title: Odor replicate 3, GFP+ cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data

value: FACS sample, GFP-


title: knock-out larvae1 rep2 (rna-seq)


title: Odor replicate 3, GFP- cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data

value: Olfactory mucosa

value: FACS sample, GFP+


title: colorectal adenoma A18

description: genomic DNA from colorectal adenoma

value: colorectal adenoma

value: primary with recurrence

value: Tubulo-villous

value: Sigmoid


title: colorectal adenoma A19

description: genomic DNA from colorectal adenoma

value: Male

value: Cecum


title: knock-out larvae1 rep1 (rna-seq)

value: whole fly


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_G6


title: Odor replicate 2, GFP- cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data

value: undecanal bourgeonal mixture


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_G7


title: Odor replicate 2, GFP+ cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data


title: wildtype larvae2 (rna-seq)

source_name: wildtype larvae

value: wildtype


title: colorectal adenoma A14

description: genomic DNA from colorectal adenoma

value: without recurrence

value: Tubular

value: Transverse


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_G5

value: Pooled male and female

value: sci-RNA-seq


title: colorectal adenoma A17

description: genomic DNA from colorectal adenoma

value: Rectum


title: Odor replicate 1, GFP- cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data

value: Olfactory mucosa


title: colorectal adenoma A15

description: genomic DNA from colorectal adenoma

value: Ascending


title: Odor replicate 1, GFP+ cells from 3 mice [Kentucky assay: undecanal bourgeonal mixture]

description: mRNA abundance data

value: FACS sample, GFP-


title: colorectal adenoma A12

description: genomic DNA from colorectal adenoma

value: colorectal adenoma


title: wildtype larvae1 rep2 (rna-seq)

value: larvae


title: colorectal adenoma A13

description: genomic DNA from colorectal adenoma

value: Female

value: Tubulo-villous


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_G4


title: colorectal adenoma A27

description: genomic DNA from colorectal adenoma

value: Male

value: primary with recurrence


title: colorectal adenoma A16

description: genomic DNA from colorectal adenoma


title: colorectal adenoma A11

description: genomic DNA from colorectal adenoma

value: Sigmoid


title: wildtype larvae1 rep1 (rna-seq)

value: whole fly

value: wildtype


title: knock-out embryo2 (rna-seq)

source_name: knock-out embryo

value: embryo

value: CG7804 knock-out


title: Vehicle replicate 4, GFP+ cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data

value: Vehicle


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_G2

value: Pooled male and female

value: sci-RNA-seq


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_G3


title: colorectal adenoma A10

description: genomic DNA from colorectal adenoma

value: without recurrence

value: Villous

value: Rectum


title: Vehicle replicate 3, GFP+ cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data

value: Olfactory mucosa

value: FACS sample, GFP-


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_G1


title: Vehicle replicate 3, GFP- cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data

value: FACS sample, GFP+


title: wildtype embryo2 rep3 (rna-seq)

source_name: wildtype embryo


title: ATRT_9379086124_R03C02

city: Heidelberg

first: Pascal

middle: David

last: Johann

address: Im Neuenheimer Feld 580

department: Pediatric Neurooncology

institute: German Cancer Research Center

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
R library minfi (v.1.28.0)
Average Beta values are reported in Normalized_calls_ATRT_MRT.txt.

source_name: DKFZ (samples profiled at the German Cancer Research Center)

growth_protocol: primary samples

extract_protocol: Qiagen Dneasy blood & tissue

treatment_protocol: primary samples

tag: tumor type

value: ATRT

value: Brain


title: wildtype embryo2 rep2 (rna-seq)


title: knock-out embryo1 (rna-seq)


title: Vehicle replicate 4, GFP- cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_G11


title: ATRT_101231000137_R06C02


title: wildtype embryo2 rep1 (rna-seq)


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_G12


title: colorectal adenoma A7

description: genomic DNA from colorectal adenoma

value: Female

value: colorectal adenoma

value: Tubulo-villous

value: Cecum


title: colorectal adenoma A23

description: genomic DNA from colorectal adenoma

value: primary with recurrence

value: Tubular

value: Transverse


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_G10

value: Pooled male and female


title: Vehicle replicate 2, GFP+ cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data

value: Vehicle


title: ATRT_9376561062_R05C01


title: wildtype embryo1 (rna-seq)

value: whole fly

value: embryo

value: wildtype


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_F9

value: sci-RNA-seq


title: colorectal adenoma A8

description: genomic DNA from colorectal adenoma

value: Male

value: without recurrence

value: Sigmoid


title: colorectal adenoma A9

description: genomic DNA from colorectal adenoma

value: Ascending


title: colorectal adenoma A5

description: genomic DNA from colorectal adenoma

value: Hepatic flexure


title: Vehicle replicate 1, GFP+ cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data

value: Olfactory mucosa

value: FACS sample, GFP-


title: Vehicle replicate 2, GFP- cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data

value: FACS sample, GFP+


title: ATRT_3999100048_R05C01

value: ATRT

value: Brain


title: Vehicle replicate 1, GFP- cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_F8


title: ATRT_9611519030_R04C02


title: ATRT_9305651060_R04C02


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_F7


title: Odor replicate 4, GFP+ cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data

source_name: Olfactory mucosa; Undecanal-stimulated

value: Undecanal


title: ATRT_9533774082_R05C01


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_F6

value: Pooled male and female


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_F5


title: CG7804_Input (chip-seq)

description: Processed data file is generated by contrasting IP to Input

library_source: genomic

data_processing:
raw reads were pre-processed with trim-galore to remove adatoprs and low quality bases
processed reads were mapped to reference genomes with bwa
reads with mapping quality score smaller than 30 were filtered using samtools
fold enrichment (IP with respect to matching INPUT) tracks were generated using MAC2
Genome_build: D. melanogaster release 6 (fly base)
Supplementary_files_format_and_content: bedgraph

extract_protocol:
Embryos were collected on standard apple juice plate. Before collection, pre-collection for 1hr was performed. Embryos were then collected for 4 hours and aged for 4 hours in 25C. ChIP was performed following standrad modEncode protocol.
Library was prepared using NuGen  Ovation Ultralow Library Systems V2

value: mixed pupae

value: GFP-tagged CG7804

tag: chip antibody


title: TBPH_Input (chip-seq)

value: GFP-tagged TBPH


title: TBPH_IP_1 (chip-seq)

value: GFP (from Kevin White's lab, University of Chicago)


title: TBPH_IP_2 (chip-seq)


title: ATRT_200091640033_R04C01


title: colorectal adenoma A3

description: genomic DNA from colorectal adenoma

value: colorectal adenoma

value: Tubulo-villous

value: Rectum


title: colorectal adenoma A4

description: genomic DNA from colorectal adenoma

value: Male

value: without recurrence

value: Tubular

value: Descending


title: colorectal adenoma A6

description: genomic DNA from colorectal adenoma

value: Villous


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_F4

tag: library construction

value: sci-RNA-seq


title: ATRT_9007225035_R03C02

value: ATRT


title: ATRT_9878820127_R06C02

value: Brain


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_F3


title: CG7804_IP_2 (chip-seq)


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_F2


title: CG7804_IP_1 (chip-seq)


title: ATRT_3998590106_R01C02


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_F1


title: eMRT_6929718026_R02C02

value: eMRT

value: Kidney


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_F12

value: Pooled male and female


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_F11


title: Odor replicate 2, GFP+ cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data

value: Olfactory mucosa

value: Undecanal

value: FACS sample, GFP-


title: eMRT_3999547168_R02C02


title: Odor replicate 1, GFP+ cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data


title: WT-P14

city: Los Angeles

first: Gerald

last: Lipshutz

address: 650 CE Young Drive, Box 957054, UCLA School of Medicine

department: Surgery

institute: UCLA

description: Array hybridization was done by the UCLA Clinical Microarray Core using their protocols.

data_processing: Raw fluorescence data was stored as .CEL.gz files was loaded into R as an AffyBatch object (using the affy package in R). This object was then processed using Robust Multi-Array Average (RMA) normalization, also part of the affy package, which removed background ‘noise’ and converted data to a log2 scale. ComBat from the sva R package was then applied to the normalized data to adjust for batch effects. Affymetrix probes were summarized and re-annotated with Ensembl gene names from the Ensembl July 2015 archive (Ensembl version 81). Finally, the dataset was filtered so that genes with a standard deviation in the 5th quantile or lower were removed.

source_name: frontal lobe (brain)

label_protocol: RNA was transcribed to double-stranded cRNA using MessageAmp Premier RNA Amplification Kit (Life Technologies, Carlsbad, CA) with an oligo(dT) primer following the manufacturer’s instructions. Following fragmentation, 11 µg of biotin-labeled cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 430 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix), then scanned with the Affymetrix GeneChip Scanner 3000 G7 (Affymetrix).

extract_protocol: Twenty milligrams of the frontal lobe of P14 mice of WT, Het, KO and treated KO (n=6 per genotype) was immediately removed after euthanizing the mice with isoflurane. RNA extraction was performed following the manufacturer’s instructions (RNeasy mini kit, Qiagen, Hilden, Germany) and DNase treatment (Roche, Basel, Switzerland) was applied.

value: WT

value: Frontal lobe (brain)

tag: sequencing batch


title: Vehicle replicate 4, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data

value: Vehicle


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_F10

data_processing:
For scRNA-seq and snRNA-seq data, scumi v0.1.0 (https://bitbucket.org/jerry00/scumi-dev/src/master/) was used to produce cell by gene sparse matrices (UMI count matrices for 3'-end methods and read count matrices for Smart-seq2). More specifically, STAR v2.6.1a was used for alignment except for Smart-seq2 and CEL-Seq2 data where HISAT v2.0.5 was used. featureCounts from the Subread package, v1.6.2 was used to tag each alignment with a gene tag. For bulk RNA-Seq data, reads were mapped to the reference genomes using Bowtie v0.12.9, and further quantified by RSEM v1.3.0 to generate transcripts per million values.
Genome_build: scRNA-seq data: a merged hg19 and mm10 geome for human and mouse mixture datasets, hg38 (GRCh38) for human PBMCs, and mm10 for mouse cortex data; bulk RNA-Seq data, hg38 (GRCh38) for human data and mm10 for mouse data
Supplementary_files_format_and_content: scRNA-seq data: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary_files_format_and_content: scRNA-seq data: cell.tsv, cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: scRNA-seq data: gene.tsv, gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: Bulk RNA-Seq data: TPM_bulk.tsv, tab-delimited text files of transcripts per million measurements of genes in each sample
Supplementary_files_format_and_content: mixture_hg19_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: mixture_hg19_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: mixture_hg19_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_count_matrix.mtx :A gene by cell count matrix in the matrix market format
Supplementary_files_format_and_content: pbmc_hg38_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: cortex_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: HEK293_PBMC_TPM_bulk.tsv :A matrix of transcripts per million measurements
Supplementary_files_format_and_content: NIH3T3_cortex_TPM_bulk.tsv :A matrix of transcripts per million measurements


title: eMRT_3999547168_R05C02


title: Odor replicate 4, GFP- cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data

value: FACS sample, GFP+


title: Odor replicate 3, GFP- cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data


title: Odor replicate 3, GFP+ cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data


title: colorectal adenoma A2

description: genomic DNA from colorectal adenoma

tag: gender

value: Male

tag: sample type

value: colorectal adenoma

value: without recurrence

value: Cecum


title: colorectal adenoma A1

description: genomic DNA from colorectal adenoma

tag: recurrence status

tag: histology

value: Tubulo-villous

value: Ascending


title: Odor replicate 2, GFP- cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_E9

tag: Sex

value: sci-RNA-seq


title: eMRT_10011071031_R04C02

value: eMRT


title: eMRT_3999547168_R01C02

value: Kidney


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_E8

value: Pooled male and female


title: WT-P15

hyb_protocol: Following fragmentation, 11 µg of biotin-labeled cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 430 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix), then scanned with the Affymetrix GeneChip Scanner 3000 G7 (Affymetrix).


title: Vehicle replicate 4, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data

tag: strain

value: Olfactory mucosa


title: TREATED-KO-P14

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix), then scanned with the Affymetrix GeneChip Scanner 3000 G7 (Affymetrix).

value: TR

tag: age


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_E7


title: TREATED-KO-P13


title: Vehicle replicate 3, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data

value: FACS sample, GFP-


title: eMRT_3999100048_R04C02


title: TREATED-KO-P15


title: KO-P15

value: KO


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_E5


title: Vehicle replicate 3, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data


title: wildtype24_3

city: Innsbruck

first: Ingo

last: Bauer

state: Tirol

address: Innrain 80-82

department: Institute of Molecular Biology

country: Austria

institute: Medical University of Innsbruck

data_processing:
The whole workflow was performed according to "RNA-seq workflow: gene-level exploratory analysis and differential expression"; https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html
Transcript abundances were estimated using Salmon with the A. nidulans FGSC A4 transcriptome downloaded from FungiDB (release 35).
Estimates were imported into R using the package tximport.
DEseq2 was used to estimate differential expression between the sample groups.
Supplementary_file PRMT_diffgene.txt includes DEseq2 results tables for contrasts wt vs∆rmtAB, wt vs∆rmtB/C, and∆rmtAB vs∆rmtBC."
Genome_build: FungiDB-37_AnidulansFGSCA4_Genome.fasta
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...

organism: Aspergillus nidulans

growth_protocol: Fungal strains were grown for 24 h as shaking cultures in liquid glucose minimal media supplemented with biotin at 37 °C

extract_protocol:
Total RNA was extracted from snap frozen fungal mycelia with TRI reagent following the manufacturer's protocol
Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries with 1 µg total RNA as input

tag: genotype

value: wild type

tag: growth time


title: Odor replicate 1, GFP- cells from 3 mice [Kentucky assay: undecanal]

description: mRNA abundance data

tag: tissue

tag: agent

value: Undecanal


title: Vehicle replicate 2, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data

value: Vehicle

tag: cell type


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_E6


title: eMRT_3999100048_R05C02


title: Vehicle replicate 2, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data

value: FACS sample, GFP+


title: HET-P15

tag: genotype/variation

value: HE

value: Frontal lobe (brain)


title: Vehicle replicate 1, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_E3


title: KO-P13


title: Odor replicate 4, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data

source_name: Olfactory mucosa; isoamyl acetate and whiskey lactone mixture-stimulated


title: HET-P14


title: HET-P13


title: Vehicle replicate 1, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_E4


title: Odor replicate 4, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data


title: ∆rmtBC24_2

value: deltarmtB/deltarmtC


title: wildtype24_2


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_E1


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_E2


title: ∆rmtBC24_1


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_E12


title: ∆rmtBC24_3


title: WT-P13

value: WT


title: wildtype24_1


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_E11


title: ∆rmtAB24_2

value: deltarmtA/deltarmtB


title: Odor replicate 3, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data


title: Odor replicate 2, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_D9

value: sci-RNA-seq


title: Odor replicate 2, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data


title: ∆rmtAB24_3


title: EE7_HET


title: EE6_Treated


title: EE8_WT


title: EE5_WT


title: ORS285_AI_14dpi_bclA_2

city: Gif sur Yvette

first: Florian

last: Lamouche

address: 1, Avenue de la Terrasse

department: Institute of Integrative Biology of the Cell (I2BC)

country: France

institute: Centre national de la Recherche Scientifique (CNRS)

data_processing:
CLC Workbench 10 software (CLC bio, Aarhus, Denmark) was used for trimming, sizing, and mapping the reads on the reference genome of Bradyrhizobium sp. ORS285 strain. Only unique gene reads mapping on 80% of their length and displaying a 90% identity have been conserved.
Genome_build: NZ_LT859959
Supplementary_files_format_and_content: tab-delimited text files including the raw counts of sequencing reads for each sample. Each sheet contains Gene Name/Region/Gene length/Unique gene reads/Total gene reads columns.

organism: Bradyrhizobium sp. ORS 285

source_name: From A. indica nodule tissues at 14 days post inoculation

growth_protocol: Bacterial culture was grown in YM rich medium. Bacteroid were obtained from nodulated plants. Aeschynomene spp. seeds were scarified and surface-sterilized using pure sulfuric acid and calcium hypochlorite, germinated in Khalys agar plates and transferred in transparent, light permissive test tubes filled with BNM medium (Erhardt et al., 1992).

extract_protocol:
Nodules were harvested at 14 days post inoculation (dpi), frozen in liquid N2 and kept at -80°C until RNA extraction. For transcriptomic analysis, total nodule RNA was extracted as previously described in Mergaert et al., 20036, and submitted to plant and bacterial rRNA and eukaryotic mRNA depletion using RiboZero kits for plants and for Gram-negative bacteria (Epicentre, Madison, USA). Total RNA of free-living cells were extracted from bacterial pellets obtained from cultures grown in YM medium at OD600= 0.5 using hot phenol and hot SDS method according to Chapelle et al. (2015).
Oriented libraries of bacterial mRNA were produced using the SOLiD total RNA-seq kit and sequenced on a SOLiD 5500XL (50bp per read).

treatment_protocol: Five days after transfer, plants were inoculated with 2mL of bacterial suspension at OD600=0.1, according to Guefrachi et al., 2015. Mock inoculations were performed when necessary using 2 mL sterile BNM medium. Plants were grown at 28°C, 80% humidity and under a 16/8 hour of light/dark photoperiod.

tag: condition

value: A. indica nodule Spherical bacteria (no phenotype of differentiation)

value: [delta]bclA strain


title: ORS285_AI_14dpi_bclA_3


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_D7

extract_protocol:
Total RNA from bulk samples was extracted using Quick-RNA Mini Prep (Zymo Research) following the vendor protocol with a DNase treatment step
For library construction methods, see SAMPLES, description: Library Construction field. For details see the Methods section in the manuscript

value: Pooled male and female


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_D8


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_E10


title: ORS285_AI_14dpi_bclA_1


title: Odor replicate 3, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data

value: Olfactory mucosa


title: EE4_HET


title: EE3_Treated

value: TR


title: Odor replicate 1, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data


title: ORS285_AA_14dpi_bclA_3

source_name: From A. afraspera nodule tissues at 14 days post inoculation

value: A. afraspera nodule Elongated bacteria (no phenotype of differentiation)


title: ∆rmtAB24_1


title: EE2_WT


title: Vehicle replicate 3, GFP+ cells from 3 mice [Kentucky assay: whiskey lactone]

description: mRNA abundance data

value: FACS sample, GFP-


title: EE10_HET


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_D5


title: ORS285_AA_14dpi_bclA_2


title: EE1_Treated


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_D4


title: ORS285_AA_14dpi_bclA_1

value: A. afraspera nodule bacteria (no phenotype of differentiation)


title: ORS285_YM_bclA_3

source_name: Culture in rich medium

value: YM culture


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_D6


title: Odor replicate 1, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate and whiskey lactone mixture]

description: mRNA abundance data


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_D2


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_D1


title: ORS285_YM_bclA_1


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_D12


title: ORS285_YM_bclA_2


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_D3


title: CC9_KO

value: KO


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_D11


title: KO-P14


title: Vehicle replicate 2, GFP+ cells from 3 mice [Kentucky assay: whiskey lactone]

description: mRNA abundance data

source_name: Olfactory mucosa; Vehicle-stimulated

value: Vehicle


title: Dpep2 vs. Wt2

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

description: biol. replicate 2, (-) polarity

hyb_protocol: Labeled samples was mixed and hybridized using Agilent Technologies habridization chambers according the supplier's recommendation. Washing of the hybridized arrays was done with a SSC protocol.

scan_protocol: Scanning of all microarrays was performed with 5µm resolution using a DNA microarray laser scanner (DNA Microarray Scanner BA, Agilent Technologies) according the manufacturers’ instructions.

data_processing: Raw microarray images were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.9.5, Agilent Technologies) using local background without spacial detrend with a grid file and GE2-NonAT_95_Feb07 (Agilent Technologies) setting. Intensities were normalized by local background correction and by rank consistency filtering with LOWESS normalization. The intensity ratios were calculated by using the most conservative estimate of error between Universal Error Model and propagated error.

organism: Escherichia coli BL21(DE3)

source_name: broth culture

label_protocol: RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies) using FullSpectrum MultiStart Primer for T7 IVT RNA Amplification (BioCat GmbH, Heidelberg, Germany) as random T7 labeling.

growth_protocol: A single colony from a freshly striped plate was picked up and inoculated 20 ml LB broth in a 50 ml tube. The cells were grown in an orbital shaker at 37°C, 220 rpm for 4 hours.  3 ml of the cultures were used to inoculate 100 ml of LB broth in a 200 ml flask and grown to the cell density of A600=0.6.

extract_protocol: The total RNA was isolated from cells for microarray analysis using the SV Total RNA Isolation kits (Promega) with modifications. Culture aliquots were removed and mixed with 1 ml of stop solution (5% water-saturated phenol (pH: 4.5), 95% ethanol). The cultures were snap-frozen in liquid nitrogen and stored at -80°C.  After thawing on ice, bacteria were pelleted by centrifugation at 8000 g at 4°C for 20 min. The cell pellets were resuspended in 100 µl distilled H2O containing 50 mg/ml lysozyme, and the suspensions incubated at room temperature for 4 min. 75 µl lysis reagents (from Promega SV total RNA purification kit) was mixed with each sample, and then 350 µl RNA dilution buffer (from kit) was added. The mixtures were heated at 70 °C for 3 min and then centrifuged at 11,580 g for 10 min at room temperature. The supernatant from each sample was mixed with 200 µl of RNase-free 95% ethanol. The mixture was transferred to a spin column (from kit) and centrifuged for 1 min at max speed. The column was washed with 600 µl wash buffer (from kit). 50 µl of DNase mix (5 µl 90 mM MnCl2, 40 µl DNase core buffer, 5 µl DNase I (from kit)) was applied to the column matrix and incubated at room temperature for 15 min, and then 200 µl DNase stop mix (from kit) was added and centrifuge 11,580 g for 1 min. The column was washed twice with 600 µl and 250 µl wash buffer, respectively. Finally, RNA was eluted into 100 µl RNase-free distilled H2O. The purified RNA was quantified on a Nanodrop machine (Nano Drop Technologies).

treatment_protocol: In the phosphosugar stress condition, the cells were grown to a density of A600=0.5. 25% glucose or α-methylglucoside was added to the cultures to a final concentration of 1% and the incubation continued for 20 min. The same procedure above-mentioned was used to isolate total RNA from cells.

value: rne-∆EBS-FLAG

value: wildtype


title: BB7_KO

value: Frontal lobe (brain)


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_D10


title: BB1_KO


title: Vehicle replicate 4, GFP+ cells from 3 mice [Kentucky assay: whiskey lactone]

description: mRNA abundance data


title: Dpep1 vs. Wt1

description: biol. replicate 1, (-) polarity


title: Vehicle replicate 2, GFP- cells from 3 mice [Kentucky assay: whiskey lactone]

description: mRNA abundance data

value: FACS sample, GFP+