title: Cerebellum_1

city: Hamburg

first: Melanie

last: Schoof

address: Martinistr. 52

institute: Research Institute Childrens Cancer Center Hamburg

data_processing:
usegalaxy and rstudio
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic (reads with quality < 20 were trimmed)
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR aligner (length of genome sequence around annotated junction = 100, using basic 2 pass-mapping,excluding alignements with indels or soft clippings, MAPQ value for unique mapper filter = 60, number of genome bins for coordinate-sorting = 50 and maximum number of loci anchor allowed to map to = 50)
Read count extraction and normalization using featureCount and VST normalized files from DESeq2 were used for downstream analysis
Assembly: mm10
Supplementary files format and content: tab-delimited text files include featureCount files for each sample, and a VST-file from DESeq2

extract_protocol:
TRIZOL
From total RNA, mRNA was extracted using the NEBNext Poly(A) mRNA Magnetic Isolation module (New England Biolabs) and RNA-Seq libraries were generated using the NEXTFLEX Rapid Directional qRNA-Seq Kit (Bioo Scientific) as per the manufacturer´s recommendations. Concentrations of all samples were measured with a Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and fragment lengths distribution of the final libraries was analyzed with the DNA High Sensitivity Chip on an Agilent 2100 Bioanalyzer (Agilent Technologies). All samples were normalized to 2nM and pooled equimolar. The library pool was sequenced on the NextSeq500 (Illumina) with 1 x 75 bp, with 16.1 to 18.6 mio reads per sample.

value: pediatric glioma tumor model

value: WT/Control


title: Olfactor_bulb_3

status: Public on Sep 25 2023

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype


title: Cerebellum_2


title: Cerebellum_3


title: Olfactor_bulb_2


title: Olfactor_bulb_1


title: X9026_Tumor_401


title: X395_mouse_shh

value: Math1-cre::SmoM2 Fl/wt


title: KRASG12D, Trametinib Sample 2

city: Dallas

first: Michael

last: Dellinger

state: Texas

address: 5323 Harry Hines Blvd

country: USA

institute: University of Texas Southwestern Medical Centre

description:
Cells were transfected with KRASG12D-expressing lentivirus particles to express Mutant KRASG12D
Tram_2_S13

data_processing:
Gene expression analyses were performed using Partek Flow software
Single-end reads were aligned to the human reference genome (hg38) using STAR
gene expression was quantified using RefSeq annotations
Expression counts were normalized using Counts Per Million (CPM). Genes with low expression in all samples were excluded.
Assembly: hg38
Supplementary files format and content: KRAS_GFP_CPM_Compiled.xlsx, xlsx File format,CPM Values,Gene ID,Gene name,P-value, FDR,Log2 Ratios, Fold Change etc.
Supplementary files format and content: Tram_vs_DMSO_CPM_Compiled.xlsx, xlsx File format,CPM Values,Gene ID,Gene name,P-value, FDR,Log2 Ratios, Fold Change etc.

organism: Homo sapiens

source_name: dermis of juvenile foreskin

growth_protocol: Primary Human Dermal Lymphatic Endothelial Cells (HDLEC) (C-12216) were maintained in EGM-2MV media (LONZA CC-3125).

extract_protocol:
RNA was then isolated with a Qiagen RNeasy Plus Mini Kit (Qiagen, #74314).
Samples were submitted to the Next Generation Sequencing Core for library preparation with the TruSeq RNA library prep kit

treatment_protocol: Primary human LECs were infected with lentivirus particles. Twenty-four hours later, the media was replaced with standard growth media. To assess the impact of trametinib on KRASG12D-LECs, primary human LECs were infected with lentivirus particles, and the media was replaced with normal growth media 24 hours later. Forty-eight hours after infecting cells, they were treated with DMSO or trametinib (10 nM) for approximately 16 hours.

value: dermis of juvenile foreskin

tag: cell line

value: HDLEC

tag: cell type

tag: treatment

value: Trametinib


title: SHH_MB_2


title: SHH_MB_3


title: X397_mouse_shh


title: X396_mouse_shh


title: Tumor1_S6


title: SHH_MB_1


title: Mouse HGG-MYCN_6

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

library_source: transcriptomic single cell

data_processing:
All samples were demultiplexed and then processed with the 10x Genomics CellRanger v6.0.2 pipeline.
For all samples, the raw 10X scRNA-seq data was converted to fastq format with CellRanger's mkfastq function.
CellRanger's count algorithm was then used to align the data against the murine reference transcriptome mm10, version 2020-A.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: brain tumor

extract_protocol:
Tumors of four hGFAP-cre::TP53Fl/Fl::lsl-MYCNFl/wt mice were isolated and minced. To prepare single-cell suspensions, samples were digested with papain and DNAse, and passed through a 40 µm cell strainer. Red blood cells were depleted using red-blood-cell  lysis buffer and non-vital cells were removed using 7-Aminoactinomycin D staining. 10,000 vital cells were used as input for scRNA-seq.
Dual-index libraries were generated with Chromium Single Cell 3’ v3.1 technology (10x Genomics) and sequenced using a NextSeq 2000 sequencing instrument (high-throughput kit, 100 cycles).

value: brain tumor

tag: age

value: 70 days

tag: Sex

value: male


title: AML irisin rep 3

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression after 24hr culture with irisin 0.5 μg/ml in media

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise.

source_name: AML12 irisin, replicate3

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced per manufacturer’s protocol.

growth_protocol: AML cells were cultured in DMEM F-12 medium supplemented with 10% fetal bovine serum

extract_protocol: RNA was isolated using Trizol reagent then purified with Rneasy mini kit.

treatment_protocol: Cells grown in 10 cm dish were cultured with or without 0.5 μg/ml irisin for 24 hr using DMEM F-12 medium supplemented with 10% fetal bovine serum as propagation medium.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

value: liver


title: AML irisin rep 1

source_name: AML12 irisin, replicate1


title: AML irisin rep 4

source_name: AML12 irisin, replicate4


title: AML control rep 3

description: Gene expression after 24hr culture without irisin

source_name: AML12 control, replicate3


title: AML control rep 2

source_name: AML12 control, replicate2


title: AML control rep 1

source_name: AML12 control, replicate1


title: AML irisin rep 2

source_name: AML12 irisin, replicate2


title: Tumor2_S7


title: X398


title: US_405


title: US_407


title: Tumor3_S8


title: X8140_Tumor_400


title: US_406


title: X399


title: X8973_Tumor_402


title: NexCre Lhx2 Mutant 1

city: Mumbai

first: Shubha

last: Tole

state: Maharashtra

address: 1, Homi Bhabha Road,, Tata Institute of Fundamental Research,

department: Dept. of Biological Sciences

country: India

institute: Tata Institute of Fundamental Research

description: Sample 7: NexM1_M

data_processing:
Alignment:  Sequenced reads were aligned on the latest   mouse reference genome assembly (mm10) using HISAT2
Conversion: SAM/BAM files were further processed using SAMtools
The number of reads per transcript was calculated and   normalized by DESeq2 using R software
Genes were considered significantly differentially expressed for FDR of <0.1. For representation, genes with fold change  cutoff of +/-1.5 were used
Mutually exclusive and overlapping genes between datasets were identified using Venny (2.1.0).
Gene ontology analysis was performed using Gene  Ontology Resource (http://geneontology.org/)
Genome_build: mm10
Supplementary_files_format_and_content: Pal et al 2020_Counts File.xlsx; Matrix table with raw gene counts for every gene and every sample

source_name: Microdissected Subplate from Somatosensory Cortex

extract_protocol:
P0 brains were dissected in ice-cold HBSS, and 200 µm-thick sections were cut using a vibratome (VT1000S). The lowermost part of the cortical plate (presumptive subplate) was visually identified and micro-dissected under stereomicroscopic guidance in ice-cold HBSS under RNase-free conditions. Microdissected subplate tissue was stored in Buffer RLT Plus (Qiagen) at -80°C and RNA was extracted using RNeasy PLUS Micro kit (Qiagen).
mRNA was isolated from total RNA, cDNA was prepared, and libraries were prepared using the IlluminaTruSeq RNA Sample preparation V2.
For RNA-seq, libraries were multiplexed and sequenced as 100 base-pairs (bp) pair-end reads using the Illumina HiSEQ2500 platform, at an expected depth of 60M single reads.

tag: strain

value: mixed

value: Cerebral Cortex region of brain

value: Postnatal day zero (P0)


title: NexCre Lhx2 Mutant 2

description: Sample 8: NexM2_P


title: Emx1Cre Lhx2 Mutant 2

description: Sample 4: EmxM2_H


title: NexCre Control 1

description: Sample 5: NexC1_I

value: WT


title: AML control rep 4

source_name: AML12 control, replicate4


title: Emx1Cre Lhx2 Mutant 1

description: Sample 3: EmxM1_D


title: Emx1Cre Control 1

description: Sample 1: EmxC1_B


title: KMS11.BATF.GNE781.1

city: Atlanta

first: Benjamin

middle: G

last: Barwick

state: GA

address: 1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37

department: Hematology and Medical Oncology

institute: Emory University

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
KBG1

data_processing:
FASTQ files were quality trimmed with TrimGalore! (v0.6.4) and CutAdapt (v2.5)
Quality and adapter trimmed FASTQ files were mapped to the GRCh38 reference genome (GRCh38.d1.vd1.fa) with the GENCODE v22 transcription database using STAR aligner (v2.5.3a)
Putative PCR duplicate reads were marked in BAM files using Samtools (v1.10)
R (v4.1.2) was used to determine read counts using the ‘summarizeOverlaps’ function of the GenomicAlignments package (v1.30.0) to identify exonic read counts
Gene expression data was normalized for sequencing depth using fragments per kilobase per million autosomal reads (FPKM)
Assembly: GRCh38 reference genome (GRCh38.d1.vd1.fa) with the GENCODE v22 transcription database
Supplementary files format and content: geneFpkm.exon.csv: comma separated file, columns defined above in description column. Sample values are Fragments per kilobase per million (FPKM) normalized as described above.
Supplementary files format and content: geneCts.exon.csv: comma separated file, columns defined above in description column. Sample values are raw read counts.

source_name: multiple myeloma

growth_protocol: RPMI 1640 supplemented with 5% FBS and 1X glutamineGlutaMAX (Gibco), without antibiotics

extract_protocol:
Qiagen Rneasy extraction according to manufacturer's recommendations
GeneWiz Standard RNA-seq

treatment_protocol: Cells were treated with 200 nM pomalidomide, 40 nM GNE-781, both, or an equivalent amount of DMSO for 48 hours

value: multiple myeloma

value: BATF


title: KMS11.BATF.Combo.2

value: 200 nM POM + 40 nM GNE-781


title: KMS11.BATF.GNE781.2

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
KBG2


title: KMS11.BATF.Combo.1

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
KBC1


title: KMS11.BATF.Pom.2

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
KBP2

value: 200 nM POM


title: Emx1Cre Control 2

description: Sample 2: EmxC2_G


title: KMS11.BATF.Pom.1

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
KBP1


title: KMS11.BATF.DMSO.1

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
KBD1

value: DMSO


title: KMS11.eGFP.Combo.2

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
KEC2

value: eGFP


title: KMS11.eGFP.GNE781.2

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
KEG2


title: KMS11.eGFP.GNE781.1

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
KEG1


title: KMS11.eGFP.Combo.1

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
KEC1


title: NexCre Control 2

description: Sample 6: NexC2_J


title: JJN3.BATF.Combo.1

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JBC1


title: KMS11.eGFP.DMSO.1

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
KED1


title: JJN3.BATF.GNE781.2

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JBG2


title: KMS11.eGFP.DMSO.2

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
KED2


title: KMS11.eGFP.Pom.2

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
KEP2


title: JJN3.BATF.Pom.1

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JBP1


title: JJN3.BATF.GNE781.1

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JBG1


title: KMS11.eGFP.Pom.1

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
KEP1


title: KMS11.BATF.DMSO.2

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
KBD2


title: JJN3.eGFP.GNE781.1

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JEG1


title: JJN3.eGFP.Pom.2

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JEP2


title: JJN3.BATF.DMSO.1

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JBD1


title: JJN3.BATF.Pom.2

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JBP2


title: JJN3.eGFP.Combo.1

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JEC1


title: JJN3.eGFP.Combo.2

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JEC2


title: JJN3.eGFP.DMSO.1

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JED1


title: biol rep 2, hiF-T, KDM1A, guide 3

city: Philadelphia

first: Naveen

last: Jain

state: PA

address: Room 415, 415 Currie Boulevard

institute: University of Pennsylvania

data_processing:
Base calling and preliminary quality scoreing was done in real time on a NextSeq 500 with RTA 2.0. The sequencing runs were stored and demultiplexed automatically on the Illumina BaseSpace website.
We aligned reads to the human genome (assembly hg38) using kallisto (Bray et al., 2016) and generated count tables with uniquely mapped reads using scripts provided at: https://github.com/arjunrajlaboratory/KallistoSleuth. We performed differential expression analysis in R using DESeq2and with data from at least 2 biological replicates for each sample and condition.
Assembly: GRCh38
Supplementary files format and content: *abundance.tsv: Gene expression values; column 1 is gene IDs, column 2 is length, column 3 is effective length, column 4 is estimated counts, column 5 is TPM

source_name: BJ skin fibroblast

extract_protocol:
RNA was extracted as per the manufacter's protocol using an RNeasy Micro kit (Qiagen #74004).
RNA-sequencing libraries were constructed as per the manufacter's protcol using a NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490L), NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L), and NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1) oligos (NEB #EE7600S).

value: BJ skin fibroblast

value: hiF-T

value: human fibroblast-like cells with inducible hTERT expression

value: KDM1A knockdown


title: biol rep 1, hiF-T, SPP1, guide 3

value: SPP1 knockdown


title: JJN3.eGFP.GNE781.2

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JEG2


title: biol rep 2, hiF-T, SPP1, guide 1


title: biol rep 1, hiF-T, SPP1, guide 2


title: JJN3.BATF.DMSO.2

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JBD2


title: biol rep 2, hiF-T, SPP1, guide 2


title: JJN3.eGFP.Pom.1

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JEP1


title: biol rep 1, hiF-T, SPP1, guide 1


title: JJN3.BATF.Combo.2

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JBC2


title: JJN3.eGFP.DMSO.2

description:
gene_id: ENSEMBL gene id (gencode v22), chr: chromosome, start: transcription start site, end: transcription termination site, strand: strand, symbol: gene name, gene_type: type of gene, source: source of gene annotation, cds.start: coding start, cds.end: coding end, protein_id: protein id
JED2


title: biol rep 1, hiF-T, KDM1A, guide 3


title: biol rep 1, hiF-T, KDM1A, guide 2


title: biol rep 2, hiF-T, KDM1A, guide 2


title: biol rep 1, hiF-T, CDKN1A, guide 2

value: CDKN1A knockdown


title: biol rep 2, hiF-T, CDKN1A, guide 2


title: biol rep 2, hiF-T, CDKN1A, guide 1


title: biol rep 1, hiF-T, CDKN1A, guide 1


title: biol rep 1, hiF-T, backbone, guide 2

value: control guide


title: biol rep 1, hiF-T, backbone, guide 1


title: biol rep 2, hiF-T, backbone, guide 1


title: biol rep 2, hiF-T, backbone, guide 2


title: NHBE IAV-dNS1 8hpi Rep2

city: Seattle

first: Daniel

last: Blanco-Melo

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Center

data_processing:
Sequencing reads were aligned to the human genome (hg19) using the STAR aligner (Dobin et al., 2013)
Differential gene expression analysis was performed using DESeq2 (Love et al., 2014), as implemented in the RNA Express application in BaseSpace (Illumina®).
Heatmap plots of statistically significant differentially expressed genes (L2FC ≥ 2, Adjusted p-value < 0.05) were constructed using the heatmap.2 function form the ggplots package in R.
Sequencing reads were also aligned to the IAV (A/Puerto Rico/8/34/Mount Sinai) genome reference using Bowtie2 (Langmead and Salzberg, 2012).
Expression of NS1 transcripts was addressed by counting the total number of reads aligning to the non-overlapping NS1 portion in segment 8 (S8:27-514) using samtools (Li et al., 2009). The viral genome references for IAV (A/Puerto Rico/8/34/Mount Sinai) were: AF389122.1, AF389121.1, AF389120.1, AF389119.1, AF389118.1, AF389117.1, AF389116.1, AF389115.1. Defective viral genomes (DVGs) identification and quantification was performed using ViReMa (Routh and Johnson, 2014) following a previously described pipeline (Alnaji et al., 2019).
hg19, AF389122.1, AF389121.1, AF389120.1, AF389119.1, AF389118.1, AF389117.1, AF389116.1, AF389115.1
Tab delimited text file including raw counts for each sample

source_name: Normal Human Bronchial Epithelial Cells

extract_protocol:
Total RNA from infected and mock treated cells was extracted using TRIzol (Thermo Fisher®) or the RNeasy Mini kit (QIAGEN®) according to the manufacturer’s instructions and treated with DNase I.
RNA-seq libraries were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina®), following manufacturer’s instructions. All sequencing runs were performed using an Illumina NextSeq 500 platform.

value: Normal Human Bronchial Epithelial Cells

value: Primary Lung Cells

value: Influenza A Virus delta-NS1 8 hours


title: NHBE IAV-dNS1 8hpi Rep1

value: WT


title: NHBE IAV-dNS1 12hpi Rep2

value: Influenza A Virus delta-NS1 12 hours


title: NHBE IAV-dNS1 16hpi Rep2

value: Influenza A Virus delta-NS1 16 hours


title: biol rep 2, hiF-T, SPP1, guide 3


title: NHBE IAV-dNS1 Rep4

value: Influenza A Virus delta-NS1


title: NHBE IAV-dNS1 Rep3


title: NHBE IAV-dNS1 12hpi Rep1


title: IB114 cas9 infected  by the bank, treated by DNAPK inhibitor

city: Bordeaux

first: Amandine

last: Crombe

address: 229 cours de l'Argonne

country: France

institute: Institut Bergonié

library_source: genomic

data_processing:
The entire genomic DNA was sequenced by Nucleus Biotech. SgRNA was amplified, and Next-Generation Sequencing (NGS) was performed on the Illumina NextSeq platform, targeting 60 million reads.
Supplementary files format and content: tab-delimited text file with CrispR cloud fold change results
Supplementary files format and content: Excel file with RIGER fold change results
Supplementary files format and content: Excel file with RIGER calculations
Supplementary files format and content: tab-delimited text file with Mageck fold change results

molecule: genomic DNA

growth_protocol: Cells were cultured in RPMI medium 1640 (Sigma Life Technologies, Saint Louis, MO) supplemented with 10% fetal calf serum (Dutscher, France)  at 37 °C with 5% CO2

extract_protocol: Genomic DNA was extracted using the DNeasy Blood and Tissue kit (Qiagen ID: 69504) following the manufacturer's protocol

treatment_protocol: Cells were treated by DMSO or  by 40µM of AZD7648 during 72h.

value: myxofibrosarcomas


title: NHBE IAV-NS1-T Rep3

value: Influenza A Virus NS1-T


title: NHBE IAV-dNS1 Rep2


title: NHBE IAV-NS1-T Rep1


title: NHBE IAV-dNS1 Rep1


title: NHBE IAV-NS1-T Rep2


title: NHBE IAV-WT Rep4

value: Influenza A Virus WT


title: NHBE IAV-WT Rep3


title: NHBE IAV-WT Rep1


title: NHBE IAV-WT Rep2


title: PASC2, scRNAseq

city: Honolulu

first: Juwon

last: Park

state: HI

address: 651 Ilalo St.

department: Tropical Medicine, Medical Microbiology and Pharmacology

institute: University of Hawaii at Manoa

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRch38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMCs

extract_protocol:
Human venous peripheral blood samples were taken and collected in ethylene diamine tetra-acetic acid (EDTA) tubes by venipuncture. Diluted blood was layered on top of Ficoll-Paque Plus and peripheral blood mononuclear cells were separated by centrifugation at 400 × g for 30 minutes at room temperature
Libraries were performed following Chromium Next GEM Single Cell 3' protocol from 10xGenomics. GEMs are generated in Chromium Controller, followed by RT and cDNA amplification. 3' Gene Expression Library construction comprises of the following steps: fragmentation, end repair, A-tailing, adapter ligation, sample index PCR. Sequencing-ready libraries are checked for their quality on Bioanlayzer DNA chip.

value: PBMCs

value: CD45+ cells


title: PASC1, scRNAseq

description: 10x Genomics


title: ctrl2, scRNAseq

description: 10x Genomics


title: IB114 cas9 infected  by the bank, treated by DMSO

value: DMSO


title: L10T

city: Houston

first: Kangyu

last: Lin

address: 1515 Holcombe Blvd

department: Department of Gastrointestinal Medical Oncology

institute: The University of Texas MD Anderson Cancer Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver tumor

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: tissue source

value: colorectal cancer (CRC) patient

value: Liver tumor


title: L11T

description: 10x Genomics


title: L9T

description: 10x Genomics


title: L11N

description: 10x Genomics

source_name: Liver normal

value: Liver normal


title: L9N

description: 10x Genomics


title: L8T2

description: 10x Genomics


title: L7N

description: 10x Genomics


title: C6T

description: 10x Genomics

source_name: Colon tumor

value: Colon tumor


title: NHBE IAV-NS1-T Rep4

value: Normal Human Bronchial Epithelial Cells


title: L8T1

description: 10x Genomics


title: C5T

description: 10x Genomics


title: C3T

description: 10x Genomics


title: L6T

description: 10x Genomics


title: C2T

description: 10x Genomics


title: C2N

description: 10x Genomics

source_name: Colon normal

value: Colon normal


title: L4T

description: 10x Genomics


title: C3N

description: 10x Genomics


title: L5N

description: 10x Genomics


title: L3N

description: 10x Genomics


title: C4T

description: 10x Genomics


title: L2N

description: 10x Genomics


title: NHBE IAV-dNS1 16hpi Rep1

value: Primary Lung Cells


title: C1T

description: 10x Genomics


title: L12T

description: 10x Genomics


title: C1N

description: 10x Genomics


title: L1T

description: 10x Genomics


title: L1N

description: 10x Genomics


title: Day 16 CorrIgG control sa19_L003

city: Boston

first: Violetta

last: Karwacki-Neisius

state: MA

address: 300 Longwood Avenue

department: Newborn Medicine

institute: Boston Children's Hospital

description: Day 16 CorrIgG control

data_processing:
CUT&RUN reads were mapped to hg38 using Bowtie2.3.5.1, with parameters --no-unal --
local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700.
Bigwig files were generated using BamCoverage in Deeptools3.3.1, with parameters --binSize 20 -- normalizeUsing BPM.
MACS2.2.6 was used to call KDM5C peaks on each replicate individually, with the --nolambda parameter. Bedtools (v2.28.0) was used to subtract blacklist regions (using bedtools subtract) and to identify peaks called in both replicates (using bedtools intersect).
The blacklist file was downloaded from https://github.com/Boyle-Lab/Blacklist/blob/master/lists/hg38-blacklist.v2.bed.gz.
Assembly: Peaks mapping to chrM and chrUn were removed, and peak annotation was performed using homer-4.11, with annotatePeaks.pl, and the fraction of peaks associated with each genomic feature was plotted in Prism 9.
Supplementary files format and content: Peaks mapping to chrM and chrUn were removed, and peak annotation was performed using homer-4.11, with annotatePeaks.pl, and the fraction of peaks associated with each genomic feature was plotted in Prism 9.

source_name: iPSCs created from human skin fibroblasts and differentiated into neuronal tissue

growth_protocol: Human iPSC were cultures on irradiated mouse embryonic fibroblast (MEF) feeder cells CF-1 (GlobalStem cat no:GSC-6201G) in DMEM/F12-15mM Hepes (STEMCELL Technologies cat no: 36254) supplemented with 20% KnockOut Serum Replacement (KSR) (Invitrogen cat no:10828-028), 100 mM 2-mercaptoethanol (2ME) (Gibco Cat no: 21985-023), 2mM L-glutamine (corning cat no:25-005-CI), 1XMEM non-essential amino acids (Invitrogen Cat.no:11140050) and 10 ng/ml bFGF (Bio Pioneer Inc cat no: HRP-0011-1). Cells were fed, inspected daily and differentiated cells at the edges of colonies were mechanically removed. Cells were passaged either manually or with collagenase (Invitrogen cat no: 17104-019). The neuronal differentiation was performed according to: Yichen Shi et al., under the title "Directed differentiation of human pluripotent stem cells to cerebral cortex neurons and neural networks" published in Nature protocols, 2012

extract_protocol:
Cells were washed with PBS and detached from plates. Cells were frozen in 50%FBS/40% growth medium and 10% DMSO. Further extraction was according to Cell Signalling technologies with modifications.
Accordingly to the Illumina library construction strategies

treatment_protocol: The neuronal differentiation was performed according to: Yichen Shi et al., under the title "Directed differentiation of human pluripotent stem cells to cerebral cortex neurons and neural networks" published in Nature protocols, 2012.


title: Day 16 CorrIgG control sa19_L002

description: Day 16 CorrIgG control

value: iPSCs created from human skin fibroblasts and differentiated into neuronal tissue


title: Day 16 MutIgG control sa17_L004

description: Day 16 MutIgG control


title: Day 16 CorrIgG control sa19_L001

description: Day 16 CorrIgG control


title: Day 16 MutIgG control sa17_L002

description: Day 16 MutIgG control


title: Day 16 MutIgG control sa17_L003

description: Day 16 MutIgG control


title: Day 16 MutIgG control sa17_L001

description: Day 16 MutIgG control


title: Day 16 Corr rep2 sa15_L003

description: Day 16 Corr rep2

tag: day

tag: cohort

value: mut


title: Day 16 Corr rep2 sa15_L002

description: Day 16 Corr rep2

value: corr


title: Day 16 Corr rep2 sa15_L004

description: Day 16 Corr rep2


title: L4N

description: 10x Genomics


title: Day 16 Corr rep2 sa15_L001

description: Day 16 Corr rep2


title: Day 16 Mut rep2 13_i22_L002

description: Day 16 Mut rep2


title: Day 16 Mut rep2 13_i22_L003

description: Day 16 Mut rep2


title: Day 16 Mut rep2 13_i22_L001

description: Day 16 Mut rep2


title: kidney, rep2, 129 strain, Akita-Renin Tg

city: Singapore

first: Jing

last: Guo

state: State...

address: 8 Collage Road, DUKE-NUS Medical School, level 5

department: Center for Computational Biology

country: Singapore

institute: Duke-NUS Medical School

description: 10x Genomics

data_processing:
Sequencing reads were aligned and quantified to the mouse genome GRCm38 (mm10-3.0.0 provided by 10x Genomics) using 10x Genomics cellranger count (v3.1.0).
Assembly: GRCm38
Supplementary files format and content: read counts file from 10x CellRanger output

source_name: Kidney tubules

extract_protocol:
Mouse kidneys was perfused, excised, minced, digested to obtain single cell suspension as described before. Cells were collected by centrifugation, subjected to live-death dye and sorted by flow cytometry using BD FACS ARIA system. For glomerular samples, mice were perfused with magnetic beads and glomeruli were isolated from kidney tissue by digestion. Then single cell suspension was obtained by further digestion from glomeruli.
Isolated living single cell suspensions were converted to barcoded scRNA-seq libraries by using the Chromium Single Cell 3′ Library, Gel Bead & Multiplex Kit, and Chip Kit V3, loading an estimated 7,000–12,000 cells per library/well, and following the manufacturer's instructions. Indexed libraries were sequenced using Illumina NovaSeq 6000 platform, where 150bp pair-end sequences were obtained.

value: Kidney tubules

value: transgenic

value: 10 weeks


title: kidney, rep2, 129 strain, wildtype

description: 10x Genomics

value: WT

value: Wildtype, 129S6


title: glomerulus, 129 strain, wildtype

description: 10x Genomics

source_name: Kidney glomerulus

value: Kidney glomerulus


title: Day 16 CorrIgG control sa19_L004

description: Day 16 CorrIgG control


title: kidney, rep1, 129 strain, Akita-Renin Tg

description: 10x Genomics


title: kidney, rep1, 129 strain, wildtype

description: 10x Genomics


title: Day 16 Corr rep1 sa11_L001

description: Day 16 Corr rep1


title: Day 16 Corr rep1 sa11_L002

description: Day 16 Corr rep1


title: Human_skin, Healthy, 5

city: Kyoto

first: Satoshi

last: NAKAMIZO

state: Kyoto

address: 54 Shogoin-Kawahara, Sakyo

country: Japan

institute: Kyoto University

description: 10x Genomics

data_processing:
The CellRanger pipeline (v3.1.0) (10x genomics) was used to generate count matrices from FASTQ files using default parameters.
Assembly: GRCh38-3.0.0

source_name: skin

extract_protocol:
For each skin sample, a 4-mm punch biopsy was obtained after local anesthesia and was placed immediately into 1 mL Bambanker freezing media (Nippon Genetic Co. Ltd., Tokyo, Japan) on ice and stored at -80 ºC until analysis (storage time was between 4 to 5 months). For cell dissociation, cryopreserved tissue was thawed in a 37 ºC water bath, transferred to 0.25% Trypsin-EDTA (Gibco, Life Technologies, USA), and incubated at 37 ºC for 15 min. The tissue was then transferred to a dissociation solution for a second round of dissociation using the abovementioned procedure, followed by dissociation with a Miltenyi Human Whole Skin Dissociation Kit (Miltenyi Biotec, Bergisch-Gladbach, Germany) for 2.5 hours according to the manufacturer's protocol. The tissue was manually disaggregated by pipetting up and down 10 times in a 1 ml-wide bore pipette. Next, cells were passed through a 70 μm cell strainer (#352340, Corning) and stored on ice. Cells were pelleted at 300g for 10 min and resuspended in 1 ml RPMI. Live cells were counted using 0.4% trypan blue (Gibco, cat. # 15250061).
Isolated cells were loaded onto a Chromium instrument (10X Genomics) according to the Chromium Single Cell 3’ Reagent Kit v3 user guide (https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v3-chemistry).

value: skin

value: M

tag: body site

value: Left upper arm

tag: disease state

value: Healthy


title: Day 16 Corr rep1 sa11_L004

description: Day 16 Corr rep1


title: Day 16 Mut rep1 sa9_L004

description: Day 16 Mut rep1


title: Human_skin, Healthy, 3

description: 10x Genomics

value: Right cheek


title: Day 16 Mut rep1 sa9_L002

description: Day 16 Mut rep1


title: Human_skin, Healthy, 1

description: 10x Genomics

value: F

value: Left cheek

value: Healthyケンジョウ


title: Human_skin, Sarcoidosis, 3

description: 10x Genomics

value: Lower lip

value: Sarcoidosis


title: Day 16 Mut rep1 sa9_L001

description: Day 16 Mut rep1

value: mut

value: iPSCs created from human skin fibroblasts and differentiated into neuronal tissue


title: glomerulus, 129 strain, Akita-Renin Tg

description: 10x Genomics

value: transgenic


title: Day 16 Mut rep2 13_i22_L004

description: Day 16 Mut rep2

value: corr


title: Human_skin, Sarcoidosis, 2

description: 10x Genomics

value: Left lower leg


title: Human_skin, Sarcoidosis, 1

description: 10x Genomics

value: Eyebrow


title: Day 32 Corr rep2

first: Shannan

last: Ho Sui

state: Massachusetts

address: 401 Park Drive, Level 3 East

department: Biostatistics

institute: Harvard T.H. Chan School of Public Health

description: iPSCs created from human male skin fibroblasts and differentiated into neuronal tissue

data_processing:
Data were processed using bcbio-nextgen 1.2.8 that includes the following steps:
Atropos trimming, v1.1.29: atropos trim --quality-cutoff=5 --minimum-length=25 --overlap 8
bwa alignment, v0.7.17: bwa aln -n 2 -k 2 -t 10 hg38.fa trimmed_reads.fq.gz
alignmentSieve to shift reads, v3.5.0: alignmentSieve  --bam <sample-sorted.bam> --ATACshift --minMappingQuality 10
macs2 peak calling, v2.2.7.1: macs2 callpeak -t <sample-sort-shifted_chrom-noMito.unique-noduplicates.bam> --nomodel  -f BAMPE -g 3217346917  --nolambda --keep-dup all
bamCoverage bigwig file creation, v3.5.0: bamCoverage --bam <sample-sort-shifted_chrom-noMito.unique-noduplicates.bam> --outFileName <sample.bw> --binSize 20 --effectiveGenomeSize 3217346917 --smoothLength 60 --extendReads 150 --centerReads --normalizeUsing CPM --ignoreForNormalization chrM
Assembly: hg38
Supplementary files format and content: bigwig signal tracks and narrowPeak peak files

source_name: Corrected IPSC

growth_protocol: Human iPSC were cultured on irradiated mouse embryonic fibroblast (MEF) feeder cells CF-1 (GlobalStem cat no:GSC-6201G) in DMEM/F12-15mM Hepes (STEMCELL Technologies cat no: 36254) supplemented with 20% KnockOut Serum Replacement (KSR) (Invitrogen cat no:10828-028), 100 mM 2-mercaptoethanol (2ME) (Gibco Cat no: 21985-023), 2mM L-glutamine (corning cat no:25-005-CI), 1XMEM non-essential amino acids (Invitrogen Cat.no:11140050) and 10 ng/ml bFGF (Bio Pioneer Inc cat no: HRP-0011-1). Cells were fed, inspected daily and differentiated cells at the edges of colonies were mechanically removed. Cells were passaged either manually or with collagenase (Invitrogen cat no: 17104-019). The neuronal differentiation was performed according to: Yichen Shi et al., under the title "Directed differentiation of human pluripotent stem cells to cerebral cortex neurons and neural networks" published in Nature protocols, 2012

extract_protocol:
Cells were washed with PBS, treated with DNase for 30 minutes and then detached from plates. 100.000 per sample were frozen in 50%FBS/40% growth medium and 10% DMSO. Further extraction was according to the Active Motif pipeline.
Accordingly to the Active Motif library construction strategies and as previously described in (Buenrostro et al. 2013) and (Corces et al. 2017).

treatment_protocol: The neuronal differentiation was performed according to: Yichen Shi et al., under the title "Directed differentiation of human pluripotent stem cells to cerebral cortex neurons and neural networks" published in Nature protocols, 2012. Cells were either cultured accordingly to the protocol only (Mutant and Corrected) or in addition in the presence or absence of a Wnt inhibitor and activator (Mutant+Inhibitor and Corrected+W) transiently.


title: Day 32 Corr+W rep2

value: corr-w


title: Human_skin, Healthy, 4

description: 10x Genomics

value: skin

value: Face


title: Day 32 Mut+inh rep2

source_name: Mutant iPSC

value: mut-inh


title: Day 16 Corr rep1 sa11_L003

description: Day 16 Corr rep1


title: Day 32 Mut rep2


title: Day 16 Mut+inh rep2


title: Human_skin, Healthy, 2

description: 10x Genomics

value: Right lower leg

value: Healthy


title: Day 16 Mut rep2


title: Day 16 Corr+W rep2


title: Day 16 Corr rep2


title: Day 12 Corr+W rep2


title: Day 12 Corr rep2


title: Day 12 Mut+inh rep2


title: Day 12 Mut rep2


title: Day 8 Corr+W rep2


title: Day 8 Corr rep2


title: Day 8 Mut rep2


title: Day 32 Corr rep1


title: Day 32 Corr+W rep1


title: Day 32 Mut+inh rep1


title: Day 32 Mut rep1


title: Day 16 Corr+W rep1


title: Day 8 Mut+inh rep2


title: Day 16 Corr rep1


title: Day 16 Mut+inh rep1


title: Day 12 Corr rep1


title: Day 12 Mut+inh rep1


title: Day 16 Mut rep1


title: Day 12 Corr+W rep1


title: Day 8 Corr+W rep1


title: Day 12 Mut rep1


title: Day 8 Corr rep1


title: Day 16 Mut rep1 sa9_L003

description: Day 16 Mut rep1


title: Day 8 Mut+inh rep1


title: Cold_input

status: Public on Sep 26 2023

city: Nanjing

first: Zexue

last: He

state: Jiangsu Province

address: Xuanwu District,1 Weigang

department: Agricultural College

country: China

institute: Nanjing Agricultural University

data_processing:
For RNA-seq analyses, the quality of raw reads was assessed using FastQC (Kroll et al. 2014). Raw reads were cleaned after removal of adapters and poor-quality bases using Trimmomatic (version 0.39) (Bolger et al. 2014). Clean reads were aligned to the rice reference genome using Hisat2 (version 2.1.0) (Kim et al. 2015). The number of reads mapped to each gene was counted using FeatureCounts (version 1.6.4) (Liao et al. 2014). FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) values were calculated to represent the gene expression levels.
For DRIP-seq data analyses, the raw data were processed for removal of adapter and low-quality bases using TrimGalore (version0.4.3,Babraham Bioinformatics). Clean reads were aligned to the rice reference genome (MSU version7.0) using Bowtie (Langmead et al. 2009) with the following parameters‐‐best‐‐strata -m 1 - x 800. Additional duplicate reads were removed by using the SAMtools rmdup,version1.4 (Li et al. 2009). The strand-specific reads were separated using flags of SAM files. The direction of R-loops was determined according to the direction of the R2 reads (R1 for the paired-end reads) aligned to the genome.
Assembly: MSU v7.0

organism: Oryza sativa Japonica Group

source_name: leaf,input,Cold

growth_protocol: Seeds of Nipponbare (Oryza sativa ssp. japonica) were pre-germinated at room temperature under dark conditions for 3 days. Uniformly germinated seeds were individually put into 96-well PCR plates with bottom cut. Each plate with germinated seeds were put into the liquid culture medium for continuing to grow under a mean temperature as 28/22°C and 12 h/12 h for a light-dark cycle in the greenhouse.

extract_protocol:
Uniformly germinated seeds were individually put into 96-well PCR plates with bottom cut. Each plate with germinated seeds were put into the liquid culture medium for continuing to grow under a mean temperature as 28/22°C and 12 h/12 h for a light-dark cycle in the greenhouse.
Total RNA was extracted from CK and COLD seedlings, respectively, using the RNeasy plant Mini kit (Qiagen, 74904). After removal of genomic DNA contamination using DNase I treatment, approximately 30 µg total RNA was used for mRNA enrichment using oligo (dT) conjugated magnetic beads.The DNA-RNA hybrid immunoprecipitation (DRIP) experiment and DRIP-seq libraries were conducted as described before

treatment_protocol: At the 13th day, a half of PCR plates with seedlings were continued to grow in the normal conditions (CK) and another half were grown at 4℃ for cold treatment. After a 24 h cold treatment (COLD), two biological replicates of CK and cold treated (COLD) seedlings were collected and stored at −80°C for later use.

value: leaf

tag: antibody

value: ChIP,input

value: After a 24 h  grown at 4℃ for cold treatment(cold)


title: 78s

type: genomic

city: Warsaw

first: Mateusz

last: Bujko

address: Roentgena 5

department: Molecular and Translational Oncology Department

country: Poland

institute: Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology

description: genomic DNA from somatotropinoma

hyb_protocol: Infinium MethylationEPIC BeadChip Array (Illumina) was used to profile whole-genome DNA methylation

scan_protocol: Scanning on an iScan Illumina instrument, call-rates generated by the Illumina GenomeStudio software

data_processing: minfi R package

source_name: somatotropinoma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was isolated using AllPrep DNA/RNA/miRNA Universal Kit (QIAGEN)

tag: gender

value: Female

tag: sample type

value: somatotropinoma

value: DG


title: 70s

description: genomic DNA from somatotropinoma

value: Male


title: 62s

description: genomic DNA from somatotropinoma

value: SG


title: Day 8 Mut rep1

value: mut


title: 90s

description: genomic DNA from somatotropinoma


title: 92s

description: genomic DNA from somatotropinoma


title: 89s

description: genomic DNA from somatotropinoma


title: 97s

description: genomic DNA from somatotropinoma


title: 88s

description: genomic DNA from somatotropinoma


title: 99s

description: genomic DNA from somatotropinoma


title: 65_16

description: genomic DNA from somatotropinoma


title: 86s

description: genomic DNA from somatotropinoma


title: 74s

description: genomic DNA from somatotropinoma


title: 93s

description: genomic DNA from somatotropinoma


title: 69_18

description: genomic DNA from somatotropinoma


title: 36_19

description: genomic DNA from somatotropinoma


title: 82s

description: genomic DNA from somatotropinoma


title: Triple-negative subtype S3

city: Sao Paulo

first: Alexis Germán

last: Murillo Carrasco

email: agmurilloc@gmail.com, agmurilloc@usp.br

state: Sao Paulo

address: Av. Dr. Arnaldo 251, Sao Paulo

country: Brazil

institute: ICESP

description: 25 ng of miRNA were loaded into the platform.

hyb_protocol: miRNAv3 NanoString® cartridges (NanoString® Technologies, cat. CSO-MIR3-12) were loaded with the mix per sample and sealed.

scan_protocol: For data collection, we transferred samples to an nCounter® Digital Analyzer device (NanoString® Technologies).

data_processing: miRNA expression data were analyzed in the nSolver™ Data Analysis v.4.0 software (NanoString® Tech.) with the default protocol by the manufacturer. For cf-miRNA, we normalize the expression of human miRNAs by the geometric mean of all negative (negative normalization) and positive (positive normalization) probes. Then, we used the top 15 more stable regions (up to 15% of the coefficient of variation) to normalize the content set data.

source_name: plasma

label_protocol: ~25 ng of cf-miRNA were hybridized for 16.5 hours with molecular barcoding for 827 experimentally validated human miRNAs (from miRBase v21) using the nCounter Master Mix (NanoString® Technologies, cat. NAA-AKIT-012).

extract_protocol: Using 200 uL of this plasma, we isolated cell-free miRNA (cf-miRNA) following the instructions of the miRNeasy Serum/plasma kit (cat. 217184, Qiagen).

tag: subtype

value: TRIPLE-NEGATIVE

value: Elderly (diagnosed after 40yo)


title: Triple-negative subtype S4


title: 96s

description: genomic DNA from somatotropinoma


title: Luminal HER2 subtype S2

value: LUMINAL HER2


title: Luminal HER2 subtype S1

value: Young (diagnosed before 40yo)


title: 84s

description: genomic DNA from somatotropinoma


title: Luminal B subtype S2

value: LUMINAL B


title: 71s

description: genomic DNA from somatotropinoma


title: 57_17

description: genomic DNA from somatotropinoma


title: 85s

description: genomic DNA from somatotropinoma


title: 64_17

description: genomic DNA from somatotropinoma


title: Triple-negative subtype S1


title: 53_15

description: genomic DNA from somatotropinoma


title: 61_18

description: genomic DNA from somatotropinoma


title: 42_19

description: genomic DNA from somatotropinoma


title: Luminal A subtype S1

value: LUMINAL A


title: HER2 subtype S3


title: Luminal B subtype S1


title: HER2 subtype S2


title: 32_12

description: genomic DNA from somatotropinoma


title: PAO1_pit4_Induced_3

city: Leuven

first: Rob

last: Lavigne

address: Kasteelpark Arenberg 21

department: Biosystems

country: Belgium

institute: KU Leuven

data_processing:
[cDNA reads quality and trimming]  The quality of the cDNA reads was analyzed using FastQC (0.11.8) (Andrews, 2010). Adapters and poor quality sequences were trimmed using Trimmomatic (v0.39) (Bolger et al., 2014).
[Allignment ]  BWA-MEM aligner 44 (v0.7.17) was used to map the read pairs to the reference genome of PAO1 (NC_002516.2), which was manually altered to carry the pit4 genomic insert in its Tn7 site.
[Normalization]  The resulting fragment counts were normalized by gene length and the total number of mapped non-rRNA fragments per sample to yield fragments per kilobase of transcript per million mapped fragments (FPKM) values
[statistics]  Principal Component Analysis (PCA) was conducted with the prcomp package in R to evaluate sample clustering. Finally, gene expression analysis was performed using the DESeq2 Bioconductor package in R (v1.30.0)
Assembly: PAO1 (NC_002516.2)
Supplementary files format and content: FeatureCounts results containing raw gene feature counts and counts normalized by fragments per kilobase per million mapped non-rRNA fragments

organism: Pseudomonas aeruginosa

source_name: bacterial cell

growth_protocol: LB overnight cultures of PAO1::empty and PAO1::pit4 were diluted a 100-fold in 50 mL LB medium to an OD600nm of 2

extract_protocol:
At OD (600 nm) = 2, 2 mL cells was harvested, 20 % ice cold stop mix solution (95 % v/v ethanol, 5 % v/v phenol, saturated pH 4.5) was added and the mixture was immediately snap-frozen in liquid nitrogen. Next, samples were thawed on ice and their pellets were collected (20 min, 4 °C, 4500 g) for resuspension in 300 µL of a 0.5 mg/mL lysozyme solution in Tris-EDTA buffer (10 mM Tris-HCl, 1 mM EDTA, pH 8). Subsequently, samples were treated via the hot phenol method, followed by ethanol precipitation to extract the RNA. Next, the samples were treated with DNase I and the RNA was further purified using ethanol purification.
RNA samples were converted into cDNA using the Illumina Stranded Total RNA Prep Ligation Ribo Zero Plus kit. The Bioanalyzer and the DNA high sensitivity kit (Aligent) were used to verify rRNA depletion and evaluate the average fragment length, aiming for fragments around 500 bp.
All samples (n = 3 per condition) were pooled together in equimolar amounts to obtain a 25 µL sample of 4 nM and the cDNA samples were paired-end sequenced via Illumina next-generation sequencing (Novaseq 6000)

treatment_protocol: Induced conditions: LB was supplemented with 1 mM IPTG

value: bacterial cell

value: single genomic integration of pit4 via pUC18mini-Tn7-lac-GW

value: 1 mM IPTG


title: 28s

description: genomic DNA from somatotropinoma


title: 29s

description: genomic DNA from somatotropinoma


title: PAO1_empty_Induced_2

value: single genomic integration of an empty pUC18mini-Tn7-lac-GW


title: HER2 subtype S1


title: PAO1_empty_Induced_3


title: PAO1_pit4_Induced_2


title: PAO1_empty_Induced_1


title: Triple-negative subtype S2


title: PAO1_pit4_Not induced_3

value: 0 mM IPTG


title: PAO1_pit4_Induced_1


title: PAO1_pit4_Not induced_2


title: IB128 cell line, GSK595 10 days, rep3

hyb_protocol: 300 ng of total purified RNA was hybridized with a Capture ProbeSet and Reporter CodeSets probes in a 15-µL reaction volume for 18 h at 65°C.

scan_protocol: Hybridized samples were then immobilized on the nCounter cartridge in the nCounter Prep Station. The cartridge was ultimately scanned with 490 Fields of View on the nCounter Digital Analyzer. Quality control assessment of the samples (imaging, binding density, positive control linearity, and limit of detection) was performed according to the Nanostring recommendations

data_processing: Raw gene expression was normalized using the RUVseq pipeline, and differential gene expression was analyzed using Deseq2 (v1.28). Pathway scoring was performed on normalized data using the single-sample GSEA method (ConsensusTME 0.0.1.9), and differences between vehicle and treated samples were evaluated for significance using Wilcoxon tests

source_name: IB128 cell line, GSK595 10 days, rep3

label_protocol: Specific oligonucleotide probe pairs that are bound to barcoded tags (Nanostring Technologies inc.) were conducted according to the manufacturer's protocol.

growth_protocol: Cells were maintained in RPMI medium 1640 GlutaMAX Supplement in the presence of 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a humidified atmosphere containing 5% CO2

extract_protocol: RNA was extracted using an RNeasy Plus Mini Kit (Qiagen). The purity and concentration of the isolated RNA were determined with a NanoDrop spectrophotometer, and capillary electrophoresis using a Bioanalyzer 2100 was carried out to determine the RNA integrity number (RIN).

treatment_protocol: Cells were untreated or treated with GSK595 at their respective IC80 every 3 days for 10 days

value: osteosarcoma


title: IB128 cell line, Control, rep3

label: Specific oligonucleotide probe pairs that are bound to barcoded tags (Nanostring Technologies inc.)

source_name: IB128 cell line, Control, rep3


title: PAO1_empty_Not induced_3


title: RC17 Master Cell Bank

city: Lund

first: Malin

last: Parmar

department: Department of Experimental Medical Science, Lund University

country: Sweden

institute: Wallenberg Neuroscience Center, MultiPark and Lund Stem Cell Centre

data_processing:
Fastq files are generated with Illumina Local Run Manager Generate Fastq workflow.
Raw data is de-multiplexed, aligned to the Human reference genome GRCh37/h19 (BWA-MEM Whole Genome Aligner v0.7.12-r1039), and genomic variant were called with DNA Amplicon analysis module (Basespace workflow v2.1.1).
The generated variant call format (vcf) files were visualized and annotated with Illumina Variant Studio software v3.0.
Genetic variants are cross-referenced to public databases (dbSNP, ClinVar, COSMIC).
The identified variants are reported as benign, pathogenic or of unknown significance based on available clinical classification.
Assembly: GRCh37/h19
Supplementary files format and content: The processed datafiles are text files (.vcf) listing the identified genomic varinats.

extract_protocol:
gDNA was extracted using the QIAamp DNA mini kit (Qiagen). 10 ng of gDNA was used for the construction of sequencing libraries.
gDNA libraries were prepared using the AmpliSeq Illumina Cancer Hotspot panel v2 Kit following manufacturer's instruction.
targeted gDNA sequencing

value: embryonic stem cells

value: embryonic stem cell culture

tag: time

value: Day 0


title: 27_18

description: genomic DNA from somatotropinoma

value: Female

value: somatotropinoma

value: SG


title: IB128 cell line, GSK595 10 days, rep2

source_name: IB128 cell line, GSK595 10 days, rep2


title: PAO1_empty_Not induced_1

tag: genotype


title: IB128cell line, Control, rep2

source_name: IB128cell line, Control, rep2


title: STEM-PD batch 1

tag: cell line

value: ventral midbrain dopaminergic precursors

value: ventral midbrain dopaminergic precursor differentiation

value: Day 16


title: PAO1_pit4_Not induced_1

tag: cell type


title: STEM-PD batch 3

data_processing:
Fastq files are generated with Illumina Local Run Manager (v2.4.0.2385) Generate Fastq workflow (v2.1.0.19)
Raw data is de-multiplexed, aligned to the Human reference genome GRCh37/h19 (BWA-MEM Whole Genome Aligner 0.7.9a-isis-1.0.2), and genomic variants were called with DNA Amplicon analysis module (3.24.1.8+master).
The generated variant call format (vcf) files were visualized and annotated with Illumina Variant Studio software v3.0.
Genetic variants are cross-referenced to public databases (dbSNP, ClinVar, COSMIC).
The identified variants are reported as benign, pathogenic or of unknown significance based on available clinical classification.
Assembly: GRCh37/h19
Supplementary files format and content: The processed datafiles are text files (.vcf) listing the identified genomic varinats.

extract_protocol:
gDNA was extracted using the QIAamp DNA mini kit (Qiagen). 10 ng of gDNA was used for the construction of sequencing libraries.
gDNA libraries were prepared using the AmpliSeq Illumina Cncer Hotspot panel v2 Kit following manufacturer's instructions.
targeted gDNA sequencing

tag: treatment


title: Tissue microarray, alopecia areata (n=2) and healthy scalp (n=2)

city: San Francisco

first: Jarish

last: Cohen

state: CA

address: 513 Parnassus Ave, HSW12 Room 1201B

department: Dermatology

institute: University of California, San Francisco

data_processing:
Libraries were pooled and sequenced on an Illumia NextSeq550 targetting 140M reads per capture area.
Fastq files were processed with the spaceranger pipeline (v 1.3.1) and were mapped to the Visium Human Transcriptome Probe Set v1.0 GRCh38-2020-A
Assembly: GRCh38
Supplementary files format and content: TIFF files are the image capture areas generated from the 10X Visium Protocol
Supplementary files format and content: PNG files are the output of the spaceranger pipeline used by Seurat in downstream analysis.
Supplementary files format and content: Filtured Feature BC Matrix Files (barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz) are the spaceranger output files generated from analysis of the fastq files
Library strategy: Spatial transcriptomics

extract_protocol:
5 micron FFPE tissue sections were placed on the 10x Visium V1 capture area. Each section contained two healthy skin samples and two samples of either scarring alopecia or alopecia areata. Slides were prepared per 10x Genomics Visium V1 Human FFPE protocol, with 3 minutes used as the Hematoxylin staining time, and 40 minutes used for tissue permeabilization. A Zeiss Axioscan.Z1 was used for image capture.
Libraries were constructed with the Visium Spatial Gene Expression Slide Kit (PN-1000185) per manufacturer protocol.

tag: tissue

value: skin


title: Tissue microarray, scarring alopecia (n=2) and healthy scalp (n=2)


title: Day 32 Corr+W rep3

data_processing:
Basecalling and demultiplexing by Illumina bcl2fastq
Alignment to human reference genome with hisat (v2.1.0) and converted
Create normalized count table using cuffdiff from Cufflinks(v2.1.1): cuffdiff -p 24 -u hg38.gtf sample1.bam sample2.bam...
genes.fpkm_tracking was modified with additional sample grouping information and removal of unused column, and used as input for Qlucore Omics Explorer (v3.7).
Assembly: hg38
Supplementary files format and content: m.genes.fpkm_tracking (tab delimited text file)

extract_protocol:
Total RNA was isolated using the TRIZOL reagent according to the manufacturer’s instructions (Life Technologies cat no: 15596018).
Illumina stranded mRNA, per the manufacturer instruction.

value: human fibroblasts to iPSCs differentiated into neurons

tag: condition

value: Corr+W

value: day 32


title: KO_Inf_lung_5

city: Riverside

first: Meera

last: Nair

address: 243 SOM Research 3401 Watkins Drive

institute: UC Riverside

description:
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.
SAMPLE 10

hyb_protocol: Lysates were hybridized to  Nanostring MouseImmunology probes sets overnight per the manufacterers protocol.

scan_protocol: Samples were loaded onto the nanostring cartrisge and read using the Nanostring nCounter Sprint.

data_processing: Data was processed using Rosalind Bio, where normalization and background subtraction were performed.

source_name: lung homogenate

growth_protocol: Lung from WT or KO mice was homogenized into a singel cell suspension, around 1M cells were separated for RNA isolation.

extract_protocol: From around 1M cells, total RNA was isolated using the Promega SV Total RNA Isolation System  kit , cat. no, Z3105.

value: KO:Retnla-/-,td tomato

value: day 30 post N. Brasiliensis infection

value: lung


title: IB128 cell line, GSK595 10 days, rep1

source_name: IB128 cell line, GSK595 10 days, rep1

value: osteosarcoma


title: IB128 cell line, Control, rep1

source_name: IB128 cell line, Control, rep1


title: Day 32 Corr rep3

source_name: iPSCs created from human skin fibroblasts and differentiated into neuronal tissue

value: Corr


title: Day 32 Mut+inh rep3

value: Mut+inh


title: IB115 cell line, GSK595 10 days, rep3

source_name: IB115 cell line, GSK595 10 days, rep3

value: dedifferentiated liposarcoma


title: PAO1_empty_Not induced_2

value: bacterial cell

value: single genomic integration of an empty pUC18mini-Tn7-lac-GW

value: 0 mM IPTG


title: Day 32 Mut rep3

value: Mut


title: Day 32 Corr+W rep2


title: 18_18

description: genomic DNA from somatotropinoma

value: Male

value: somatotropinoma

value: DG


title: KO_Inf_lung_4

description:
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.
SAMPLE 9


title: Day 32 Corr rep2

value: human fibroblasts to iPSCs differentiated into neurons


title: IB115 cell line, Control, rep3

source_name: IB115 cell line, Control, rep3


title: WT_Inf_Lung_5

description:
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.
SAMPLE 7

value: WT


title: Day 32 Mut+inh rep2

value: day 32


title: IB115 cell line, GSK595 10 days, rep2

source_name: IB115 cell line, GSK595 10 days, rep2


title: Day 32 Mut rep2


title: WT_Inf_Lung_4

description:
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.
SAMPLE 6


title: IB115 cell line, Control, rep2

source_name: IB115 cell line, Control, rep2


title: WT_Inf_Lung_3

description:
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.
SAMPLE 5


title: Day 32 Mut+inh rep1


title: Day 32 Corr+W rep1

value: Corr+W


title: Day 32 Corr rep1


title: KO_Inf_lung_3

description:
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.
SAMPLE 8

value: KO:Retnla-/-,td tomato

value: day 30 post N. Brasiliensis infection


title: Day 32 Mut rep1


title: KO_Inf_lung_2

description:
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.
SAMPLE 4

value: lung


title: 172s

description: genomic DNA from somatotropinoma

value: Female


title: IB115 cell line, Control, rep1

source_name: IB115 cell line, Control, rep1


title: IB115 cell line, GSK595 10 days, rep1

source_name: IB115 cell line, GSK595 10 days, rep1


title: Day 16 Corr+W rep3

value: day 16


title: 173s

description: genomic DNA from somatotropinoma

source_name: somatotropinoma


title: 23s

description: genomic DNA from somatotropinoma


title: WT_Inf_Lung_2

description:
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.
SAMPLE 3


title: Day 16 Corr rep3

value: Corr


title: Day 16 Mut+inh rep3

value: Mut+inh


title: Day 16 Mut rep3


title: Day 16 Corr+W rep2


title: 160s

description: genomic DNA from somatotropinoma

value: SG


title: IB114 cell line, Control, rep3

source_name: IB114 cell line, Control, rep3

value: mixofibrosarcoma


title: WT_Inf_Lung_1

description:
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.
SAMPLE 2


title: Day 16 Corr rep2


title: KO_Inf_lung_1

description:
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.
SAMPLE 1


title: 164s

description: genomic DNA from somatotropinoma


title: Day 16 Mut rep2

value: Mut


title: CC10Cre+_Inf_lung_5

scan_protocol: Samples were loaded onto the nanostring cartridge and read using the Nanostring nCounter Sprint.

growth_protocol: Lung from CC10 Cre- or CC10 Cre+ mice was homogenized into a singel cell suspension, around 1M cells were separated for RNA isolation.

value: CC10 Cre+

tag: infection status


title: Day 16 Mut+inh rep2


title: IB114 cell line, GSK595 10 days, rep2

source_name: IB114 cell line, GSK595 10 days, rep2


title: 18_13

description: genomic DNA from somatotropinoma

value: Male

value: somatotropinoma


title: Day 16 Corr+W rep1

value: human fibroblasts to iPSCs differentiated into neurons


title: Day 16 Corr rep1


title: IB114 cell line, Control, rep2

source_name: IB114 cell line, Control, rep2


title: 129s

description: genomic DNA from somatotropinoma

value: DG


title: 168s

description: genomic DNA from somatotropinoma


title: Day 16 Mut+inh rep1


title: 170s

description: genomic DNA from somatotropinoma


title: 176s

description: genomic DNA from somatotropinoma


title: 169s

description: genomic DNA from somatotropinoma


title: 113s

description: genomic DNA from somatotropinoma


title: Gp130+/+ stomach (antrum)

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

country: Australia

institute: Monash University

description:
Wildtype gastric cells, antrum
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using cellCounts a function within Rsubread (https://rdrr.io/bioc/Rsubread/man/cellCounts.html).
Quality control was performed by filtering genes that failed to express (an expressed gene has at least 1 UMI count) in at least 3 cells in at least 1 as well as cells with <200 detected gene or cells with >6000 detected genes together with cells having mitochondrial content>40% and ribosomal content > 40% were excluded from the rest of the analysis.
After removing unwanted cells from the dataset, the data was normalized using a global-scaling normalization method “LogNormalize” that normalizes the feature expression measurements for each cell by the total expression, multiplies this by a scale factor (10,000 by default), and log-transforms the result.
A linear transformation (‘scaling’) was applied to the normalised data prior to dimensional reduction techniques using the ScaleData function in Seurat.
Clustering is performed using 20 dimensions with a resolution of 0.6.
Assembly: mm10
Supplementary files format and content: Processed_counts.RData: R data object file containing a Seurat object of processed and normalised counts together with clustering metadata.
Supplementary files format and content: Wild_type_Antrum_barcodes.tsv: Tab-separated file containing barcodes used in the analysis.
Supplementary files format and content: Wild_type_Antrum_genes.tsv: Tab-separated file containing details of genes included in the analysis.
Supplementary files format and content: Wild_type_Antrum_matrix.mtx: Tab-separated file containing sparse matrix of UMI counts.
Supplementary files format and content: Wild_type_Corpus_barcodes.tsv: Tab-separated file containing barcodes used in the analysis.
Supplementary files format and content: Wild_type_Corpus_genes.tsv: Tab-separated file containing details of genes included in the analysis.
Supplementary files format and content: Wild_type_Corpus_matrix.mtx: Tab-separated file containing sparse matrix of UMI counts.
Supplementary files format and content: FF_Antrum_barcodes.tsv: Tab-separated file containing barcodes used in the analysis.
Supplementary files format and content: FF_Antrum_genes.tsv: Tab-separated file containing details of genes included in the analysis.
Supplementary files format and content: FF_Antrum_matrix.mtx: Tab-separated file containing sparse matrix of UMI counts.
Supplementary files format and content: FF_Corpus_barcodes.tsv: Tab-separated file containing barcodes used in the analysis.
Supplementary files format and content: FF_Corpus_genes.tsv: Tab-separated file containing details of genes included in the analysis.
Supplementary files format and content: FF_Corpus_matrix.mtx: Tab-separated file containing sparse matrix of UMI counts.

source_name: Gastric (antrum)

extract_protocol:
Freshly collected gastric tissue from Gp130F/F and wildtype Gp130+/+ mice was cut into 1 mm pieces and digested in Collagenase/Dispase (Roche) and DNase I (Roche) in Ca2+- and Mg2+-free Hanks medium plus 5% FCS for 30 minutes at 37°C with gentle shaking. Samples were then vortexed for 15 seconds, filtered and washed in PBS plus 5% FCS. Single cell suspensions were blocked with FC block (Invitrogen) for 20 minutes at 4°C, before staining with fluorophore-conjugated primary antibodies for EpCAM and CD45.2 for 20 minutes at 4°C in the dark. Cells were washed twice and re-suspended in PBS supplemented with 5% FCS prior to staining with Sytox blue for viability and sorted with an Aria III cell sorter.
Library was performed according to the manufacturer’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: CD45 and EpCAM cells

value: Gastric (antrum)

tag: age

value: 8-12 weeks


title: Gp130+/+ stomach (corpus)

description:
Wildtype gastric cells, corpus
10x Genomics

source_name: Gastric (corpus)

value: Gastric (corpus)


title: 17s

description: genomic DNA from somatotropinoma


title: MTN_123

first: Junhyong

last: Kim

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

description: MTN, 4 Weeks, Batch 2

data_processing:
Basecalling was done with bcl2fastq v2.17. Reads were trimmed for adapters, low quality base calls, and poly-A sequence using both in-house software and cutadapt v2.10 (Martin, Marcel. 2011), and then mapped to the mouse genome (mm10) using STAR v2.7.2d (Dobin et al. 2013). Uniquely mapped reads were used for gene quantification using VERSE v0.1.4 with parameters "-s 0 -z 3 --nonemptyModified" (Zhu et al. 2016)
Assembly: mm10
Supplementary files format and content: Tab-separated values files; gene counts

source_name: Brainstem

extract_protocol:
DPA and MTN neurons were labeled with 1,1'-Dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI) from the maxillary first molars of C57BL/6  mouse, then isolated in acute culture from the TG tissues and from brainstem slices, respectively. Afterwards, they were manually collected using a glass micropipette containing RNase inhibitor; each neuron was also photographed prior to collection, and the images were used for cell body area (μm2) measurements using ImageJ software.
Neurons were individually digested and reverse-transcribed into non-stranded cDNA using poly-T primers. The resulting cDNA was amplified using SMART-Seq v4 Ultra Low Input RNA kit according to the manufacturer’s instructions, but with the following modifications: 1) ERCC RNA Spike-In controls were added at the cell lysis step 2) 18 PCR cycles were performed to amplify cDNA libraries. The libraries were diluted accordingly and used to make DNA sequencing libraries by following the Nextera XT DNA Library Preparation Kit protocol. Library size distribution and quality were measured using Agilent's BioAnalyzer High Sensitivity DNA assay prior to sequencing.

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

value: Brainstem

tag: strain

value: 4 weeks old


title: 157s

description: genomic DNA from somatotropinoma

value: Female


title: IB114 cell line, GSK595 10 days, rep3

source_name: IB114 cell line, GSK595 10 days, rep3


title: 163s

description: genomic DNA from somatotropinoma


title: MTN_122

description: MTN, 4 Weeks, Batch 2


title: 125s

description: genomic DNA from somatotropinoma


title: MTN_121

description: MTN, 4 Weeks, Batch 2


title: 16_12

description: genomic DNA from somatotropinoma


title: MTN_120

description: MTN, 4 Weeks, Batch 2


title: 100s

description: genomic DNA from somatotropinoma


title: IB111 cell line, GSK595 10 days, rep3

source_name: IB111 cell line, GSK595 10 days, rep3

value: dedifferentiated liposarcoma


title: IB111 cell line, GSK595 10 days, rep2

source_name: IB111 cell line, GSK595 10 days, rep2


title: IB111 cell line, Control, rep3

source_name: IB111 cell line, Control, rep3


title: MTN_117

description: MTN, 4 Weeks, Batch 2


title: MTN_116

description: MTN, 4 Weeks, Batch 2


title: MTN_119

description: MTN, 4 Weeks, Batch 2


title: CC10Cre+_Inf_lung_4

source_name: lung homogenate

value: day 30 post N. Brasiliensis infection


title: MTN_118

description: MTN, 4 Weeks, Batch 2


title: MTN_115

description: MTN, 4 Weeks, Batch 2


title: MTN_114

description: MTN, 4 Weeks, Batch 2


title: IB111 cell line, Control, rep1

source_name: IB111 cell line, Control, rep1


title: CC10Cre-_Inf_lung_4

value: CC10 Cre-


title: MTN_113

description: MTN, 4 Weeks, Batch 2


title: Cells, control day 13 3

city: Rehovot

first: Or

last: Eliason

address: 234 Hertzk

country: Israel

institute: The Weizmann Institute of Science

data_processing:
UTAP (Kohen R, Barlev J, Hornung G, et al. UTAP: User-friendly Transcriptome Analysis Pipeline. BMC Bioinformatics. 2019;20(1):154. doi:10.1186/s12859-019-2728-2)
Assembly: GIZZ01000000
Supplementary files format and content: tab-delimited text file includes raw read counts for each sample
Supplementary files format and content: tab-delimited text file includes UMI read counts for each sample
Supplementary files format and content: tab-delimited text file includes UMI counts for each sample and statistical analysis

organism: Emiliania huxleyi

source_name: cells

growth_protocol: The axenic algal strain of Emiliania huxleyi CCMP3266 was purchased from the National Center for Marine Algae and Microbiota (Bigelow Laboratory for Ocean Sciences, Maine, USA). Algae were grown in artificial sea water according to Goyet and Poisson 83 and supplemented with L1 medium according to Guillard and Hargraves 84, with the exception that Na2SiO3 was omitted following the cultivation recommendations for this strain. Algae were grown in standing cultures in borosilicate Erlenmeyers with an initial inoculum of 330 cells/ml, placed in a growth chamber at 18°C under a light/dark cycle of 16/8 hr. PAR intensity during the light period was 130 µmoles photonsm-2 s-1. Cultures volume was 50 ml except for cultures used to measure growth rates under vitamin D treatment (fig. S1) which were grown in 20 ml.

extract_protocol:
Algal cultures were harvested for RNA extraction by centrifugation at 4000 rpm for 5 min at 18°C. RNA was extracted using the Isolate II RNA mini kit (Meridian Bioscience, London, UK) according to manufacturer instructions. Cells were ruptured in RLT buffer containing 1% β-mercapto-ethanol by bead beating for 5 min at 30 mHz. RNA was then treated with 3 µl Turbo DNAse (ThermoFisher, Waltham, USA) in a 50 µl reaction volume, followed by a cleaning step using RNA Clean & ConcentratorTM-5 kit (Zymo Research, Irvine, CA, USA) according to manufacturer instructions. RNA was used for generating transcriptomic data and qPCR analysis.
MARS-seq2.0 (Keren-Shaul H, Kenigsberg E, Jaitin DA, et al. MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing. Nat Protoc. 2019;14(6):1841-1862. doi:10.1038/s41596-019-0164-4)

treatment_protocol: Continuous UV irradiation was achieved by placing a UV-emitting light source (Exo Terra Reptile UVB150, Hagen, Montreal, Canada) inside the algal growth chamber. Algal cultures experienced UV-A intensity of 0.5 w/m2, UV-B intensity of 0.07 w/m2 and UV-C intensity of 0.026 w/m2, measured using an ALMENO 2570 device (Ahlborn, Budapest, Hungary) placed within the Erlenmeyer. The UV-B intensity employed in this study was selected to replicate the UV-B radiation encountered at the ocean surface 29. The UV light-source was operating daily for 14 hours in parallel to the PAR light period, starting one hour after PAR illumination started, and ending one hour before PAR illumination ended. This irradiation regime was employed because in thought of imitating a simplified natural day cycle including a dawn and dusk period.

value: cells

value: control


title: CC10Cre-_Inf_lung_1


title: IB111 cell line, GSK595 10 days, rep1

first: Amandine

last: Crombe

institute: Institut Bergonié

source_name: IB111 cell line, GSK595 10 days, rep1


title: Cells, control day 13 1


title: Cells, control day 13 2


title: IB111 cell line, Control, rep2

source_name: IB111 cell line, Control, rep2


title: MTN_111

city: Philadelphia

description: MTN, 4 Weeks, Batch 2


title: Cells, UV day 13 3

value: Constant UV


title: MTN_110

description: MTN, 4 Weeks, Batch 2


title: Cells, UV day 13 2


title: MTN_107

description: MTN, 4 Weeks, Batch 2


title: MTN_108

description: MTN, 4 Weeks, Batch 2


title: MTN_109

description: MTN, 4 Weeks, Batch 2


title: Cells, UV day 13 1


title: MTN_105

description: MTN, 4 Weeks, Batch 2


title: Cells, control day 10 3


title: MTN_112

description: MTN, 4 Weeks, Batch 2


title: MTN_106

description: MTN, 4 Weeks, Batch 2


title: MTN_104

description: MTN, 4 Weeks, Batch 2


title: MTN_103

description: MTN, 4 Weeks, Batch 2


title: MTN_102

description: MTN, 4 Weeks, Batch 2


title: Gp130F/F stomach and tumour (corpus)

description:
Gp130F/F gastric cells, corpus
10x Genomics

source_name: Gastric and gastric tumour (corpus)

value: Gastric and gastric tumour (corpus)


title: MTN_101

description: MTN, 4 Weeks, Batch 2


title: Cells, control day 10 2


title: Cells, control day 10 1


title: MTN_99

description: MTN, 4 Weeks, Batch 1


title: MTN_97

description: MTN, 4 Weeks, Batch 1


title: Cells, UV day 10 3


title: Mouse MB, SHH 3

city: Hamburg

first: Melanie

last: Schoof

address: Martinistr. 52

institute: Research Institute Childrens Cancer Center Hamburg

description: MB SHH mouse tumor 3

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Mouse Methylation Beadchip array (MM285) using standard Illumina protocol

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

data_processing: Rstudio

label: Cy5 and Cy3

source_name: Tumor biopsy

extract_protocol: genomic DNA was extracted and purified from tumor samples using Maxwell DNA isolation kit according to standard instructions

value: fresh frozen

value: brain


title: MTN_96

description: MTN, 4 Weeks, Batch 1


title: MTN_95

description: MTN, 4 Weeks, Batch 1


title: Cells, UV day 10 2


title: Mouse MB, SHH 2

description: MB SHH mouse tumor 2


title: IB114 cell line, GSK595 10 days, rep1

city: Bordeaux

address: 229 cours de l'Argonne

source_name: IB114 cell line, GSK595 10 days, rep1

value: mixofibrosarcoma


title: MTN_94

description: MTN, 4 Weeks, Batch 1


title: MTN_93

description: MTN, 4 Weeks, Batch 1


title: Day 16 Mut rep1

source_name: iPSCs created from human skin fibroblasts and differentiated into neuronal tissue

value: human fibroblasts to iPSCs differentiated into neurons

value: Mut

tag: day

value: day 16


title: AdipoKO_BAT-4 251486841802_1_4

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

institute: NIEHS

description:
AdipoKO_BAT-4
Gene expression from knockout brown adipose tissue

data_processing: The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise

source_name: Brown Adipose Tissue

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: RNA was prepared using the Qiagen RNeasy Kit for total RNA isolation

value: adipose tissue

tag: Sex


title: MTN_92

description: MTN, 4 Weeks, Batch 1

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

value: Brainstem


title: AdipoKO_BAT-3 251486841801_1_4

description:
AdipoKO_BAT-3
Gene expression from knockout brown adipose tissue

value: Female


title: IB114 cell line, Control, rep1

source_name: IB114 cell line, Control, rep1


title: AdipoKO_BAT-2 251486841798_1_4

description:
AdipoKO_BAT-2
Gene expression from knockout brown adipose tissue


title: Mouse MB, SHH 1

description: MB SHH mouse tumor 1


title: Mouse Glioma, MYCN_2

description: Glioma MYCN mouse tumor 2


title: MTN_91

description: MTN, 4 Weeks, Batch 1

value: 4 weeks old


title: Cells, control day 7 3


title: CTL_BAT-4 251486841802_1_2

description:
CTL_BAT-4
Gene expression from control brown adipose tissue


title: MTN_90

description: MTN, 4 Weeks, Batch 1


title: Mouse Glioma, MYCN_1

description: Glioma MYCN mouse tumor 1


title: Cells, control day 7 2


title: Mouse Glioma, MYCN_3

description: Glioma MYCN mouse tumor 3


title: Cells, control day 7 1


title: MTN_89

description: MTN, 4 Weeks, Batch 1


title: MTN_88

description: MTN, 4 Weeks, Batch 1


title: MTN_86

description: MTN, 4 Weeks, Batch 1


title: AdipoKO_BAT-1 251486841797_1_4

description:
AdipoKO_BAT-1
Gene expression from knockout brown adipose tissue


title: MTN_83

description: MTN, 4 Weeks, Batch 1


title: Cells, UV day 7 3


title: Gp130F/F stomach and tumour (antrum)

description:
Gp130F/F gastric cells, antrum
10x Genomics

source_name: Gastric and gastric tumour (antrum)

value: CD45 and EpCAM cells

value: Gastric and gastric tumour (antrum)

value: 8-12 weeks


title: MTN_81

description: MTN, 4 Weeks, Batch 1

source_name: Brainstem


title: Cells, UV day 10 1

value: cells


title: CC10Cre+_Inf_lung_2

value: CC10 Cre+

value: day 30 post N. Brasiliensis infection


title: Cells, UV day 7 2

value: Constant UV


title: CTL_BAT-2 251486841797_1_2

description:
CTL_BAT-2
Gene expression from control brown adipose tissue


title: CTL_BAT-1 251486841801_1_2

description:
CTL_BAT-1
Gene expression from control brown adipose tissue


title: CTL_BAT-3 251486841798_1_2

description:
CTL_BAT-3
Gene expression from control brown adipose tissue


title: Cells, UV day 7 1


title: MTN_79

description: MTN, 4 Weeks, Batch 1


title: MTN_74

description: MTN, 3 Weeks, Batch 2

value: 3 weeks old


title: MTN_73

description: MTN, 3 Weeks, Batch 2


title: AdipoKO_WAT-4 251486841801_1_3

description:
AdipoKO_WAT-4
Gene expression from knockout white adipose tissue

source_name: White Adipose Tissue


title: MTN_82

description: MTN, 4 Weeks, Batch 1


title: MTN_84

description: MTN, 4 Weeks, Batch 1


title: MTN_75

description: MTN, 3 Weeks, Batch 2


title: Young TNBC_3

description: vesicular miRNA from 1mL of plasma were loaded into the platform.

data_processing:
miRNA expression data were analyzed in the nSolver™ Data Analysis v.4.0 software (NanoString® Tech.) with the default protocol by the manufacturer. For cf-miRNA, we normalize the expression of human miRNAs by the geometric mean of all negative (negative normalization) and positive (positive normalization) probes. Then, we used the top 15 more stable regions to normalize the content set data.
Data were exported in comma-separated value (*.csv) format for further analysis.

label: miRNA reported and capture probes

source_name: plasma (Evs)

label_protocol: All miRNA concentrated per each sample were hybridized for 16.5 hours with molecular barcoding for 827 experimentally validated human miRNAs (from miRBase v21) using the nCounter Master Mix (NanoString® Technologies, cat. NAA-AKIT-012).

extract_protocol: Using 1mL of human plasma, we isolated extracellular vesicles using the qEV Izon columns. Then, we isolated vesicular miRNA following the instructions of the miRNeasy Serum/plasma kit (cat. 217184, Qiagen).

value: Young

value: TNBC

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: III

tag: tumor relapse

value: No

tag: os

value: Alive

tag: os.time (days)

tag: race

value: White

tag: bmi

value: Eutrophic

tag: physical activity

tag: drug use

tag: cigarrette use

value: Never

tag: alcohol use

tag: cancer family history

tag: previous surgeries

tag: diabetes mellitus

tag: hbp

tag: dpoc

tag: gastritis

tag: first kindgree (cancer cases)

tag: first kindgree (breast/ovarian cancer cases)

tag: menopause status

tag: tubular grade

tag: nuclear grade

tag: mitotic index

tag: histologic grade

tag: estrogen receptor

value: Negative

tag: progesterone receptor

tag: her2 (ihc)

value: 0 (Negative)

tag: t

tag: n

tag: m

tag: neoadjuvant treatment


title: MTN_70

description: MTN, 3 Weeks, Batch 2

tag: cell type

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

tag: tissue

value: Brainstem

tag: strain

tag: age


title: MTN_71

description: MTN, 3 Weeks, Batch 2


title: MTN_72

description: MTN, 3 Weeks, Batch 2


title: MTN_69

description: MTN, 3 Weeks, Batch 2


title: Young TNBC_2

tag: subtype

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: I

tag: tumor relapse

tag: os

tag: os.time (days)

tag: Sex

value: Female

tag: race

value: Brown

tag: bmi

value: Overweight

tag: physical activity

value: With regularity

tag: drug use

tag: cigarrette use

tag: alcohol use

tag: cancer family history

tag: previous surgeries

value: Yes

tag: diabetes mellitus

tag: hbp

tag: dpoc

tag: gastritis

tag: first kindgree (cancer cases)

tag: first kindgree (breast/ovarian cancer cases)


title: AdipoKO_WAT-2 251486841798_1_3

description:
AdipoKO_WAT-2
Gene expression from knockout white adipose tissue

tag: tissue

value: adipose tissue


title: Young TNBC_1

value: Young

tag: subtype

value: TNBC

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: II

tag: tumor relapse

tag: os

tag: os.time (days)

value: Obese

tag: menopause status

tag: tubular grade

tag: nuclear grade

tag: mitotic index

tag: histologic grade

tag: estrogen receptor

tag: progesterone receptor

tag: her2 (ihc)

tag: t

tag: n

tag: m

tag: neoadjuvant treatment


title: MTN_67

description: MTN, 3 Weeks, Batch 2

tag: cell type

tag: tissue

tag: strain

tag: age

value: 3 weeks old


title: CC10Cre+_Inf_lung_3

description:
50ng of total RNA was hybridized using the Mouse Immunology probeset from Nanstring which includes 561 target genes and 15 internal reference genes.
SAMPLE 6

tag: genotype

value: CC10 Cre+

tag: infection status

value: day 30 post N. Brasiliensis infection


title: MTN_68

description: MTN, 3 Weeks, Batch 2


title: MTN_76

description: MTN, 4 Weeks, Batch 1

value: 4 weeks old


title: AdipoKO_WAT-3 251486841797_1_3

description:
AdipoKO_WAT-3
Gene expression from knockout white adipose tissue

tag: Sex


title: CTL_WAT-4 251486841802_1_1

description:
CTL_WAT-4
Gene expression from control white adipose tissue


title: Young TNBC_4

tag: subtype

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: III

tag: tumor relapse

value: No

tag: os

value: Alive

tag: os.time (days)

tag: race

value: White

tag: bmi

tag: physical activity

tag: drug use

tag: cigarrette use

value: Never

tag: alcohol use

value: In the past

tag: cancer family history

tag: previous surgeries

tag: diabetes mellitus

tag: hbp

tag: dpoc

tag: gastritis

tag: first kindgree (cancer cases)

tag: first kindgree (breast/ovarian cancer cases)

tag: menopause status

tag: tubular grade

tag: nuclear grade

value: Negative

value: 0 (Negative)

tag: her2 (fish)


title: Elderly TNBC_6

value: Elderly

tag: subtype

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: I

tag: tumor relapse

tag: os

tag: os.time (days)

tag: Sex

value: Female

tag: race

value: Brown

tag: bmi

value: Eutrophic

value: Still in use

value: Yes

tag: mitotic index

tag: histologic grade

tag: estrogen receptor

tag: progesterone receptor

tag: her2 (ihc)

tag: t

tag: n

tag: m


title: MTN_66

description: MTN, 3 Weeks, Batch 2

tag: cell type

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

tag: tissue

value: Brainstem

tag: strain

tag: age

value: 3 weeks old


title: AdipoKO_WAT-1 251486841802_1_3

description:
AdipoKO_WAT-1
Gene expression from knockout white adipose tissue

value: adipose tissue


title: MTN_65

description: MTN, 3 Weeks, Batch 2


title: MTN_62

description: MTN, 3 Weeks, Batch 2


title: MTN_64

description: MTN, 3 Weeks, Batch 2


title: MTN_59

description: MTN, 3 Weeks, Batch 2


title: CTL_WAT-3 251486841801_1_1

description:
CTL_WAT-3
Gene expression from control white adipose tissue


title: Elderly TNBC_4

tag: subtype

value: TNBC

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: II

tag: tumor relapse

value: No

tag: os

value: Alive

value: Overweight

tag: physical activity

value: Sporadically

tag: cigarrette use

tag: alcohol use

tag: cancer family history

tag: previous surgeries

tag: diabetes mellitus

tag: hbp

tag: dpoc

tag: gastritis

tag: first kindgree (cancer cases)

tag: first kindgree (breast/ovarian cancer cases)

tag: menopause status

tag: tubular grade

tag: nuclear grade

tag: neoadjuvant treatment


title: CTL_WAT-2 251486841798_1_1

description:
CTL_WAT-2
Gene expression from control white adipose tissue

tag: tissue

tag: Sex


title: MTN_58

description: MTN, 3 Weeks, Batch 2

tag: cell type

tag: strain

tag: age


title: Elderly TNBC_3

value: Elderly

tag: subtype

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

tag: tumor relapse

tag: os

tag: os.time (days)

tag: race

value: Black

tag: bmi

tag: physical activity

tag: cigarrette use

tag: alcohol use

value: Never

tag: cancer family history

tag: mitotic index

tag: histologic grade

tag: estrogen receptor

value: Negative

tag: progesterone receptor

tag: her2 (ihc)

value: 0 (Negative)

tag: t

tag: n

tag: m


title: MTN_56

description: MTN, 3 Weeks, Batch 2

tag: cell type

tag: tissue

tag: strain

tag: age


title: MTN_57

description: MTN, 3 Weeks, Batch 2


title: Elderly TNBC_1

tag: subtype

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: I

tag: tumor relapse

tag: Sex

value: Female

tag: race

value: Obese

tag: drug use

tag: previous surgeries

tag: diabetes mellitus

tag: hbp

tag: dpoc

tag: gastritis

tag: first kindgree (cancer cases)

tag: first kindgree (breast/ovarian cancer cases)

tag: menopause status

tag: tubular grade

tag: nuclear grade

tag: her2 (fish)


title: MTN_53

description: MTN, 3 Weeks, Batch 2

tag: cell type

value: Mesencephalic Trigeminal Nucleus (MTN) Neurons

tag: tissue

value: Brainstem

tag: strain

tag: age


title: MTN_54

description: MTN, 3 Weeks, Batch 2

value: 3 weeks old


title: Elderly TNBC_2

tag: subtype

value: TNBC

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

value: III

tag: tumor relapse

tag: os

value: Death

tag: os.time (days)

tag: Sex

tag: race

tag: bmi

tag: physical activity

tag: cigarrette use

tag: alcohol use

tag: cancer family history

value: Yes

tag: mitotic index

tag: histologic grade

tag: estrogen receptor

tag: progesterone receptor

tag: her2 (ihc)

tag: t

tag: n

tag: m

tag: neoadjuvant treatment


title: Young Luminal HER2_4

value: Young

tag: subtype

value: Luminal HER2

tag: current age

tag: age at biobank entrance

tag: age at dx

tag: cid code

tag: clinical stage

tag: tumor relapse

value: No

tag: os

value: Alive

tag: os.time (days)

value: Brown

value: Eutrophic

tag: drug use

tag: previous surgeries

tag: diabetes mellitus

tag: hbp

tag: dpoc

tag: gastritis

tag: first kindgree (cancer cases)

tag: first kindgree (breast/ovarian cancer cases)

tag: menopause status

tag: tubular grade

tag: nuclear grade

value: Positive

tag: her2 (fish)

value: Tis


title: MTN_55

description: MTN, 3 Weeks, Batch 2

tag: cell type

tag: tissue

tag: strain

tag: age