title: n-Myc_control,lenalidomide,rep2

city: San Francisco

first: Xiaokun

last: Shu

address: 555 Mission Bay Boulevard South, CVRI,RM484

institute: University of California, San Francisco

data_processing:
Raw FASTQ files were quality checked using FASTQC . Then fastp was used to quality trim FASTQ files using default setting.
Clean reads were processed to pseudo-align to human genome (hg38) using star.
HT-seq was used for gene counts quantification
Differential expressed genes were defined by edgeR with |log2FC| > 0.58,  p-value < 0.01, FDR < 0.05. DEGs based hypergeometric test and gene set enrichment analysis were produced by clusterProfiler.C56
Assembly: human genome (hg38)
Supplementary files format and content: csv files include raw counts

source_name: SH-EP

extract_protocol:
Total RNA was extracted by Quick-RNA Microprep Kit (Zymo Reserch, R1051).
Library was prepapred by Novogen

value: SH-EP

value: lenalidomide ON


title: SH-EP, baseline,rep1

status: Public on Feb 28 2024

type: SRA

state: CA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: treatment

value: Mock


title: n-Myc_control,DMSO,rep1

value: DMSO ON


title: n-Myc_control,DMSO,rep3


title: SH-EP, baseline,rep2


title: n-Myc_control,DMSO,rep2


title: SH-EP, baseline,rep3


title: DLBCL tissue PDX intermediate passage 4 RNA [PDX_4_HD_int ]

city: New York

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

description:
PDX_4_HD_int
logCPM_Normalized_human_PDX.csv

data_processing:
Illumina Casava-1.8.2 software used for basecalling
STAR v2.6.1a was used to align
XenofilteR v0.99 used to deconvolute PDX samples
Salmon v1.3.0 used for quantification post deconvolution
Assembly: hg38, mm10 (for PDX TME reads)
Supplementary files format and content: csv file includes Salmon TPM values

molecule: total RNA

source_name: DLBCL

extract_protocol:
Qiagen total RNA
TruSeq mRNA
polyA selection and stranded RNA-seq

tag: tissue

value: DLBCL

tag: tissue type

value: DLBCL tissue PDX intermediate passage


title: A. wentii CBS141173 NaCl + sorbitol 1

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of A nidulans FGSC A4 or A. wentii CBS141173 with hisat2 (version 2.1.0).
DESeq2 (version 1.24.0) (Love et al. 2014) was used to determine differentially expressed genes.
RPKM values were calculated with the edgeR package (“rpkm” function).
Assembly: https://fungidb.org/common/downloads/release-65/AnidulansFGSCA4/fasta/data/FungiDB-65_AnidulansFGSCA4_Genome.fasta; https://fungidb.org/common/downloads/release-65/AnidulansFGSCA4/gff/data/FungiDB-65_AnidulansFGSCA4.gff; https://fungidb.org/common/downloads/release-65/AwentiiDTO134E9/fasta/data/FungiDB-65_AwentiiDTO134E9_Genome.fasta; https://fungidb.org/common/downloads/release-65/AwentiiDTO134E9/gff/data/FungiDB-65_AwentiiDTO134E9.gff
Supplementary files format and content: excell file includes count and RPKM values for each Sample

organism: Aspergillus wentii

source_name: mycelium

growth_protocol: Barratt’s minimal broth (100 mL in 500 mL Erlenmeyer flask) inoculated with 1x108 conidia was incubated in a rotary shaker at 25 °C, 220 rpm (approx. 3.7 Hz). A. nidulans mycelia were harvested after 36 h (THS30) or 38 h (ΔgfdB), meanwhile A. wentii mycelia were harvested after 65 h (both CBS141173 and 'c gfdB) cultivation. Different incubation times were used in order we collect exponentially phase mycelia with similar physiological conditions in the case of each strain

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.

treatment_protocol: Mycelia were collected, washed and then transferred into 100 mL fresh Barratt’s minimal broth or Barratt’s minimal broth supplemented with 2 M sorbitol, 1 M NaCl, or 1 M NaCl + 2 M sorbitol. Cultures were further incubated at 25 °C and 220 rpm and samples were taken after 0.5 h for RNA isolation.

value: mycelium

tag: genotype

value: CBS141173 reference strain

value: NaCl+sorbitol treated


title: n-Myc_control,lenalidomide,rep1


title: 10astroko

city: Jerusalem

first: Oded

last: Behar

address: Ein Kerem. P.O. Box 12271, The Hebrew University Faculty ,, building 3, floor 2, room 3213

department: Developmental Biology and Cancer Research

country: Israel

institute: The Hebrew University

data_processing:
Poly-A/T stretches and Illumina adapters were trimmed from the reads using cutadapt (54); resulting reads shorter than 30bp were discarded. Reads were mapped to the M. musculus GRCm38 reference genome using STAR (55), supplied with gene annotations downloaded from Ensembl release 92 (STAR was run with EndToEnd option and outFilterMismatchNoverLmax 0.04). Expression levels for each gene were quantified using htseq-count (56). Differentially expressed genes were identified using DESeq2 (57) with the betaPrior, cooksCutoff and independent filtering parameters set to False. The pipeline was run using snakemake (58).
Assembly: Mus_musculus.GRCm38.dna
Supplementary files format and content: Immune cell fraction Sema4B-/- versus Sema4B+/- upregulated genes. Xlsx file
Supplementary files format and content: Astrocyte cell fraction Sema4B-/- versus Sema4B+/- upregulated genes. Xlsx file

organism: Mus musculus

source_name: brain (cortex)

extract_protocol: To test the changes in gene expression systematically and within specific cell types, Sema4B+/- and Sema4B -/- mice inflicted cortical injury. A 3x3mm square around the injured site was dissected out 12h after injury and dissociated into cells. Using immunopanning astrocytes (collecting the cells adhering to the Acsa-2 plate isolate) and immune cells (collecting cells adhering to a secondary-only plate and CD45 plate). The isolated cell populations were used to extract RNA and perform RNAseq.

value: brain (cortex)

tag: cell type

value: astrcocytes

value: cortical injury


title: n-Myc_SPARK-ON,DMSO,rep3


title: 9microko

value: immune cells


title: 8microko


title: n-Myc_SPARK-ON,DMSO,rep2


title: n-Myc_SPARK-ON,DMSO,rep1


title: 7microko


title: n-Myc_SPARK-ON,lenalidomide,rep3


title: n-Myc_SPARK-ON,lenalidomide,rep2


title: 6astrohet


title: 4astrohet


title: n-Myc_SPARK-ON,lenalidomide,rep1


title: 3microhet


title: 2microhet


title: 1microhet


title: Patient 8 Replicate 1

city: Chicago

first: Rogan

middle: A

last: Grant

state: IL

address: 303 E Superior St, Simpson Querrey Biomedical Research Center 5-522

department: Pulmonary and Critical Care Medicine

institute: Northwestern University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Data were processed using the Cell Ranger 7.0.1 pipeline (10x Genomics) with intronic reads disabled. To enable detection of viral RNA, reads were aligned to a custom hybrid genome containing GRCh38.93 and SARS-CoV-2 (NC_045512.2). An additional negative strand transcript spanning the entirety of the SARS-CoV-2 genome was then added to the GTF and GFF files to enable detection of SARS-CoV-2 replication as described in (33). Samples were genetically demultiplexed using the supplied “common_variants_grch38.vcf” reference, stripped of genetically-defined doublet cells.
Assembly: GRCh38
Supplementary files format and content: FASTQ

source_name: Brain, frontal lobe

extract_protocol:
During routine brain autopsy, sections of the frontal cortex were removed by dissection and placed in sufficient pre-cooled HypoThermosol solution (BioLife Solutions 101104) to cover. Postmortem interval for all samples is reported in Supplemental Table S1. Under aseptic conditions, any remaining arachnoid mater was removed on ice and discarded. Samples were then divided into 2 sections. The minor section was fixed in ice-cold fresh 4% formaldehyde (Electron Microscopy Sciences 15714) in 1X PBS for 48-72 hours, before being transferred to 1X PBS (Corning 21-040-CM) + 0.01% sodium azide (Sigma S2002) indefinitely. The major section was chopped into ~3mm strips, stored at 4˚C in HypoThermosol FRS (BioLife Solutions 101102), and processed for flow cytometry sorting as described below 0-48 hours later. Free-floating sections were placed on ice and rinsed briefly with 1X HBSS (Fisher Scientific 21023CM) and strained. Tissues were then chopped thoroughly in 1mL ice-cold digest buffer consisting of 1X Papain Dissociation System (Fisher NC9212788; 1 vial dissolved in 5mL HBSS to yield 20U of papain/mL in 1mM L-cysteine with 0.5mM EDTA) and 1mg/mL DNAse I (Roche 10104159001) with curved scissors. Chopped tissue was then transferred to gentleMACS C-tubes (Miltenyi 130-093-237) and mixed with 1mL HBSS. Samples were then mechanically dissociated using a gentleMACS Octo Dissociator using the stock program “m_brain_03_01”. Samples were then shaken at 200rpm, 37˚C for 30 minutes, followed by a second round of mechanical dissociation. Digestion was then stopped by mixing samples with 18mL ice-cold, sterile-filtered 1% BSA (Sigma SLBW2268) in 1X HBSS. Cell suspensions were then mashed through a 70-µm filter with 3x10mL ice-cold 1% BSA in HBSS into a fresh 50mL conical tube. The resulting single-cell suspension was then pelleted at 400g for 10 minutes at 4˚C and resuspended in 25mL RT 30% Percoll (Millipore-Sigma GE17-0891-01) in 1X HBSS without calcium or magnesium (Gibco 14185-052). The resultant suspension was then slowly layered on top of 5mL 70% Percoll in 1X HBSS without calcium or magnesium. Density centrifugation was performed at 600g, brake: 0, acceleration: 4 for 30 minutes at room temperature. Myelin and debris were removed using a vacuum apparatus, and 5-10mL of the cell-containing interphase was transferred to a fresh 50-mL conical tube, discarding the RBC/debris pellet. The purified cell suspension was then diluted 3:1 in ice-cold 1X HBSS and pelleted at 400g for 5 minutes at 4˚C. Cells were then resuspended in 15mL ice-cold 1x HBSS and again pelleted at 400g for 5 minutes at 4˚C and resuspended in 500µL ice-cold MACS buffer (Miltenyi 130-091-221). A 10-µL aliquot was then mixed with 10µL 2X AOPI (Nexcelom NC1412892) and counted using a Cellometer K2. Remaining cells were then pelleted at 400g for 5 minutes at 4˚C and resuspended at 1x106 cells/mL in ice-cold BamBanker medium (Bulldog Bio BB02). Cell suspensions were aliquoted at 2.5-5.0x105 cells and frozen directly at -80˚C until sorting. Frozen human brain single-cell suspensions were thawed rapidly in a 37˚C water bath with swirling and transferred to fresh 50-mL conical tubes. Cell suspensions were then diluted slowly with pre-warmed RPMI 1640 (Fisher MT10041CV) + 5% FBS (Gibco 26140079), 50µL every 5 seconds with agitation until 1.5mL, 100µL every 5 seconds with agitation until 5mL total volume. The resultant suspension was then filtered through a 70µm strainer and washed with 500µL RPMI + 5% FBS and spun down at 400g for 10 minutes at RT. Cells were then resuspended in 50µL ice-cold 1:10 human TruStain FcX (BioLegend 422302) in MACS buffer and incubated for at least 5 minutes on ice. A 2µL aliquot was then counted on a Cellometer K2 as above. Samples were then mixed with 50µL antibody cocktail / 1x106 cells (minimum 50µL; see cocktail below) and incubated at 4˚C in the dark for 30 minutes. Cells were then diluted with 900µL ice-cold MACS buffer and pelleted at 400g for 5 minutes at 4˚C, and resuspended in 400µL ice-cold MACS buffer. Immediately before sorting, suspensions were filtered through a 70-µm filter, rinsed with 100-600µL MACS buffer. SYTOX stain was then added at 1µL and the suspension was mixed thoroughly. Cells were then sorted into PBS + 4% BSA (Millipore-Sigma A1595-50ML) in DNA lo-bind tubes (Eppendorf 022431005) using a FACS ARIA SORP in a BioProtect IV-LE-Bio Containment Hood with a 100µm nozzle. For scRNA-seq, cells were sorted as singlet, non-debris, live (SYTOX-), CD56-, CD15-, CD45+, HLA-DR+ events. Microglia were further subdivided as [CD14/CD3/CD19]- events for flow cytometry. Sorted cells were diluted to 1.5mL with BamBanker medium and immediately pelleted at 400g for 5 minutes at 4˚C. Cells were then resuspended in PBS + 4% BSA at ~1x106 cells/mL. Cell concentrations and viability were confirmed using a Cellometer K2 as above. Libraries were then generated using the 10X Genomics 5’ V2 kit, according to manufacturer’s instructions (CG000331 Rev A), using a 10X Genomics Chromium Controller. After quality checks, single-cell RNA-seq libraries were pooled and sequenced on a NovaSeq 6000 instrument using an S1 flow cell (Illumina 20028319).
10X Genomics 3' V3.1

value: Brain, frontal lobe

value: Neuro-immune cells

tag: group

value: Control

tag: Sex

value: Male

tag: race

value: Other

tag: ethnicity

value: Not Hispanic or Latino

tag: bmi

tag: cognitive impairment

value: Not Diagnosed


title: Patient 6 Replicate 1

description: 10X Genomics

value: White


title: T-cell Activated 0h untreated rep3 [Ribo-seq]

city: Evry-Courcouronnes

first: Emmanuel

last: Labaronne

address: Genopôle Campus  4 rue Pierre Fontaine - Pépinière du Génopôle

country: France

institute: ADLIN science

description:
For RiboSeq
Tmac-3

data_processing:
Library strategy: Ribo-seq
Trimming with FASTX-Toolkits
Filtering with bowtie2.2.4 with -t –fast options  against mouse 18S, 28S, 45S, 5S, and 5.8S rRNA, tRNAs
Mapping with TopHat 2 (v2.0.13) with --bowtie1 (bowtie version 1.1.1.0) --library-type fr-secondstrand --b2-sensitive -i 30 -m 1 -g 10 --max-coverage-intron 1000000 options
Count with Htseq with htseq-count -f sam -r pos -s yes -a 10 -m intersection-nonempty options
Genome_build: mm10
Supplementary_files_format_and_content: coma-delimited text files include read counts for each Sample for each gene

source_name: Sleen and lymph nodes

growth_protocol: Primary CD4+ T cells were obtained from 6 week old C57BL/6J female mice. Briefly, the spleen as well as the inguinal, axillary, brachial, cervical and mesenteric lymph nodes were collected, followed by ficoll separation to remove red blood cells from splenocytes. CD4+ T cells were then purified by negative selection using the CD4+ T Cell Isolation kit (Myltenyi Biotec, Cat:130-104-454) following the manufacturer's protocol. Isolated cells were grown in RPMI medium supplemented with 10% foetal calf serum (FCS) and 50µM β-mercaptoethanol. CD4+ T cell activation was performed using magnetic beads coupled with CD3/CD28 antibodies (Thermo Fisher Scientific, Cat: 11452D) following the manufacturer’s protocol

extract_protocol:
total RNA was extrated using Trizol reagent, following manufacturer‘s procedure
High-throughput sequencing libraries were prepared as described in Heyer E et al., 2015 NAR

treatment_protocol: cells were incubated in the presence of 5,6-Dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) at a final concentration of 65µM or Triptolide (Sigma-Aldrich, Cat: T3652) at a final concentration of 25µM for 15min, 1h or 3h. At each time point (0, 15min, 1h and 3h), cells were collected, counted and total RNA was extracted from the same amount of cells at each time point. o monitor mRNA stability in conditions where mRNA translation is impaired, cells were incubated in the presence of either DRB or Triptolide and Cycloheximide (final concentration of 100µg.ml-1) or Harringtonine (final concentration of 2µg.ml-1) for 1 or 3h and total RNA extracted.

tag: strain

value: T-cell

tag: cell status

value: Activated

tag: biological replicate

value: Replicate 3

value: untreated

tag: treatment time


title: T-cell Activated 0h untreated rep4 [Ribo-seq]

description:
For RiboSeq
Tmac-5

value: Replicate 4


title: T-cell Resting 0h untreated rep3 [Ribo-seq]

description:
For RiboSeq
Tmac-4

value: Resting


title: PANC-1_EB_4

city: Qingyuan

first: Qingtian

last: Huang

address: 35 Yinquan North Road, Qingcheng District

country: China

institute: Guangzhou Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample

source_name: cell line

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: cell line

value: Human pancreatic cancer cell

value: 10uM Eupalinolide B


title: Patient 2 Replicate 1

description: 10X Genomics

value: Brain, frontal lobe

value: Female

value: Black or African-American

value: Diagnosed


title: T-cell Resting 0h untreated rep2 [Ribo-seq]

description:
For RiboSeq
Tmac-2

value: Replicate 2


title: T-cell Resting 0h untreated rep4 [Ribo-seq]

description:
For RiboSeq
Tmac-6


title: Patient 1 Replicate 1

description: 10X Genomics

value: Neuro-immune cells

value: Male

value: Not Hispanic or Latino


title: Patient 3 Replicate 1

description: 10X Genomics


title: PANC-1_EB_3


title: T-cell Activated 0h untreated rep4 [PAS-seq]

description:
For PASeq
PAS_Activated_CD4_T_cells_A3

data_processing:
Library strategy: PAS-seq
Trimming with FASTX-Toolkits
Filtering with bowtie2.2.4 with -t –fast options  against mouse 18S, 28S, 45S, 5S, and 5.8S rRNA, tRNAs
Mapping with TopHat 2 (v2.0.13) with --bowtie1 (bowtie version 1.1.1.0) --library-type fr-secondstrand --b2-sensitive -i 30 -m 1 -g 10 --max-coverage-intron 1000000 options
Count with Htseq with htseq-count -f sam -r pos -s yes -a 10 -m intersection-nonempty options
PASeq analysis was done as described in Ashar-Patel et.al, 2017 Sci Rep
Genome_build: mm10
Supplementary_files_format_and_content: coma-delimited text of each peak for each sample with count and genomic location

value: T-cell


title: PANC-1_EB_2


title: 5astrohet

value: brain (cortex)

value: astrcocytes

value: cortical injury


title: T-cell Activated 0h untreated rep3 [PAS-seq]

description:
For PASeq
PAS_Activated_CD4_T_cells_A2

value: Activated

value: Replicate 3

value: untreated


title: PANC-1_EB_1

value: cell line

value: Human pancreatic cancer cell


title: PANC-1_DMSO_4

value: DMSO


title: T-cell Resting 0h untreated rep4 [PAS-seq]

description:
For PASeq
PAS_Resting_CD4_T_cells_R3

value: Resting

value: Replicate 4


title: T-cell Resting 0h untreated rep3 [PAS-seq]

description:
For PASeq
PAS_Resting_CD4_T_cells_R2


title: Patient 7 Replicate 1

description: 10X Genomics

value: Brain, frontal lobe

value: Control

value: White

value: Not Diagnosed


title: PANC-1_DMSO_3


title: PANC-1_DMSO_2


title: T-cell Resting 0h untreated rep2 [PAS-seq]

description:
For PASeq
PAS_Resting_CD4_T_cells_R1

value: Replicate 2


title: Patient 5 Replicate 1

description: 10X Genomics

value: Neuro-immune cells

value: Male

value: Hispanic or Latino


title: PANC-1_DMSO_1


title: T-cell Resting 1h Harringtonine rep4

data_processing:
Trimming with FASTX-Toolkits
Filtering with bowtie2.2.4 with -t –fast options  against mouse 18S, 28S, 45S, 5S, and 5.8S rRNA, tRNAs
Mapping with TopHat 2 (v2.0.13) with --bowtie1 (bowtie version 1.1.1.0) --library-type fr-secondstrand --b2-sensitive -i 30 -m 1 -g 10 --max-coverage-intron 1000000 options
Count with Htseq with htseq-count -f sam -r pos -s yes -a 10 -m intersection-nonempty options
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample for each gene

value: T-cell

value: Harringtonine


title: T-cell Activated 0h untreated rep2 [Ribo-seq]

description:
For RiboSeq
Tmac-1

value: Activated


title: Patient 4 Replicate 1

description: 10X Genomics

value: Asian

value: Not Hispanic or Latino


title: T-cell Resting 3h CHX rep4

value: Cycloheximide


title: Monocyte, Patient5

city: Xiamen

first: dang

last: buyun

state: Fujian

address: Xiang 'an District Xiang Annan Road

institute: xiamen university

library_source: genomic

data_processing:
ATAC-seq reads trimmed for adaptor sequence/low-quality using trim_galore. Discarding reads left with < 50bp
ATAC-seq reads were aligned to the hg19 genome by bowtie2
Coverage profiles represent Reads Per Kilobase Million (RPKM) values, calculated using deeptools2 bamCoverage
Peaks were called by MACS2
Assembly: hg19
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: PBMCs

extract_protocol:
Cells were centrifuged at 500 g for 5 min and then lysed for 10 min at 4°C with pre-cold lysis buffer .
ATAC-seq was carried out using the TruePrep DNA Library Prep Kit V2 for Illumina following manufacturer's protocols.

treatment_protocol: Monocytes in  peripheral blood mononuclear cells (PBMCs) from patients diagnosed with atopic dermatitis and urticaria were collected for ATAC-seq.

value: Monocyte

tag: condition

value: atopic dermatitis and urticaria

value: Patient


title: Monocyte, Patient6


title: Monocyte, Patient4


title: T-cell Activated 0h untreated rep2 [PAS-seq]

description:
For PASeq
PAS_Activated_CD4_T_cells_A1

value: untreated


title: T-cell Resting 1h CHX rep4

value: Resting

value: Replicate 4


title: T-cell Resting 3h Triptolide rep4

value: Triptolide


title: T-cell Resting 0h Triptolide rep4


title: Monocyte, Patient3


title: T-cell Resting 1h Triptolide rep4


title: Monocyte, Patient2


title: T-cell Resting 1h untreated rep4


title: T-cell Resting 0h untreated rep4


title: Monocyte, Healthy2

value: control

value: Healthy


title: Monocyte, Patient1


title: T-cell Resting 3h untreated rep4


title: T-cell Resting 3h Triptolide Harr rep4

value: Triptolide and Harringtonine


title: Monocyte, Healthy3


title: T-cell Resting 1h Triptolide CHX rep4

value: Triptolide and Cycloheximide


title: T-cell Resting 1h Triptolide Harr rep4

value: T-cell


title: T-cell Resting 3h Harringtonine rep4

value: Harringtonine


title: T-cell Resting 1h Harringtonine rep3

value: Replicate 3


title: T-cell Resting 3h Triptolide CHX rep4


title: T-cell Resting 3h CHX rep3


title: T-cell Resting 1h CHX rep3


title: Monocyte, Healthy1


title: T-cell Resting 3h Triptolide rep3


title: N21_Day_1

city: Parkville

first: Katherine

middle: R.

last: Martin

state: VIC

address: 1G Royal Parade!

department: John T. Reid Trusts Laboratory

country: Australia

institute: WEHI

data_processing:
Images were analysed in real time by the NovaSeq Control Software v1.6.0 and Real Time Analysis 3 (RTA3) software v3.4.4. RTA performs real-time base calling on the NovaSeq instrument. The Illumina bcl2fastq 2.20.0.422 pipeline was then used to generate sequence data.
Sequenced reads were mapped to human reference genome GRCh38.p12 using Star (v2.6.1) with default parameters, except for the quantMode TranscriptomeSAM setting
Reads were summarised at the gene level using the featureCounts tool from the Subread package (v1.6.4), in a strand-specific manner.
Differential expression was analysed using limma (v3.40.6) from the bioconductor package, following a limma-voom RNASeq123 published workflow
Assembly: GRCh38.p12
Supplementary files format and content: CSV, raw counts
Supplementary files format and content: CSV, normalized counts log2 FPKM

source_name: Whole Blood

extract_protocol:
Whole blood total RNA was extracted using the PAXgene blood RNA extraction kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions. Extracted RNA samples were quality checked using the Agilent 2100 Bioanalyzer platform (Agilent Technologies, Santa Clara, USA).
cDNA libraries were prepared for sequencing using strand specific TrueSeq kits, with ribosomal RNA and globin mRNA depletion. At least 30 million 150 bp paired-end reads were generated per sample using Illumina NovaSeq 6000 (Illumina, San Diego, USA), employing standard protocols at the Victoria Clinical Genetics Services facility (Melbourne, Australia).

value: Whole Blood

tag: patientid

tag: rin

value: Lauren

tag: gender

value: male

tag: ancestry

value: Caucasian

value: TRUE

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

value: Cags

tag: txa

tag: ddavp

tag: stroke

tag: pneumonia

tag: batch

tag: sirs

value: SIRS_days 2


title: N21_60V

tag: tissue

tag: group

tag: bmi


title: T-cell Resting 1h Triptolide rep3

tag: strain

tag: cell type

tag: cell status

value: Resting

tag: biological replicate

tag: treatment

tag: treatment time


title: N21_60A

tag: patientid

tag: rin

tag: gender

tag: ancestry

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes


title: T-cell Resting 1h untreated rep3

value: untreated


title: N20_Day_1

tag: tissue

value: female

tag: procedure

tag: txa

tag: ddavp

tag: stroke

tag: pneumonia

tag: batch

tag: sirs

value: SIRS_days 4


title: T-cell Resting 3h untreated rep3

tag: strain

tag: cell type

tag: cell status

tag: biological replicate

tag: treatment

tag: treatment time


title: N20_60V

tag: patientid

tag: group

tag: rin

tag: gender

tag: ancestry

tag: bmi

tag: smoking

tag: hypertension


title: Monocyte, Healthy4

value: Monocyte

tag: condition

value: control

value: Healthy


title: T-cell Resting 0h Triptolide rep3

value: T-cell

value: Triptolide


title: N21_PRE

tag: tissue

value: PRE

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

tag: txa

tag: ddavp

tag: stroke

tag: pneumonia

tag: batch


title: T-cell Resting 0h untreated rep3

tag: strain

tag: cell type

tag: cell status

tag: biological replicate

value: Replicate 3

tag: treatment

tag: treatment time


title: N20_60A

value: Whole Blood

tag: patientid

tag: group

tag: rin

value: Lauren

tag: gender

tag: ancestry

tag: bmi

tag: smoking

tag: hypertension

tag: sirs


title: T-cell Resting 1h Triptolide Harr rep3

value: Triptolide and Harringtonine


title: T-cell Resting 3h Triptolide Harr rep3


title: T-cell Resting 3h Triptolide CHX rep3

value: Triptolide and Cycloheximide


title: T-cell Resting 1h Triptolide CHX rep3


title: N19_Day_1

tag: tissue

value: male

value: Caucasian

value: TRUE

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

value: AVR

tag: txa

tag: ddavp

tag: stroke

tag: pneumonia


title: N19_60V

tag: patientid

tag: batch

value: SIRS_days 2


title: N20_PRE

tag: group

tag: rin

value: female

value: Cags

value: SIRS_days 4


title: T-cell Resting 3h Harringtonine rep3

tag: strain

tag: cell type

tag: cell status

value: Resting

tag: biological replicate

tag: treatment

value: Harringtonine

tag: treatment time


title: T-cell Resting 1h Harringtonine rep2

value: T-cell

value: Replicate 2


title: N19_PRE

tag: tissue

value: PRE

tag: gender

tag: ancestry

tag: bmi

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: sirs


title: N19_60A

value: Whole Blood

tag: patientid

tag: diabetes

tag: procedure

tag: txa

tag: ddavp

tag: stroke

tag: pneumonia

tag: batch


title: T-cell Resting 3h CHX rep2

tag: strain

tag: cell type

tag: cell status

tag: biological replicate

tag: treatment

value: Cycloheximide

tag: treatment time


title: T-cell Resting 1h CHX rep2


title: N18_Day_1

tag: tissue

tag: group

tag: rin

value: Lauren

tag: gender

tag: ancestry

tag: bmi

tag: smoking

tag: hypertension

value: SIRS_days 3


title: N18_60A

tag: patientid

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

tag: txa

tag: ddavp

tag: stroke

tag: sirs


title: T-cell Resting 3h Triptolide rep2

tag: strain

tag: cell type

tag: cell status

tag: biological replicate

tag: treatment

value: Triptolide

tag: treatment time


title: N18_60V

tag: tissue

tag: group

tag: rin

tag: gender

tag: ancestry

value: Caucasian

tag: bmi

tag: pneumonia

tag: batch


title: T-cell Resting 1h Triptolide rep2


title: N18_PRE

tag: patientid

value: TRUE

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

tag: txa

tag: ddavp


title: N17_Day_1

value: male

value: Cags and MVR

tag: stroke

tag: sirs


title: T-cell Resting 0h Triptolide rep2

tag: strain

tag: cell type

tag: cell status

tag: biological replicate

tag: treatment

tag: treatment time


title: T-cell Resting 3h untreated rep2

value: untreated


title: T-cell Resting 1h untreated rep2


title: N17_60A

tag: tissue

tag: group

tag: rin

tag: gender

tag: ancestry

tag: bmi

tag: pneumonia

tag: batch


title: N17_PRE

tag: patientid

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

tag: txa

tag: ddavp


title: T-cell Resting 0h untreated rep2

tag: strain

tag: cell type

tag: cell status

tag: biological replicate

tag: treatment

tag: treatment time


title: N16_Day_1

tag: tissue

tag: group

tag: rin

tag: gender

tag: ancestry

tag: bmi

value: cags

tag: stroke

tag: sirs


title: T-cell Resting 3h Triptolide Harr rep2

value: Triptolide and Harringtonine


title: T-cell Resting 1h Triptolide Harr rep2

value: Resting


title: N16_60A

tag: patientid

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

tag: pneumonia

tag: batch

value: SIRS_days 4


title: N16_PRE

tag: txa

tag: ddavp


title: T-cell Resting 1h Triptolide CHX rep2

tag: strain

tag: cell type

value: T-cell

tag: cell status

tag: biological replicate

tag: treatment

value: Triptolide and Cycloheximide

tag: treatment time


title: T-cell Resting 3h Harringtonine rep2

value: Replicate 2

value: Harringtonine


title: T-cell Activated 1h Triptolide rep4

value: Activated

value: Replicate 4


title: N15_60V

tag: tissue

value: Whole Blood

tag: group

tag: rin

value: Lauren

tag: gender

tag: ancestry

tag: bmi

value: Cags

tag: stroke

tag: sirs

value: SIRS_days 3


title: N15_60A

tag: patientid

value: male

value: Caucasian

value: TRUE

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

tag: pneumonia

tag: batch


title: T-cell Activated 3h Triptolide rep4

tag: strain

tag: cell type

tag: cell status

tag: biological replicate

tag: treatment

value: Triptolide

tag: treatment time


title: T-cell Activated 3h DRB rep4

value: DRB


title: T-cell Activated 0h Triptolide rep4


title: T-cell Activated 1h DRB rep4


title: N15_PRE

tag: tissue

tag: group

value: PRE

tag: rin

tag: gender

tag: ancestry

tag: bmi

tag: txa

tag: ddavp


title: N14_60V

tag: patientid

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

value: 20 post CPB

tag: stroke

tag: sirs

value: SIRS_days 4


title: T-cell Activated 0h DRB rep4

tag: strain

tag: cell type

value: T-cell

tag: cell status

tag: biological replicate

tag: treatment

tag: treatment time


title: N14_60A

tag: tissue

tag: group

tag: rin

tag: gender

tag: ancestry

tag: bmi

tag: pneumonia

tag: batch


title: N17_60V

tag: patientid

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

value: Cags and MVR

tag: txa

tag: ddavp


title: T-cell Activated 3h untreated rep4

tag: strain

tag: cell type

tag: cell status

tag: biological replicate

tag: treatment

value: untreated

tag: treatment time


title: N13_Day_1

tag: tissue

tag: group

tag: rin

tag: gender

tag: ancestry

tag: bmi

value: yes

tag: stroke

tag: sirs

value: SIRS_days 2


title: N16_60V

value: Whole Blood

tag: patientid

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

value: cags

tag: pneumonia

tag: batch


title: T-cell Resting 3h Triptolide CHX rep2

tag: strain

tag: cell type

tag: cell status

value: Resting

tag: biological replicate

value: Replicate 2

tag: treatment

value: Triptolide and Cycloheximide

tag: treatment time


title: T-cell Activated 1h untreated rep4

value: Activated

value: Replicate 4


title: T-cell Activated 3h Triptolide Harr rep4

value: Triptolide and Harringtonine


title: N13_PRE

tag: tissue

tag: group

tag: rin

value: Lauren

tag: gender

value: male

tag: ancestry

value: Caucasian

value: TRUE

tag: bmi

value: Cags

tag: txa

tag: ddavp


title: T-cell Activated 1h Triptolide Harr rep4

value: T-cell


title: N15_Day_1

tag: patientid

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

tag: stroke

tag: sirs

value: SIRS_days 3


title: N12_PRE

value: PRE

value: FALSE

value: CAGS

tag: pneumonia

tag: batch

value: SIRS_days 0


title: T-cell Activated 3h Triptolide CHX rep4

tag: strain

tag: cell type

tag: cell status

tag: biological replicate

tag: treatment

tag: treatment time


title: T-cell Activated 1h Triptolide CHX rep4


title: N14_Day_1

tag: tissue

value: Whole Blood

tag: group

tag: rin

tag: gender

tag: ancestry

tag: bmi

tag: txa

tag: ddavp

value: 20 post CPB

value: SIRS_days 4


title: N12_60A

tag: patientid

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

tag: stroke

tag: sirs


title: N12_60V

tag: pneumonia

tag: batch


title: T-cell Activated 3h DRB Harr rep4

tag: strain

tag: cell type

tag: cell status

value: Activated

tag: biological replicate

tag: treatment

value: DRB and Harringtonine

tag: treatment time


title: N11_Day_1

tag: tissue

tag: group

tag: rin

tag: gender

tag: ancestry

tag: bmi

tag: txa

tag: ddavp


title: T-cell Activated 1h DRB Harr rep4

value: Replicate 4


title: N11_60V

tag: patientid

value: Lauren

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

tag: stroke

tag: sirs


title: T-cell Activated 3h DRB CHX rep4

tag: strain

tag: cell type

tag: cell status

tag: biological replicate

tag: treatment

value: DRB and Cycloheximide

tag: treatment time


title: N11_PRE

tag: tissue

tag: group

tag: rin

tag: gender

value: male

tag: ancestry

value: Caucasian

tag: bmi

tag: pneumonia

tag: batch


title: N11_60A

tag: patientid

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

tag: txa

tag: ddavp

value: TRUE


title: N10_Day_1

tag: stroke

tag: sirs


title: N10_60V

tag: tissue

tag: group


title: T-cell Activated 3h Harringtonine rep4

tag: strain

tag: cell type

value: T-cell

tag: cell status

tag: biological replicate

tag: treatment

value: Harringtonine

tag: treatment time


title: N14_PRE

tag: patientid

value: PRE

tag: rin

tag: gender

tag: ancestry

tag: bmi

tag: smoking

value: Cags

tag: pneumonia

tag: batch


title: T-cell Activated 1h DRB CHX rep4


title: T-cell Activated 1h Harringtonine rep4


title: N10_60A

value: FALSE

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

value: CAGS

tag: txa

tag: ddavp

tag: stroke

tag: sirs

value: SIRS_days 3


title: N12_Day_1

tag: tissue

value: Whole Blood

tag: group

value: SIRS_days 0


title: N9_Day_1

tag: patientid

tag: rin

value: 1 to 6


title: T-cell Activated 1h CHX rep4

tag: strain

tag: cell type

tag: cell status

value: Activated

tag: biological replicate

tag: treatment

value: Cycloheximide

tag: treatment time


title: N10_PRE

value: Lauren

tag: gender

tag: ancestry

tag: bmi

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: pneumonia

tag: batch


title: T-cell Activated 0h untreated rep4

value: Replicate 4

value: untreated


title: T-cell Activated 3h Triptolide rep3

value: Replicate 3

value: Triptolide


title: T-cell Activated 1h Triptolide rep3

value: T-cell


title: N9_60V

tag: tissue

tag: group

value: male

value: Caucasian

tag: diabetes

tag: procedure

tag: txa

tag: ddavp

tag: stroke

tag: sirs

value: TRUE


title: N9_60A

tag: patientid

tag: rin

value: FALSE


title: T-cell Activated 0h Triptolide rep3

tag: strain

tag: cell type

tag: cell status

tag: biological replicate

tag: treatment

tag: treatment time


title: N8_Day_1

tag: gender

tag: ancestry

tag: bmi

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

value: CAGS

tag: pneumonia

tag: batch

value: SIRS_days 2


title: T-cell Activated 1h DRB rep3

value: DRB


title: N8_60V

tag: tissue

value: Whole Blood

tag: group

tag: diabetes

tag: procedure

tag: txa

tag: ddavp

tag: stroke

tag: sirs


title: N8_60A

tag: patientid

tag: rin

value: 1 to 6


title: T-cell Activated 3h untreated rep3

tag: strain

tag: cell type

tag: cell status

value: Activated

tag: biological replicate

tag: treatment

tag: treatment time


title: N8_PRE

value: PRE

tag: gender

tag: ancestry

tag: bmi

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

tag: pneumonia

tag: batch


title: T-cell Activated 0h untreated rep3


title: N7_60V

tag: tissue

tag: group

value: Lauren

tag: diabetes

tag: procedure

value: REDO CAGS

tag: txa

tag: ddavp

tag: stroke

tag: sirs

value: SIRS_days 4


title: N7_PRE

tag: patientid

tag: rin


title: N7_Day_1

tag: gender

tag: ancestry


title: T-cell Activated 3h CHX rep4

tag: strain

tag: cell type

tag: cell status

tag: biological replicate

value: Replicate 4

tag: treatment

value: Cycloheximide

tag: treatment time


title: T-cell Activated 1h Triptolide Harr rep3

value: T-cell

value: Replicate 3

value: Triptolide and Harringtonine


title: T-cell Activated 3h Triptolide CHX rep3

value: Triptolide and Cycloheximide


title: T-cell Activated 1h Triptolide CHX rep3


title: T-cell Activated 1h DRB Harr rep3

value: DRB and Harringtonine


title: N6_60V

tag: tissue

tag: group

value: Tsin

value: female

value: Caucasian

value: FALSE

tag: bmi

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

value: CAGS

value: 3 to9

tag: pneumonia

tag: batch

value: TRUE


title: T-cell Activated 3h DRB Harr rep3

value: Activated


title: N6_60A

value: Whole Blood

tag: patientid

tag: rin

tag: diabetes

tag: procedure

tag: txa

tag: ddavp

tag: stroke

tag: sirs

value: SIRS_days 2


title: T-cell Activated 3h DRB rep3

tag: strain

tag: cell type

tag: cell status

tag: biological replicate

tag: treatment

value: DRB

tag: treatment time


title: T-cell Activated 1h DRB CHX rep3

value: DRB and Cycloheximide


title: N5_Day_1

tag: tissue

tag: group

tag: gender

tag: ancestry

tag: bmi

tag: smoking

tag: hypertension

tag: hypercholesterolaemia

value: SIRS_days 0


title: T-cell Activated 3h DRB CHX rep3

value: T-cell

value: Replicate 3


title: T-cell Activated 0h DRB rep3


title: N6_PRE

tag: patientid

value: PRE

tag: rin

tag: diabetes

tag: procedure

tag: txa

tag: ddavp

tag: pneumonia

tag: batch


title: T-cell Activated 3h Harringtonine rep3

tag: strain

tag: cell type

tag: cell status

tag: biological replicate

tag: treatment

value: Harringtonine

tag: treatment time


title: N5_60A

tag: tissue

tag: group

value: Tsin

tag: gender

tag: ancestry

tag: bmi

tag: smoking

tag: stroke

tag: sirs


title: N9_PRE

tag: patientid

tag: rin

value: Lauren

value: male

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

tag: txa

tag: ddavp

value: 1 to 6

value: SIRS_days 3


title: N5_PRE

value: female

value: Caucasian

value: FALSE

value: CAGS

tag: pneumonia

tag: batch


title: T-cell Activated 3h CHX rep3

tag: strain

tag: cell type

tag: cell status

value: Activated

tag: biological replicate

tag: treatment

value: Cycloheximide

tag: treatment time


title: T-cell Activated 1h Harringtonine rep3


title: T-cell Activated 1h untreated rep3

value: untreated


title: N4_Day_1

tag: tissue

value: Whole Blood

tag: group

tag: gender

tag: ancestry

tag: bmi

tag: smoking

tag: stroke

tag: sirs

value: TRUE

value: SIRS_days 2


title: N4_60V

tag: patientid

tag: rin

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

tag: txa

tag: ddavp


title: T-cell Activated 3h Triptolide rep2

tag: strain

tag: cell type

value: T-cell

tag: cell status

tag: biological replicate

value: Replicate 2

tag: treatment

value: Triptolide

tag: treatment time


title: N4_60A

tag: tissue

tag: group

value: Tsin

tag: gender

tag: ancestry

tag: bmi

tag: smoking

tag: pneumonia

tag: batch


title: T-cell Activated 1h CHX rep3

value: Replicate 3


title: N7_60A

tag: patientid

tag: rin

value: Lauren

value: male

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

value: REDO CAGS

tag: stroke

tag: sirs

value: SIRS_days 4


title: N6_Day_1

value: female

value: Caucasian

value: FALSE

tag: txa

tag: ddavp

value: 3 to9


title: N4_PRE

tag: tissue

tag: group

value: PRE

value: CAGS


title: T-cell Activated 1h Triptolide rep2

tag: strain

tag: cell type

tag: cell status

value: Activated

tag: biological replicate

tag: treatment

tag: treatment time


title: N3_60V

value: Whole Blood

tag: patientid

tag: rin

tag: gender

tag: ancestry

tag: bmi

tag: smoking

value: AVR+MVR

tag: pneumonia

tag: batch

value: TRUE

value: SIRS_days 3


title: T-cell Activated 0h Triptolide rep2

value: T-cell

value: Replicate 2

value: Triptolide


title: N3_60A

value: Tsin

value: male

tag: hypertension

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

tag: txa

tag: ddavp

tag: stroke

tag: sirs


title: Six weeks  Fed pigID=64

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

data_processing:
RNA preparation, library construction and sequencing on BGISEQ-500 was performed at Beijing Genomics Institute.
Reads were aligned to the pig genome (Sus_scrofa.Sscrofa11.1.104) using STAR  (-runThreadN 2 --genomeDir --readFilesIn  --readFilesCommand gunzip -c --outFileNamePrefix  --outSAMtype BAM SortedByCoordinate --outSAMunmapped None --outSAMattrIHstart 0 --outFilterType BySJout --sjdbGTFfile /Sus_scrofa.Sscrofa11.1.104.gtf --quantMode TranscriptomeSAM
Reads were quantified using Htseq
Assembly: Sus_scrofa.Sscrofa11.1.104
Supplementary files format and content: Raw counts using HTSeq

organism: Sus scrofa

source_name: jejunum small intestine scraping

extract_protocol:
Piglets were anasthesized using a mixture of Zoletil+Xylazine (5:2 ratio, 1 mg/10 kg BW), and euthanized by lethal injection with pentobarbital (24 mg/kg BW), followed by exanguination. The intestine was isolated, and mid-jejunum was identified at 50% of the small intestinal length. Intestine was washed in cold PBS, dabbed dry and mucosa was scraped off using clean glass slides. Collected tissue was snap frozen in liquid nitrogen and stored at -80°C until further analysis. Total RNA was extracted by grinding frozen muscle tissue and dissolving approximately 5-10 mg in RLT buffer containing b-mercaptoethanol. Further RNA isolation was performed according to the RNAeasy mini kit instructions (Qiagen). RNA concentration was measured using NanoDrop spectrophotometer (Thermofisher). RNA integrity was measured using RNA Screentape on the 2200 Tapestation (Agilent).
RNA preparation, library construction and sequencing on BGISEQ-500 was performed at Beijing Genomics Institute.

treatment_protocol: Gene expression profiles from pig jejunum scrapings either fed or fasted at four and six weeks of age (n=16 per group). Piglets were kept at a commercial farm and did not receive any creep feed, and remained with the sow until four weeks of age, after which they were weighed and assigned to one of  four groups: four-week-old fed piglets remained with the sow until time of slaugther, which occured on the farm at the same time as the four-week-old fasted piglets. Four-week-old fasted piglets  were placeced in a seperate pen on the farm and were slaughtered 48h after the start of the intervention. Six-wweek-old piglets were transferred to the experimental research facility of Wageningen University at four weeks of age, and were pair-housed throughout the remainer of the study. They received a standard weaning diet for two-weeks, after which the fed piglets kept receiving feed for the 48h long intervention period, while the fasted piglets did not receive any feed starting 48h before slaughter. All piglets had ad libitum acces to water at all times.

tag: Sex

tag: strain

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

tag: diet

value: Standard weaning diet

tag: age

value: Six weeks

tag: treatment

value: Fed


title: T-cell Activated 3h DRB rep2

tag: cell type

tag: cell status

tag: biological replicate

value: DRB

tag: treatment time


title: Six weeks  Fasted pigID=63

value: female

value: Fasted


title: T-cell Activated 0h DRB rep2

value: Activated


title: T-cell Activated 3h untreated rep2

value: untreated


title: N3_PRE

tag: tissue

value: Whole Blood

tag: patientid

tag: group

value: PRE

tag: rin

tag: gender

tag: ancestry

value: Caucasian

value: FALSE

tag: bmi

tag: smoking

tag: hypertension

value: AVR+MVR

tag: pneumonia

tag: batch


title: T-cell Activated 1h DRB rep2

tag: strain

value: T-cell

value: Replicate 2


title: N5_60V

value: Tsin

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

value: CAGS

tag: txa

tag: ddavp

tag: stroke

tag: sirs

value: SIRS_days 0


title: Six weeks  Fed pigID=62

tag: Sex

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

tag: diet

value: Standard weaning diet

tag: age

value: Six weeks

tag: treatment


title: T-cell Activated 1h untreated rep2

tag: cell type

tag: cell status

tag: biological replicate

tag: treatment time


title: T-cell Activated 1h Triptolide Harr rep2

value: Triptolide and Harringtonine


title: T-cell Activated 3h Triptolide Harr rep2


title: Six weeks  Fasted pigID=61

value: female

value: Fasted


title: Six weeks  Fed pigID=60

value: Fed


title: T-cell Activated 3h Triptolide CHX rep2

value: Activated

value: Triptolide and Cycloheximide


title: T-cell Activated 0h untreated rep2

value: untreated


title: T-cell Activated 3h DRB Harr rep2

value: DRB and Harringtonine


title: Six weeks  Fasted pigID=59


title: T-cell Activated 1h Triptolide CHX rep2


title: N2_PRE

tag: tissue

value: Whole Blood

tag: patientid

tag: group

value: PRE

tag: rin

tag: gender

tag: ancestry

value: Arabic

value: FALSE

tag: bmi

tag: smoking

tag: hypertension

tag: pneumonia

tag: batch

value: TRUE

value: SIRS_days 4


title: T-cell Activated 3h Triptolide Harr rep3

tag: strain

value: T-cell

value: Replicate 3


title: T-cell Activated 1h DRB Harr rep2

value: Replicate 2

tag: treatment


title: N1_PRE

value: Tsin

value: male

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

value: AVR, Ascending aorta replacement and lung wedge resection

tag: txa

tag: ddavp

tag: stroke

tag: sirs

value: SIRS_days 2


title: Six weeks  Fed pigID=58

tag: Sex

value: female

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

tag: diet

value: Standard weaning diet

tag: age

value: Six weeks

value: Fed


title: T-cell Activated 3h DRB CHX rep2

tag: cell type

tag: cell status

value: Activated

tag: biological replicate

value: DRB and Cycloheximide

tag: treatment time


title: T-cell Activated 1h DRB CHX rep2


title: T-cell Activated 3h Harringtonine rep2

value: Harringtonine


title: T-cell Activated 3h CHX rep2

value: Cycloheximide


title: N2_60V

tag: tissue

value: Whole Blood

tag: patientid

tag: group

tag: rin

tag: gender

tag: ancestry

value: Arabic

value: FALSE

tag: bmi

tag: smoking

tag: hypertension

value: CAGS

tag: pneumonia

tag: batch

value: TRUE

value: SIRS_days 4


title: Six weeks  Fed pigID=56

tag: Sex

tag: strain

tag: diet

tag: treatment


title: Six weeks  Fasted pigID=57

tag: age

value: Fasted


title: T-cell Activated 1h CHX rep2

tag: cell type

value: T-cell

tag: cell status

tag: biological replicate

value: Replicate 2

tag: treatment time


title: N2_60A

tag: tissue

tag: patientid

tag: group

tag: rin

value: Tsin

value: female

tag: hypercholesterolaemia

tag: diabetes

tag: procedure

tag: txa

tag: ddavp

tag: stroke

tag: sirs


title: T-cell Activated 1h Harringtonine rep2

tag: strain

tag: treatment


title: Patient7 3D

city: toulouse

first: gael

last: jalowicki

address: iuct

institute: iuct

data_processing:
STAR
htseq
deseq2
Assembly: hg38
Supplementary files format and content: *.fastq.gz: raw sequencing reads
Supplementary files format and content: raw_counts.tsv: counts from htseq
Supplementary files format and content: deseq2_result.csv: differential expression matrix for the contrast 3D vs 2D

extract_protocol:
Extracted using Direct-zol RNA Minipep kits – Zymo Research
QuantSeq 3’mRNA-Seq Library Prep Kit-FWD

tag: cell type

value: FL-PDLS

tag: genotype

value: Patient 7

value: growth medium


title: Patient7 2D

value: FL cells from lymph nodes


title: Six weeks  Fasted pigID=55

tag: Sex

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

tag: diet

value: Standard weaning diet

tag: age

value: Six weeks


title: PC52_Mixed

city: Suwon

first: Jae-Il

last: Choi

address: 164, World cup-ro, Yeongtong-gu

department: Pathology

country: South Korea

institute: Ajou University School of Medicine

description: 10x Genomics

data_processing:
The resulting reads were trimmed and aligned to the GRCh38-2020-A reference genome using Cell Ranger (v7.0) software
Assembly: GRCh38-2020-A
Supplementary files format and content: The output files of Cell Ranger

source_name: Pancreas

extract_protocol:
Patient tumor tissue were dissociated using collagenase and DNase. Patient-derived PCO, and mixed PCO-CAF were dissociated using TrypLE™ Express (Thermo Fisher Scientific). Then, scRNA were performed after cell counting and viability analysis.
Single-cell RNA sequencing was performed by using the Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics Inc., Pleasanton, CA, USA) and was sequenced on a Novaseq 6000 platform according to the manufacturer's instructions

tag: tissue

value: Pancreas

value: Mixed

tag: disease

value: Pancreatic cancer


title: PC52_Organoid

description: 10x Genomics

value: Organoid


title: PC52_Tissue

description: 10x Genomics

value: Tissue


title: Patient3 3D

value: Patient 3


title: KLE cells,LATS1/2-dKO#3

city: 上海

first: Qian

middle: lan

last: Yang

state: 上海

address: 上海市浦东新区芳芯路210弄

institute: Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji

data_processing:
Raw paired-end fastq reads were filtered by TrimGaloreto discard the adapters and low quality bases via calling the Cutadapt tool
The clean reads obtained were then aligned to the  hg19 human genome using HISAT2, followed by reference genome-guided transcriptome assembly and gene expression quantification using StringTie .
Differentially expressed genes (DEGs) were identified by DEseq2 with a cut-off value of log2|fold-change|>1 and p-adjust <0.05.
The clusterProfiler was used to perform functional enrichment analysis for the annotated significant DEGs, the potential genes in identified modules based on gene ontology (GO) and KEGG pathway categories.
Terms with pvalue<0.05 were considered significant. Gene set enrichment analysis (GSEA) was performed by the function in package clusterProfiler with a gene list sorted by log2 fold-change.
Assembly: hg19

source_name: KLE cells

extract_protocol:
Total RNA was isolated using a TRIzol total RNA extraction kit (TIANGEN,Cat.No.DP424), which yielded > 2 μg of total RNA per sample. RNA quality was examined by 0.8% agarose gel electrophoresis and spectrophotometry. High-quality RNA  with a 260/280 absorbance ratio of 1.8-2.2 was used for library construction and sequencing.
Illumina library construction was performed according to the manufacturer's instructions (Illumina,USA). Oligo-dT primers are used to transverse mRNA to obtain cDNA(APExBIO, Cat. No. K1159). Amplify cDNA for the synthesis of the second chain of cDNA. Purify cDNA products by AMPure XP system (Beckman Coulter, Beverly, USA). After library construction, library fragments were enriched by PCR amplification and selected according to a fragment size of 350-550 bp. The library was quality-assessed using an Agilent 2100 Bioanalyzer (Agilent, USA).The library was sequenced using the Illumina NovaSeq 6000 sequencing platform (Paired end150) to generate raw reads.

tag: cell line

value: KLE cells

value: LATS1/2 double knockout


title: KLE cells,LATS1/2-dKO#2

address: 上海市浦东新区芳芯路210弄


title: Six weeks  Fed pigID=54

value: Fed


title: Patient2 3D

value: Patient 2


title: Patient2 2D


title: Six weeks  Fasted pigID=53

value: female

value: Fasted


title: KLE cells,LATS1/2-dKO#1

address: 上海市浦东新区芳芯路210弄


title: PC79_Mixed

data_processing:
The raw data was removed for adapter sequences using Cutadapt (v1.18) and were checked using FastQC (v0.11.8).
Alignment, gene count, and normalization were performed using STAR (v2.7.10a), FeatureCounts (v2.0.1), and edgeR (v3.36.0).
Assembly: GRCh38
Supplementary files format and content: Text files includes feature counts for each sample

extract_protocol:
Total RNAs were isolated using Trizol
The construction of the library was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit


title: PC79_Organoid


title: KLE cells,Parental#3

address: 上海市浦东新区芳芯路210弄

value: WT


title: Six weeks  Fasted pigID=51


title: PC70_Mixed


title: PC70_Organoid


title: Six weeks  Fed pigID=50


title: Six weeks  Fasted pigID=49


title: KLE cells,Parental#2

address: 上海市浦东新区芳芯路210弄


title: PC70_Tissue


title: PC55_Organoid


title: PC55_Mixed


title: PC55_Tissue


title: Six weeks  Fed pigID=48


title: primary mammary tumor, pre-treatment, Patient95

city: Liège

first: Claire

last: Josse

state: Liège

address: rue de l'hopital, 1

department: Medical Oncology

country: Belgium

institute: CHU Liege

data_processing:
The CLC Genomics v22 software (Qiagen) is used to remove low-quality reads from raw NGS sequences, perform trimming and mapping to the Homo sapiens genome hg38 and the RNA database v91
Supplementary files format and content: the processed datafile is containing the raw counts of reads. The colums are Gene Names, Chromosomes, coordinates, ensembl identifiers, and raw counts for each of the 122 libraries

source_name: mammary tumor

extract_protocol:
deparaffinization and extraction steps were carried out using the AllPrep DNA/RNA FFPE kit (#80234, Qiagen), according to manufacturer’s recommendations and DNA was removed from the samples with the TURBO DNA-free™ kit (#AM1907, Thermo Fisher Scientific), by following manufacturer’s instructions. Total RNA samples were then quantified by using Quant-it™ RiboGreen RNA Assay kit (#R11490, Thermo Fisher Scientific
ribosomal RNA depletion were performed with the NEBNext rRNA Depletion kit (Human/Mouse/Rat) with sample purification beads (#E6350, New England Biolabs). Libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep with Beads kit (#E7765, New England Biolabs). Adaptors and primers used for the library preparation were from NEBNext Multiplex Oligos for Illumina (Dual Index Set 1), 96 rxns (#E7760, New England Biolabs). The quality of the libraries was evaluated using High Sensitivity DNA kit (chips and reagents) (#5067 and #4626, Agilent) with a 2100 Bioanalyzer system (Agilent). Sequence reads were generated on the Illumina NovaSeq 6000 sequencer, on an S4 cartridge (300 bp). RNA sequencing was performed in 3 distinct batches
bulk stranded total RNA sequencing after depletion of rRNA. Paired-end, 2 x 150bp.

treatment_protocol: Formalin-fixed paraffin-embedded slides from diagnostic biopsies were cut with a depth of 4 µm. Delimitation of the tumoral zone was done by the pathologist after HE staining on one slide, and reported on the other slides. On average, the tumoral zones of 15-20 slides were scratched.

value: mammary tumor

tag: timing biopsies

value: pre-surgery

tag: patient id

tag: age diagnostic

tag: statut menopausal

value: yes

tag: molecular category

tag: rcb category

value: no residual disease

tag: unifocal

value: no

tag: grade

tag: node invasion

tag: nac category

value: anthracyclines and taxanes

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: primary mammary tumor, pre-treatment, Patient94

tag: tissue

tag: timing biopsies

tag: Sex

value: Luminal B

value: moderate residual disease

value: Femara


title: Six weeks  Fasted pigID=47

tag: strain

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

tag: diet

value: Standard weaning diet

tag: age

value: Six weeks

tag: treatment


title: PC53_Mixed

value: Pancreas

tag: disease

value: Pancreatic cancer

tag: cell type

value: Mixed


title: KLE cells,Parental#1

address: 上海市浦东新区芳芯路210弄

tag: cell line

value: KLE cells

tag: genotype


title: PC53_Organoid

value: Organoid


title: Patient3 2D

value: FL cells from lymph nodes

value: Patient 3

value: growth medium


title: PC79_Tissue

value: Tissue


title: PC52_Mixed


title: PC53_Tissue


title: primary mammary tumor, pre-treatment, Patient93

value: mammary tumor

value: pre-surgery

tag: patient id

value: female

tag: age diagnostic

tag: statut menopausal

value: no

tag: molecular category

tag: rcb category

value: minimal residual disease

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

tag: nac herceptin_binary

value: yes

tag: breast conservative_surgery


title: Six weeks  Fed pigID=52

tag: Sex

tag: strain

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

tag: diet

value: Standard weaning diet

tag: age

value: Fed


title: PC52_Organoid

tag: tissue

value: Pancreas

tag: disease

value: Pancreatic cancer

tag: cell type


title: primary mammary tumor, pre-treatment, Patient92

tag: timing biopsies

tag: patient id

tag: age diagnostic

value: Luminal B

value: anthracyclines and taxanes

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

value: Nolvadex

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: Six weeks  Fasted pigID=45

value: Six weeks

tag: treatment

value: Fasted


title: PC52_Tissue

value: Tissue


title: 782_RET_2

city: Saint-Viance

first: Adèle

last: Mauroux

address: ZAC de la Nau

institute: SILAB

data_processing:
Reads were mapped to the human genome reference and quantified using RSEM (Li et al. 2011) to obtain raw read counts and transcript per kilobase million (TPM).
Differential gene expression was performed using DESeq2 package (Love et al. 2014)  with a filtering step (TPM>20 in at least two samples were considered as expressed) and corrections
Genes with distinct fold change threshold were further analysed
Only genes with a threhold of at least 1,5 and a p-value≤0,05 were considered as differrentially expressed.
Supplementary_files_format_and_content: Matrix table that contains transcript per kilobase million for every gene and every sample

source_name: abdominal skin

growth_protocol: Primary papillary and reticular fibroblasts were cultivated at high density (20 000c/cm2) in 6well petri dishes.

extract_protocol:
mRNA were extracted from the 6 well dishes using Nucleospin RNA kit (Macherey-Nagel). RNA quantity was determined using Qubit 2.0 fluorometer (Thermofisher) and RNA quality was checked using Tapestation 2-200  RNA screetape assay (Agilent technologies). All the samples had an RNA integrity number superior to 9.6.
The 12 librairies were built using SENSE mRNA-Seq Library Prep kit V2 (Lexogen) with 2µg starting material and following the manufactors instructions. The librairies were pooled in equimolar ratio and sequenced using Illumina NextSeq 500 platform in single end (75pb).

treatment_protocol: Cells were cultivated for one week with ECGM2 medium depleted in VEGF and FGF to stimulate angiogenic factors secretion and matrix deposition.

value: primary reticular skin fibroblast


title: primary mammary tumor, pre-treatment, Patient91

value: mammary tumor

value: pre-surgery

tag: statut menopausal

tag: molecular category

tag: rcb category

value: no residual disease

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

tag: nac herceptin_binary

tag: breast conservative_surgery


title: 782_RET_1

tag: cell type


title: Six weeks  Fed pigID=44

tag: Sex

value: female

tag: strain

tag: diet

tag: age


title: 782_PAP_2

value: primary papillary skin fibroblast


title: primary mammary tumor, pre-treatment, Patient90

tag: tissue

tag: timing biopsies

tag: patient id

tag: age diagnostic

value: no

value: minimal residual disease

value: yes

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch


title: Six weeks  Fasted pigID=43

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

value: Standard weaning diet

tag: treatment


title: primary mammary tumor, pre-treatment, Patient89

tag: statut menopausal

tag: molecular category

value: TNBC

tag: rcb category

value: moderate residual disease

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

value: others

tag: mapped to_intergenic_(%_reads)


title: 782_PAP_1

tag: cell type


title: primary mammary tumor, pre-treatment, Patient88

tag: tissue

tag: timing biopsies

tag: Sex

value: extensive residual disease

value: anthracyclines and taxanes

tag: nac herceptin_binary

tag: breast conservative_surgery

value: Tamoxifen


title: 752_PAP_3

source_name: breast skin


title: 752_RET_2

value: primary reticular skin fibroblast


title: 752_PAP_2


title: Six weeks  Fed pigID=42

tag: strain

tag: diet

tag: age

value: Six weeks

value: Fed


title: 714_RET_1


title: 714_RET_2


title: 714_PAP_2


title: Six weeks  Fasted pigID=41

tag: treatment

value: Fasted


title: Six weeks  Fed pigID=46

value: female


title: primary mammary tumor, pre-treatment, Patient86

value: mammary tumor

value: pre-surgery

tag: patient id

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: no residual disease

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch


title: Six weeks  Fasted pigID=39


title: 714_PAP_1

tag: cell type

value: primary papillary skin fibroblast


title: Six weeks  Fed pigID=40

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands


title: Six weeks  Fed pigID=38

value: Standard weaning diet


title: primary mammary tumor, pre-treatment, Patient85

tag: tissue

tag: timing biopsies

value: yes

value: Luminal B

tag: rcb category

tag: unifocal

value: no

tag: grade

tag: node invasion

tag: nac category

value: Femara

tag: mapped to_intergenic_(%_reads)


title: ileum, 25C, no infection (TNc)-Rep 4

city: Athens

first: Samuel

middle: E

last: Aggrey

state: GA

address: 110 Cedar Street

department: Poultry Science

institute: University of Georgia

data_processing:
Sequence reads were trimmed using Trimmomatic v.0.36.
Reads were aligned to the chicken reference genome  using STAR aligner
Expressed genes and transcripts were detected using Cufflinks v 2.2.1
Frangements per kilobase of exon per million mapped fragments for each sample was determined using Cuffdiff v 2.11
Orthogonal differences of differentially expressed genes among the treatments were tested using DESeq2
Assembly: Gallus gallus 5.0.90, Ensembl

organism: Gallus gallus

source_name: ileum

extract_protocol:
RNA was extracted using the trizol-chloroform method and purified with Rneasy Mini kit
4 µg total RNA using the TruSeq RNA Sample Preparation Kit to acquire cDNA fragments with an average size of 229 bp, or 355 bp inclusive of the adapter sequences.

value: ileum

tag: genotype

tag: treatment

value: TNc


title: primary mammary tumor, pre-treatment, Patient84

tag: patient id

tag: Sex

tag: age diagnostic

tag: statut menopausal

value: anthracyclines and taxanes

tag: nac herceptin_binary

tag: breast conservative_surgery


title: ileum, 25C, no infection (TNc)-Rep 3


title: ileum, 25C, no infection (TNc)-Rep 2


title: ileum, 25C, no infection (TNc)-Rep 1


title: Six weeks  Fasted pigID=37

tag: strain

tag: diet

tag: age

value: Six weeks


title: ileum, 35C,  infection (HSi)-Rep 5

tag: tissue

value: HSi


title: primary mammary tumor, pre-treatment, Patient83

tag: timing biopsies

tag: molecular category

tag: rcb category

value: extensive residual disease

tag: unifocal

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch


title: 752_RET_1

tag: cell type

value: primary reticular skin fibroblast


title: ileum, 35C,  infection (HSi)-Rep 4

tag: genotype

tag: treatment


title: Six weeks  Fed pigID=36

tag: Sex

value: female

value: Fed


title: primary mammary tumor, pre-treatment, Patient87

value: mammary tumor

value: pre-surgery

tag: patient id

tag: age diagnostic

tag: statut menopausal

value: minimal residual disease

tag: grade

tag: node invasion

tag: nac category

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: mapped to_intergenic_(%_reads)


title: ileum, 35C,  infection (HSi)-Rep 2

tag: tissue


title: ileum, 35C,  infection (HSi)-Rep 3


title: ileum, 35C,  infection (HSi)-Rep 1


title: primary mammary tumor, pre-treatment, Patient81

tag: timing biopsies

tag: molecular category

value: TNBC

tag: rcb category

value: no residual disease

tag: unifocal

tag: sentinel lymph_node

tag: radiotherapy binary


title: primary mammary tumor, pre-treatment, Patient82

tag: Sex

value: yes

tag: hormonotherapy type_category

tag: sequencing batch


title: Six weeks  Fasted pigID=35

tag: strain

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

tag: diet

value: Standard weaning diet

tag: age

tag: treatment

value: Fasted


title: Six weeks  Fed pigID=34


title: primary mammary tumor, pre-treatment, Patient80

tag: patient id

tag: age diagnostic

tag: statut menopausal

value: no

tag: grade

tag: node invasion

tag: nac category

tag: nac herceptin_binary


title: ileum, 35C, no infection (HSc)-Rep 4

tag: tissue

value: ileum

tag: genotype

value: HSc


title: primary mammary tumor, pre-treatment, Patient79

tag: timing biopsies

tag: molecular category

tag: rcb category

tag: unifocal

value: anthracyclines and taxanes

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: mapped to_intergenic_(%_reads)


title: ileum, 35C, no infection (HSc)-Rep 3

tag: treatment


title: ileum, 35C, no infection (HSc)-Rep 5


title: ileum, 35C, no infection (HSc)-Rep 1


title: Six weeks  Fasted pigID=33

tag: Sex

tag: strain

tag: diet

tag: age

value: Six weeks


title: primary mammary tumor, pre-treatment, Patient78

tag: patient id

tag: age diagnostic

tag: statut menopausal

tag: grade

tag: node invasion

tag: nac category

tag: hormonotherapy type_category

tag: sequencing batch


title: ileum, 25C, infection (TNi)-Rep 4

tag: tissue

tag: genotype

value: TNi


title: Four weeks Fasted pigID=32

value: female

value: Sow's milk

value: Four weeks


title: ileum, 25C, infection (TNi)-Rep 2


title: ileum, 25C, no infection (TNc)-Rep 5

value: TNc


title: primary mammary tumor, pre-treatment, Patient76

value: mammary tumor

tag: timing biopsies

value: pre-surgery

tag: molecular category

value: Luminal B

tag: rcb category

value: moderate residual disease

tag: unifocal

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

value: Arimidex


title: Four weeks Fed pigID=31

tag: Sex

tag: strain

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

tag: diet

tag: age

tag: treatment

value: Fed


title: ileum, 25C, infection (TNi)-Rep 1


title: Four weeks Fed pigID=29


title: primary mammary tumor, pre-treatment, Patient75

tag: patient id

tag: age diagnostic

tag: statut menopausal

value: yes

value: minimal residual disease

value: no

tag: grade

tag: node invasion

tag: nac category

tag: hormonotherapy type_category

tag: mapped to_intergenic_(%_reads)


title: primary mammary tumor, pre-treatment, Patient74

tag: tissue

tag: timing biopsies

tag: molecular category

value: TNBC

tag: rcb category

tag: unifocal

value: anthracyclines and taxanes

tag: nac herceptin_binary

tag: sequencing batch


title: ileum, 35C, no infection (HSc)-Rep 2

value: ileum

tag: genotype

value: HSc


title: Four weeks Fasted pigID=28

tag: Sex

value: female

tag: strain

tag: diet

value: Sow's milk

tag: age

tag: treatment

value: Fasted


title: primary mammary tumor, pre-treatment, Patient73

value: mammary tumor

tag: patient id

tag: age diagnostic

tag: statut menopausal

value: no residual disease

tag: grade

tag: node invasion

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

value: Femara


title: Four weeks Fed pigID=27

value: Four weeks


title: Four weeks Fasted pigID=26


title: ileum, 25C, infection (TNi)-Rep 5

tag: tissue

value: TNi


title: primary mammary tumor, pre-treatment, Patient77

tag: timing biopsies

value: pre-surgery

tag: molecular category

tag: rcb category

tag: unifocal

tag: nac category

tag: nac herceptin_binary

tag: hormonotherapy type_category

tag: mapped to_intergenic_(%_reads)


title: ileum, 25C, infection (TNi)-Rep 3

tag: genotype

tag: treatment


title: Four weeks Fed pigID=25

tag: Sex

tag: strain

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

tag: diet

tag: age

value: Fed


title: AILNCaP14 cells, AR siRNA (s1539) #2

city: Tokyo

first: Eijiro

last: Nakamura

state: Not in USA

address: Tukiji 5-1-1

department: Urology

country: Japan

institute: National Cancer Center Japan

description:
KN8
LNCaP AILNCaP14 AR siRNA

data_processing:
CAGE bar code tags were sequenced on an Illumina HiSeq 2000 sequencer and mapped to the mouse mm9 genome using BWA software (v0.5.9) after discarding ribosomal or non-A/C/G/T base-containing RNAs.
For tag clustering, CAGE tag 5’ coordinates were input for Reclu clustering, with a maximum irreproducible discovery rate of 0.1 and minimum count per million (CPM) of 0.1.
The samples were normalized using the relative log expression method, and differential analyses were conducted using edgeR.
Assembly: hg19
Supplementary files format and content: Excel file containing raw counts for each sample.

growth_protocol: LNCaP cells were cultured in RPMI 1640 medium supplemented with 10% (v/v) FBS 100 U/mL penicillin and 100 U/mL streptomycin at 37 °C in 5% CO2. AILNCaP14 cells were cultured in phenol red-free RPMI 1640 medium supplemented with 10% CSFBS, 100 U/mL penicillin, and 100 U/mL streptomycin at 37 °C in 5% CO2

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (250).
CAGE libraries were prepared from the purified RNA samples, as follows: briefly, first-strand cDNAs were transcribed to the 5’ ends of capped RNAs and attached to CAGE bar code tags.

treatment_protocol: The siRNA for AR and a non-targeting negative control were purchased from Thermo Fisher Scientific (siRNA ID: s1538, s1539). Electroporation was performed using a NEPA21 Type II instrument. (Nepa Gene)

tag: cell line

tag: cell type

value: Human prostate cancer

value: siRNA (s1539)


title: AILNCaP14 cells, AR siRNA (s1539) #3

description:
KN9
LNCaP AILNCaP14 AR siRNA


title: AILNCaP14 cells, siControl #3

description:
KN3
LNCaP AILNCaP14 AR siRNA

value: siControl


title: primary mammary tumor, pre-treatment, Patient71

tag: tissue

tag: patient id

tag: age diagnostic

tag: statut menopausal

value: yes

value: TNBC

value: minimal residual disease

tag: grade

tag: node invasion

value: no

value: anthracyclines and taxanes

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: sequencing batch


title: AILNCaP14 cells, AR siRNA (s1538) #2

description:
KN5
LNCaP AILNCaP14 AR siRNA

tag: treatment

value: siRNA (s1538)


title: primary mammary tumor, pre-treatment, Patient72

value: mammary tumor

tag: timing biopsies

tag: Sex

value: female

tag: molecular category

value: Luminal B

tag: rcb category

value: moderate residual disease

tag: unifocal

tag: nac category

tag: nac herceptin_binary

tag: hormonotherapy type_category

tag: mapped to_intergenic_(%_reads)


title: AILNCaP14 cells, siControl #2

description:
KN2
LNCaP AILNCaP14 AR siRNA

tag: cell line

tag: cell type


title: AILNCaP14 cells, AR siRNA (s1538) #1

description:
KN4
LNCaP AILNCaP14 AR siRNA


title: AILNCaP14 cells, siControl #1

description:
KN1
LNCaP AILNCaP14 AR siRNA


title: AILNCaP14 cells, AR siRNA (s1538) #3

description:
KN6
LNCaP AILNCaP14 AR siRNA


title: LNCaP cells, AR siRNA (s1539) #3

description:
Nk9
LNCaP AILNCaP14 AR siRNA

source_name: LNCaP

value: LNCaP


title: Four weeks Fasted pigID=30

tag: strain

tag: diet

value: Sow's milk

tag: age

value: Four weeks

value: Fasted


title: Four weeks Fed pigID=24

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

value: Fed


title: AILNCaP14 cells, AR siRNA (s1539) #1

description:
KN7
LNCaP AILNCaP14 AR siRNA

value: Human prostate cancer

value: siRNA (s1539)


title: LNCaP cells, AR siRNA (s1539) #1

description:
Nk7
LNCaP AILNCaP14 AR siRNA


title: Four weeks Fasted pigID=23


title: primary mammary tumor, pre-treatment, Patient70

tag: tissue

value: pre-surgery

tag: patient id

tag: age diagnostic

tag: statut menopausal

value: yes

value: TNBC

value: no residual disease

tag: grade

tag: node invasion

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary


title: LNCaP cells, AR siRNA (s1539) #2

description:
Nk8
LNCaP AILNCaP14 AR siRNA

tag: treatment


title: LNCaP cells, AR siRNA (s1538) #2

description:
Nk5
LNCaP AILNCaP14 AR siRNA

value: siRNA (s1538)


title: LNCaP cells, AR siRNA (s1538) #3

description:
Nk6
LNCaP AILNCaP14 AR siRNA


title: LNCaP cells, AR siRNA (s1538) #1

description:
Nk4
LNCaP AILNCaP14 AR siRNA


title: primary mammary tumor, pre-treatment, Patient69

value: mammary tumor

tag: timing biopsies

tag: Sex

value: no

tag: molecular category

tag: rcb category

tag: unifocal

tag: nac category

value: anthracyclines and taxanes

tag: nac herceptin_binary

tag: hormonotherapy type_category

value: Femara

tag: sequencing batch


title: primary mammary tumor, pre-treatment, Patient68

tag: tissue

tag: patient id

value: female

tag: age diagnostic

tag: mapped to_intergenic_(%_reads)


title: Four weeks Fed pigID=22

tag: strain

tag: diet

value: Sow's milk

tag: age


title: Four weeks Fasted pigID=21

value: Four weeks

tag: treatment


title: LNCaP cells, siControl #1

description:
Nk1
LNCaP AILNCaP14 AR siRNA

tag: cell line

value: LNCaP

tag: cell type

value: siControl


title: primary mammary tumor, pre-treatment, Patient67

tag: timing biopsies

tag: Sex

tag: statut menopausal

tag: molecular category

tag: grade

tag: node invasion

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary


title: LNCaP cells, siControl #2

description:
Nk2
LNCaP AILNCaP14 AR siRNA


title: Four weeks Fed pigID=20

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

value: Fed


title: primary mammary tumor, pre-treatment, Patient64

tag: tissue

tag: patient id

tag: age diagnostic

tag: rcb category

tag: unifocal

tag: nac category

tag: nac herceptin_binary

tag: hormonotherapy type_category

tag: sequencing batch


title: primary mammary tumor, pre-treatment, Patient65

tag: timing biopsies

tag: Sex

value: minimal residual disease

value: Nolvadex

tag: mapped to_intergenic_(%_reads)


title: primary mammary tumor, pre-treatment, Patient66

value: pre-surgery

tag: statut menopausal

value: yes

tag: molecular category

tag: grade


title: AILNCaP14 cells #3

description:
AILNCaP14 #3 TAC50
LNCaP AILNCaP14 data

tag: cell line

tag: cell type

value: Human prostate cancer


title: Four weeks Fed pigID=18

tag: strain

tag: diet

tag: age

tag: treatment


title: Four weeks Fasted pigID=17

value: Fasted


title: LNCaP cells, #2

description:
LNCap FBS # 2 GGCTAC
LNCaP AILNCaP14 data


title: AILNCaP14 cells #1

description:
AILNCaP14 #1 ATG50
LNCaP AILNCaP14 data


title: Four weeks Fasted pigID=19


title: AILNCaP14 cells #2

description:
AILNCaP14 #2 GCG50
LNCaP AILNCaP14 data


title: LNCaP cells, #1

description:
LNCap FBS # 1 TAGCTT
LNCaP AILNCaP14 data


title: LNCaP cells, #3

description:
LNCap FBS #3 CTTGTA
LNCaP AILNCaP14 data


title: Z93

city: Houston

first: Zejuan

last: Li

state: Texas

address: 6565 Fannin St, MC227

department: Department of Pathology and Genomic Medicine

institute: Houston Methodist Hospital

data_processing:
library strategy: nano-hmC-Seal
Basecalls were converted using bcl2fastq2.
Sequencing quality of raw reads were evaluated using FastQC, and trimmed adaptors and low quality reads (Phred quality score < 15) using Trimmomatic
High quality reads were mapped to hg38  genome using bowtie2 with end-to-end mode
Duplicate reads were removed using samtools.
The reads were counted for Refseq annotated gene body regions using featureCounts.
Assembly: hg38
Supplementary files format and content: txt file for all sample with raw reads count summarised to Refseq annotated gene bodies.

source_name: Plasma

extract_protocol:
Plasma was separated from whole blood by centrifuge 1350 g for 10 minutes at 4 °C. Plasma cfDNA was extracted using QIAamp Circulating Nucleic Acid Kit (QIAGEN, Germantown, MD) following manufacturer’s instructions.
Briefly, cfDNA was ligated with barcode adaptors after end repair and A-tailing. Then cfDNA was purified and was incubated with 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, 100 μM N3-UDP-azide-glucose and 1 μM T4 Phage β-gulcosyltransferase at 37 °C for 1 hour. After purification, cfDNA was incubated with 1 μL DBCO-PEG4-DBCO (a click chemistry tool, 4.5 mM stock in DMSO) at 37 °C for 2 hours. Next, the cfDNA was purified and incubated with 5 μL pre-washed C1 Streptavidin beads (Thermo Fisher Scientific, Waltham, MA) for 15 min. The beads were subsequently washed for 5 minutes eight times. The captured DNA fragments were amplified with 15-18 cycles of PCR. The PCR products were purified with AMPure XP beads according to the manufacturer’s instructions. The concentration of DNA library was measured using a Qubit Fluorometer with dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA) and Bioanalyzer 2100 with Agilent High Sensitivity Kit (Agilent Technologies, Santa Clara, CA).

tag: tissue

value: Plasma

tag: gender

tag: training/validation group in pan-cancer diagnostic model


title: Z74

value: male


title: Z52


title: Four weeks Fasted pigID=16


title: primary mammary tumor, pre-treatment, Patient63

value: mammary tumor

tag: patient id

tag: age diagnostic

value: TNBC

tag: rcb category

value: extensive residual disease

tag: unifocal

value: no

tag: node invasion

tag: nac category

value: others

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category


title: primary mammary tumor, pre-treatment, Patient62

tag: timing biopsies

tag: Sex

value: female

tag: statut menopausal

tag: molecular category

tag: grade

value: anthracyclines and taxanes

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: Z60

tag: tissue

tag: gender

tag: age

tag: training/validation group in pan-cancer diagnostic model


title: Four weeks Fed pigID=15

tag: strain

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

tag: diet

value: Sow's milk

value: Four weeks

tag: treatment


title: LNCaP cells, siControl #3

description:
Nk3
LNCaP AILNCaP14 AR siRNA

tag: cell line

value: LNCaP

tag: cell type

value: siControl


title: Z48


title: Z119

value: Control


title: primary mammary tumor, pre-treatment, Patient61

value: pre-surgery

tag: patient id

tag: age diagnostic

value: yes

tag: rcb category

value: no residual disease

tag: unifocal

tag: node invasion

tag: nac category

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category


title: Z13

tag: tissue

value: Plasma

tag: gender

tag: age

tag: training/validation group in pan-cancer diagnostic model


title: Four weeks Fasted pigID=14

tag: Sex

tag: strain

tag: diet

tag: treatment

value: Fasted


title: primary mammary tumor, pre-treatment, Patient60

value: mammary tumor

tag: timing biopsies

tag: patient id

tag: age diagnostic

tag: statut menopausal

tag: molecular category

tag: rcb category

tag: grade

value: Femara

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: Z15

tag: tissue


title: Four weeks Fed pigID=13

value: Fed


title: primary mammary tumor, pre-treatment, Patient59

value: no

tag: unifocal

tag: node invasion

tag: nac category

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category


title: Z51

tag: gender

value: male

tag: age

tag: training/validation group in pan-cancer diagnostic model

value: Training


title: Z4

value: female


title: Four weeks Fasted pigID=12

tag: Sex

tag: strain

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

tag: diet

value: Sow's milk

tag: treatment


title: Z31


title: Z33


title: Z57


title: Four weeks Fed pigID=11

value: Four weeks


title: primary mammary tumor, pre-treatment, Patient57

tag: timing biopsies

tag: patient id

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: Luminal B

tag: rcb category

tag: grade

value: anthracyclines and taxanes

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: primary mammary tumor, pre-treatment, Patient58

tag: tissue

value: pre-surgery

value: moderate residual disease

tag: unifocal

tag: node invasion

tag: nac category

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category


title: Four weeks Fasted pigID=10

tag: Sex

tag: strain

tag: diet

tag: age

tag: treatment


title: Z7

tag: gender

tag: training/validation group in pan-cancer diagnostic model

value: Validation


title: primary mammary tumor, pre-treatment, Patient56

tag: timing biopsies

tag: patient id

tag: age diagnostic

tag: statut menopausal

value: yes

tag: molecular category

tag: rcb category

tag: grade

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: Z11

tag: tissue

value: Plasma


title: Z27


title: Z9


title: primary mammary tumor, pre-treatment, Patient55

value: mammary tumor

tag: Sex

value: no residual disease

tag: unifocal

tag: node invasion

tag: nac category

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

value: Nolvadex


title: Four weeks Fed pigID=9

tag: strain

tag: diet

tag: age

tag: treatment

value: Fed


title: primary mammary tumor, pre-treatment, Patient54

tag: timing biopsies

tag: patient id

tag: age diagnostic

tag: statut menopausal

tag: molecular category

value: TNBC

tag: rcb category

value: extensive residual disease

tag: grade

value: no


title: Z21

tag: tissue

tag: gender

value: male

tag: training/validation group in pan-cancer diagnostic model

value: Training


title: Z18

value: female


title: Z23


title: Z53


title: Z6


title: Four weeks Fasted pigID=7

tag: Sex

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

value: Sow's milk

value: Four weeks

value: Fasted


title: primary mammary tumor, pre-treatment, Patient53

value: pre-surgery

tag: unifocal

tag: node invasion

tag: nac category

value: anthracyclines and taxanes

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: Four weeks Fed pigID=6

tag: strain

tag: diet

tag: age

tag: treatment


title: Z43

tag: tissue

value: Plasma


title: primary mammary tumor, pre-treatment, Patient52

value: mammary tumor

tag: timing biopsies

tag: patient id

tag: age diagnostic

tag: statut menopausal

value: yes

tag: molecular category

tag: rcb category

tag: grade

tag: hormonotherapy type_category


title: Z109

tag: gender

tag: training/validation group in pan-cancer diagnostic model


title: Four weeks Fasted pigID=5

tag: Sex


title: Z35

value: Validation


title: Z56


title: Four weeks Fed pigID=4

value: Fed


title: Z10


title: Z37


title: Z58


title: Four weeks Fed pigID=8


title: Z34


title: Z8


title: primary mammary tumor, pre-treatment, Patient48

value: Luminal B

value: minimal residual disease

tag: unifocal

tag: node invasion

tag: nac category

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

value: Femara

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: Z111

tag: tissue

value: male

tag: age


title: Z16

value: Training


title: Four weeks Fasted pigID= 1

value: female

tag: strain

tag: diet

tag: treatment


title: Z118

tag: gender


title: captured CTM_3, circulating tumor micro-embolus captured from mice

city: Nanjing

first: Xiaoxiang

last: Guan

state: None Selected

address: Guangzhoulu

department: Department of Oncology

institute: The First Affiliated Hospital of Nanjing Medical University

data_processing:
we used HISAT2 software (https://daehwankimlab.github.io/hisat2/, version: hisat2-2.0.4) to map reads to the genome
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Expression levels of all transcripts were estimated and performed as calculating FPKM (FPKM = [total exon fragments / mapped reads (millions) × exon length (kB)]). The differentially expressed mRNAs were selected with fold change>2 or fold change<0.5 and p-value<0.05 by edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html). Gene ontology terms (http://www.geneontology.org/) and KEGG pathways (http://www.genome.jp/kegg/) of these differentially expressed mRNAs were also annotated.
Assembly: mm8
Supplementary files format and content: gene_count_matrix.xlsx

source_name: circulating tumor cell cluster

growth_protocol: 4T1 cells were cultured under standard conditions of 37 °C and 5% CO2 atmosphere, and grown in  DMEM medium supplemented with 10% fetal bovine serum (FBS) respectively and 1% Penicillin-streptomycin

extract_protocol:
RNA was harvested using The SMART-Seq v4 Ultra Low Input RNA Kit
RNA library construction was using The SMART-Seq v5 Ultra Low Input RNA Kit following manufacturer's protocol

value: circulating tumor cell cluster

tag: cell type

value: tumor cell cluster


title: Z55

tag: training/validation group in pan-cancer diagnostic model


title: primary mammary tumor, pre-treatment, Patient46

tag: timing biopsies

tag: patient id

tag: Sex

tag: age diagnostic

tag: statut menopausal

value: no

tag: molecular category

tag: rcb category

value: no residual disease

tag: unifocal

tag: grade

tag: hormonotherapy type_category


title: captured CTM_2, circulating tumor micro-embolus captured from mice

tag: tissue


title: Z1

tag: age


title: primary mammary tumor, pre-treatment, Patient45

value: pre-surgery

value: Luminal A

value: moderate residual disease

tag: node invasion

tag: nac category

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: sequencing batch

tag: mapped to_intergenic_(%_reads)


title: primary mammary tumor, pre-treatment, Patient51

value: mammary tumor

tag: timing biopsies

tag: patient id

tag: Sex

tag: age diagnostic

value: anthracyclines and taxanes


title: Z14

value: Plasma

tag: gender

tag: training/validation group in pan-cancer diagnostic model


title: captured CTM_1, circulating tumor micro-embolus captured from mice

tag: cell type


title: primary mammary tumor, pre-treatment, Patient44

tag: tissue

tag: statut menopausal

value: yes

tag: molecular category

tag: rcb category

value: extensive residual disease

tag: unifocal

tag: grade

tag: hormonotherapy type_category


title: Z2

tag: age

value: Validation


title: Z3


title: Z40


title: primary mammary tumor, pre-treatment, Patient49

value: TNBC

tag: node invasion

tag: nac category

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: sequencing batch


title: 4T1 cell lines, control_3, low adherence culture

source_name: 4T1 cell lines

tag: cell line

value: 4T1 cell lines

value: tumor cell


title: Four weeks Fasted pigID=3

tag: Sex

value: female

tag: strain

value: TN20; Large White x Norwegian Landrace, TopigsNorsvin, Vught, The Netherlands

tag: diet

value: Sow's milk

value: Four weeks

tag: treatment

value: Fasted


title: primary mammary tumor, pre-treatment, Patient50

tag: tissue

tag: timing biopsies

value: pre-surgery

tag: patient id

tag: age diagnostic

tag: statut menopausal

tag: molecular category

tag: rcb category

value: no

tag: mapped to_intergenic_(%_reads)


title: Z44

tag: gender

tag: age

tag: training/validation group in pan-cancer diagnostic model


title: Four weeks Fed pigID=2

value: Fed


title: primary mammary tumor, pre-treatment, Patient43

value: mammary tumor

value: Luminal B

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

tag: nac herceptin_binary

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

value: Nolvadex

tag: sequencing batch


title: Z105

tag: tissue

value: Plasma

value: Training


title: 4T1 cell lines, control_2, low adherence culture

tag: cell line

tag: cell type


title: primary mammary tumor, pre-treatment, Patient47

tag: timing biopsies

tag: patient id

tag: Sex

tag: age diagnostic

tag: statut menopausal

tag: molecular category

tag: rcb category

value: no residual disease

value: anthracyclines and taxanes

value: yes

value: Aromasin

tag: mapped to_intergenic_(%_reads)


title: primary mammary tumor, pre-treatment, Patient42

value: female

value: TNBC

tag: unifocal

tag: grade

tag: node invasion

tag: nac category

tag: nac herceptin_binary


title: ATAC_iXist-ChrX-Cast_SmD5_NPC_d7

city: Oxford

first: Joseph

middle: S

last: Bowness

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
Paired-end fastq files from ATAC-seq were mapped using bowtie2 (v2.3.5.1; Langmead and Salzberg, 2012) to a mm10 genome N-masked at positions of SNPs between M. musculus domesticus (129/Sv) or M. musculus castaneous (CAST) strains. The parameters “--very sensitive --no-discordant --no-mixed -X 2000” were used for mapping and any unmapped read pairs were removed. Aligned bam files were then sorted by samtools and PCR duplicates were marked and removed using the “MarkDuplicates” programme in the Picard toolkit (Broad Institute).
Aligned reads were assigned to separate files corresponding to either the CAST (“genome1”) or 129/Sv (“genome2”) genomes by SNPsplit (v0.2.0; Krueger and Andrews, 2016) using the “--paired” parameter and a strain-specific SNP file compiled from UCSC annotations.
Bigwig files were generated by bamCoverage (deeptools v3.5.0; Ramirez et al., 2014) using the total library size as a normalisation scale factor.
For quantitative allelic analysis of RE accessibility over the timecourse of XCI, consensus chrX REs identified from our initial analysis of WT iXist-ChrX time-courses (GSE240677) were labelled and parsed into gtf file format by awk commands. These were used as input for featureCounts (Liao et al. 2014) to count sequencing fragments overlapping REs in both the total and allele-specific alignment files for each time point. Counts matrices were loaded into RStudio for further analysis. Alllelic filters were performed separately for the two paired time-courses (ie. iXist-ChrX-Dom WT vs SmA3 was treated as one dataset) as follows: only peaks containing at least 10 allelically-assigned fragments in >80% of samples and showing biallelic signal in uninduced mESCs (0.15 < allelic ratio < 0.85) were retained. Allelic ratios (Xi/(Xi + Xa)) were then calculated for all sample time points and used for further analysis.
Assembly: mm10
Supplementary files format and content: Bigwig files of ATAC-seq tracks (unspit and allelic) for all samples
Supplementary files format and content: Tables of allelic ratios for WT vs SmHD1mut for iXist-ChrX-Cast and iXist-ChrX-Dom time-courses (.txt)

source_name: iXist-ChrX-Dom

growth_protocol: mESCs were maintained in Dulbecco’s Modified Eagle Medium (DMEM; Life Technologies) with 10% foetal calf serum (FCS; ThermoFisher), 2 mM L-glutamine, 0.1 mM non-essential amino acids, 50 μM β-mercaptoethanol, 100 U/mL penicillin/ 100 μg/mL streptomycin (all from Life Technologies) and 1000 U/mL LIF made in-house. Cells were grown on gelatin-coated plates under standard cell culture conditions (37oC, 5% CO2, humid) on a ‘feeder’ layer of SNLP mouse fibroblasts mitotically inactivated by Mitomycin-C (Sigma Aldrich). mESCs were routinely passaged at ~80% confluency every 2-3 days using TrypLE Express (ThermoFisher), and were pre-plated off feeders for 30-40 min before experiments. For NPC differentiation, mESCs were first extensively isolated from feeder cells by four rounds of pre-plating, each for 35-40 min. 0.5x106 mESCs were plated to gelatin-coated T25 flasks in N2B27 media (50:50 DMEM/F-12:Neurobasal (Gibco) supplemented with 1X N2 and 1X B27 (ThermoFisher), 1 mM L-glutamine, 100 μM β-mercaptoethanol, 50 U/mL penicillin / 50 μg/mL streptomycin (all from Life Technologies) with 1 μg/ml doxycycline for continuous Xist induction. After 7 days, cells were detached with Accutase (Merck Life Sciences) and 3 x 106 cells were plated to grow in suspension in 90 mm bacterial petri dishes containing N2B27 media supplemented with 1 μg/ml doxycycline and 10 ng/ml EGF and FGF (Peprotech). Embryoid-body-like aggregates were collected by mild centrifugation (100 g for 2 min) on day 10 and re-plated to 90 mm gelatinised cell culture dishes in N2B27 + dox + FGF/EGF media. Upon reaching ~80% confluency, NPC outgrowths were passaged using Accutase at a 1:3 - 1:4 ratio to new cell culture dishes until the establishment of a homogenous cellular population of NPCs from approximately day 17.

extract_protocol:
Chromatin accessibility was assayed by ATAC-seq using a protocol adapted from “Omni-ATAC” (Corces et al. 2017). Briefly, 1-5x106 cells were harvested as pellets, washed with PBS, and nuclei were isolated by incubation for 1 min at room temperature in 600 μl HS Lysis buffer (50 mM KCl, 10 mM MgSO4.7H2O, 5 mM HEPES, 0.05% NP40 (IGEPAL CA630), 1 mM PMSF, 3 mM DTT). Nuclei were then centrifuged at 1200 g for 5 min at 4oC, followed by three washes with cold RSB buffer (10 mM NaCl, 10 mM Tris pH 7.4, 3 mM MgCl2). After counting, 5x105 nuclei were centrifuged (1500g for 5min at 4oC) and resuspended in 50 μl H2O. 5x104 nuclei (5 μl) were taken for each transposition assay, performed in technical duplicate for each sample in a 50 μl transposition mix of: 1X Tn5 reaction buffer (10 mM TAPS, 5 mM MgCl2, 10% dimethyl- formamide), 0.1% Tween-20 (Sigma), 0.01% Digitonin (Promega), 2.5 μl Tagment DNA TDE1 enzyme (Illumina), 16.5 μl PBS and 5 μl H2O. As controls for transposition and mapping bias, tn5-digested ‘input’ controls were made by performing tagmentation for 50 ng iXist-ChrX genomic DNA by a basic 50 μl transposition mix of 1X TDE buffer and 2.5 μl TDE1 Enzyme (Illumina) in H2O. Both sample and input mixes were incubated at 37oC for 35 minutes in a thermomixer at 1000 rpm, then cleaned-up with ChIP DNA Clean and Concentrator kit (Zymo) and eluted in 14 μl elution buffer for storage at -20oC.
ATAC-seq libraries were prepared by ∼8 cycles of PCR using NEBNext High Fidelity 2X PCR Master Mix (NEB) and primers containing Illumina barcodes (Buenrostro et al. 2013). Libraries were purified and size selected using Agencourt AMPure XP bead clean-up (Beckman Coulter) to ensure a size distribution containing mono-, di- and tri-nucleosomal fragments between 150-800bp.
2x79bp paired-end

treatment_protocol: Xist expression from the TetOn promoter was induced by addition of 1  µg/ml doxycycline (Sigma, D9891) to the culture medium.

tag: xist (dox)_induction

value: iXist-ChrX-Dom

value: mESC to NPC intermediate

tag: strain

value: Dom/129S x Cast

value: Female


title: ATAC_iXist-ChrX-Cast_SmD5_NPC_d15

tag: cell line

value: Neural progenitor cell (NPC)


title: 4T1 cell lines, control_1, low adherence culture

value: 4T1 cell lines

tag: cell type

value: tumor cell


title: ATAC_iXist-ChrX-Cast_SmD5_NPC_d5


title: residual primary mammary tumor, post-treatment, Patient92

tag: tissue

value: mammary tumor

tag: timing biopsies

value: post-surgery

value: no

value: Luminal B

value: minimal residual disease

tag: breast conservative_surgery

tag: sentinel lymph_node

tag: radiotherapy binary

tag: hormonotherapy type_category

tag: sequencing batch


title: ATAC_iXist-ChrX-Cast_SmD5_NPC_d3

tag: Sex


title: ATAC_iXist-ChrX-Cast_WT_NPC_d7


title: ATAC_iXist-ChrX-Cast_WT_NPC_d5


title: residual primary mammary tumor, post-treatment, Patient90

tag: patient id

tag: age diagnostic

tag: statut menopausal

tag: molecular category

tag: rcb category

tag: unifocal

value: anthracyclines and taxanes

value: Nolvadex

tag: mapped to_intergenic_(%_reads)


title: ATAC_iXist-ChrX-Cast_WT_NPC_d3

tag: xist (dox)_induction

tag: cell line

tag: strain