title: whole_blood_tropical_ambient_d0_F [MA0050_4_87]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430299


title: whole_blood_temperate_30C_d3_F [MA0050_4_82]

status: Public on Mar 17 2026

type: RNA

city: CASTANET-TOLOSAN cedex

first: Laure

last: GRESS

address: 24 chemin de Borde Rouge CS52627

department: Occitanie-Toulouse

country: France

institute: INRAE

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310262

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Pig GE 8x60K (AMID 37880)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 037880_D_F_20120213). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R for each microarray analysis serial using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 8 out of the total number of microarrays per serial. The mean signal of the different washing batches were substracted to individuals signals to correct the batch effect of the multiple serials observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has ?????  rows each corresponding to a unique ProbeName (provided as data Matrix).
log2 normalized signal

molecule: total RNA

organism: Sus scrofa

source_name: whole blood,3 days at 30 degrees

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: F1 pigs were obtained from 10 F0 purebred Large White dams inseminated with 5 F0 boars of the Créole breed. Among F1 pigs, 10 were selected for back crossing 130 genetically related Large White sows in two experimental facilities (70 and 60 sows in the tropical and temperate the facility, respectively). The backcross generation resulted in herds of 664 pigs in the tropical facility and 634 pigs in the temperate facility, each composed of females and castrated males.   The temperate animals farm is located in Poitou-Charente, France (INRAE-GenESI, Poitou-Charentes, France; 46° N, 0.45° W); and the tropical farm is located in a French Indies Island (INRAE-PTEA, Guadeloupe, French West Indies; 16° N, 61° W). Data were collected from April 2013 to October 2014.   The average temperature difference between environment was about 1.1°C (25.2°C in temperate, 26.3°C in tropical, on average), the temperature-humidity index difference was 2.4°C (22.9°C in temperate, 25.3 in tropical, on average), resulting in pigs from the tropical facility growing in a heat-stress environment.   Whole blood transcriptome data were generated from a subset of 361 backcross animals: 181 pigs from the tropical facility and 180 pigs from the temperate facility.

extract_protocol: 800µL whole blood (with EDTA anticoagulant) was mixed with 800µL DL buffer (lysis buffer of the RNA extraction kit). Aliquots were then frozen at -20°C for 4 hours prior to freezing at -80°C.  Whole blood RNA extractions were performed using the NucleoSpin 96 RNA Blood, 96-well kit (Macherey-Nagel), following the manufacturer instructions (centrifuge processing). Minor laboratory adaptations were applied: (i) Membrane desalting steps with RB3 buffer were performed twice. (ii) Twice the amount of reconstituted rDNase was used in the rDNase reaction mixture for a 30-minute treatment. (iii) RNA was eluted in a volume of 60 µL.

treatment_protocol: Blood samples were obtained at 23 weeks of age in each facility (noted as d0). Pigs raised in the temperate facility underwent an experimental heat stress challenge. The experimental heat stress period occurred from Monday of week 24 until the end of week 26 (3 weeks), during which pigs were subject to a 30°C temperature. The animals were further sampled for blood at two timepoints: on Thursday of week 24 (noted as d3) and at the end of week 26 (noted as d18).

tag: experimental facility

value: temperate

tag: gender

value: female

tag: breeding batch

tag: condition

tag: wash batch

tag: analysis serial


title: RNA_WT-SL_rep3

type: SRA

city: Toyonaka

first: Takamasa

last: Ito

state: Osaka

address: 1-1 Machikaneyama

department: Biological Science

country: Japan

institute: Osaka University

description: Library name: RNA_WT-SL_rep3

library_source: genomic

data_processing:
eads were trimmed using Trim Galore (v0.6.10) and aligned to the mm10 genome using STAR (v2.7.11b). Read counts per gene were counted using featureCounts command in Subread package (v2.0.6). Raw count data were normalized, and differential gene expression analysis was performed using DESeq2 (v1.44.0). Differentially expressed genes (DEGs) were defined by an adjusted p-value < 0.05 and |Log2(fold change)| > 1.
Assembly: mm10
Supplementary files format and content: bigwig

molecule: genomic DNA

organism: Mus musculus

growth_protocol: TT2 mESCs are kindly gifted from Dr. Tachibana in Osaka university. mESCs were cultured on dishes coated with 0.1% gelatin in DMEM (Nacalai, 08458-16) supplemented with 10% Knockout Serum Replacement (Gibco, 10828028), 1% FBS (HyClone, SH30070.03), 1× sodium pyruvate (Wako, 190-14881), 1× non-essential amino acids (Wako, 139-15651), 0.1 mM 2-mercaptoethanol (Wako, 133-14571), penicillin-streptomycin (Gibco, 15140122), and LIF (produced in-house) at 37˚C with 5% CO2. mESCs were passaged every 2-3 days using 0.05% trypsin-EDTA (Nacalai, 32777-44).  For retinoic acid differentiation, cells were cultured in ES medium without LIF and supplemented with 5 µM retinoic acid. After 72 hours of induction, the cells were used for subsequent analysis.

extract_protocol:
Total RNA was extracted using ISOGEN according to the manufacturer's instructions.
Libraries were prepared from three biological replicates per sample and sequenced with Illumina NovaSeq X plus using a paired-end 150 bp system at Novogene (Beijing, China).

tag: cell line

tag: cell type

value: mouse embryoic stem cell

tag: genotype

value: WT


title: RNA_WT-SL_rep2

description: Library name: RNA_WT-SL_rep2


title: whole_blood_temperate_24C_d0_M [MA0050_4_79]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310271

source_name: whole blood,24 degrees

value: male


title: ChIP_DKO-SL_Zmym3

description: Library name: ChIP_DKO-SL_Zmym3

data_processing:
Reads were trimmed using Trim Galore (v0.6.10) and aligned to the mm10 genome using Bowtie2 (v2.5.4) with --very-sensitive, --no-unal ,--no-mixed and --no-discordant options. Reads with low mapping quality (MAPQ < 5) were discarded using Samtools. PCR duplicates were removed using MarkDuplicates command in Picard (v3.3.0, Broad Institute). BigWig files were created using bamCoverage command in deepTools (v3.5.5) with --normaliseUsing CPM, --binSize 25, --smoothLength 100, --extendReads and --centerReads options. Log2(ChIP/input) was caluculated using bigwigCompare command in deepTools.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
ChIP was performed as described previously (Nozawa et al., NCB, 2010) with a few modifications. Approximately 1×107 cells were prepared in 10 cm culture dishes and crosslinked with 5% formaldehyde (Thermo Fisher Scientific, 28908) for 5 min. Crosslinking was quenched with 200 mM glycine for 5 min and then cells were lysed with the lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 0.5% NP-40 or 0.5% IGEPAL CA-630, 0.1mM PMSF, 2 µg/ml leupeptin) for 7 min. Cells were collected in 1.5 ml tubes and centrifuged at 800g for 3 min. The supernatant was then discarded, and pellets were resuspended with the SDS lysis buffer (50 mM Tris-HCl, 10 mM EDTA, 1% SDS, 0.1mM PMSF, 2 µg/ml leupeptin). Lysates were diluted with ChIP dilution buffer (50 mM Tris-HCl, 167 mM NaCl, 1.1% Triton X-100, 0.11% SDS, 0.1mM PMSF, 2 µg/ml leupeptin) and sonicated for 24 cycles (15 s ON/30 s OFF per cycle) using Bioruptor (Cosmo Bio, UCD-250). The sonicated chromatin was centrifuged at 16,000g for 15 min and the supernatant was collected. The chromatin was then snap-frozen in liquid nitrogen and stored at -80˚C until further use. 50 µl of Dynabeads M-280 Sheep anti-Mouse IgG (Thermo Fisher Scientific, 11202D) for mouse IgG or Dynabeads Protein A (Thermo Fisher Scientific, 10002D) for rabbit IgG were incubated with 1 µg of purified IgG or 10 µl of hybridoma culture supernatant at 4°C for 2 hours. Chromatin from 3–5×106 cells was incubated with the pre-incubated beads at 4˚C for 2 hours, followed by washing once with RIPA-150 buffer (50 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 0.1 mM PMSF, 2 µg/ml leupeptin), once with RIPA-500 buffer (50 mM Tris-HCl, 500 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 0.1 mM PMSF, 2 µg/ml leupeptin), and twice with TE buffer (10 mM Tris-HCl, 1 mM EDTA, 0.1 mM PMSF, 2 µg/ml leupeptin). Reverse-crosslinking and elution were performed with ChIP direct elution buffer (10 mM Tris-HCl, 300 mM NaCl, 5 mM EDTA, 0.5% SDS, 0.1 mM PMSF, 2 µg/ml leupeptin) at 65°C overnight. The eluted chromatin was treated with 0.5 µg/ml RNase at 37°C for 30 minutes, followed by the addition of 50 µg/ml Proteinase K at 55°C for 1 hour. ChIPed or input DNA was purified using a QIAquick PCR Purification Kit (Qiagen, 28104).
ChIP libraries were prepared with up to 20 ng of DNA using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645L). Library quality control was performed using a Qubit 4 Fluorometer (Thermo Fisher Scientific, Q33238) and an Agilent 2100 Bioanalyzer (Agilent Technologies), followed by sequencing on an Illumina NovaSeq X Plus platform with a paired-end 150 bp system (Macrogen Japan Inc.).

value: Rlf/Zfp292 KO


title: RNA_WT-SL_rep1

description: Library name: RNA_WT-SL_rep1


title: whole_blood_temperate_30C_d3_F [MA0050_4_81]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201316043


title: ChIP_DKO-SL_PolIIS5P

description: Library name: ChIP_DKO-SL_PolIIS5P


title: ChIP_DKO-SL_H3K4me1

description: Library name: ChIP_DKO-SL_H3K4me1


title: ChIP_DKO-SL_H3K27ac

description: Library name: ChIP_DKO-SL_H3K27ac


title: ChIP_DKO-SL_Input

description: Library name: ChIP_DKO-SL_Input


title: whole_blood_temperate_24C_d0_M [MA0050_4_78]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201312475


title: whole_blood_temperate_24C_d0_F [MA0050_4_73]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201312442


title: ChIP_DKO-SL_H3K27me3

description: Library name: ChIP_DKO-SL_H3K27me3


title: ChIP_DKO-SL_H3K4me3

description: Library name: ChIP_DKO-SL_H3K4me3


title: whole_blood_tropical_ambient_d0_M [MA0050_4_77]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331590

source_name: whole blood,ambient

value: tropical


title: ChIP_DKO-SL_H3K9me3

description: Library name: ChIP_DKO-SL_H3K9me3


title: whole_blood_tropical_ambient_d0_M [MA0050_4_76]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330311


title: whole_blood_temperate_24C_d0_F [MA0050_4_67]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313203


title: whole_blood_temperate_30C_d3_M [MA0050_4_75]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201411223


title: ChIP_WT-SL_Zmym3

description: Library name: ChIP_WT-SL_Zmym3


title: whole_blood_temperate_24C_d0_M [MA0050_4_74]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313208


title: ChIP_WT-SL_PolIIS5P

description: Library name: ChIP_WT-SL_PolIIS5P


title: ChIP_RLF-FLAG-SL_Input

description: Library name: ChIP_RLF-FLAG-SL_Input

value: RLF-FLAG


title: whole_blood_tropical_ambient_d0_M [MA0050_4_72]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330315


title: ChIP_WT-SL_LSD1

description: Library name: ChIP_WT-SL_LSD1


title: whole_blood_temperate_24C_d0_M [MA0050_4_70]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201312437


title: whole_blood_tropical_ambient_d0_F [MA0050_4_71]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330983


title: ChIP_WT-SL_H3K9me3

description: Library name: ChIP_WT-SL_H3K9me3


title: ChIP_WT-SL_H3K27me3

description: Library name: ChIP_WT-SL_H3K27me3


title: whole_blood_temperate_30C_d3_F [MA0050_4_64]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310892


title: whole_blood_tropical_ambient_d0_M [MA0050_4_65]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330746


title: whole_blood_temperate_30C_d3_M [MA0050_4_66]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201411301


title: whole_blood_temperate_30C_d18_M [MA0050_4_68]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410525

source_name: whole blood,18 days at 30 degrees


title: ChIP_WT-SL_H3K27ac

description: Library name: ChIP_WT-SL_H3K27ac


title: ChIP_ZFP292-FLAG-SL_Input

description: Library name: ChIP_ZFP292-FLAG-SL_Input


title: whole_blood_temperate_24C_d0_F [MA0050_4_69]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201312425


title: ChIP_ZFP292-FLAG-SL_FLAG

description: Library name: ChIP_ZFP292-FLAG-SL_FLAG


title: whole_blood_temperate_30C_d18_F [MA0050_4_61]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315301


title: whole_blood_tropical_ambient_d0_F [MA0050_4_63]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330773


title: ChIP_WT-SL_H3K4me3

description: Library name: ChIP_WT-SL_H3K4me3


title: whole_blood_temperate_24C_d0_M [MA0050_4_60]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313234


title: BLM_BT2_3

city: wuhan

first: Jie

last: Yao

state: 湖北

address: wuhan hubei province

country: China

institute: wuhan university

description: Library name: Sample54

library_source: transcriptomic

data_processing:
We performed quality control using FastQC for all of the samples. The raw reads were trimmed using Trim-galore to remove adapters. We mapped the clean reads to the mouse reference genome (mm39) using Hisat2. The number of reads mapped to each gene was counted using the featureCounts program of the Subread. We performed differentially expressed genes (DEGs) analysis using the DESeq2. Then, we performed Gene Ontology (GO) enrichment analysis and KEGG pathway analysis to DEGs using clusterProfiler. The normalized counts were also variance-stabilizing transformed and scaled to plot the heatmap.
Assembly: mm39
Supplementary files format and content: csv files include TPM values for each Sample

source_name: lung

growth_protocol: Primary mouse lung fibroblasts (MLFs) were maintained in DMEM/F-12 medium supplemented with 10% FBS (LONSERA) and 1% penicillin-streptomycin (Gibco) at 37°C under 5% O₂ and 5% CO₂.  10–12-week-old male C57BL/6 mice were provided free access to food and water and kept in a colony room on a 12:12 h light/dark cycle.

extract_protocol:
Total RNA of cells was extracted by using EASYspin RNA Mini Kit (Aidlab, RN07). Total RNA extraction from heart tissue was performed using TRIzol reagent (Vazyme, R401).
The library construction process for eukaryotic transcriptome sequencing involves several key steps. Firstly, sample quality is assessed using spectrophotometry and capillary electrophoresis to ensure the purity, concentration, and integrity of RNA. Subsequently, eukaryotic mRNAs are enriched from Total RNA using Oligo(dT) magnetic beads and then fragmented. The fragmented mRNAs serve as templates for cDNA synthesis, which involves first-strand synthesis with random hexamer primers and second-strand synthesis followed by purification. After end-repairing and A-tailing, sequencing adapters are added to the cDNA fragments, which are then size-selected to yield approximately 350 bp cDNA. Finally, PCR amplification is performed to enrich the cDNA library, preparing it for sequencing.

treatment_protocol: In vitro: MLFs were cultured in three media conditions: complete medium (Complete), BCAA-free medium (Free), or BCAA-free medium supplemented with BCAAs (Free+BCAA) or BCKA (Free+BCKA) for 24 hours prior to TGF-β1 (20 ng/mL) stimulation for 48 hours. In vivo: Comparative RNA-seq profiling was performed on lung tissues from three experimental groups: PBS-treated controls, bleomycin (BLM)-exposed mice, and BLM-treated mice receiving BCAA supplementation (3 mmol/L in drinking water) or BCAA-free diets or BT2 treatment.

tag: tissue

value: lung

tag: treatment

tag: batch


title: ChIP_RLF-FLAG-SL_FLAG

description: Library name: ChIP_RLF-FLAG-SL_FLAG


title: whole_blood_temperate_24C_d0_F [MA0050_4_51]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201314542


title: whole_blood_temperate_24C_d0_F [MA0050_4_52]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315552


title: ChIP_WT-SL_H3K4me1

description: Library name: ChIP_WT-SL_H3K4me1


title: BLM_BT2_2

description: Library name: Sample53


title: whole_blood_tropical_ambient_d0_F [MA0050_4_59]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331139


title: whole_blood_temperate_24C_d0_M [MA0050_4_50]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313946


title: whole_blood_temperate_24C_d0_M [MA0050_4_58]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410497


title: BLM_BT2_1

description: Library name: Sample52


title: BLM_DMSO_3

description: Library name: Sample51

value: BLM


title: BLM_ND_4

description: Library name: Sample41

value: Normal diet (ND) and BLM


title: whole_blood_temperate_30C_d3_M [MA0050_4_57]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310888


title: BLM_DMSO_1

description: Library name: Sample49


title: BLM_ND_3

description: Library name: Sample40


title: ChIP_WT-SL_Input

description: Library name: ChIP_WT-SL_Input


title: BLM_DMSO_2

description: Library name: Sample50


title: PBS_DMSO_3

description: Library name: Sample48

value: PBS


title: whole_blood_tropical_ambient_d0_F [MA0050_4_54]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430095


title: whole_blood_temperate_24C_d0_M [MA0050_4_56]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410695


title: PBS_DMSO_2

description: Library name: Sample47


title: BLM_BCAA_free_4

description: Library name: Sample45

value: BCAA_free diet and BLM


title: PBS_DMSO_1

description: Library name: Sample46


title: BLM_BCAA_free_1

description: Library name: Sample42


title: whole_blood_temperate_30C_d18_M [MA0050_4_49]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311494


title: whole_blood_temperate_30C_d3_M [MA0050_4_42]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201312437


title: BLM_BCAA_1

description: Library name: Sample31

value: Water with BCAA and BLM


title: whole_blood_temperate_30C_d3_M [MA0050_4_62]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313852


title: BLM_BCAA_free_3

description: Library name: Sample44


title: whole_blood_tropical_ambient_d0_F [MA0050_4_53]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331527


title: BLM_BCAA_free_2

description: Library name: Sample43


title: whole_blood_temperate_24C_d0_F [MA0050_4_46]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313935


title: whole_blood_temperate_30C_d18_F [MA0050_4_48]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315551


title: whole_blood_temperate_30C_d3_F [MA0050_4_47]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313227


title: whole_blood_tropical_ambient_d0_M [MA0050_4_39]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430548


title: PBS_ND_4

description: Library name: Sample37

value: Normal diet (ND) and PBS


title: whole_blood_temperate_30C_d3_M [MA0050_4_55]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410595


title: whole_blood_temperate_30C_d3_M [MA0050_4_35]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315307


title: whole_blood_tropical_ambient_d0_M [MA0050_4_45]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330679


title: BLM_ND_2

description: Library name: Sample39


title: whole_blood_temperate_30C_d18_M [MA0050_4_43]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310243


title: BLM_ND_1

description: Library name: Sample38


title: whole_blood_temperate_30C_d3_M [MA0050_4_41]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313949


title: whole_blood_temperate_24C_d0_M [MA0050_4_31]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315283


title: PBS_ND_3

description: Library name: Sample36


title: whole_blood_temperate_30C_d3_F [MA0050_4_38]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310878


title: whole_blood_temperate_24C_d0_F [MA0050_4_44]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410691


title: BLM_BCAA_2

description: Library name: Sample32


title: whole_blood_tropical_ambient_d0_F [MA0050_4_40]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330735


title: whole_blood_temperate_30C_d18_M [MA0050_4_33]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410695


title: BLM_BCAA_3

description: Library name: Sample33


title: PBS_ND_1

description: Library name: Sample34


title: whole_blood_temperate_30C_d18_M [MA0050_4_29]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313988


title: PBS_ND_2

description: Library name: Sample35


title: PBS_NW_3

description: Library name: Sample27

value: Normal water (NW) and PBS


title: BLM_NW_3

description: Library name: Sample30

value: Normal water (NW) and BLM


title: BLM_NW_1

description: Library name: Sample28


title: BLM_NW_2

description: Library name: Sample29


title: whole_blood_tropical_ambient_d0_F [MA0050_4_30]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330130


title: whole_blood_tropical_ambient_d0_F [MA0050_4_36]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330736


title: whole_blood_temperate_30C_d3_F [MA0050_4_34]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410726

value: temperate


title: PBS_NW_2

description: Library name: Sample26


title: Free_add_BCKA_TGFb_2

description: Library name: Sample23

source_name: MLF

value: MLF

value: Primary mouse lung fibroblasts

value: BCAA free+BCKA_TGF-β1


title: Free_add_BCKA_TGFb_3

description: Library name: Sample24

value: WT


title: whole_blood_tropical_ambient_d0_F [MA0050_4_32]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430585

value: female


title: whole_blood_temperate_30C_d18_M [MA0050_4_37]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310904

value: male


title: whole_blood_temperate_30C_d3_F [MA0050_4_25]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410517


title: Free_add_BCAA_TGFb_2

description: Library name: Sample17

value: BCAA free+BCAA_TGF-β1


title: whole_blood_temperate_30C_d3_M [MA0050_4_27]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315281


title: whole_blood_temperate_30C_d18_F [MA0050_4_23]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310275


title: Free_add_BCKA_PBS_3

description: Library name: Sample21

value: BCAA free+BCKA_PBS


title: whole_blood_temperate_30C_d3_M [MA0050_4_26]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313229


title: Free_add_BCKA_TGFb_1

description: Library name: Sample22


title: Free_add_BCKA_PBS_1

description: Library name: Sample19


title: whole_blood_tropical_ambient_d0_F [MA0050_4_28]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330370

value: tropical


title: PBS_NW_1

description: Library name: Sample25

value: lung


title: Free_add_BCAA_TGFb_3

description: Library name: Sample18


title: Free_add_BCAA_PBS_1

description: Library name: Sample13

value: BCAA free+BCAA_PBS


title: Free_add_BCKA_PBS_2

description: Library name: Sample20


title: whole_blood_temperate_30C_d18_M [MA0050_4_22]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201312444


title: whole_blood_temperate_24C_d0_M [MA0050_4_13]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410525


title: Free_add_BCAA_TGFb_1

description: Library name: Sample16


title: whole_blood_tropical_ambient_d0_F [MA0050_4_14]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330348


title: whole_blood_temperate_24C_d0_F [MA0050_4_24]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201314543


title: Complete_TGFb_1

description: Library name: Sample4

value: BCAA complete_TGF-β1


title: whole_blood_temperate_30C_d3_M [MA0050_4_19]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313988


title: Free_TGFb_2

description: Library name: Sample11

value: BCAA free_TGF-β1


title: whole_blood_tropical_ambient_d0_M [MA0050_4_10]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331165


title: whole_blood_temperate_30C_d3_M [MA0050_4_21]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315284


title: whole_blood_temperate_30C_d3_F [MA0050_4_20]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410515


title: Free_add_BCAA_PBS_3

description: Library name: Sample15


title: Free_TGFb_1

description: Library name: Sample10


title: Free_add_BCAA_PBS_2

description: Library name: Sample14


title: Free_PBS_2

description: Library name: Sample8

value: BCAA free_PBS


title: Free_TGFb_3

description: Library name: Sample12


title: Free_PBS_3

description: Library name: Sample9


title: whole_blood_tropical_ambient_d0_M [MA0050_4_15]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330103


title: whole_blood_temperate_30C_d18_M [MA0050_4_16]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201316049


title: whole_blood_tropical_ambient_d0_F [MA0050_4_18]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330372


title: Complete_TGFb_3

description: Library name: Sample6


title: Complete_TGFb_2

description: Library name: Sample5


title: whole_blood_temperate_30C_d3_F [MA0050_4_11]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201316131


title: Free_PBS_1

description: Library name: Sample7


title: BCAA_TGFb_H3K27ac_2

description: Library name: Sample18

data_processing:
We performed quality control using FastQC on all samples. The raw reads were trimmed using Trim-galore to remove adapters. The clean reads were mapped to mouse reference genome (mm39) using Bowtie2 with the “--end-to-end --very-sensitive -I 10 -X 700 --no-mixed" option.  Low-quality mapped reads and those mapped to mitochondrial reads were filtered using Samtools. The duplicated reads were removed using Sambamba. The Counts Per Million mapped reads (CPM) normalization method was used to transform alignment bam files into read coverage files in bigWig format on deepTools. Peak calling was performed using MACS2. Differentially accessible peaks were identified using the DiffBind. Motif enrichment analysis was performed using the HOMER.
Assembly: mm39
Supplementary files format and content: bigWig for each Sample
Library strategy: CUT&Tag

growth_protocol: Primary mouse lung fibroblasts (MLFs) were maintained in DMEM/F-12 medium supplemented with 10% FBS (LONSERA) and 1% penicillin-streptomycin (Gibco) at 37°C under 5% O₂ and 5% CO₂.

extract_protocol:
CUT&Tag assay was performed using CUT&Tag High‐Sensitivity Kit (Novoprotein, N259-YH01) according to the manufacturer’s recommendation.
CUT&Tag assay was performed using CUT&Tag High‐Sensitivity Kit (Novoprotein, N259-YH01) according to the manufacturer’s recommendation.

treatment_protocol: MLFs were cultured in two media conditions: complete medium (Complete) or BCAA-free medium (Free) for 24 hours prior to TGF-β1 (20 ng/mL) stimulation for 48 hours. H3K4me3, H3K27ac, H3K27me3, H3K36me3, and H3K9me3 CUT&Tag analyses were conducted on treated MLFs.


title: whole_blood_temperate_24C_d0_M [MA0050_4_2]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311718


title: Complete_PBS_3

description: Library name: Sample3

value: BCAA complete_PBS


title: BCAA_TGFb_H3K4me3_2

description: Library name: Sample14


title: whole_blood_temperate_30C_d18_F [MA0050_3_96]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313871


title: BCAA_TGFb_H3K4me3_1

description: Library name: Sample13


title: Complete_PBS_2

description: Library name: Sample2


title: whole_blood_temperate_30C_d3_M [MA0050_4_7]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315549


title: Complete_PBS_1

description: Library name: Sample1


title: whole_blood_temperate_24C_d0_F [MA0050_3_95]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310261


title: Free_TGFb_H3K27me3_2

description: Library name: Sample12


title: whole_blood_temperate_30C_d18_F [MA0050_4_9]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410726


title: whole_blood_tropical_ambient_d0_F [MA0050_4_5]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330940


title: whole_blood_temperate_24C_d0_M [MA0050_4_3]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313876


title: Free_TGFb_H3K27ac_2

description: Library name: Sample20


title: whole_blood_temperate_30C_d3_F [MA0050_4_6]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313203


title: whole_blood_tropical_ambient_d0_M [MA0050_4_8]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331299


title: Free_TGFb_H3K4me3_2

description: Library name: Sample16


title: whole_blood_temperate_30C_d18_M [MA0050_4_4]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310268


title: BCAA_TGFb_H3K27ac_1

description: Library name: Sample17


title: Free_TGFb_H3K9me3_1

description: Library name: Sample7


title: whole_blood_temperate_24C_d0_F [MA0050_3_90]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315300


title: Free_TGFb_H3K4me3_1

description: Library name: Sample15


title: whole_blood_temperate_24C_d0_F [MA0050_3_89]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313125


title: Free_TGFb_H3K36me3_2

description: Library name: Sample4


title: whole_blood_temperate_30C_d3_F [MA0050_4_12]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313868


title: Free_TGFb_H3K27ac_1

description: Library name: Sample19


title: Free_TGFb_H3K27me3_1

description: Library name: Sample11


title: whole_blood_temperate_24C_d0_F [MA0050_4_1]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310263


title: BCAA_TGFb_H3K27me3_1

description: Library name: Sample9


title: whole_blood_temperate_30C_d3_M [MA0050_3_93]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313137


title: BCAA_TGFb_H3K36me3_1

description: Library name: Sample1


title: whole_blood_temperate_30C_d3_M [MA0050_3_92]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313876


title: whole_blood_temperate_30C_d3_M [MA0050_3_83]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201312476


title: BCAA_TGFb_H3K27me3_2

description: Library name: Sample10


title: whole_blood_temperate_30C_d3_F [MA0050_3_94]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313975


title: whole_blood_temperate_24C_d0_M [MA0050_4_17]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311719


title: whole_blood_tropical_ambient_d0_M [MA0050_3_91]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331740


title: PPARg_TGFb_1

description: Library name: Sample3

treatment_protocol: MLFs were treated with TGF-β1 (20 ng/mL) for 48 h.

tag: cut&tag antibody

value: PPARγ (abcam, #ab45038)


title: Free_TGFb_H3K9me3_2

description: Library name: Sample8


title: BCAA_TGFb_H3K9me3_2

description: Library name: Sample6


title: whole_blood_temperate_30C_d3_M [MA0050_3_80]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310950

value: temperate


title: whole_blood_temperate_30C_d18_M [MA0050_3_79]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313247


title: BCAA_TGFb_H3K9me3_1

description: Library name: Sample5

value: MLF


title: whole_blood_temperate_30C_d3_F [MA0050_3_88]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311724


title: Free_TGFb_H3K36me3_1

description: Library name: Sample3

value: Primary mouse lung fibroblasts


title: whole_blood_temperate_30C_d18_M [MA0050_3_87]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311720


title: whole_blood_temperate_24C_d0_F [MA0050_3_85]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310894


title: ATAC_Free+BCAA_TGFb_1

description: Library name: Sample11

data_processing:
We performed quality control using FastQC on all samples. The raw reads were trimmed using Trim-galore to remove adapters. The clean reads were mapped to mouse reference genome (mm39) using Bowtie2 with the “--very-sensitive -X 1000" option.  Low-quality mapped reads and those mapped to mitochondrial reads were filtered using Samtools. The duplicated reads were removed using Sambamba. The Counts Per Million mapped reads (CPM) normalization method was used to transform alignment bam files into read coverage files in bigWig format on deepTools. Peak calling was performed using MACS2 with the parameter "--SPMR --nomodel --shift -100 --extsize 200". Differentially accessible peaks were identified using the DiffBind. Motif enrichment analysis was performed using the HOMER.
Assembly: mm39
Supplementary files format and content: bigWig for each Sample

extract_protocol:
ATAC-seq libraries were generated using a TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD711) according to the manufacturer’s instructions.
ATAC-seq libraries were generated using a TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD711) according to the manufacturer’s instructions.

treatment_protocol: MLFs were cultured in three media conditions: complete medium (Complete), BCAA-free medium (Free), or BCAA-free medium supplemented with BCAAs (Free+BCAA) for 24 hours prior to TGF-β1 (20 ng/mL) stimulation for 48 hours.


title: ATF4_PBS_2

description: Library name: Sample6

value: PBS

value: ATF4 (Proteintech, #10835-1-AP)


title: whole_blood_tropical_ambient_d0_M [MA0050_3_86]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430345


title: whole_blood_temperate_30C_d3_F [MA0050_3_81]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313867

value: female


title: whole_blood_temperate_30C_d18_M [MA0050_3_74]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313919

value: male


title: whole_blood_temperate_30C_d18_F [MA0050_3_84]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201316035


title: ATAC_Free_TGFb_1

description: Library name: Sample7

value: WT


title: BCAA_TGFb_H3K36me3_2

description: Library name: Sample2


title: whole_blood_temperate_24C_d0_M [MA0050_3_76]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310268


title: PPARg_PBS_2

description: Library name: Sample2

value: PPARγ (abcam, #ab45037)


title: PPARg_PBS_1

description: Library name: Sample1

value: PPARγ (abcam, #ab45036)


title: whole_blood_temperate_30C_d18_F [MA0050_3_82]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310944


title: whole_blood_temperate_24C_d0_F [MA0050_3_75]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201316035


title: ATAC_Free+BCAA_PBS_1

description: Library name: Sample9


title: ATF4_PBS_1

description: Library name: Sample5


title: whole_blood_temperate_30C_d3_M [MA0050_3_77]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310781


title: whole_blood_temperate_30C_d18_M [MA0050_3_78]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313983


title: whole_blood_temperate_24C_d0_M [MA0050_3_69]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201314552


title: ATAC_Complete_TGFb_2

description: Library name: Sample4


title: PPARg_TGFb_2

description: Library name: Sample4

value: PPARγ (abcam, #ab45039)


title: whole_blood_tropical_ambient_d0_F [MA0050_3_68]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430304

value: tropical


title: ATAC_Free_TGFb_2

description: Library name: Sample8


title: ATAC_Free+BCAA_TGFb_2

description: Library name: Sample12

value: BCAA free+BCAA_TGF-β1


title: ATAC_Complete_PBS_2

description: Library name: Sample2


title: whole_blood_tropical_ambient_d0_M [MA0050_3_70]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331323


title: ATAC_Free+BCAA_PBS_2

description: Library name: Sample10

value: BCAA free+BCAA_PBS


title: ATAC_Complete_PBS_1

description: Library name: Sample1


title: ATAC_Free_PBS_2

description: Library name: Sample6

value: BCAA free_PBS


title: whole_blood_tropical_ambient_d0_F [MA0050_3_72]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331524


title: whole_blood_temperate_24C_d0_M [MA0050_3_73]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315218


title: Bone marrow-derived macrophage, Pacc1-/-, stimulated, biological replicate 6

city: Boston

first: Markus

last: Bosmann

state: MA

address: 72 E Concord Street

department: Pulmonary Centre, Department of Medicine

country: USA

institute: Boston University

description: Library name: SKO6

data_processing:
After adapter trimming of the fastq reads using trim galore, the sequences were aligned to the reference mouse genome of Mus musculus (Gencode version M36; GRCm39) using the STAR aligner (version 2.7.10b).
The aligned reads were indexed and sorted using samtools (version 1.10) and quantified with the featureCounts function of the subread (version 2.0.3) software.
Exploratory data analysis and differential expression analysis were performed using DESeq2 (version 1.46.0) using the counts data, after excluding the Gencode suffix from the Ensembl IDs of the mouse genes. False Discovery Rate was set to 0.05.
Assembly: Mus musculus: GRCm39; Gencode version M36
Supplementary files format and content: tab-limited text file includes raw counts which were used as input matrix to DESeq2 (the uploaded file excludes the Gencode suffix)

source_name: Bone marrow derived macrophage

extract_protocol:
RNA was extracted using Qiagen RNAeasy Plus mini kit. 200 ng was used for the construction of sequencing libraries. Novogene performed quality control on all RNA samples.
RNA libraries were constructed and sequenced using the standard mRNA library preparation (poly A enrichment) protocol with paired-end sequencing (150 bp) by Novogene Corporation Inc. (Sacramento CA). This included messenger RNA purification from total RNA using poly-T oligo-attached magnetic beads, followed by fragmentation, cDNA synthesis, end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was quality checked using Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina NovaSeq X Plus.

value: Bone marrow derived macrophage

tag: strain

value: stimulated with E. coli pHrodo Bioparticles


title: whole_blood_temperate_24C_d0_M [MA0050_3_64]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313851

value: temperate


title: Bone marrow-derived macrophage, Pacc1-/-, stimulated, biological replicate 4

description: Library name: SKO4


title: ATAC_Free_PBS_1

description: Library name: Sample5

value: MLF


title: whole_blood_temperate_30C_d18_F [MA0050_3_62]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410592


title: Bone marrow-derived macrophage, Pacc1-/-, stimulated, biological replicate 5

description: Library name: SKO5


title: whole_blood_temperate_30C_d3_M [MA0050_3_71]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410525


title: Bone marrow-derived macrophage, Pacc1-/-, stimulated, biological replicate 2

description: Library name: SKO2


title: whole_blood_tropical_ambient_d0_M [MA0050_3_61]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331039


title: whole_blood_temperate_24C_d0_M [MA0050_3_65]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201314551


title: whole_blood_temperate_30C_d18_F [MA0050_3_67]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315277


title: whole_blood_temperate_24C_d0_M [MA0050_3_60]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201314565


title: whole_blood_tropical_ambient_d0_F [MA0050_3_66]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331217


title: whole_blood_temperate_30C_d18_M [MA0050_3_59]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310900


title: Bone marrow-derived macrophage, Pacc1-/-, stimulated, biological replicate 3

description: Library name: SKO3


title: ATAC_Complete_TGFb_1

description: Library name: Sample3

value: Primary mouse lung fibroblasts

value: BCAA complete_TGF-β1


title: whole_blood_temperate_24C_d0_F [MA0050_3_63]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310227


title: Bone marrow-derived macrophage, Pacc1-/-, stimulated, biological replicate 1

description: Library name: SKO1


title: whole_blood_temperate_30C_d3_M [MA0050_3_56]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311730


title: whole_blood_temperate_24C_d0_F [MA0050_3_54]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313934


title: Bone marrow-derived macrophage, wild type, stimulated, biological replicate 6

description: Library name: SWT6

value: wild type


title: Bone marrow-derived macrophage, wild type, stimulated, biological replicate 1

description: Library name: SWT1


title: whole_blood_temperate_30C_d18_M [MA0050_3_57]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311730


title: whole_blood_temperate_24C_d0_F [MA0050_3_58]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313126

value: female


title: Bone marrow-derived macrophage, wild type, stimulated, biological replicate 2

description: Library name: SWT2


title: Bone marrow-derived macrophage, wild type, stimulated, biological replicate 5

description: Library name: SWT5


title: Bone marrow-derived macrophage, wild type, stimulated, biological replicate 3

description: Library name: SWT3


title: whole_blood_temperate_30C_d3_M [MA0050_3_51]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313958

value: male


title: Bone marrow-derived macrophage, wild type, stimulated, biological replicate 4

description: Library name: SWT4


title: whole_blood_tropical_ambient_d0_F [MA0050_3_52]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430139


title: whole_blood_temperate_30C_d3_F [MA0050_3_49]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313935


title: whole_blood_temperate_30C_d3_M [MA0050_3_55]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201316038


title: Bone marrow-derived macrophage, Pacc1-/-, unstimulated control, biological replicate 4

description: Library name: CKO4

value: unstimulated control


title: whole_blood_temperate_30C_d3_M [MA0050_3_50]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313877


title: Bone marrow-derived macrophage, Pacc1-/-, unstimulated control, biological replicate 5

description: Library name: CKO5


title: whole_blood_temperate_30C_d3_M [MA0050_3_53]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201312434


title: Bone marrow-derived macrophage, Pacc1-/-, unstimulated control, biological replicate 1

description: Library name: CKO1


title: Bone marrow-derived macrophage, Pacc1-/-, unstimulated control, biological replicate 3

description: Library name: CKO3


title: Bone marrow-derived macrophage, Pacc1-/-, unstimulated control, biological replicate 6

description: Library name: CKO6


title: whole_blood_temperate_24C_d0_M [MA0050_3_47]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313207


title: whole_blood_temperate_30C_d18_F [MA0050_3_48]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313869


title: whole_blood_temperate_24C_d0_M [MA0050_3_46]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310781


title: Bone marrow-derived macrophage, wild type, unstimulated control, biological replicate 5

description: Library name: CWT5


title: whole_blood_temperate_24C_d0_F [MA0050_3_44]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310892


title: Bone marrow-derived macrophage, Pacc1-/-, unstimulated control, biological replicate 2

description: Library name: CKO2


title: whole_blood_tropical_ambient_d0_F [MA0050_3_42]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330966


title: Bone marrow-derived macrophage, wild type, unstimulated control, biological replicate 1

description: Library name: CWT1


title: whole_blood_tropical_ambient_d0_F [MA0050_3_45]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430124


title: whole_blood_temperate_30C_d18_F [MA0050_3_40]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313975


title: Bone marrow-derived macrophage, wild type, unstimulated control, biological replicate 3

description: Library name: CWT3


title: Bone marrow-derived macrophage, wild type, unstimulated control, biological replicate 4

description: Library name: CWT4


title: gill filaments, vehicle, rep3

city: Saratoga Springs

first: Jason

last: Breves

state: New York

address: 815 N. Broadway

department: Biology

institute: Skidmore College

description:
Library name: Veh-3
Column name in raw_counts_all_sample.txt: Veh-3

data_processing:
Raw sequence data (.bcl files) generated by Illumina NovaSeq were converted to fastq files and demultiplexed using Illumina bcl2fastq 2.20.
Trimmomatic v.0.36 was used to remove adapter sequences.
The trimmed reads were mapped to the Oreochromis_niloticus reference genome available on ENSEMBL with STAR aligner v.2.5.2b
Assembly: Oreochromis_niloticus
Supplementary files format and content: txt file includes raw counts for each sample.

organism: Oreochromis mossambicus

source_name: gill filaments

extract_protocol:
Total RNA was extracted from homogenized filaments using TRI Reagent according to the manufacturer’s protocol (MRC, Cincinnati, OH).
RNA sequencing libraries were prepared using a NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA).

value: gill filaments

tag: Sex

value: vehicle (saline)

tag: surgery

value: Hx


title: whole_blood_temperate_30C_d18_F [MA0050_3_41]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313845


title: Bone marrow-derived macrophage, wild type, unstimulated control, biological replicate 6

description: Library name: CWT6


title: whole_blood_tropical_ambient_d0_M [MA0050_3_33]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330494

value: tropical


title: day 30, Mock - MuHV4 - del73, mRNA, AbSeq

city: Liège

first: Bénédicte

last: Machiels

state: Liège

address: Avenue de Cureghem 7b, B43b

department: DMI

country: Belgium

institute: Uliège

description: Library name: day 30

data_processing:
Aligment, demultiplexing, barcoded processing and features counting were made using the BD Rhapsody WTA Analysis Pipeline Version 2.0b2
Assembly: GRCm38-PhiX/gencodevM19
Supplementary files format and content: Features count in csv Tab-separated values files
Supplementary files format and content: Sample Tag in csv Tab-separated values files
Library strategy: CITE-seq

molecule: polyA RNA

source_name: Blood - Bone marrow

extract_protocol:
Whole bone marrow (BM) cells were incubated for 20 min with a purified rat IgG2a anti-mouse CD16/CD32 antibody (BioLegend) to block Fc receptor-mediated nonspecific binding. Cells were then stained for 30 min at 4°C with APC-conjugated antibodies against lineage markers (CD3, B220, Gr-1, Ter119, NK1.1, SiglecF, and CD11b). The cell suspension was subsequently incubated with anti-APC magnetic beads (BioLegend) for 15 min. Cells were passed through LS columns, and the negative (flow-through) fraction was collected and used for subsequent sorting of LSK cells. For bone marrow monocytes, T cells, CMP/GMP populations, and blood monocytes, cells were incubated with an Fc receptor–blocking antibody followed by staining with fluorochrome-conjugated antibodies against surface markers. Cell sorting was performed using a BD FACSAria™ III cell sorter. Gating strategies are shown in the manuscript.
Libraries  for single-cell immune profiling were constructed following ™ HT Single-Cell Analysis System protocols from BD rhapsody manufacturer.

treatment_protocol: MuHV-4 infections were performed by intratracheal (i.t.)  injection under isoflurane anesthesia with 3 × 104 plaque forming units (P.F.U.) in 50 µl of PBS. For mock mice, viruses were replaced by PBS.

value: Female

tag: age

value: 7-8 weeks

value: Blood - Bone marrow

value: Bone marrow LSK - Blood monocytes

tag: time

value: day 30

value: Mock - MuHV4 - del73


title: whole_blood_temperate_30C_d3_F [MA0050_3_34]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201312442

tag: experimental facility

value: temperate

tag: gender


title: Chd8_control_rep1

city: Kanazawa

first: Kenta

last: Nitahara

state: Ishikawa

address: 13-1, Takaramachi

department: Department of Histology and Cellular Biology

institute: Kanazawa Univeristy

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: forebrain

extract_protocol:
Forebrains were harvested from mice at P5 and digested using the Papain Dissociation Kit (Worthington Bio-chemical Corporation). The target cells were isolated by fluorescence-activated cell sorting (FACS).
Library was prepared using Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics) with the input of 5000 cells after manufacturer's instructions.

value: forebrain

value: neuronal cells


title: Bone marrow-derived macrophage, wild type, unstimulated control, biological replicate 2

description: Library name: CWT2

value: Bone marrow derived macrophage

value: wild type


title: whole_blood_tropical_ambient_d0_M [MA0050_3_32]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331168

value: male

tag: breeding batch

tag: condition


title: Chd8_mutant_rep2

description: 10x Genomics


title: whole_blood_tropical_ambient_d0_M [MA0050_3_35]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331296

tag: wash batch

tag: analysis serial


title: Chd8_mutant_rep1

description: 10x Genomics

tag: cell type


title: gill filaments, ovine Prl, rep2

description:
Library name: oPrl-2
Column name in raw_counts_all_sample.txt: oPrl-2

tag: genotype

value: ovine Prl


title: whole_blood_tropical_ambient_d0_M [MA0050_3_43]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330153


title: whole_blood_temperate_30C_d3_M [MA0050_3_39]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311494


title: Chd8_control_rep2

description: 10x Genomics

tag: tissue


title: whole_blood_temperate_30C_d3_F [MA0050_3_29]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201316035

value: female


title: whole_blood_tropical_ambient_d0_F [MA0050_3_36]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330319


title: whole_blood_temperate_30C_d3_F [MA0050_3_38]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410692


title: gill filaments, vehicle, rep2

description:
Library name: Veh-2
Column name in raw_counts_all_sample.txt: Veh-2

value: gill filaments

tag: treatment

value: vehicle (saline)


title: whole_blood_temperate_30C_d18_F [MA0050_3_37]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313126


title: gill filaments, vehicle, rep1

description:
Library name: Veh-1
Column name in raw_counts_all_sample.txt: Veh-1

value: Hx


title: whole_blood_temperate_30C_d3_F [MA0050_3_31]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201411263


title: whole_blood_tropical_ambient_d0_M [MA0050_3_25]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330329

value: tropical


title: day 120, Mock - MuHV4 - del73, mRNA, AbSeq

description: Library name: day 120

value: Female

value: 7-8 weeks

value: day 120


title: whole_blood_temperate_24C_d0_M [MA0050_3_24]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315549


title: ORG-0159_IO360_20230117 histologically normal breast tissue

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

description: Original RCC file: 20230117_Radisky35 IO360 run3_ORG-0159_11.RCC; Selected renamed RCC file: ORG-0159_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run3; Lane: 11; MD5: 7609cf43b3573b9c514b208e212d9d19

hyb_protocol: RNA was hybridized for 18 h at 65°C to the NanoString BC360 or IO360 CodeSet. Cartridges were processed on the nCounter Prep Station.

scan_protocol: Cartridges were scanned at 555 fields of view on the nCounter Digital Analyzer. All samples passed manufacturer QC thresholds used in the manuscript: imaging QC score > 0.85, binding density 0.1–2.25 spots/µm², and positive-control linearity R² > 0.95.

data_processing: The IO360_Raw_Matrix.xlsx values are complete raw NanoString counts extracted directly from the selected IO360 RCC files. This IO360 matrix contains 784 probes/features across 74 specimens (750 endogenous genes, 20 housekeeping probes, 8 negative controls, 6 positive controls). Raw RCC files were matched to specimens by exact specimen ID; when multiple candidate raw RCC files existed for the same specimen and panel, the latest RCC date was selected. The processed workbook sample ORG-0098 was matched to raw IO360 specimen ORG-0098 R per submitter instruction. Supplementary file IO360_processed_matrix.tsv retains the analyzed normalized values supplied in Combined IO360 and BC360.xlsx.

label: nanostring

organism: Homo sapiens

source_name: histologically normal breast tissue

label_protocol: NanoString nCounter direct digital counting with panel-specific reporter and capture probes according to the manufacturer protocol; no separate external labeling step was performed.

growth_protocol: Not applicable. These are human surgical FFPE specimens and were not grown or cultured before RNA extraction.

extract_protocol: From each FFPE block, three consecutive 10 µm scrolls (approximately 50 mm² total tissue area) were deparaffinized in xylene and rehydrated through graded ethanol. RNA was extracted using the Qiagen RNeasy FFPE Kit (Cat. 73504) according to the manufacturer instructions. RNA integrity was assessed by spectrophotometry (A260/280 > 1.8) and DV200 (>40% required for inclusion). One hundred nanograms of RNA were used per hybridization.

treatment_protocol: Not applicable. Tissue was collected at surgery with no experimental ex vivo treatment before NanoString profiling.

value: breast

value: FFPE surgical specimen

value: not specified

tag: panel

value: NHW

value: White

tag: ethnicity

value: Not Hispanic/Latino

value: Pre

tag: parity

value: Parous

tag: breastfed

value: Yes

tag: density

value: HD

tag: involution

value: Partial

value: Other

tag: diagnosis

value: L IDC w/ DCIS

value: L DCIS

value: no


title: gill filaments, ovine Prl, rep1

description:
Library name: oPrl-1
Column name in raw_counts_all_sample.txt: oPrl-1

value: gill filaments

tag: Sex

value: male

value: wild type

value: ovine Prl

tag: surgery

value: Hx


title: ORG-0152_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run3_ORG-0152_09.RCC; Selected renamed RCC file: ORG-0152_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run3; Lane: 9; MD5: 086eb741b8828e31445bed9b8c0cf37c

value: breast

value: FFPE surgical specimen

value: not specified

value: NHW

value: ED

value: Right Mastectomy, Left Prophylactic Mastectomy

value: R IDC

value: unknown


title: whole_blood_temperate_24C_d0_F [MA0050_3_30]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315551

tag: experimental facility

value: temperate

tag: gender

value: female

tag: breeding batch


title: whole_blood_temperate_30C_d18_F [MA0050_3_28]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311724

tag: condition

tag: wash batch

tag: analysis serial


title: whole_blood_temperate_30C_d18_F [MA0050_3_26]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313868


title: ORG-0146_R1_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run3_ORG-0146 R1_04.RCC; Selected renamed RCC file: ORG-0146_R1_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run3; Lane: 4; MD5: a1d10796e838f2e5f8594e408d4f9e2c

tag: tissue

value: NHB

value: Black

value: Not Hispanic/Latino

value: Pre

value: Parous

value: Yes

value: Missing

value: Partial

value: Breast Reduction

value: No


title: whole_blood_temperate_30C_d3_M [MA0050_3_17]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201411222

value: male


title: ORG-0143_L2_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run3_ORG-0143 L2_03.RCC; Selected renamed RCC file: ORG-0143_L2_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run3; Lane: 3; MD5: e308114d176087d70e0ff8e2630f05a9

value: breast

value: FFPE surgical specimen

value: NHW

value: White

value: Fg

value: IDC

value: no


title: ORG-0139_L1_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run3_ORG-0139 L1_01.RCC; Selected renamed RCC file: ORG-0139_L1_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run3; Lane: 1; MD5: d079038b2059fbe34bb265f406a4cd07

value: HD

value: Left Mastectomy, Right Prophylactic Mastectomy

value: unknown


title: whole_blood_temperate_30C_d3_M [MA0050_3_20]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311729

value: temperate


title: NanoString CosMx data from  WT and Chd8 mutant adult brain

first: Atsuki

last: Kawamura

address: 13-1 Takaramachi

department: Department of Histology and Cell Biology

institute: Graduate School of Medical Sciences, Kanazawa University

hyb_protocol: Hybridization was conducted using the CosMx Spatial Molecular Imager (Nanostring) to capture spatial transcriptomics data from the prepared tissue sections.

scan_protocol: Imaging was conducted using the CosMx Spatial Molecular Imager (Nanostring) to capture spatial transcriptomics data from the prepared tissue sections.

data_processing: Spatial transcriptomic data were processed using the Scanpy (v1.9.3) and Squidpy (v1.2.4) Python packages. Cells with fewer than 200 total counts were removed, and only cells with at least 120 detected genes were retained. Dimensionality reduction and clustering were conducted using PCA and Leiden clustering, followed by UMAP for visualization. Batch effects were corrected using scVI, and differential expression analysis was performed using the Wilcoxon rank-sum test.

label: SMI imaging barcodes

source_name: Mouse brain at 8 weeks  of age

label_protocol: One section each from control and mutant tissues was placed on the same VWR premium superfrost plus microscope slide and analyzed using the CosMx Spatial Molecular Imager (Nanostring) with 1000-Plex RNA Mouse Neuroscience Panel.

extract_protocol: The brains were removed from the skull, slice to a thickness of 5 mm, and postfixed overnight with 10% neutral-buffered formalin at room temperature. The brain tissues were then dehydrated through an ethanol gradient and embedded in paraffin. Coronal sections 1 mm anterior to Bregma were obtained by slicing the tissue into 5 µm thick sections using a microtome.

value: Male

tag: strain

value: Brain

tag: Stage

value: 8 weeks of age


title: day 8, Mock - MuHV4 - del73, mRNA, AbSeq

description: Library name: day 8

value: Female

tag: age

value: 7-8 weeks

value: Blood - Bone marrow

tag: cell type

value: Bone marrow LSK - Blood monocytes

tag: time

value: day 8

tag: treatment

value: Mock - MuHV4 - del73


title: ORG-0151_R1_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run3_ORG-0151 R1_08.RCC; Selected renamed RCC file: ORG-0151_R1_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run3; Lane: 8; MD5: 7d5f2181ff142930d8465000e2699c18

value: breast

value: FFPE surgical specimen

tag: panel

value: NHW

value: White

tag: ethnicity

value: Not Hispanic/Latino

value: Pre

tag: parity

value: Nulliparous

tag: breastfed

value: Unknown

tag: density

tag: involution

value: Partial

value: Other

value: L IDC


title: gill filaments, ovine Prl, rep3

description:
Library name: oPrl-3
Column name in raw_counts_all_sample.txt: oPrl-3

value: gill filaments

tag: Sex

value: male

tag: genotype

value: wild type

value: ovine Prl

tag: surgery

value: Hx


title: whole_blood_temperate_24C_d0_F [MA0050_3_22]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310241

tag: experimental facility

value: temperate

tag: gender

value: female

tag: breeding batch

tag: condition

tag: wash batch

tag: analysis serial


title: ORG-0154_L3_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run3_ORG-0154 L3_10.RCC; Selected renamed RCC file: ORG-0154_L3_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run3; Lane: 10; MD5: 5d08d85a5c824ea33aa3675603b9dc93

tag: tissue

value: breast

value: FFPE surgical specimen

value: unknown

value: ED

tag: diagnosis

value: R IDC w/ DCIS

value: no


title: ORG-0141_R4_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run3_ORG-0141 R4_02.RCC; Selected renamed RCC file: ORG-0141_R4_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run3; Lane: 2; MD5: ebbca20acb8274865f0e69012ae3879c

tag: panel

value: NHW

value: White

value: Not Hispanic/Latino

value: Pre

value: Nulliparous

value: Unknown

value: Right Mastectomy, Left Prophylactic Mastectomy

value: IDC w/ DCIS


title: whole_blood_tropical_ambient_d0_M [MA0050_3_21]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331697

value: tropical

value: male


title: whole_blood_temperate_30C_d3_F [MA0050_3_23]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313238

value: temperate

value: female


title: whole_blood_temperate_30C_d3_F [MA0050_3_27]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313957


title: whole_blood_temperate_30C_d18_F [MA0050_3_13]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313240


title: whole_blood_temperate_30C_d18_M [MA0050_3_12]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315284


title: ORG-0136_R2_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run2_ORG-0136 R2_11.RCC; Selected renamed RCC file: ORG-0136_R2_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run2; Lane: 11; MD5: 16dc235bb53049db8d0541a0cc94c516

value: breast

value: FFPE surgical specimen

tag: ethnicity

value: Post

value: Parous

value: No

value: HD

value: Partial

value: IDC


title: ORG-0138_R1_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run2_ORG-0138 R1_12.RCC; Selected renamed RCC file: ORG-0138_R1_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run2; Lane: 12; MD5: 2ab6ae72441b0c1ad491f183886bd692

value: NHW

value: White

value: unknown

value: Pre

tag: parity

value: Breast Reduction

value: No (Reduc)

value: no


title: whole_blood_temperate_24C_d0_F [MA0050_3_19]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201314558

value: temperate


title: whole_blood_temperate_24C_d0_F [MA0050_3_10]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315277

value: female


title: ORG-0150_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run3_ORG-0150_07.RCC; Selected renamed RCC file: ORG-0150_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run3; Lane: 7; MD5: 151a7ae71a5a0383b24816b75afd3a9d

value: breast

value: not specified

value: Not Hispanic/Latino

tag: breastfed

value: Yes

value: Other

value: L IDC


title: ORG-0147_R4_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run3_ORG-0147 R4_05.RCC; Selected renamed RCC file: ORG-0147_R4_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run3; Lane: 5; MD5: 3bd2953d29f6f3a7b4e3022c8769a3cb

value: FFPE surgical specimen

value: NHB

value: Black

value: Parous

tag: density

value: HD

value: Partial


title: whole_blood_temperate_30C_d18_M [MA0050_3_16]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201312434

value: male


title: whole_blood_tropical_ambient_d0_M [MA0050_3_18]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430532

value: tropical


title: ORG-0163_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run3_ORG-0163_12.RCC; Selected renamed RCC file: ORG-0163_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run3; Lane: 12; MD5: 478c49b029d0d28536be3d307a8d29d3

value: Post

value: unknown

tag: involution

value: Breast Reduction

value: no


title: whole_blood_temperate_24C_d0_F [MA0050_3_5]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313843

value: temperate

value: female


title: ORG-0148_R1_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run3_ORG-0148 R1_06.RCC; Selected renamed RCC file: ORG-0148_R1_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run3; Lane: 6; MD5: 0e76f4ac3ca5ebb01aa061367f52b36b

value: breast

value: NHW

value: White

value: Not Hispanic/Latino

value: Pre

value: Yes

value: IDC


title: whole_blood_temperate_30C_d18_F [MA0050_3_11]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201411221


title: whole_blood_tropical_ambient_d0_M [MA0050_3_15]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330505


title: whole_blood_temperate_24C_d0_M [MA0050_3_14]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315282


title: whole_blood_temperate_30C_d18_F [MA0050_3_9]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313128


title: whole_blood_tropical_ambient_d0_M [MA0050_3_4]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430118


title: ORG-0136_L1_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run2_ORG-0136 L1_10.RCC; Selected renamed RCC file: ORG-0136_L1_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run2; Lane: 10; MD5: 00eff08f2f698230fff0e3e44310d82e

value: FFPE surgical specimen

value: Parous

value: No

value: HD

value: Right Mastectomy, Left Prophylactic Mastectomy


title: ORG-0134_R1_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run2_ORG-0134 R1_08.RCC; Selected renamed RCC file: ORG-0134_R1_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run2; Lane: 8; MD5: 4bb0ee90768493c22c59dcddcdd6367e

value: Partial

value: Left Mastectomy, Right Prophylactic Mastectomy

value: unknown


title: ORG-0133_L2_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run2_ORG-0133 L2_07.RCC; Selected renamed RCC file: ORG-0133_L2_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run2; Lane: 7; MD5: b048063b19f49fc55e6499432f6a37c0

value: no


title: ORG-0120_L_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run2_ORG-0120 L_02.RCC; Selected renamed RCC file: ORG-0120_L_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run2; Lane: 2; MD5: fc923d7617efb17c2726e63e1b75ca00

value: L

value: Breast Reduction


title: whole_blood_temperate_24C_d0_F [MA0050_3_7]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311649

value: temperate

value: female


title: whole_blood_tropical_ambient_d0_M [MA0050_3_8]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330678

value: tropical

value: male


title: ORG-0135_L_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run2_ORG-0135 L_09.RCC; Selected renamed RCC file: ORG-0135_L_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run2; Lane: 9; MD5: 5d8b305812fe6ba69c417d44f9938529

value: breast

value: NHB

value: Black

value: Pre

value: Nulliparous

value: Unknown


title: whole_blood_temperate_30C_d18_F [MA0050_3_6]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201314540


title: whole_blood_temperate_24C_d0_M [MA0050_3_2]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313962


title: whole_blood_temperate_30C_d3_M [MA0050_3_3]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315218


title: ORG-0125_L_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run2_ORG-0125 L_05.RCC; Selected renamed RCC file: ORG-0125_L_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run2; Lane: 5; MD5: 5bbca70b137238581d3d0ca95e479240

value: FFPE surgical specimen

value: NHW

value: White

value: No


title: ORG-0130_R1_IO360_20220614 histologically normal breast tissue

description: Original RCC file: 20220614_Radisky BC360 IO360 rerun_ORG-0130 R1_05.RCC; Selected renamed RCC file: ORG-0130_R1_IO360_20220614.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220614; Cartridge: Radisky BC360 IO360 rerun; Lane: 5; MD5: e40954dea2a8594747397c489993a1d2

value: Not Hispanic/Latino

value: Parous

value: Yes

value: HD

value: Left Mastectomy, Right Prophylactic Mastectomy

value: IDC

value: unknown

value: no


title: ORG-0123_R1_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run2_ORG-0123 R1_04.RCC; Selected renamed RCC file: ORG-0123_R1_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run2; Lane: 4; MD5: 87f84f16f8e8717ace6acff7bee0a31f

value: breast

value: ED


title: ORG-0131_L2_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run2_ORG-0131 L2_06.RCC; Selected renamed RCC file: ORG-0131_L2_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run2; Lane: 6; MD5: 2670511e08d5e4aae253fa3b7367a1ae

value: Pre

value: Partial

value: Right Mastectomy, Left Prophylactic Mastectomy

value: DCIS


title: whole_blood_temperate_30C_d18_F [MA0050_3_1]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201411263

value: temperate

value: female


title: whole_blood_temperate_30C_d3_M [MA0050_2_96]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313983

value: male


title: whole_blood_temperate_24C_d0_M [MA0050_2_95]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313232


title: ORG-0128_R_IO360_20220608 histologically normal breast tissue

description: Original RCC file: 20220608_Radisky BC360 IO360 run1_ORG-0128 R_12.RCC; Selected renamed RCC file: ORG-0128_R_IO360_20220608.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220608; Cartridge: Radisky BC360 IO360 run1; Lane: 12; MD5: 51a6806fb46ac3c9d2086fdeaf9aaef4

value: FFPE surgical specimen

value: R

value: NHW

value: White

value: Hispanic/Latino

value: Post

value: Fg

value: Complete

value: Breast Reduction

value: No


title: ORG-0121_R4_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run2_ORG-0121 R4_03.RCC; Selected renamed RCC file: ORG-0121_R4_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run2; Lane: 3; MD5: d670859c09974f492729d9fc24c8197a

value: breast

value: Asian/White

value: Not Hispanic/Latino

value: Pre

value: Nulliparous

value: unknown

value: Unknown

value: HD

value: Left Mastectomy, Right Prophylactic Mastectomy

value: IDC

value: no


title: ORG-0112_IO360_20211019 histologically normal breast tissue

description: Original RCC file: 20211019_Radisky IO360 run 2_ORG-112_06.RCC; Selected renamed RCC file: ORG-0112_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 2; Lane: 6; MD5: c081521a1087f85ba15f2398d026ea8a

value: FFPE surgical specimen

value: not specified

value: NHW

value: White

value: Parous

value: Partial

value: R IDC


title: whole_blood_temperate_24C_d0_F [MA0050_2_94]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315297

value: temperate

value: female


title: ORG-0115_L2_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run1_ORG-0115 L2_11.RCC; Selected renamed RCC file: ORG-0115_L2_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run1; Lane: 11; MD5: 4084476b70e31c4e497d2a4769368aa7

value: breast

value: Not Hispanic/Latino

value: Pre

value: Yes

value: Complete

value: PD (padget's disease)


title: ORG-0119_L4_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run2_ORG-0119 L4_01.RCC; Selected renamed RCC file: ORG-0119_L4_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run2; Lane: 1; MD5: 7d9c647fa7dcab57cfa2a152378e3899

value: Nulliparous

value: unknown

value: Unknown

value: ED

value: Right Mastectomy, Left Prophylactic Mastectomy

value: DCIS


title: ORG-0118_L1_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run1_ORG-0118 L1_12.RCC; Selected renamed RCC file: ORG-0118_L1_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run1; Lane: 12; MD5: 18b918fee28048ea2a5609c0ed63494e

value: FFPE surgical specimen

value: NHW

value: White

value: Breast Reduction

value: No

value: no


title: whole_blood_temperate_24C_d0_M [MA0050_2_91]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311643

value: temperate

value: male


title: ORG-0111_IO360_20211019 histologically normal breast tissue

description: Original RCC file: 20211019_Radisky IO360 run 2_ORG-111_05.RCC; Selected renamed RCC file: ORG-0111_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 2; Lane: 5; MD5: fee25eb4ff4bc10f400ab4cbc7f4dc30

value: breast

value: not specified

value: NHB

value: Black

value: Not Hispanic/Latino

value: Post

value: Parous

value: HD

value: Partial

value: Left Mastectomy, Right Prophylactic Mastectomy


title: whole_blood_temperate_24C_d0_F [MA0050_2_93]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311726

value: female


title: whole_blood_temperate_30C_d3_F [MA0050_2_90]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310241


title: whole_blood_tropical_ambient_d0_F [MA0050_2_92]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331046

value: tropical


title: ORG-0110_IO360_20211019 histologically normal breast tissue

description: Original RCC file: 20211019_Radisky IO360 run 2_ORG-110_04.RCC; Selected renamed RCC file: ORG-0110_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 2; Lane: 4; MD5: 489f948f58203f49e06968b20aa2b383

value: FFPE surgical specimen

value: Pre

value: Nulliparous

value: unknown

value: Unknown

value: Breast Reduction


title: whole_blood_tropical_ambient_d0_M [MA0050_2_88]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330135

value: male


title: ORG-0105_R1_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run1_ORG-0105 R1_10.RCC; Selected renamed RCC file: ORG-0105_R1_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run1; Lane: 10; MD5: d4eae3bfe10621161ee288e83e275a49

value: breast

value: NHW

value: White

value: Yes

value: ED

value: Right Mastectomy, Left Prophylactic Mastectomy

value: IDC

value: no


title: whole_blood_temperate_30C_d18_F [MA0050_2_87]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201411262

value: temperate

value: female


title: ORG-0109_IO360_20211019 histologically normal breast tissue

description: Original RCC file: 20211019_Radisky IO360 run 2_ORG-109_03.RCC; Selected renamed RCC file: ORG-0109_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 2; Lane: 3; MD5: ed9b064abfeafe6e1e8085f530eb7c5e

value: FFPE surgical specimen

value: not specified

value: NHB

value: Black

value: Not Hispanic/Latino

value: No


title: ORG-0103_IO360_20220329 histologically normal breast tissue

description: Original RCC file: 20220329_Radisky IO360 run 1_ORG-0103_12.RCC; Selected renamed RCC file: ORG-0103_IO360_20220329.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220329; Cartridge: Radisky IO360 run 1; Lane: 12; MD5: 8c8420f12fcf1a29afb4c445996c1314

value: Pre

value: Parous

value: HD

value: Partial

value: Left Mastectomy, Right Prophylactic Mastectomy

value: unknown


title: ORG-0102_IO360_20220329 histologically normal breast tissue

description: Original RCC file: 20220329_Radisky IO360 run 1_ORG-0102 _11.RCC; Selected renamed RCC file: ORG-0102_IO360_20220329.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220329; Cartridge: Radisky IO360 run 1; Lane: 11; MD5: db8f2ba5f449874edab58a40b4244c03

value: breast

value: NHW

value: White

value: Yes

value: ED

value: Right Mastectomy, Left Prophylactic Mastectomy

value: DCIS


title: whole_blood_temperate_24C_d0_F [MA0050_2_89]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313868

value: temperate

value: female


title: whole_blood_tropical_ambient_d0_F [MA0050_2_86]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331700

value: tropical


title: ORG-0101_L2_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run1_ORG-0101 L2_08.RCC; Selected renamed RCC file: ORG-0101_L2_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run1; Lane: 8; MD5: f1c46e5dcd237ae6d746bc587400f552

value: FFPE surgical specimen

value: Not Hispanic/Latino

value: Post

value: Nulliparous

value: Unknown

value: IDC

value: no


title: ORG-0100_IO360_20220329 histologically normal breast tissue

description: Original RCC file: 20220329_Radisky IO360 run 1_ORG-0100 _10.RCC; Selected renamed RCC file: ORG-0100_IO360_20220329.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220329; Cartridge: Radisky IO360 run 1; Lane: 10; MD5: 6059eb766d38d6d7b6f4b0b8ccff9714

value: breast

value: not specified

value: Parous

value: HD

value: Partial

value: Left Mastectomy, Right Prophylactic Mastectomy

value: unknown


title: ORG-0104_L2_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run1_ORG-0104 L2_09.RCC; Selected renamed RCC file: ORG-0104_L2_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run1; Lane: 9; MD5: 6f1aed0bb8a5eeb66a65f867f7299697

value: NHW

value: White

value: Pre

value: ED

value: Complete

value: IDC & DCIS


title: whole_blood_temperate_30C_d3_F [MA0050_2_85]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410691

value: temperate

value: female


title: whole_blood_temperate_30C_d3_F [MA0050_2_83]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201314542


title: whole_blood_temperate_30C_d3_F [MA0050_2_82]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310030


title: ORG-0098_R_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run1_ORG-0098 R_07.RCC; Selected renamed RCC file: ORG-0098_R_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run1; Lane: 7; MD5: 59781e99e6ec448fb2005a2576ead39c; Processed workbook sample ORG-0098 mapped to raw RCC specimen ORG-0098 R for IO360 per submitter instruction.

value: FFPE surgical specimen

value: R

value: NHB

value: Black

value: Not Hispanic/Latino

value: Nulliparous

value: Unknown

value: Breast Reduction

value: No


title: ORG-0093_IO360_20220329 histologically normal breast tissue

description: Original RCC file: 20220329_Radisky IO360 run 2_ORG-0093_01.RCC; Selected renamed RCC file: ORG-0093_IO360_20220329.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220329; Cartridge: Radisky IO360 run 2; Lane: 1; MD5: c568b7a68cd854f976e9b5af1a6167f1

value: breast

value: not specified

value: Parous

value: Yes

value: HD

value: Partial

value: Right Mastectomy, Left Prophylactic Mastectomy

value: R IDC

value: unknown

value: no


title: whole_blood_temperate_30C_d3_F [MA0050_2_80]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201316134

value: temperate

value: female


title: whole_blood_temperate_30C_d18_F [MA0050_2_79]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311725


title: ORG-0095_IO360_20220329 histologically normal breast tissue

description: Original RCC file: 20220329_Radisky IO360 run 1_ORG-0095_09.RCC; Selected renamed RCC file: ORG-0095_IO360_20220329.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220329; Cartridge: Radisky IO360 run 1; Lane: 9; MD5: 28fd4aabd88bbd425e57ba6f358730d1

value: FFPE surgical specimen

value: NHB

value: Black

value: Not Hispanic/Latino

value: Pre

value: R DCIS


title: whole_blood_temperate_24C_d0_F [MA0050_2_84]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315548


title: whole_blood_temperate_30C_d18_M [MA0050_2_81]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201312474

value: male


title: ORG-0092_IO360_20220329 histologically normal breast tissue

description: Original RCC file: 20220329_Radisky IO360 run 1_ORG-0092_08.RCC; Selected renamed RCC file: ORG-0092_IO360_20220329.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220329; Cartridge: Radisky IO360 run 1; Lane: 8; MD5: 22708b6e85a4a6b121770767a343b2cb

value: breast

value: not specified

value: NHW

value: White

value: Parous

value: Left Mastectomy, Right Prophylactic Mastectomy

value: L IDC


title: whole_blood_temperate_24C_d0_F [MA0050_2_78]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311710


title: whole_blood_temperate_30C_d18_F [MA0050_2_77]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313203


title: ORG-0091_IO360_20220329 histologically normal breast tissue

description: Original RCC file: 20220329_Radisky IO360 run 1_ORG-0091_07.RCC; Selected renamed RCC file: ORG-0091_IO360_20220329.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220329; Cartridge: Radisky IO360 run 1; Lane: 7; MD5: 356e5145ce12b906aae8bbed08783796

value: Post

value: Yes

value: HD

value: Complete

value: Bilateral Prophylactic Mastectomies

value: No

value: IDC

value: no


title: ORG-0087_IO360_20220609 histologically normal breast tissue

description: Original RCC file: 20220609_Radisky BC360 IO360 run3_ORG-0087_02.RCC; Selected renamed RCC file: ORG-0087_IO360_20220609.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220609; Cartridge: Radisky BC360 IO360 run3; Lane: 2; MD5: 56539721b7bff6b0c80eea20f49a9aa3

value: FFPE surgical specimen

value: Not Hispanic/Latino

value: Pre

value: Nulliparous

value: unknown

value: Unknown

value: Partial

value: Right Mastectomy, Left Prophylactic Mastectomy

value: R ILC


title: ORG-0090_IO360_20220329 histologically normal breast tissue

description: Original RCC file: 20220329_Radisky IO360 run 1_ORG-0090 _06.RCC; Selected renamed RCC file: ORG-0090_IO360_20220329.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220329; Cartridge: Radisky IO360 run 1; Lane: 6; MD5: 27f97bdcdc6e8d712af64a858593292d

value: breast

value: not specified

value: NHW

value: White

value: Post

value: Parous

value: No (prophy)


title: whole_blood_temperate_24C_d0_M [MA0050_2_76]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310913

value: temperate

value: male


title: whole_blood_temperate_30C_d3_M [MA0050_2_75]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313234


title: whole_blood_temperate_30C_d3_M [MA0050_2_74]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313946


title: ORG-0081_IO360_20211019 histologically normal breast tissue

description: Original RCC file: 20211019_Radisky IO360 run 1_ORG-81_12.RCC; Selected renamed RCC file: ORG-0081_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 1; Lane: 12; MD5: 66441f826daf2e9c7f56fa7c1c888e37

value: FFPE surgical specimen

value: NHB

value: Black

value: Breast Reduction

value: No

value: no


title: whole_blood_temperate_30C_d18_F [MA0050_2_72]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201411265

value: female


title: ORG-0070_IO360_20220608 histologically normal breast tissue

description: Original RCC file: 20220608_Radisky BC360 IO360 run1_ORG-0070 _11.RCC; Selected renamed RCC file: ORG-0070_IO360_20220608.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220608; Cartridge: Radisky BC360 IO360 run1; Lane: 11; MD5: 67b163beb76791e2dd682c42c974042b

value: Not Hispanic/Latino

value: Pre

value: Nulliparous

value: unknown

value: Unknown

value: HD

value: Complete

value: Right Mastectomy, Left Prophylactic Mastectomy

value: R IDC