title: ORG-0073_IO360_20220329 histologically normal breast tissue

description: Original RCC file: 20220329_Radisky IO360 run 1_ORG-0073_05.RCC; Selected renamed RCC file: ORG-0073_IO360_20220329.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220329; Cartridge: Radisky IO360 run 1; Lane: 5; MD5: 474032303298cd5a6fa0d0bd7ed6351b

value: breast

value: not specified

value: NHW

value: White

value: Parous

value: Yes

value: Partial

value: R DCIS


title: ORG-0068_IO360_20211019 histologically normal breast tissue

status: Public on Mar 17 2026

type: RNA

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

country: USA

institute: Mayo Clinic

description: Original RCC file: 20211019_Radisky IO360 run 1_ORG-68_11.RCC; Selected renamed RCC file: ORG-0068_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 1; Lane: 11; MD5: 76af2e59d49279df66c5a3e228007faa

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

molecule: total RNA

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.

tag: tissue

value: FFPE surgical specimen

tag: panel

tag: ethnicity

value: unknown

value: Pre

tag: parity

tag: breastfed

tag: density

tag: involution

value: Breast Reduction

tag: diagnosis

value: No

value: no


title: ORG-0067_IO360_20211019 histologically normal breast tissue

description: Original RCC file: 20211019_Radisky IO360 run 1_ORG-67_10.RCC; Selected renamed RCC file: ORG-0067_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 1; Lane: 10; MD5: 30d1b716173ef14ec170e27883f70b5c

value: Nulliparous

value: Unknown


title: whole_blood_temperate_24C_d0_M [MA0050_2_71]

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 in temperate facility at 24 degrees for individual FR17MAG201411107

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

organism: Sus scrofa

source_name: whole blood,24 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: male

tag: breeding batch

tag: condition

tag: wash batch

tag: analysis serial


title: whole_blood_temperate_24C_d0_F [MA0050_2_73]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310275

value: female


title: ORG-0064_IO360_20211019 histologically normal breast tissue

description: Original RCC file: 20211019_Radisky IO360 run 1_ORG-64_09.RCC; Selected renamed RCC file: ORG-0064_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 1; Lane: 9; MD5: 800357a4fe2b0eb2b3788c288ec2ccc7

value: breast

value: not specified

value: NHB

value: Black

value: Not Hispanic/Latino

value: ED

value: Right Mastectomy, Left Prophylactic Mastectomy

value: R IDC


title: whole_blood_temperate_30C_d18_M [MA0050_2_70]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313155

source_name: whole blood,18 days at 30 degrees


title: ORG-0063_IO360_20211019 histologically normal breast tissue

description: Original RCC file: 20211019_Radisky IO360 run 1_ORG-63_08.RCC; Selected renamed RCC file: ORG-0063_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 1; Lane: 8; MD5: 60a9c3a2dea81f137f7be28871d1c078

value: FFPE surgical specimen

value: NHW

value: White

value: unknown

value: Pre

value: Partial


title: ORG-0062_IO360_20220329 histologically normal breast tissue

description: Original RCC file: 20220329_Radisky IO360 run 1_ORG-0062_04.RCC; Selected renamed RCC file: ORG-0062_IO360_20220329.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220329; Cartridge: Radisky IO360 run 1; Lane: 4; MD5: 8979f3d90a172cc7d4523863edf17359

value: Parous

value: Yes

value: HD

value: Left Mastectomy, Right Prophylactic Mastectomy

value: L DCIS

value: no


title: whole_blood_temperate_30C_d18_F [MA0050_2_67]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313915

value: temperate

value: female


title: whole_blood_temperate_30C_d3_M [MA0050_2_66]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410523

source_name: whole blood,3 days at 30 degrees

value: male


title: whole_blood_tropical_ambient_d0_M [MA0050_2_69]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330732

source_name: whole blood,ambient

value: tropical


title: whole_blood_temperate_30C_d3_F [MA0050_2_65]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310227


title: ORG-0055_R_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run1_ORG-0055 R_04.RCC; Selected renamed RCC file: ORG-0055_R_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run1; Lane: 4; MD5: 125d8c605e62a7cc2a7ad5cd866d8e7f

value: breast

value: R

value: Nulliparous

value: Unknown

value: Complete

value: Breast Reduction

value: No


title: whole_blood_temperate_24C_d0_M [MA0050_2_62]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310888


title: ORG-0051_IO360_20211019 histologically normal breast tissue

description: Original RCC file: 20211019_Radisky IO360 run 1_ORG-51_06.RCC; Selected renamed RCC file: ORG-0051_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 1; Lane: 6; MD5: cb53462537a093ea6cfade75a1ce2085

value: FFPE surgical specimen

value: not specified

value: NHB

value: Black

value: Not Hispanic/Latino

value: Pre

value: Parous

value: unknown

value: Partial


title: ORG-0059_L_IO360_20220608 histologically normal breast tissue

description: Original RCC file: 20220608_Radisky BC360 IO360 run1_ORG-0059 L_10.RCC; Selected renamed RCC file: ORG-0059_L_IO360_20220608.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220608; Cartridge: Radisky BC360 IO360 run1; Lane: 10; MD5: bb182bac3443d65f9c9103a0c111b6ce

value: L

value: NHW

value: White

value: Hispanic/Latino

value: Yes

value: ED

value: Other

value: L IDC

value: no


title: whole_blood_temperate_30C_d18_F [MA0050_2_63]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311710

value: temperate

value: female


title: whole_blood_temperate_30C_d18_M [MA0050_2_64]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313958

value: male


title: whole_blood_temperate_30C_d18_M [MA0050_2_61]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315281


title: ORG-0054_IO360_20220609 histologically normal breast tissue

description: Original RCC file: 20220609_Radisky BC360 IO360 run3_ORG-0054_07.RCC; Selected renamed RCC file: ORG-0054_IO360_20220609.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220609; Cartridge: Radisky BC360 IO360 run3; Lane: 7; MD5: b950dbd3dc1d56edf52c2d6aac842432

value: breast

value: FFPE surgical specimen

value: not specified

value: Nulliparous

value: Unknown

value: Breast Reduction

value: No


title: ORG-0058_IO360_20211019 histologically normal breast tissue

description: Original RCC file: 20211019_Radisky IO360 run 1_ORG-58_07.RCC; Selected renamed RCC file: ORG-0058_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 1; Lane: 7; MD5: 5f33a891ef500b4a4911c40ea18d6cdc

value: NHW

value: White

value: Not Hispanic/Latino

value: Post

value: Parous

value: Fg

value: Partial

value: Bilateral Prophylactic Mastectomies

value: unknown


title: whole_blood_temperate_30C_d3_M [MA0050_2_59]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313854

value: temperate

value: male


title: whole_blood_temperate_30C_d3_M [MA0050_2_60]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310914


title: ORG-0049_IO360_20211019 histologically normal breast tissue

description: Original RCC file: 20211019_Radisky IO360 run 1_ORG-49_05.RCC; Selected renamed RCC file: ORG-0049_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 1; Lane: 5; MD5: 3810a6c83728a22197ad2fbbcb8e60f9

value: breast

value: FFPE surgical specimen

value: Pre

value: Yes

value: HD

value: Right Mastectomy, Left Prophylactic Mastectomy

value: R IDC

value: no


title: ORG-0048_IO360_20220614 histologically normal breast tissue

description: Original RCC file: 20220614_Radisky BC360 IO360 rerun_ORG-0048_03.RCC; Selected renamed RCC file: ORG-0048_IO360_20220614.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220614; Cartridge: Radisky BC360 IO360 rerun; Lane: 3; MD5: 773da15d3f575c33acdef794bbfeb3e4; Selection rule: latest RCC date chosen from 2 candidate raw RCC files for this specimen/panel.

value: not specified

value: NHW

value: White

value: Hispanic/Latino

value: ED

value: Left Mastectomy, Right Prophylactic Mastectomy

value: L DCIS


title: ORG-0050_L_IO360_20220614 histologically normal breast tissue

description: Original RCC file: 20220614_Radisky BC360 IO360 rerun_ORG-0050 L_04.RCC; Selected renamed RCC file: ORG-0050_L_IO360_20220614.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220614; Cartridge: Radisky BC360 IO360 rerun; Lane: 4; MD5: ee2175331f0c10a8b129218fb43510fd; Selection rule: latest RCC date chosen from 2 candidate raw RCC files for this specimen/panel.

value: L

value: Unknown

value: Hispanic or Latino

value: Parous

value: R DCIS

value: unknown


title: ORG-0046_IO360_20220609 histologically normal breast tissue

description: Original RCC file: 20220609_Radisky BC360 IO360 run3_ORG-0046_06.RCC; Selected renamed RCC file: ORG-0046_IO360_20220609.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220609; Cartridge: Radisky BC360 IO360 run3; Lane: 6; MD5: 0dd54b0cefbf51f6c49258e2036b68dc

value: breast

value: FFPE surgical specimen

value: Not Hispanic/Latino

value: Pre

value: Nulliparous

value: Complete

value: Breast Reduction

value: No


title: whole_blood_tropical_ambient_d0_M [MA0050_2_58]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430259

value: tropical

value: male


title: ORG-0047_R3_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run1_ORG-0047 R3_03.RCC; Selected renamed RCC file: ORG-0047_R3_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run1; Lane: 3; MD5: 14b9752edfa33e0eca505c83e7f60105

value: NHW

value: White

value: Yes

value: ED

value: Partial

value: Right Mastectomy, Left Prophylactic Mastectomy

value: R IDC

value: no


title: ORG-0047_IO360_20211019 histologically normal breast tissue

description: Original RCC file: 20211019_Radisky IO360 run 1_ORG-47_04.RCC; Selected renamed RCC file: ORG-0047_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 1; Lane: 4; MD5: 87b70161a424ab3c17b78c2d47984a5e

value: breast

value: FFPE surgical specimen

value: not specified

value: Parous

value: unknown


title: ORG-0042_IO360_20211019 histologically normal breast tissue

description: Original RCC file: 20211019_Radisky IO360 run 1_ORG-42_03.RCC; Selected renamed RCC file: ORG-0042_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 1; Lane: 3; MD5: 3c3403edfdb766fa64c1a5c81f6bb337

value: Hispanic/Latino

value: Pre

value: Nulliparous

value: Unknown

value: HD

value: Bilateral Prophylactic Mastectomies

value: R Papilloma w/ atypia


title: whole_blood_temperate_30C_d18_M [MA0050_2_56]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310913

value: temperate

value: male


title: ORG-0022_IO360_20220329 histologically normal breast tissue

description: Original RCC file: 20220329_Radisky IO360 run 1_ORG-0022_03.RCC; Selected renamed RCC file: ORG-0022_IO360_20220329.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220329; Cartridge: Radisky IO360 run 1; Lane: 3; MD5: 675289c3cbaaf4d608a351aee7d23b14

value: NHW

value: White

value: Not Hispanic/Latino

value: Partial

value: Right Mastectomy, Left Prophylactic Mastectomy

value: IDC


title: whole_blood_temperate_30C_d18_M [MA0050_2_55]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201411105


title: whole_blood_temperate_24C_d0_M [MA0050_2_54]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311654


title: ORG-0017_IO360_20211019 histologically normal breast tissue

description: Original RCC file: 20211019_Radisky IO360 run 1_ORG-17_02.RCC; Selected renamed RCC file: ORG-0017_IO360_20211019.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20211019; Cartridge: Radisky IO360 run 1; Lane: 2; MD5: 83e2f9339fd0ae0588956eb5ed6d344a

value: breast

value: FFPE surgical specimen

value: not specified

value: ED

value: R IDC

value: no


title: ORG-0016_IO360_20220609 histologically normal breast tissue

description: Original RCC file: 20220609_Radisky BC360 IO360 run3_ORG-0016_05.RCC; Selected renamed RCC file: ORG-0016_IO360_20220609.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220609; Cartridge: Radisky BC360 IO360 run3; Lane: 5; MD5: c4a1c8e43da94e057a0ae29933c02b8d

value: Pre

value: Unknown

value: unknown

value: Fg


title: Tumor_sWAT_biol rep 3 (forward strand)

type: SRA

city: New York

first: Christine

last: Chio

state: NY

address: 1130 St. Nicholas Ave

institute: Columbia University Medical Center

library_source: transcriptomic

data_processing:
Libraries were sequenced using Element AVITI at the Columbia Genome Center.
Samples were multiplexed in each lane, yielding a targeted number of paired-end 75bp reads for each sample.
Bases2fastq version 1.4.0.833301531 was used for converting BCL to fastq format, coupled with adaptor trimming.
Differentially expressed genes were analyzed using DESeq2 R packages designed to test differential expression between two experimental groups from RNA-seq counts data.
Following the differential expression analysis, we performed Gene Set Enrichment Analysis (GSEA) using annotated gene sets from the Molecular Signatures Database (MSigDB) to determine whether a predefined set of genes shows statistically significant, concordant differences between two biological states.
Assembly: Mouse:GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

organism: Mus musculus

source_name: subcutaneous white adipose tissue

extract_protocol:
Total RNA (RIN value > 7) was extracted from adipose tissues, and poly-A pull-down was performed to enrich mRNAs.
Library construction was performed using Illumina TruSeq chemistry, with the final PCR step being modified using the KAPA HiFi HotStart Ready Mix.

value: subcutaneous white adipose tissue

tag: genotype

value: MSRA full-body KO

tag: treatment

value: Orthotopic transplant


title: whole_blood_temperate_30C_d18_F [MA0050_2_47]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311726

value: temperate

value: female


title: whole_blood_temperate_24C_d0_F [MA0050_2_51]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201316043


title: whole_blood_tropical_ambient_d0_F [MA0050_2_57]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330775

value: tropical


title: whole_blood_temperate_30C_d18_F [MA0050_2_53]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410692


title: whole_blood_tropical_ambient_d0_M [MA0050_2_49]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330508

value: male


title: whole_blood_temperate_30C_d3_F [MA0050_2_52]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313240


title: ORG-0021_IO360_20220329 histologically normal breast tissue

description: Original RCC file: 20220329_Radisky IO360 run 1_ORG-0021_02.RCC; Selected renamed RCC file: ORG-0021_IO360_20220329.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220329; Cartridge: Radisky IO360 run 1; Lane: 2; MD5: dde0b9c51002868ab79aae18ad28b020

value: breast

value: NHW

value: White

value: Not Hispanic/Latino

value: Parous

value: Yes

value: Partial

value: Bilateral Prophylactic Mastectomies

value: Atypia

value: Left DCIS 2019


title: whole_blood_tropical_ambient_d0_F [MA0050_2_50]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330687


title: Tumor_sWAT_biol rep 1 (forward strand)

value: subcutaneous white adipose tissue


title: ORG-0018_IO360_20220614 histologically normal breast tissue

description: Original RCC file: 20220614_Radisky BC360 IO360 rerun_ORG-0018_06.RCC; Selected renamed RCC file: ORG-0018_IO360_20220614.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220614; Cartridge: Radisky BC360 IO360 rerun; Lane: 6; MD5: 8d00564e23ec05cb0766f173021d67fb; Selection rule: latest RCC date chosen from 2 candidate raw RCC files for this specimen/panel.

value: FFPE surgical specimen

value: not specified

value: NHB

value: Black

value: Pre

value: Unknown

value: unknown

value: HD

value: Left Mastectomy, Right Prophylactic Mastectomy

value: L IDC

value: no


title: whole_blood_temperate_24C_d0_F [MA0050_2_48]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313915

value: temperate

value: female


title: ORG-0012_IO360_20220608 histologically normal breast tissue

description: Original RCC file: 20220608_Radisky BC360 IO360 run1_ORG-0012_02.RCC; Selected renamed RCC file: ORG-0012_IO360_20220608.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220608; Cartridge: Radisky BC360 IO360 run1; Lane: 2; MD5: 60b24338cf0f94aa8b11826ea7fb781b

value: breast

value: NHW

value: White

value: Not Hispanic/Latino

value: Partial

value: L ILC


title: whole_blood_temperate_24C_d0_M [MA0050_2_46]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201312476

value: male


title: whole_blood_temperate_30C_d18_F [MA0050_2_68]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410517


title: ORG-0011_IO360_20220609 histologically normal breast tissue

description: Original RCC file: 20220609_Radisky BC360 IO360 run3_ORG-0011_04.RCC; Selected renamed RCC file: ORG-0011_IO360_20220609.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20220609; Cartridge: Radisky BC360 IO360 run3; Lane: 4; MD5: 4a03ce901fb78c21b30c7674567093e7

value: FFPE surgical specimen

value: not specified

value: NHB

value: Black

value: Post

value: Fg

value: Right Mastectomy, Left Prophylactic Mastectomy

value: R IDC


title: WT_sWAT_biol rep 3 (forward strand)

value: subcutaneous white adipose tissue

value: MSRA WT

value: Orthotopic transplant


title: WT_sWAT_biol rep 2 (forward strand)


title: ORG-0027_L_IO360_20230117 histologically normal breast tissue

description: Original RCC file: 20230117_Radisky35 IO360 run1_ORG-0027 L_02.RCC; Selected renamed RCC file: ORG-0027_L_IO360_20230117.RCC; Panel: nCounter PanCancer IO 360 Panel [NS_IO_360_v1.0]; Run date: 20230117; Cartridge: Radisky35 IO360 run1; Lane: 2; MD5: a9b6da78164149faf380f64db838fece

value: breast

value: L

value: NHW

value: Pre

value: Parous

value: Unknown

value: ED

value: R DCIS

value: unknown

value: no


title: WT_sWAT_biol rep 1 (forward strand)


title: whole_blood_temperate_24C_d0_M [MA0050_2_43]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315284

value: temperate

value: male


title: whole_blood_temperate_24C_d0_F [MA0050_2_45]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311724

value: female


title: whole_blood_temperate_30C_d18_F [MA0050_2_42]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313935


title: PBS_Light_265

city: Tromsø

first: Alexander

middle: Christopher

last: West

state: Troms

address: Framstredet 39, Tromsø

department: Arctic Chronobiology and Physiology

country: Norway

institute: Universitetet i Tromsø

description: Library name: Sample 11

data_processing:
Prior to transcript quantification, adaptor sequences were trimmed off using fastp 0.23.2. Transcripts from single and paired-end RNAseq data were quantified based on the Atlantic salmon reference transcriptome version 3 (Ssal_v3.1, GCA_905237065.2) by using Salmon (v 1.1.0.) on mapping-mode. Library size was set to automatic detection, and we included the --gcBias flag which corrects for fragment-level GC biases in the input data and bootstrapping was set to 100. We loaded the salmon annotation file (.gff3) into R by using the package ‘ape’.  Output files from Salmon containing read count estimates for each transcript were processed further in R studio (v 2023.6.0) and the package tidyR.
Assembly: Ssal_v3.1, GCA_905237065.2
Supplementary files format and content: name, length, effective length, TPM, num reads

organism: Salmo salar

source_name: heart

extract_protocol:
RNA from hearts were extracted using QIAgen RNeasy® Universal mini kit
Library preparation and sequencing was performed by BGI (Hong Kong) who provided 20 million clean pair-end reads (PE100).

value: heart

value: Aquagen, commercial strain

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP PBS injection light-dark timepoint. Collect after 14 days. Bio rep 5


title: whole_blood_temperate_30C_d18_M [MA0050_2_41]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310781


title: PBS_Light_266

description: Library name: Sample 12

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP PBS injection light-dark timepoint. Collect after 14 days. Bio rep 6


title: Tumor_sWAT_biol rep 2 (forward strand)

value: subcutaneous white adipose tissue

value: MSRA full-body KO

value: Orthotopic transplant


title: whole_blood_temperate_30C_d3_M [MA0050_2_39]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201411105


title: PBS_Light_260

description: Library name: Sample 7

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP PBS injection light-dark timepoint. Collect after 14 days. Bio rep 4


title: PBS_Dark_262

description: Library name: Sample 8

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP PBS injection mid-dark timepoint. Collect after 14 days. Bio rep 4


title: PBS_Dark_263

description: Library name: Sample 9

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP PBS injection mid-dark timepoint. Collect after 14 days. Bio rep 5


title: whole_blood_tropical_ambient_d0_F [MA0050_2_40]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331344

value: tropical


title: whole_blood_temperate_30C_d3_F [MA0050_2_36]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311726


title: whole_blood_temperate_30C_d3_F [MA0050_2_37]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311711


title: PBS_Light_259

description: Library name: Sample 6

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP PBS injection light-dark timepoint. Collect after 14 days. Bio rep 3


title: whole_blood_temperate_24C_d0_M [MA0050_2_33]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313854


title: PBS_Dark_264

description: Library name: Sample 10

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP PBS injection mid-dark timepoint. Collect after 14 days. Bio rep 6


title: whole_blood_temperate_30C_d18_M [MA0050_2_35]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201411223


title: whole_blood_temperate_24C_d0_M [MA0050_2_34]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313949


title: PBS_Light_257

description: Library name: Sample 4

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP PBS injection light-dark timepoint. Collect after 14 days. Bio rep 1


title: PBS_Dark_256

description: Library name: Sample 3

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP PBS injection mid-dark timepoint. Collect after 14 days. Bio rep 3


title: whole_blood_temperate_30C_d3_F [MA0050_2_38]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313871

value: temperate


title: PBS_Dark_254

description: Library name: Sample 2

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP PBS injection mid-dark timepoint. Collect after 14 days. Bio rep 2


title: PBS_Light_258

description: Library name: Sample 5

value: heart

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP PBS injection light-dark timepoint. Collect after 14 days. Bio rep 2


title: whole_blood_temperate_24C_d0_M [MA0050_2_32]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313155

value: male


title: whole_blood_temperate_30C_d18_F [MA0050_2_31]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313934

value: female


title: PBS_Dark_253

description: Library name: Sample 1

value: Aquagen, commercial strain

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP PBS injection mid-dark timepoint. Collect after 14 days. Bio rep 1


title: SAV3_Light_255

description: Library name: Sample 27

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP PBS injection mid-dark timepoint. Collect after 14 days. Bio rep 7


title: whole_blood_tropical_ambient_d0_M [MA0050_2_29]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430379


title: SAV3_Light_282

description: Library name: Sample 25

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP SAV3 injection light-dark timepoint. Collect after 14 days. Bio rep 4


title: SAV3_Light_284

description: Library name: Sample 26

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP SAV3 injection light-dark timepoint. Collect after 14 days. Bio rep 5


title: whole_blood_temperate_30C_d3_F [MA0050_2_27]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310881


title: SAV3_Light_281

description: Library name: Sample 24

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP SAV3 injection light-dark timepoint. Collect after 14 days. Bio rep 3


title: SAV3_Dark_280

description: Library name: Sample 23

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP SAV3 injection mid-dark timepoint. Collect after 14 days. Bio rep 7


title: whole_blood_temperate_30C_d18_M [MA0050_2_22]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201312437


title: whole_blood_temperate_24C_d0_M [MA0050_2_25]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201316036


title: whole_blood_tropical_ambient_d0_M [MA0050_2_24]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330714

value: tropical


title: whole_blood_temperate_24C_d0_M [MA0050_2_23]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313947


title: whole_blood_temperate_30C_d18_F [MA0050_2_20]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315548


title: whole_blood_temperate_30C_d3_F [MA0050_2_26]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310944


title: SAV3_Dark_278

description: Library name: Sample 21

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP SAV3 injection mid-dark timepoint. Collect after 14 days. Bio rep 5


title: SAV3_Light_273

description: Library name: Sample 18

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP SAV3 injection light-dark timepoint. Collect after 14 days. Bio rep 1


title: whole_blood_temperate_24C_d0_F [MA0050_2_21]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310276


title: whole_blood_temperate_24C_d0_F [MA0050_2_30]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315212


title: SAV3_Dark_279

description: Library name: Sample 22

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP SAV3 injection mid-dark timepoint. Collect after 14 days. Bio rep 6


title: SAV3_Dark_270

description: Library name: Sample 16

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP SAV3 injection mid-dark timepoint. Collect after 14 days. Bio rep 2


title: SAV3_Dark_271

description: Library name: Sample 17

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP SAV3 injection mid-dark timepoint. Collect after 14 days. Bio rep 3


title: whole_blood_tropical_ambient_d0_M [MA0050_2_19]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331514


title: SAV3_Dark_277

description: Library name: Sample 20

value: heart

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP SAV3 injection mid-dark timepoint. Collect after 14 days. Bio rep 4


title: whole_blood_tropical_ambient_d0_F [MA0050_2_28]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330368


title: SAV3_Light_274

description: Library name: Sample 19

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP SAV3 injection light-dark timepoint. Collect after 14 days. Bio rep 2


title: SAV3_Dark_269

description: Library name: Sample 15

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP SAV3 injection mid-dark timepoint. Collect after 14 days. Bio rep 1


title: whole_blood_temperate_30C_d3_M [MA0050_2_17]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201314551

value: temperate

value: male


title: PBS_Light_267

description: Library name: Sample 13

value: Aquagen, commercial strain

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP PBS injection light-dark timepoint. Collect after 14 days. Bio rep 7


title: whole_blood_temperate_24C_d0_M [MA0050_2_16]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315281


title: WT-L3-P5-HD

city: Rochester

first: Justin

last: Brennan

address: 601 Elmwood Ave.

department: Microbiology & Immunology

institute: University of Rochester Medical Center

description: Library name: Sample 48

data_processing:
The obtained reads were processed by ViReMa which first aligned the obtained reads to the human reference genome GRCh38 human reference genome.
The unmapped reads were further applied to ViReMa (v0.25) to identify junction reads from cbDVGs
The final cbDVG junction reads from ViReMa were used to graph the cbDVG break and rejoin point distribution in R. The reference RSV genome used for ViReMa was the whole genome plasmid sequence of the reverse genetic system backbone pSynkRSV-line19F
Assembly: pSynkRSV-line19F
Supplementary files format and content: hg38
Supplementary files format and content: ViReMa file includes the break and rejoin points, and counts for each cbDVG detected.

organism: Respiratory syncytial virus

growth_protocol: HEp2 cells were maintained in DMEM supplemented with 10% fetal bovine serum and gentamicin. Cultured in a humidified atmosphere at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from virus containing supernatants with Trizol-LS according to the manufacturer's instructions.
Figure 3: All WT and R2-10U samples: Library construction proceeded with 200ng of total RNA using the TruSeq Stranded Total Sample Preparation kit (Illumina) with Ribo-Zero ribosomal RNA depletion. Figure 6 and 7: WT< R2-10U and R2-8U sequencing was performed on a NovaSeq X Plus sequencer (Illumina) generating paired-end reads giving ~20 million reads per end.

treatment_protocol: High MOI infections to enrich cbDVG proceeded for 3 days per passage. Low MOI infections to deplete cbDVGs proceeded for 5 days per passage

tag: cell line

value: WT


title: whole_blood_tropical_ambient_d0_M [MA0050_2_18]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331166


title: whole_blood_tropical_ambient_d0_F [MA0050_2_15]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330751

value: female


title: WT-L3-P4-LD

description: Library name: Sample 47


title: whole_blood_tropical_ambient_d0_M [MA0050_2_13]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331755


title: whole_blood_temperate_24C_d0_F [MA0050_2_14]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311711


title: WT-L3-P3-HD

description: Library name: Sample 44


title: PBS_Light_268

description: Library name: Sample 14

tag: tissue

value: 6 weeks short photoperiod, 6 weeks long photoperiod, IP PBS injection light-dark timepoint. Collect after 14 days. Bio rep 8


title: whole_blood_temperate_30C_d3_M [MA0050_2_12]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201312475


title: WT-L3-P2

description: Library name: Sample 43


title: WT-L3-P3-LD

description: Library name: Sample 45


title: whole_blood_tropical_ambient_d0_F [MA0050_2_10]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330161

value: tropical


title: WT-L3-P4-HD

description: Library name: Sample 46


title: WT-L3-P0-2

description: Library name: Sample 41


title: whole_blood_tropical_ambient_d0_M [MA0050_2_8]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331307


title: WT-L3-P1

description: Library name: Sample 42


title: whole_blood_temperate_30C_d3_F [MA0050_2_11]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311649


title: whole_blood_temperate_24C_d0_M [MA0050_2_4]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313877


title: WT-L2-P4-HD

description: Library name: Sample 38


title: WT-L2-P3-LD

description: Library name: Sample 37


title: whole_blood_temperate_30C_d18_F [MA0050_2_3]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315300


title: whole_blood_temperate_30C_d3_F [MA0050_2_6]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313128


title: whole_blood_tropical_ambient_d0_M [MA0050_2_2]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430104


title: WT-L2-P5-HD

description: Library name: Sample 40


title: whole_blood_temperate_30C_d3_M [MA0050_2_5]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310904


title: 10U-IVT

description:
Library name: Sample 49
In vitro transcribed RNA

source_name: In vitro transcribed RNA

value: In vitro transcribed RNA

tag: cell type


title: WT-L2-P0-2

description: Library name: Sample 33


title: WT-L2-P1_R2

description: Library name: Sample 34


title: whole_blood_tropical_ambient_d0_F [MA0050_2_9]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430044


title: WT-L2-P3-HD

description: Library name: Sample 36


title: whole_blood_temperate_30C_d3_M [MA0050_1_93]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201312474


title: whole_blood_temperate_30C_d18_F [MA0050_1_94]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310262


title: WT-L2-P2

description: Library name: Sample 35


title: 10U-L3-P4-HD

description: Library name: Sample 30


title: 10U-L3-P3-LD

description: Library name: Sample 29


title: 10U-L3-P3-HD

description: Library name: Sample 28


title: whole_blood_temperate_30C_d18_M [MA0050_1_95]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410524


title: WT-L2-P4-LD

description: Library name: Sample 39


title: whole_blood_tropical_ambient_d0_M [MA0050_1_92]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430243


title: 10U-L3-P4-LD

description: Library name: Sample 31


title: whole_blood_temperate_30C_d3_F [MA0050_1_91]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313933


title: whole_blood_temperate_24C_d0_M [MA0050_2_1]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201316045


title: 10U-L3-P5-HD

description: Library name: Sample 32


title: whole_blood_tropical_ambient_d0_F [MA0050_1_90]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331538


title: whole_blood_temperate_30C_d3_F [MA0050_1_96]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201312426


title: 10U-L3-P1

description: Library name: Sample 26


title: 10U-L3-P2

description: Library name: Sample 27


title: whole_blood_temperate_30C_d18_F [MA0050_1_89]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410515


title: whole_blood_temperate_30C_d3_F [MA0050_1_86]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201316133


title: 10U-L3-P0-2

description: Library name: Sample 25


title: whole_blood_temperate_30C_d3_F [MA0050_1_84]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310230


title: whole_blood_temperate_30C_d18_M [MA0050_2_7]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201314551


title: whole_blood_temperate_30C_d18_M [MA0050_1_83]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201316036


title: whole_blood_tropical_ambient_d0_M [MA0050_1_82]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330347


title: whole_blood_temperate_24C_d0_M [MA0050_1_80]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201312444


title: 10U-L1-P4-HD

description: Library name: Sample 22


title: whole_blood_temperate_30C_d18_F [MA0050_1_81]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201312426


title: 10U-L1-P1

description: Library name: Sample 18


title: whole_blood_temperate_24C_d0_F [MA0050_1_87]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313867


title: 10U-L1-P5-HD

description: Library name: Sample 24


title: whole_blood_temperate_24C_d0_M [MA0050_1_85]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313247


title: 10U-L1-P4-LD

description: Library name: Sample 23


title: whole_blood_tropical_ambient_d0_M [MA0050_1_75]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330510


title: 10U-L1-P3-LD

description: Library name: Sample 21


title: 8U-L3-P3-LD

description: Library name: Sample 13


title: 8U-L3-P4-HD

description: Library name: Sample 14


title: 8U-L3-P5-HD

description: Library name: Sample 16


title: whole_blood_temperate_24C_d0_F [MA0050_1_77]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313957


title: whole_blood_temperate_30C_d18_M [MA0050_1_79]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201411300


title: 10U-L1-P3-HD

description: Library name: Sample 20


title: whole_blood_tropical_ambient_d0_F [MA0050_1_78]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330750


title: 8U-L3-P0-2

description: Library name: Sample 9


title: whole_blood_temperate_24C_d0_M [MA0050_1_73]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313248


title: whole_blood_tropical_ambient_d0_F [MA0050_1_70]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430316


title: 8U-L3-P2

description: Library name: Sample 11


title: 8U-L3-P4-LD

description: Library name: Sample 15


title: whole_blood_temperate_30C_d18_F [MA0050_1_74]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313227


title: 8U-L3-P3-HD

description: Library name: Sample 12


title: 8U-L1-P4-LD

description: Library name: Sample 7


title: 8U-L1-P4-HD

description: Library name: Sample 6


title: whole_blood_temperate_24C_d0_M [MA0050_1_67]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311729


title: 8U-L1-P5-HD

description: Library name: Sample 8


title: whole_blood_temperate_30C_d3_F [MA0050_1_76]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310276


title: whole_blood_tropical_ambient_d0_M [MA0050_1_71]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330743


title: whole_blood_temperate_30C_d18_M [MA0050_1_69]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310272


title: whole_blood_temperate_30C_d3_F [MA0050_1_72]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315548


title: 8U-L1-P2

description: Library name: Sample 3


title: whole_blood_temperate_30C_d3_M [MA0050_1_66]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315559


title: whole_blood_tropical_ambient_d0_F [MA0050_1_61]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331601


title: whole_blood_tropical_ambient_d0_F [MA0050_1_59]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430557


title: whole_blood_temperate_30C_d18_F [MA0050_1_68]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410691


title: 8U-L1-P3-HD

description: Library name: Sample 4


title: whole_blood_temperate_30C_d18_F [MA0050_1_65]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313867


title: R2-8U P6 HD

data_processing:
The obtained reads were processed by ViReMa which first aligned the obtained reads to the human reference genome GRCh38 human reference genome.
The unmapped reads were further applied to ViReMa (v0.25) to identify junction reads from cbDVGs
The final cbDVG junction reads from ViReMa were used to graph the cbDVG break and rejoin point distribution in R. The reference RSV genome used for ViReMa was the whole genome plasmid sequence of the reverse genetic system backbone pSynkRSV-line19F
Assembly: hg38
Supplementary files format and content: ViReMa file includes the break and rejoin points, and counts for each cbDVG detected.

extract_protocol:
Total RNA was extracted from virus containing supernatants with Trizol-LS according to the manufacturer's instructions.
All WT and R2-10U samples: Library construction proceeded with 200ng of total RNA using the TruSeq Stranded Total Sample Preparation kit (Illumina) with Ribo-Zero ribosomal RNA depletion. R2-8U: Total RNA Library preparation kit (Illumina) with ribosomal RNA depletion.

value: High cbDVG


title: Mock_ATAC

city: Liège

first: Bénédicte

last: Machiels

state: Liège

address: Avenue de Cureghem 7b, B43b

department: DMI

country: Belgium

institute: Uliège

description: Library name: Mock_ATAC

library_source: genomic single cell

data_processing:
Reads were aligned to the hg38 reference genome and transcriptome. Data processing, including filtering, counting, and peak calling, was performed using cellranger-arc count.
For each sample, we generate a fragment object using CreateFragmentObject function and a feature-cell matrix was created by running FeatureMatrix function with default parameters. CreateChromatinAssay function was used to Create a ChromatinAssay. Seurat objects containing both RNA were generated using the CreateSeuratObject() function.
Assembly: GRCh38
Supplementary files format and content: Fragment and bed files,
Supplementary files format and content: feature matrix.h5

molecule: genomic DNA

source_name: 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 were generated using the Chromium Single Cell Multiome ATAC + Gene Expression Kit (10x Genomics) following the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform.

tag: strain

value: MISTRG

value: Bone marrow

value: human CD34+

value: LSK, GMP, CMP, Monocyte

value: Humanized

value: Mock


title: whole_blood_temperate_24C_d0_F [MA0050_1_64]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313975


title: 10U-L1-P2

description: Library name: Sample 19


title: whole_blood_tropical_ambient_d0_M [MA0050_1_55]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330960


title: EBV_GEX

description: Library name: EBV_GEX

library_source: transcriptomic single cell

molecule: polyA RNA

value: EBV


title: 8U-L1-P1

description: Library name: Sample 2


title: whole_blood_temperate_24C_d0_F [MA0050_1_60]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311636

value: temperate


title: Mock_GEX

description: Library name: Mock_GEX


title: 8U-L1-P0-2

description: Library name: Sample 1


title: MuHV4 D120

description: Library name: MuHV4 D120

data_processing:
The obtained fastq files were mapped to the reference genome provided by 10x Genomics (GRCm38 reference genome). The cellranger-atac count function was used to align reads and generate single cell accessibility counts. The peak-cell matrix and fragment file for each sample were imported in R and preprocessed individually with Seurat v5.1.0, Signac v1.14.0.
Assembly: GRCm38
Supplementary files format and content: Fragment and bed files,
Supplementary files format and content: feature matrix.h5

extract_protocol:
Cells were collected and washed with PBS, nuclei isolation was conducted following the 10x demonstrated protocol CG000169
The library was sequenced using the NovaSeq 6000 (Illumina) according to the manufacturer’s instructions. Libraries were sequenced following the manufacturer’s protocol.

tag: Sex

value: Female

tag: age

value: 7-8 weeks

value: monocytes

tag: time

value: day 120


title: 8U-L1-P3-LD

description: Library name: Sample 5


title: whole_blood_temperate_30C_d3_M [MA0050_1_57]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201411107

value: male


title: whole_blood_tropical_ambient_d0_F [MA0050_1_54]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430253

value: female


title: whole_blood_temperate_24C_d0_M [MA0050_1_62]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313960


title: whole_blood_tropical_ambient_d0_M [MA0050_1_56]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330964

value: tropical


title: whole_blood_tropical_ambient_d0_M [MA0050_1_53]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330949


title: EBV_ATAC

description: Library name: EBV_ATAC


title: whole_blood_temperate_30C_d18_F [MA0050_1_58]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310227


title: Del73 D120

description: Library name: Del73 D120


title: MuHV4_D8_Rep2

description: Library name: MuHV4_D8_Rep2

library_source: genomic

data_processing:
Paired-end sequencing was performed on an Illumina NovaSeq 6000 platform.
Adapter trimming was performed using Trimmomatic v0.36 with Nextera adapter
Paired-end reads were aligned to the mouse mm10 reference genome using Bowtie2
Peak calling was performed using MACS2
Assembly: mm10
Supplementary files format and content: bigwig files

source_name: 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.
Nuclei were resuspended in 50 µl of transposition reaction mix. Transposition was carried out for 30 min at 37°C. DNA was purified using the MinElute PCR Purification Kit. Purified DNA was amplified and indexed by PCR with 10–12 cycles. Amplified libraries were purified using the MinElute PCR Purification Kit, followed by double AMPure XP purification.

value: bone marrow

value: monocyte

value: day 8


title: whole_blood_temperate_30C_d18_F [MA0050_1_52]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310263


title: Mock D120

description: Library name: Mock D120

value: Bone marrow


title: Mock_D8_Rep1

description: Library name: Mock_D8_Rep1


title: whole_blood_tropical_ambient_d0_M [MA0050_1_50]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331695


title: MuHV4_D8_Rep1

description: Library name: MuHV4_D8_Rep1


title: MuHV4_D8_Rep3

description: Library name: MuHV4_D8_Rep3


title: 8U-L3-P1

description: Library name: Sample 10


title: whole_blood_tropical_ambient_d0_M [MA0050_1_46]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330729


title: Del73_D8_Rep3

description: Library name: Del73_D8_Rep3


title: whole_blood_tropical_ambient_d0_M [MA0050_1_49]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330965


title: Del73_D8_Rep2

description: Library name: Del73_D8_Rep2


title: whole_blood_temperate_30C_d18_F [MA0050_1_47]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315215


title: 10U-L1-P0-2

description: Library name: Sample 17


title: whole_blood_tropical_ambient_d0_F [MA0050_1_48]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331303


title: whole_blood_temperate_30C_d18_M [MA0050_1_45]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313135


title: MuHV4_D120_Rep2

description: Library name: MuHV4_D120_Rep2


title: whole_blood_temperate_30C_d18_M [MA0050_1_51]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201312475


title: Del73_D8_Rep1

description: Library name: Del73_D8_Rep1


title: whole_blood_temperate_24C_d0_F [MA0050_1_44]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311725


title: Mock_D8_Rep2

description: Library name: Mock_D8_Rep2


title: whole_blood_temperate_30C_d18_M [MA0050_1_42]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313876


title: Mock_D120_Rep2

description: Library name: Mock_D120_Rep2


title: MuHV4_D120_Rep3

description: Library name: MuHV4_D120_Rep3


title: whole_blood_temperate_24C_d0_M [MA0050_1_40]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313988


title: whole_blood_temperate_24C_d0_M [MA0050_1_41]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310235


title: whole_blood_temperate_30C_d3_F [MA0050_1_39]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410591


title: Mock_D120_Rep3

description: Library name: Mock_D120_Rep3


title: Del73_D120_Rep2

description: Library name: Del73_D120_Rep2


title: whole_blood_temperate_30C_d18_F [MA0050_1_43]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311636


title: Del73_D120_Rep3

description: Library name: Del73_D120_Rep3


title: whole_blood_temperate_30C_d18_M [MA0050_1_38]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313962


title: Mock_D120_Rep1

description: Library name: Mock_D120_Rep1


title: whole_blood_temperate_30C_d3_F [MA0050_1_33]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201411262


title: Del73_D120_Rep1

description: Library name: Del73_D120_Rep1


title: whole_blood_temperate_30C_d18_F [MA0050_1_30]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313204


title: MuHV4_D120_Rep1

description: Library name: MuHV4_D120_Rep1


title: whole_blood_temperate_30C_d3_M [MA0050_1_32]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201312444


title: whole_blood_tropical_ambient_d0_F [MA0050_1_35]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331715


title: whole_blood_temperate_30C_d3_M [MA0050_1_36]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315304


title: whole_blood_temperate_24C_d0_M [MA0050_1_31]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201411300


title: whole_blood_temperate_30C_d18_F [MA0050_1_29]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315297


title: whole_blood_temperate_24C_d0_M [MA0050_1_34]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410524


title: whole_blood_temperate_30C_d18_M [MA0050_1_37]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313947


title: Bru.LC.5_33.1

city: New Haven

first: Rong

last: Fan

state: CT

address: 55 prospect street

institute: Yale University

description:
Library name: Bru.LC.5
FFPE spatial transcriptomic sequencing

data_processing:
Read 2 from the FASTQ file was processed to extract unique molecular identifiers (UMIs) and spatial Barcodes A and B. Read 1, containing cDNA sequences, was aligned to the mouse GRCm39 or human GRCh38 reference genome using STAR V2.7.8a. Spatial barcode sequences were demultiplexed with ST_Pipeline V1.8.1, using the predefined coordinates of the microfluidic channels, and ENSEMBL IDs were converted to gene names. This generated a gene-by-spot expression matrix for downstream analysis. Entries in the matrix that corresponded to spot positions without tissue were excluded.
The spatial transcriptomic data from Bru.LC.6 was preprocessed following the ASTRO Pipeline(Zhang, D. et al. ASTRO: Automated Spatial Whole-Transcriptome RNA-Expression Workflow (Cold Spring Harbor Laboratory, 2025), also utilized in Bai, Z. et al. Cell (2024).
Assembly: GRCm39 (mouse) and GRCh38 (human)
Supplementary files format and content: Black and white contrasted image of the region of interest for generating the position file. File format (.png)
Supplementary files format and content: Image of the region of interest (ROI). File format (.png)
Supplementary files format and content: Position of spatial pixels aligned to ROI image. File format (.txt)
Supplementary files format and content: Gene expression matrix. File format (.tsv)
Supplementary files format and content: sgRNA expression matrix. File format (.txt)
Library strategy: Spatial Transcriptomics

source_name: Mouse lung

extract_protocol:
Tissue Collection and Embedding Tissue specimens harvested from the experimental mouse models including B16-OVA subcutaneous tumors, AAV-induced GEMM liver tumors, HT29/E0771 lung metastases, and SMARTA splenic tissues were processed as either fresh frozen (FF) or formalin-fixed paraffin-embedded (FFPE) blocks. Fresh tissues were embedded in OCT compound immediately upon harvest, while fixed samples were preserved in PFA prior to paraffin embedding. To maintain RNA, DNA, and protein integrity for downstream spatial transcriptomics, all procedures from collection to embedding were conducted in a strict contamination-free environment. Suitability for analysis was confirmed by histological examination of adjacent sections. Sectioning and Slide Preparation For Perturb-DBiT profiling, both paraffin and OCT blocks were sliced into 7–10 µm thick sections. Sections were carefully mounted in the center of poly-L-lysine-coated glass slides (63478-AS, Electron Microscopy Sciences) to ensure proper alignment with the microfluidic device channels. FFPE Samples: Sectioning of archived FFPE liver and lung tissue blocks was performed by Yale Pathology Tissue Services (YPTS). Fresh Frozen Samples: Sectioning of frozen blocks was carried out in-house. Following preparation, all slides were stored at -80°C until the time of the experiment to prevent transcript degradation. Regulatory Compliance Tissue retrieval and distribution were conducted in accordance with approved protocols (Yale University Institutional Review Board IRB #1401013259) and under the oversight of the Tissue Resource Oversight Committee. All samples were handled in strict compliance with relevant institutional research policies and diagnostic requirements.
The SEQuoia RiboDepletion Kit was used to remove rRNA and mitochondrial rRNA from the amplified cDNA, following the manufacturer’s instructions. 20 ng of cDNA was used as the input amount, and three rounds of depletion were performed. 11 PCR cycles was sufficient to directly ligate sequencing primers, using a 100 μl system consisting of 50 μl 2X KAPA HiFi HotStart ReadyMix, ~42 μl solution from the rRNA removal step, 4 μl 10 μM Modified N501 Primer, and 4 μl 10 μM P7 Primer. The library product was purified using SPRIselect beads at a 0.8X ratio, according to the manufacturer's standard protocol.

value: Mouse lung

value: NSG


title: Bru.LC.1_33.3

description:
Library name: Bru.LC.1_33.3
FFPE spatial transcriptomic sequencing


title: Brie.LU.1

description:
Library name: Brie.LU.1
Fresh frozen spatial transcriptomic sequencing


title: Bru.LC.6_33.1

description:
Library name: Bru.LC.6
FFPE spatial transcriptomic sequencing


title: mTSG.LV.3

description:
Library name: mTSG.LV.3
FFPE spatial transcriptomic sequencing

source_name: Mouse liver

value: Mouse liver


title: Bru.LC.8

description:
Library name: Bru.LC.8
FFPE spatial transcriptomic sequencing


title: whole_blood_temperate_30C_d3_M [MA0050_1_27]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313960


title: mTSG.LV.2_MSTGN3R

description:
Library name: mTSG.LV.2
FFPE spatial transcriptomic sequencing


title: Bru.LC.7

description:
Library name: Bru.LC.7
FFPE spatial transcriptomic sequencing


title: Bru.LC.4_33.1

description:
Library name: Bru.LC.4
FFPE spatial transcriptomic sequencing


title: Bru.LC.3_33.1

description:
Library name: Bru.LC.3
FFPE spatial transcriptomic sequencing


title: whole_blood_tropical_ambient_d0_F [MA0050_1_25]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330334


title: Rat heart bulk RNA-seq, sonogenetic (MscL-G22S), 8 months, biological replicate 3

city: Los Angeles

first: Jun

last: Chen

state: CA

address: 420 Westwood Plaza 5121 Engineering V

department: Bioengineering

institute: University of California, Los Angeles

description:
Library name: RNAseq_RatHeart_ST_8mo_Rep3
Bulk RNA-seq from rat heart tissue.
8MONTH.txt (ST-8-MONTH-3)

data_processing:
Stereo-seq data were processed with SAW (v8.1.3) to generate GEF outputs and associated spatial/QC files.
Assay-specific processing details and file formats are provided in the corresponding RNA-seq and Spatial Transcriptomics metadata templates.
Assembly: Bulk RNA-seq: Rattus norvegicus reference genome. Spatial transcriptomics: Mus musculus GRCm38 (mm10) with custom MSCLG22S sequence included.
Supplementary files format and content: This Series includes raw FASTQ files and processed expression matrices for bulk RNA-seq, and GEF files, spatial images, and associated QC outputs for Stereo-seq spatial transcriptomics. Detailed file lists are provided in the assay-specific templates.

organism: Rattus norvegicus

source_name: heart tissue

growth_protocol: Rodents were housed under standard conditions with ad libitum access to food and water and maintained on a regular light/dark cycle, following institutional guidelines.

extract_protocol:
For bulk RNA-seq, total RNA was extracted from heart tissue using standard RNA isolation methods. For spatial transcriptomics, fresh-frozen heart sections were processed on Stereo-seq capture chips according to the manufacturer’s protocol.
Bulk RNA-seq libraries were prepared from total RNA following standard library preparation protocols. Spatial transcriptomics libraries were prepared using the Stereo-seq library preparation workflow compatible with SAW processing.

treatment_protocol: Animals were assigned to WT control or sonogenetic groups (AAV2/9-cTnT-MscL-G22S-mCherry). Samples were collected at defined time points for bulk RNA-seq and/or spatial transcriptomics.

value: heart tissue

value: 8 months


title: Rat heart bulk RNA-seq, sonogenetic (MscL-G22S), 8 months, biological replicate 1

description:
Library name: RNAseq_RatHeart_ST_8mo_Rep1
Bulk RNA-seq from rat heart tissue.
8MONTH.txt (ST-8-MONTH-1)


title: whole_blood_temperate_30C_d18_F [MA0050_1_24]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313953

value: temperate


title: whole_blood_temperate_24C_d0_F [MA0050_1_23]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201411221


title: Rat heart bulk RNA-seq, WT, 6 months, biological replicate 3

description:
Library name: RNAseq_RatHeart_WT_6mo_Rep3
Bulk RNA-seq from rat heart tissue.
6MONTH.txt (WT-6-Month-3)

value: WT

value: 6 months


title: whole_blood_tropical_ambient_d0_M [MA0050_1_22]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331326


title: Rat heart bulk RNA-seq, sonogenetic (MscL-G22S), 8 months, biological replicate 2

description:
Library name: RNAseq_RatHeart_ST_8mo_Rep2
Bulk RNA-seq from rat heart tissue.
8MONTH.txt (ST-8-MONTH-2)


title: Bru.LC.2_33.1

description:
Library name: Bru.LC.2
FFPE spatial transcriptomic sequencing


title: Rat heart bulk RNA-seq, sonogenetic (MscL-G22S), 6 months, biological replicate 2

description:
Library name: RNAseq_RatHeart_ST_6mo_Rep2
Bulk RNA-seq from rat heart tissue.
6MONTH.txt (ST-6-Month-2)


title: Ep.Tu.1

description:
Library name: Ep.Tu.1
Fresh frozen spatial transcriptomic sequencing

source_name: Mouse tumor

value: Mouse tumor


title: Rat heart bulk RNA-seq, sonogenetic (MscL-G22S), 6 months, biological replicate 3

description:
Library name: RNAseq_RatHeart_ST_6mo_Rep3
Bulk RNA-seq from rat heart tissue.
6MONTH.txt (ST-6-Month-3)


title: Rat heart bulk RNA-seq, sonogenetic (MscL-G22S), 2 months, biological replicate 2

description:
Library name: RNAseq_RatHeart_ST_2mo_Rep2
Bulk RNA-seq from rat heart tissue.
2MONTH.txt (ST-2-Month-2)

value: 2 months


title: Rat heart bulk RNA-seq, WT, 2 months, biological replicate 2

description:
Library name: RNAseq_RatHeart_WT_2mo_Rep2
Bulk RNA-seq from rat heart tissue.
2MONTH.txt (WT-2-Month-2)


title: NTC.SP.1

description:
Library name: NTC.SP.1
Fresh frozen spatial transcriptomic sequencing

source_name: Mouse spleen

value: Mouse spleen

value: SMARTA-TCR-transgenic


title: whole_blood_tropical_ambient_d0_M [MA0050_1_21]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331339

value: tropical

value: male


title: Rat heart bulk RNA-seq, WT, 6 months, biological replicate 2

description:
Library name: RNAseq_RatHeart_WT_6mo_Rep2
Bulk RNA-seq from rat heart tissue.
6MONTH.txt (WT-6-Month-2)


title: Bru.LC.1_33.1

description:
Library name: Bru.LC.1
FFPE spatial transcriptomic sequencing


title: whole_blood_temperate_30C_d3_F [MA0050_1_20]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313843

value: female


title: whole_blood_tropical_ambient_d0_M [MA0050_1_26]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430308


title: Rat heart bulk RNA-seq, WT, 6 months, biological replicate 1

description:
Library name: RNAseq_RatHeart_WT_6mo_Rep1
Bulk RNA-seq from rat heart tissue.
6MONTH.txt (WT-6-Month-1)


title: Rat heart bulk RNA-seq, sonogenetic (MscL-G22S), 2 months, biological replicate 1

description:
Library name: RNAseq_RatHeart_ST_2mo_Rep1
Bulk RNA-seq from rat heart tissue.
2MONTH.txt (ST-2-Month-1)


title: whole_blood_tropical_ambient_d0_M [MA0050_1_28]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331706


title: whole_blood_temperate_30C_d18_M [MA0050_1_19]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201316045


title: Bone marrow derived cells, DHT

first: Kiana

middle: Lee

state: New York

address: 601 Elmwood Avenue

description:
Library name: Sample 1
DHT-treated cells

data_processing:
Samples were demultiplexed using 'cellranger mkfastq' within 10X provided cellranger-7.0.1 using default parameters. Samples were aligned to 10X provided reference refdata-gex-GRCh38-2020-A OR refdata-gex-mm10-2020-A (human OR mouse) using 'cellranger count' within cellranger-7.0.1 using default parameters.
Assembly: GRCh38-2020
Supplementary files format and content: gene list (_genes.tsv) and cell barcodes (_barcodes.tsv) as well as gene/barcode matrices (_matrix.mtx) are provided for each time sample

growth_protocol: Bone marrow-derived cells from a 3-month-old male C57BL/6J mouse were plated in hormone-depleted media supplemented with 5ng/mL of recombinant M-CSF, and 10-9M of 5ɑ-dihydrotestosterone or vehicle control. Cells were incubated for 48 hours before a change in media containing 100ng/mL of recombinant M-CSF, 30ng/mL of RANKL, 10ng/mL of human TNFɑ, and 10-9M of DHT or vehicle control. After 24 hours, adherent cells were collected for single-cell RNA-sequencing.

extract_protocol:
Adherent cells in culture were collected by removing media, washing the cells in PBS twice, and incubating cells in 0.02M EDTA in PBS for 10 minutes at room temperature. Cells were lifted from plate surface using a sterile cell scraper and submitted for scRNA-Seq.
Cell suspensions were processed to generate single-cell RNA-Seq libraries using Chromium Next GEM Single Cell 3′ GEM, Library and Gel Bead Kit v3.1 (10x Genomics), per the manufacturer’s recommendations, as summarized below. Samples were loaded on a Chromium Single-Cell Instrument (10x Genomics, Pleasanton, CA, USA) to generate single-cell GEMs (Gel Bead-in-Emulsions). GEM reverse transcription (GEM-RT) was performed to produce a barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, GEMs were broken, the pooled GEM-RT reaction mixtures were recovered, and cDNA was purified with silane magnetic beads (DynaBeads MyOne Silane Beads, ThermoFisher Scientific). The purified cDNA was further amplified by PCR to generate sufficient material for library construction. Enzymatic fragmentation and size selection was used to optimize the cDNA amplicon size and indexed sequencing libraries were constructed by end repair, A-tailing, adaptor ligation, and PCR. Final libraries contain the P5 and P7 priming sites used in Illumina bridge amplification. Sequence data was generated using Illumina’s NovaSeq 6000.

treatment_protocol: Cells were treated with either 10-9M of 5ɑ-dihydrotestosterone or an equal volume of the vehicle control, ethanol.

value: Mouse primary cells

value: Osteoclast precursors

value: Wild-type

tag: batch


title: Panc02, allograft 8

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

country: Germany

institute: Martin Luther University Halle-Wittenberg

description:
Library name: N797
part2_polyARNA.featureCounts

data_processing:
Sequenced strand specific paired-end reads were trimmed for adaptor sequences and low quality sequence using Cutadapt (v 4.4) with parameters -j 0 -q 20 -O 7 -m 20 –trim-n.
Trimmed reads were mapped against the human genome (mm39 UCSC) using HiSat2 (v 2.2.1) with parameters -q --rna-strandness RF --dta -k 5.
Secondary alignments were filtered out using samtools (v 1.19.2).
Mapped reads were summarized using featureCounts (v 2.0.6) with parameterst -p -s 2 -T 8 -M -t exon -g gene_id and Ensembl gene annotations (GRCm39.113).
Assembly: mm39
Supplementary files format and content: Tab-separated featureCounts file including raw counts for each sample.

source_name: allograft tumor in male mouse

extract_protocol:
RNA from positively sorted NK cells was extracted using Dynabeads™ Oligo(dT)25 RNA isolation kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Quality of RNA was assessed by agarose gel electrophoresis. Reverse transcription was performed with a reverse transcription system (Promega). Total RNA from cell experiments or allograft tumors was isolated by TriZOL® (Thermo Fisher Scientific) according to the manufacturer’s instructions as described before (29). For allograft tumors, tissue was dispersed using an Ultra Turrax (IKA®). RNA integrity was determined by the RNA Pico kit using a Bioanalyzer 2100. Samples with RIN values between 8.5 and 10 were considered. The isolated RNA served as a template for RNA sequencing.
Libraries for RNA sequencing were conducted according to the manufacturer’s instructions (Illumina). For a total of 100 ng (cell culture) or 500 ng (allograft), polyA enrichment with oligo dT beads was performed, before strand-specific libraries were generated using Stranded mRNA Prep kit (Illumina).

value: allograft tumor in male mouse

value: pancreatic cancer derived cell line


title: Rat heart bulk RNA-seq, sonogenetic (MscL-G22S), 6 months, biological replicate 1

description:
Library name: RNAseq_RatHeart_ST_6mo_Rep1
Bulk RNA-seq from rat heart tissue.
6MONTH.txt (ST-6-Month-1)

value: heart tissue


title: Rat heart bulk RNA-seq, WT, 2 months, biological replicate 1

description:
Library name: RNAseq_RatHeart_WT_2mo_Rep1
Bulk RNA-seq from rat heart tissue.
2MONTH.txt (WT-2-Month-1)


title: Ripk2 WT, Biol rep 4, TSB

city: Toronto

first: Stephen

middle: E

last: Girardin

state: ON

address: 1 King's College Cir

country: Canada

institute: University of Toronto

description: Library name: WT_RIP2_4TSB_RNA_08_23_23

data_processing:
Adaptors are trimmed using Trim Galore. The raw trimmed reads are aligned to the reference genome using the STAR aligner.
Assembly: Genome reference sequence: GRCm39, M34 Gencode gene models.
Supplementary files format and content: Tab-delimited text file includes rawcounts for each sample

source_name: Primary Ileal Organoids

extract_protocol:
Total RNA was isolated using the GeneJET RNA purification kit following the manufacturer’s instructions (ThermoFisher, K0732)
32.00 Stranded poly(A) mRNA library preparation (NEBNext)

value: Primary Ileal Organoids

value: TSB Control


title: Ripk2 WT, Biol rep 4, Uninfected

description: Library name: WT_RIP2_4_UI_RNA_08_23_23

value: Uninfected Control


title: Bone marrow derived cells, Vehicle

description:
Library name: Sample 2
Vehicle-treated cells

value: Bone marrow

value: Vehicle control (ethanol)


title: Panc02, allograft 7

description:
Library name: N799
part2_polyARNA.featureCounts


title: whole_blood_temperate_30C_d18_M [MA0050_1_18]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313246

value: temperate


title: Panc02, allograft 5

description:
Library name: N794
part2_polyARNA.featureCounts


title: Panc02, allograft 6

description:
Library name: N798
part2_polyARNA.featureCounts


title: Ripk2 WT, Biol rep 4, M90T

description: Library name: WT_RIP2_4_M90T_RNA_08_23_23

value: M90T Shigella


title: Panc02, allograft 4

description:
Library name: N788
part2_polyARNA.featureCounts

source_name: allograft tumor in female mouse

value: allograft tumor in female mouse


title: whole_blood_temperate_30C_d3_F [MA0050_1_15]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310893


title: whole_blood_temperate_30C_d18_F [MA0050_1_16]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310893


title: Panc02, allograft 3

description:
Library name: N787
part2_polyARNA.featureCounts


title: Ripk2 WT, Biol rep 3, Uninfected

description: Library name: WT_RIP2_3_UI_RNA_08_23_23


title: whole_blood_temperate_24C_d0_M [MA0050_1_17]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315307

source_name: whole blood,24 degrees


title: Panc02, cell line2

description:
Library name: PANC02-2
part2_polyARNA.featureCounts

source_name: cell line

value: cell line

value: monoculture


title: Panc02, allograft 1

description:
Library name: N785
part2_polyARNA.featureCounts


title: Ripk2 WT, Biol rep 3, TSB

description: Library name: WT_RIP2_3_TSB_RNA_08_23_23


title: Panc02, cell line1

description:
Library name: PANC02-1
part2_polyARNA.featureCounts


title: co-culture, sample 5

description:
Library name: M5_PANC
part1_polyARNA.featureCounts

source_name: spleen

value: spleen

value: primary murine NK cells from a male murine donor

value: coculture


title: NK only, sample 5

description:
Library name: M5_NKO
part1_polyARNA.featureCounts


title: whole_blood_temperate_30C_d18_M [MA0050_1_13]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201314807

source_name: whole blood,18 days at 30 degrees

value: male


title: Ripk2 WT, Biol rep 3, M90T Supernantant

description: Library name: WT_RIP2_3_M90T_SUP_RNA_08_23_23

value: Sterile M90T Supernatant


title: whole_blood_temperate_30C_d3_M [MA0050_1_14]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313962

source_name: whole blood,3 days at 30 degrees


title: ctrl, sample 5

description:
Library name: M5_INPUT
part1_polyARNA.featureCounts

value: fresh


title: co-culture, sample 4

description:
Library name: M4_PANC
part1_polyARNA.featureCounts


title: whole_blood_tropical_ambient_d0_F [MA0050_1_12]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330159

source_name: whole blood,ambient

value: tropical

value: female


title: whole_blood_temperate_24C_d0_F [MA0050_1_11]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201314540


title: Ripk2 WT, Biol rep 2, Uninfected

description: Library name: 2_WT_Rip2_Ui_RNA_08_23_23

value: Primary Ileal Organoids


title: Panc02, allograft 2

description:
Library name: N786
part2_polyARNA.featureCounts

value: pancreatic cancer derived cell line


title: co-culture, sample 2

description:
Library name: M2_PANC
part1_polyARNA.featureCounts

value: primary murine NK cells from a female murine donor


title: NK only, sample 4

description:
Library name: M4_NKO
part1_polyARNA.featureCounts


title: ctrl, sample 4

description:
Library name: M4_INPUT
part1_polyARNA.featureCounts


title: Ripk2 WT, Biol rep 2, TSB

description: Library name: 2_WT_Rip2_TSB_RNA_08_23_23

value: TSB Control


title: NK only, sample 2

description:
Library name: M2_NKO
part1_polyARNA.featureCounts


title: ctrl, sample 2

description:
Library name: M2_INPUT
part1_polyARNA.featureCounts


title: Ripk2 WT, Biol rep 2, M90T Supernantant

description: Library name: 2_WT_Rip2_M9S_RNA_08_23


title: whole_blood_temperate_30C_d18_M [MA0050_1_10]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315307

value: temperate


title: Ripk2 WT, Biol rep 3, M90T

description: Library name: WT_RIP2_3_M90T_RNA_08_23_23

value: M90T Shigella


title: whole_blood_temperate_24C_d0_F [MA0050_1_9]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201316134


title: Ripk2 WT, Biol rep 2, M90T

description: Library name: 2_WT_Rip2_M90T_RNA_08_23


title: whole_blood_temperate_30C_d3_M [MA0050_1_8]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313947


title: co-culture, sample 1

description:
Library name: M1_PANC
part1_polyARNA.featureCounts


title: CIN612 cells, shA3B-11, biol rep 2

city: Chicago

first: Conor

last: Templeton

address: 300 E Superior Street

institute: Northwestern University

description: Library name: Sample6

data_processing:
The single-stranded sequences were uploaded to Galaxy EU for bioinformatic analyses, such as DESeq2, and pathway analysis was completed through ShinyGo.
Briefly, a quality check of the RNA-Seq reads was done with FASTQC (Galaxy Version 0.74+galaxy1). Adaptors and low-quality bases were removed with Trimmomatic (Galaxy Version 0.39+galaxy2).
BAM files were created from the FATSQ files with RNA STAR (Galaxy Version 2.7.11a+galaxy1).
Duplicates of mapping were marked by Picard Collect Sequencing Artifact Metrics (Galaxy Version 3.1.1.0).
These transcripts were used to obtain feature counts with FeatureCounts (2.0.6+galaxy0), and differential expression was determined from these counts by DESeq2 (2.11.40.8+galaxy0).
Assembly: The alignments were assembled into potential transcripts with StringTie (Galaxy Version 2.2.3+galaxy0).
Supplementary files format and content: DESeq2 as a tabular file: DESeq2_shAPOBEC3B.tabular

source_name: cervical

growth_protocol: CIN612 9E cells, a clonal cell line derived from a cervical biopsy that stably maintains episomes of HPV31, were co-cultured with mitomycin treated 3T3 J2 fibroblasts in E media.

extract_protocol: Confluent 10 cm plates of these knockdown cell lines were treated with Versene to remove the feeder cells before being harvested and RNA was extracted from the cell pellets using Trizol extraction before being sent for RNA sequencing.

treatment_protocol: The ampicillin-resistant E. coli glycerol stocks expressing shRNAs targeting A3B were grown up in Terrific broth with ampicillin and then purified for lentivirus generation. The plasmids were transfected into HEK293T cells with Lipofectamine 2000 and then the CIN612 9E cells were transduced. The cells were selected for with puromycin.

value: cervical

value: CIN612 9E

value: keratinocyte


title: NK only, sample 1

description:
Library name: M1_NKO
part1_polyARNA.featureCounts

value: spleen

value: monoculture


title: ctrl, sample 1

description:
Library name: M1_INPUT
part1_polyARNA.featureCounts


title: Ripk2 WT, Biol rep 1, Uninfected

description: Library name: 1_WT_Rip2_Ui_RNA_08_23_23

value: Uninfected Control


title: CIN612 cells, shA3B-11, biol rep 1

description: Library name: Sample5


title: whole_blood_temperate_30C_d18_M [MA0050_1_6]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201411222

value: male


title: whole_blood_tropical_ambient_d0_F [MA0050_1_7]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331340


title: CIN612 cells, shA3B-01, biol rep 2

description: Library name: Sample4


title: CIN612 cells, shSCRM, biol rep 2

description: Library name: Sample2

value: shSCRM


title: whole_blood_temperate_30C_d3_M [MA0050_1_5]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313155


title: HDLEC_CTR_3

first: Bruce

middle: D

last: Gelb

address: 1470 Madison Ave

department: Pediatrics and Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: Library name: HDLEC_CTR_3

data_processing:
fastq, salmon
hisat2 and featureCounts
Assembly: grch38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Human primary cell

growth_protocol: We use CHIR, bFGF, BMP4, VEGF-A, EGF, and VEGF-C to differentiate iPSCs into LECs

extract_protocol:
Buffer RLT with b-mercaptoethanol
novogene

value: Human primary cell

value: WT


title: CIN612 cells, shA3B-01, biol rep 1

description: Library name: Sample3


title: CIN612 cells, shSCRM, biol rep 1

description: Library name: Sample1


title: whole_blood_temperate_30C_d3_M [MA0050_1_4]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201316045


title: HDLEC_CTR_2

description: Library name: HDLEC_CTR_2


title: HDLEC_CTR_1

description: Library name: HDLEC_CTR_1


title: Ripk2 WT, Biol rep 1, TSB

description: Library name: 1_WT_Rip2_TSB_RNA_08_23_23


title: Ripk2 KO, Biol rep 4, Uninfected

description: Library name: KO_RIP2_4_UI_RNA_08_23_23

value: Nlrc4-/- Ripk2-/-


title: Ripk2 WT, Biol rep 4, M90T Supernantant

description: Library name: WT_RIP2_4_M90T_SUP_RNA_08_23_23

value: Primary Ileal Organoids

value: Sterile M90T Supernatant


title: ACTN2_4_D18

description: Library name: ACTN2_4_D18

value: mono-allelic ACTN2-mEGFP

value: EGF, VEGFC, D18


title: whole_blood_tropical_ambient_d0_M [MA0050_1_2]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330367

value: tropical


title: Ripk2 WT, Biol rep 1, M90T

description: Library name: 1_WT_Rip2_M90T_RNA_08_23

value: M90T Shigella


title: whole_blood_temperate_24C_d0_M [MA0050_1_3]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201316049

value: temperate


title: ACTN2_2_D18

description: Library name: ACTN2_2_D18


title: Ripk2 WT, Biol rep 1, M90T Supernantant

description: Library name: 1_WT_Rip2_M9S_RNA_08_23


title: whole_blood_temperate_30C_d18_F [MA0050_1_1]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311649

value: female


title: ACTN2_3_D18

description: Library name: ACTN2_3_D18


title: Ripk2 KO, Biol rep 4, M90T Supernantant

description: Library name: KO_RIP2_4_M90T_SUP_RNA_08_23_23


title: ACTN2_4_D14

description: Library name: ACTN2_4_D14

value: EGF, VEGFC, D14


title: ACTN2_1_D18

description: Library name: ACTN2_1_D18


title: ACTN2_3_D14

description: Library name: ACTN2_3_D14


title: ACTN2_1_D14

description: Library name: ACTN2_1_D14


title: ACTN2_3_VEC

description: Library name: ACTN2_3_VEC

value: EGF,bFGF


title: Ripk2 KO, Biol rep 4, TSB

description: Library name: KO_RIP2_4_TSB_RNA_08_23_23

value: TSB Control


title: ACTN2_2_D14

description: Library name: ACTN2_2_D14


title: whole_blood_temperate_24C_d0_F [MA0050_2_44_h2]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313128


title: ACTN2_4_VEC

description: Library name: ACTN2_4_VEC


title: Ripk2 KO, Biol rep 3, TSB

description: Library name: KO_RIP2_3_TSB_RNA_08_23_23


title: whole_blood_tropical_ambient_d0_F [MA0050_7_49_m2]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330129


title: whole_blood_temperate_30C_d18_F [MA0050_8_48]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310881


title: ACTN2_2_VEC

description: Library name: ACTN2_2_VEC


title: ACTN2_1_VEC

description: Library name: ACTN2_1_VEC


title: Ripk2 KO, Biol rep 3, M90T Supernantant

description: Library name: KO_RIP2_3_M90T_SUP_RNA_08_23_23


title: whole_blood_temperate_24C_d0_M [MA0050_8_47]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313983


title: Ripk2 KO, Biol rep 4, M90T

description: Library name: KO_RIP2_4_M90T_RNA_08_23_23


title: Ripk2 KO, Biol rep 2, Uninfected

description: Library name: 2_KO_Rip2_Ui_RNA_08_23

value: Uninfected Control


title: NC210219_HNDS0059-01_C_mut

city: Boston

first: Madison

middle: Rose

last: Glass

state: MA

address: 3 Blackfan St

department: Neurobiology

institute: Boston Children's Hospital

description: Library name: IonCode_0112

data_processing:
The Torrent Suite was used to preprocess the data and generate a matrix of read counts for each sample and gene probe.
Ampliseq read counts were normalized to counts per million.
Assembly: hg38
Supplementary files format and content: AmpliSeqGeneMapping.txt contains information to covert target names to gene IDs.
Supplementary files format and content: CDD_Ampliseq_NormalizedData_combined.txt contains the normalized counts for each target and sample (labeled with IonCode). Metadata_CDD_Ampliseq_features_p162.txt enables the conversion of Ioncoe to sample name.

source_name: induced neurons

growth_protocol: See experimental details in https://doi.org/10.1016/j.nbd.2025.107093

extract_protocol:
RNA was extracted from lysed live cells or frozen cell pellets using TakaraBio's Nucleospin kit (Takara Bio catalog #740971), and then converted into cDNA using using SuperScript IV VILO (Thermofisher Scientific #11756050).
The Ion Ampliseq Transcriptome Human Gene Expression Kit (Thermo Fisher Scientific #A31446) in an automated Ion Chef instrument was used to generate libraries that were then sequenced on an IonTorrent S5 Sequencer (Thermofisher Scientific).

treatment_protocol: no treatment

value: induced neurons


title: Human primary NK cells, TGFBR2 gene knock-out, rep 2

city: Seoul

first: Mihue

last: Jang

address: 5, Hwarang-ro 14-gil, Seongbuk-gu

department: Medicinal Materials Research Center, Biomedical Research Division

country: South Korea

institute: Korea Institute of Science and Technology

description: Library name: KO 2

data_processing:
Sequencing reads were preprocessed with Trimmomatic v0.39.
Trimmed sequence reads were mapped to GRCh38 using STAR v2.7.11b.
Read count extraction and normalization were performed using RSEM v1.3.3.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes expected count for each sample.

source_name: Human promary NK cells

extract_protocol:
Total RNA was isolated from human primary NK cells using RiboEx™ Total RNA isolation solution (GeneAll, South Korea)
The libraries were prepared for 150bp paired-end sequencing using TruSeq Stranded mRNA Sample Prep Kit (Illumina, CA, USA)

value: Human primary NK cells

value: NK cell

value: TGFBR2 knock-out

value: control

value: Batch 2


title: Ripk2 KO, Biol rep 3, Uninfected

description: Library name: KO_RIP2_3_UI_RNA_08_23_23

value: Primary Ileal Organoids

value: Nlrc4-/- Ripk2-/-


title: Human primary NK cells, TGFBR2 gene knock-out and CAR gene knock-in , rep 1

description: Library name: KI 1

value: TGFBR2 knock-out and CAR gene knock-in

value: Batch 1