title: WT L2 P10 HD

city: Rochester

first: Justin

last: Brennan

state: NY

address: 601 Elmwood Ave.

department: Microbiology & Immunology

institute: University of Rochester Medical Center

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.

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.
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.

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

value: WT

value: High cbDVG


title: WT L2 P5 LD

status: Public on Mar 17 2026

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: cell line

tag: genotype

tag: treatment

value: Low cbDVG


title: VEDS CTL, rep3

city: Baltimore

first: Tyler

middle: J

last: Creamer

state: Maryland

address: 733 N Broadway

department: Genetic Medicine

institute: Johns Hopkins University

description: Library name: D3769

library_source: transcriptomic single cell

data_processing:
Illumina’s BaseSpace software and alignment is completed using 10X Genomics CellRanger software (version cellranger-7.1.0). CellRanger software was used to process, align, (mm10), and aggregate (--normalize=none) the raw data.
Assembly: mm10
Supplementary files format and content: There are 3 matricies containing all of the cells from all the samples prior to filtering (barcodes.tsv.gz, matrix.mtx.gz, and features.tsv.gz) and the SampleOrderforAllSamplesMatrix.docx is a Microsoft Word file with the order of the samples within the matricies.

molecule: nuclear RNA

organism: Mus musculus

source_name: Untreated VEDS control

extract_protocol:
Between 10am and 1pm, the aorta was perfused with 10mL ice cold 1x DPBS (ThermoFisher Scientific, J67670-K2) through the right ventricle of the heart. The descending thoracic aorta (proximal to the left subclavian down to the diaphragm) was collected and the adventitia was stripped from the aortas using forceps. The aortas were then flash frozen in an empty cryovial and stored in liquid nitrogen at -154°C until processing. Within a treatment group (N = 3), aortas were randomized to determine processing order. Aortas were processed in batches containing one aorta per treatment group (total aortas per batch N = 6). Within a batch, aortas were randomized to minimize processing order bias. For each batch, the first 3 aortas were processed on wet ice by cutting the aorta into pieces in a cross hatched manner. These pieces were put into the lysis buffer from the Chromium Nuclear Isolation Kit (10x Genomics). Each aorta was manually homogenized with the supplied pestle by twisting 10 times then releasing pressure, this was repeated 4 times. Then the Chromium Nuclear Isolation Kit was used according to the manufacturer’s instructions until the samples were in the 1mL Wash and Resuspension Buffer containing RNase inhibitor. At this point, the 3 processed aortas remained on wet ice and the remaining 3 samples (which had remained frozen on dry ice) were processed just like the first 3 aortas. Once all 6 aortas were in the Wash and Resuspension Buffer containing RNase inhibitor, all 6 samples were spun down and resuspended in 50uL Wash and Resuspension Buffer. Then samples were submitted on wet ice to the Johns Hopkins Single Cell & Transcriptomics core for QC and cDNA synthesis.
Briefly, nuclei were combined with RT reagents and loaded onto 10X Next GEM Chip M along with 3’ HT gel beads. The NextGEM protocol was run on the 10X Chromium X to create GEMs which are broken using Recovery Agent and cDNA is cleaned, following manufacturer’s instructions using MyOne SILANE beads. Fragmentation, end repair, and A-tailing are completed, and samples are cleaned up using double sided size selection (0.6X, 0.8X) with SPRIselect beads. Libraries are sequenced on the Illumina NovaSeq 6000 using v1.5 kits, targeting 50K reads/cell, at read lengths of 28 (R1), 10 (i7), 10 (i5), 91 (R2).

treatment_protocol: Mice were left untreated until 21 days of age, after which they were treated with 50mg/kg/day bicalutamide, 100mg/kg/dayspironolactone, or 5mg/kg/day finerenone in medicated chow until 60 days of age when tissue was harvested. Fludrocortisone treated mice were left untreated until 21 days of age, after which they were treated 10ug/kg/day fludrocortisone in medicated water until 60 days of age when tissue was harvested. Untreated controls remained untreated throughout the experiment.

tag: tissue

value: descending thoracic aorta

tag: Sex

value: Male

tag: strain

tag: age

value: 60 days

value: Untreated


title: Spleen, CD23+ B cell, Xist tat KO, 0h naïve, H3K27me3, biol rep 1

city: Philadelphia

first: Montserrat

last: Anguera

state: PA

address: 3800 Spruce Street, Rosenthal Room 390EB

department: Biomedical Sciences

institute: University of Pennsylvania School of Veterinary Medicine

library_source: genomic

data_processing:
Adaptors were removed using Trimmomatic v0.32
Reads were aligned to mm10 using Bowtie2 v2.3.4.1 with parameters [-q --local --very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant --phred33 -I 10 -X 1000]
Duplicates were removed using Picard MarkDuplicates v1.141
Reads mapped to regions from the ENCODE blacklist were removed
CPM normalized bigwig files were generated using deepTools bamCoverage v3.5.1 with options [--effectiveGenomeSize 2652783500 --normalizeUsing CPM --ignoreForNormalization chrX]
Assembly: mm10
Supplementary files format and content: CPM normalized bigwig files for each Sample
Supplementary files format and content: mean CPM normalized bigwig files for each group of biological replicates
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: Spleen

growth_protocol:
Splenic CD23+ B cells were isolated using biotin anti-mouse CD23 Antibody (Cat #101604, Biolegend)
Naïve samples for both in vivo and ex vivo experiments were immediately subjected to CUT&RUN. In vivo deletion samples were stimulated with 1uM CpG for 24 hours followed by CUT&RUN. Ex vivo deletion samples were treated with 80ug TAT-cre for 45 minutes, then stimulated with 1uM CpG for 24 hours followed by CUT&RUN.

extract_protocol:
Cells were collected at respective timepoint and immobilized on concanavalin A-coated beads in Wash Buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 1x Protease Inhibitor Cocktail). 3ug (H3K27me3, H3K27ac) or 1.5ug  (H2AK119Ub) of antibody was incubated with immobilized cells at 4°C for 5 hours with rotation in Antibody Buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 1x PIC, 0.05% Digitonin, 2mM EDTA). Cells were washed then incubated with pA-MNase fusion protein at 4°C for 1 hour with rotation in Digitonin Wash Buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 1x PIC, 0.05% Digitonin). Digestion was performed in Digitonin Wash Buffer at 0°C for 30 minutes by adding CaCl2 to 2mM. The digestion was stopped by adding one volume of 2X STOP Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 0.02% Digitonin, 50ug/mL RNase A, 50ug/mL Linear Acrylamide, 2pg/mL Yeast Spike-In DNA). Chromatin was released from cells by shaking beads at 300rpm at 37°C for 10 minutes. The supernatant was incubated at 70°C for 10 min with SDS to 0.1% and 50ug of Proteinase K. DNA was then isolated with phenol:chloroform:isoamyl alcohol followed by precipitation with ammonium acetate.
Libraries were constructed with 5ng of CUT&RUN DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturor's protocol

value: Spleen

value: Female

tag: cell type

value: CD23+ B cell

value: Xist fl/fl

tag: antibody

value: unstimulated


title: Spleen, CD23+ B cell, WT tat, 24h stimulated, H3K27me3, biol rep 3

value: TAT-cre treated then stimulated with CpG for 24 hours


title: WT L1 P10 HD


title: whole_blood_temperate_30C_d18_M [MA0050_7_35]

type: RNA

city: CASTANET-TOLOSAN cedex

first: Laure

last: GRESS

address: 24 chemin de Borde Rouge CS52627

department: Occitanie-Toulouse

country: France

institute: INRAE

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313137

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,18 days at 30 degrees

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

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

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

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

tag: experimental facility

value: temperate

tag: gender

value: male

tag: breeding batch

tag: condition

tag: wash batch

tag: analysis serial


title: Spleen, CD23+ B cell, WT tat, 24h stimulated, H3K27me3, biol rep 2


title: WT L1 P5 LD


title: VEDS CTL, rep1

description: Library name: D3709


title: R2-10U L3 P5 LD


title: whole_blood_temperate_30C_d18_F [MA0050_7_36]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313933

value: female


title: whole_blood_temperate_24C_d0_M [MA0050_7_37]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310272

source_name: whole blood,24 degrees


title: VEDS CTL, rep2

description: Library name: D3714


title: Spleen, CD23+ B cell, Xist tat KO, 24h stimulated, H3K27me3, biol rep 3


title: R2-10U L3 P10 HD


title: Wild type CTL, rep3

description: Library name: D3712

source_name: Untreated wild type control


title: Spleen, CD23+ B cell, WT tat, 24h stimulated, H3K27me3, biol rep 1


title: Spleen, CD23+ B cell, WT tat, 0h naïve, H3K27me3, biol rep 3


title: R2-10U L2 P5 LD


title: whole_blood_temperate_24C_d0_M [MA0050_7_32]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310904


title: Spleen, CD23+ B cell, WT tat, 0h naïve, H3K27me3, biol rep 2


title: whole_blood_tropical_ambient_d0_F [MA0050_7_33]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330162

source_name: whole blood,ambient

value: tropical


title: R2-10U L2 P10 HD


title: Wild type CTL, rep1

description: Library name: D3768


title: mouse miRNA-seq Spleen WT 1655

city: Greifswald

first: Stefan

last: Simm

address: Walter-Rathenau-Straße 48

department: Bioinformatics

country: Germany

institute: University Medicine Greifswald

description:
Library name: 22Jan49-D01-L2_S13_L001_R1_001
miRNA-seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Spleen_tissue_wise_diff_expr.csv

library_source: other

data_processing:
Samples sequenced across 2 flowcells are concatenated
Adapter sequences are cut from reads and the first and last 4 nucleotides are trimmed
Samples are mapped to the mouse genome GRCm39 using NextGenMap (v0.5.5)
Genes are counted using featureCounts (subread-2.0.3) with the full Ensembl annotation (v108) filtered to only miRNAs with missing miRBase miRNAs added to their blasted position (50 added)v108)
DESeq2 is used organ-wise to perform differential expression analysis
Assembly: GRCm39, annotation version 108
Supplementary files format and content: DESeq2 output of each experiment as csv-file

molecule: other

growth_protocol: All mice were fed ad libitum and had acces to water until euthanization

extract_protocol:
Tissues were extracted and frozen on dry ice. A bead mill (Retsch, Düsseldorf, Germany) was used to pulverize the tissue. RNA was subsequently extracted from the tissue powder using PeqGold TRIFAST, a phenol-based extraction protocol, (VWR, Germany) according to the manufacturer's protocol. RNA integrity was visualized using a Bioanalyzer (Agilent, Santa Clara, CA, USA)
Each sample was prepared for library construction separately. All 30 libraries were prepared using the NEXTflex small RNA-Seq kit v3 (BIOO Scientific, Austin, TX, USA) according to the manufacturer's recommendations

treatment_protocol: No special treatments were carried out

value: 4 months old

value: whole Spleen tissue

value: WT

tag: batch


title: Wild type CTL, rep2

description: Library name: D3786

value: descending thoracic aorta


title: whole_blood_temperate_24C_d0_F [MA0050_7_31]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315301


title: Spleen, CD23+ B cell, WT tat, 0h naïve, H3K27me3, biol rep 1


title: whole_blood_temperate_30C_d3_M [MA0050_7_30]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313247

source_name: whole blood,3 days at 30 degrees


title: R2-10U L1 P5 LD

value: Low cbDVG


title: mouse miRNA-seq Spleen WT 1653

description:
Library name: 22Jan49-H01-L2_S27_L001_R1_001
miRNA-seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Spleen_tissue_wise_diff_expr.csv


title: Spleen, CD23+ B cell, Xist mb1 cKO, 24h stimulated, H3K27ac, biol rep 3

value: Xist fl/fl ; mb1-cre+

value: stimulated with CpG for 24 hours


title: mouse miRNA-seq Spleen WT 1646

description:
Library name: 22Jan49-A04-L2_S4_L001_R1_001
miRNA-seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Spleen_tissue_wise_diff_expr.csv

value: Spleen


title: Colony 137 Nurse Day 26 Replicate 3

city: Edmonton

first: Olav

last: Rueppell

state: Alberta

address: 11355 - Saskatchewan Drive

department: Biological Sciences

country: Canada

institute: University of Alberta

description:
Library name: Sample 96
All samples were prepared together using an in-house TagSeq library preparation.

data_processing:
FastQC
TagTrimmer.pl & RemovePCRDups.pl
HiSat2
Samtools
Deseq2 in R
Assembly: GCF_003254395.2
Supplementary files format and content: csv files containing the cumulative read counts for genes for each sample from Deseq2

organism: Apis mellifera

source_name: Whole bee

growth_protocol: 1-day-old adults were equally dispered to three different nuclear hives with existing queens and honey frames. Bees inside the colony were undisturbed.

extract_protocol:
Honey bees were captured on days 7 and 26 in order. Nurses and foragers were grabbed and frozen on dry ice and left in -80 until further analysis
RNA libraries were created using an in-house TagSeq protocol

treatment_protocol: Untreated

value: Whole bee

value: untreated


title: Colony 137 Nurse Day 26 Replicate 2 #2

description:
Library name: Sample 95
All samples were prepared together using an in-house TagSeq library preparation.


title: R2-10U L1 P10 HD

value: High cbDVG


title: Spleen, CD23+ B cell, Xist mb1 cKO, 24h stimulated, H3K27ac, biol rep 1

value: Female

value: CD23+ B cell


title: whole_blood_temperate_30C_d3_M [MA0050_7_34]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201314807

value: temperate


title: whole_blood_temperate_24C_d0_M [MA0050_7_29]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410595

value: male


title: whole_blood_tropical_ambient_d0_F [MA0050_7_28]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331526

value: female


title: mouse miRNA-seq Spleen Ftsj1_DF 1656

description:
Library name: 22Jan49-E03-L2_S19_L001_R1_001
miRNA-seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Spleen_tissue_wise_diff_expr.csv


title: mouse miRNA-seq Spleen Ftsj1_DF 1654

description:
Library name: 22Jan49-D02-L2_S14_L001_R1_001
miRNA-seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Spleen_tissue_wise_diff_expr.csv


title: whole_blood_tropical_ambient_d0_M [MA0050_7_27]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331311

value: tropical


title: Spleen, CD23+ B cell, Xist mb1 cKO, 24h stimulated, H3K27ac, biol rep 2


title: mouse miRNA-seq Spleen Ftsj1_DF 1647

description:
Library name: 22Jan49-A03-L2_S3_L001_R1_001
miRNA-seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Spleen_tissue_wise_diff_expr.csv

value: 4 months old


title: Colony 137 Nurse Day 26 Replicate 2

description:
Library name: Sample 94
All samples were prepared together using an in-house TagSeq library preparation.


title: whole_blood_temperate_30C_d18_F [MA0050_7_26]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313151


title: whole_blood_temperate_30C_d3_M [MA0050_7_25]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311719


title: mouse miRNA-seq Liver WT 1653

description:
Library name: 220100000049-F04_22Jan49-F04-L8_S27_L002_R1_001
miRNA-seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L007-L008 = lane 7-8. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male. Batch 2 comprises samples that had to be redone because of low sequencing depth (E04, A02) or were missing entirely (F04)
mirna_Liver_tissue_wise_diff_expr.csv

source_name: Liver

value: Liver

value: whole Liver tissue


title: Colony 137 Nurse Day 26 Replicate 1

description:
Library name: Sample 93
All samples were prepared together using an in-house TagSeq library preparation.

value: WT


title: Spleen, CD23+ B cell, Xist mb1 cKO, 0h naïve, H3K27ac, biol rep 2

value: unstimulated


title: whole_blood_temperate_30C_d18_M [MA0050_7_23]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315558


title: whole_blood_temperate_30C_d18_M [MA0050_7_24]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410595


title: Colony 137 Forager Day 26 Replicate 2 #2

description:
Library name: Sample 91
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, Xist mb1 cKO, 0h naïve, H3K27ac, biol rep 1

value: Xist fl/fl ; mb1-cre+


title: Colony 137 Forager Day 26 Replicate 3

description:
Library name: Sample 92
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, Xist mb1 cKO, 0h naïve, H3K27ac, biol rep 3


title: mouse miRNA-seq Liver Ftsj1_DF 1656

description:
Library name: 22Jan49-G02-L2_S25_L001_R1_001
miRNA-seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Liver_tissue_wise_diff_expr.csv


title: Spleen, CD23+ B cell, WT mb1, 24h stimulated, H3K27ac, biol rep 3

value: WT (mb1-cre+)

value: stimulated with CpG for 24 hours


title: Colony 137 Forager Day 26 Replicate 2

description:
Library name: Sample 90
All samples were prepared together using an in-house TagSeq library preparation.

value: Whole bee


title: Spleen, CD23+ B cell, WT mb1, 24h stimulated, H3K27ac, biol rep 2

value: Spleen


title: whole_blood_temperate_30C_d3_F [MA0050_7_22]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315280


title: Colony 137 Forager Day 26 Replicate 1

description:
Library name: Sample 89
All samples were prepared together using an in-house TagSeq library preparation.

value: untreated


title: mouse miRNA-seq Liver Ftsj1_DF 1654

description:
Library name: 22Jan49-B04-L2_S8_L001_R1_001
miRNA-seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Liver_tissue_wise_diff_expr.csv


title: Spleen, CD23+ B cell, WT mb1, 0h naïve, H3K27ac, biol rep 3

value: Female


title: mouse miRNA-seq Liver WT 1655

description:
Library name: 22Jan49-D03-L2_S15_L001_R1_001
miRNA-seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Liver_tissue_wise_diff_expr.csv


title: mouse miRNA-seq Liver WT 1646

description:
Library name: 22Jan49-A01-L2_S1_L001_R1_001
miRNA-seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Liver_tissue_wise_diff_expr.csv


title: whole_blood_tropical_ambient_d0_M [MA0050_7_20]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430119


title: Colony 137 Nurse Day 7 Replicate 2 #2

description:
Library name: Sample 87
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, WT mb1, 0h naïve, H3K27ac, biol rep 2

value: CD23+ B cell


title: Spleen, CD23+ B cell, WT mb1, 0h naïve, H3K27ac, biol rep 1


title: Colony 137 Nurse Day 7 Replicate 3

description:
Library name: Sample 88
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse miRNA-seq Liver Ftsj1_DF 1647

description:
Library name: 22Jan49-F01-L2_S21_L001_R1_001
miRNA-seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Liver_tissue_wise_diff_expr.csv


title: Spleen, CD23+ B cell, WT mb1, 24h stimulated, H3K27ac, biol rep 1


title: whole_blood_temperate_30C_d18_M [MA0050_7_19]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315559

value: temperate


title: Spleen, CD23+ B cell, Xist mb1 cKO, 24h stimulated, H2AK119Ub, biol rep 3


title: Spleen, CD23+ B cell, Xist mb1 cKO, 24h stimulated, H2AK119Ub, biol rep 2


title: mouse miRNA-seq Kidney WT 1646

description:
Library name: 220100000049-A02_22Jan49-A02-L6_S25_L002_R1_001
miRNA-seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L007-L008 = lane 7-8. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male. Batch 2 comprises samples that had to be redone because of low sequencing depth (E04, A02) or were missing entirely (F04)
mirna_Kidney_tissue_wise_diff_expr.csv

source_name: Kidney

value: Kidney

value: male

value: whole Kidney tissue


title: Colony 137 Nurse Day 7 Replicate 2

description:
Library name: Sample 86
All samples were prepared together using an in-house TagSeq library preparation.


title: whole_blood_temperate_24C_d0_M [MA0050_7_21]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310243


title: whole_blood_temperate_30C_d3_F [MA0050_7_18]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313151

value: female


title: whole_blood_temperate_24C_d0_F [MA0050_7_17]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313227


title: mouse miRNA-seq Kidney Ftsj1_DF 1647

description:
Library name: 22Jan49-F02-L2_S22_L001_R1_001
miRNA-seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Kidney_tissue_wise_diff_expr.csv

value: 4 months old


title: mouse miRNA-seq Kidney Ftsj1_DF 1656

description:
Library name: 22Jan49-C04-L2_S12_L001_R1_001
miRNA-seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Kidney_tissue_wise_diff_expr.csv


title: mouse miRNA-seq Kidney Ftsj1_DF 1654

description:
Library name: 22Jan49-B01-L2_S5_L001_R1_001
miRNA-seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Kidney_tissue_wise_diff_expr.csv


title: Colony 137 Nurse Day 7 Replicate 1

description:
Library name: Sample 85
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, Xist mb1 cKO, 24h stimulated, H2AK119Ub, biol rep 1


title: whole_blood_temperate_30C_d18_M [MA0050_7_13]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315218


title: Colony 137 Forager Day 7 Replicate 2

description:
Library name: Sample 82
All samples were prepared together using an in-house TagSeq library preparation.


title: whole_blood_temperate_30C_d3_F [MA0050_7_14]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410513


title: Colony 137 Forager Day 7 Replicate 3

description:
Library name: Sample 84
All samples were prepared together using an in-house TagSeq library preparation.


title: Colony 127 Nurse Day 26 Replicate 3

description:
Library name: Sample 80
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse miRNA-seq Kidney WT 1653

description:
Library name: 22Jan49-B03-L2_S7_L001_R1_001
miRNA-seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Kidney_tissue_wise_diff_expr.csv


title: whole_blood_temperate_24C_d0_M [MA0050_7_16]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201411105


title: Spleen, CD23+ B cell, Xist mb1 cKO, 0h naïve, H2AK119Ub, biol rep 2


title: Colony 127 Nurse Day 26 Replicate 2

description:
Library name: Sample 79
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse miRNA-seq Kidney WT 1655

description:
Library name: 22Jan49-G03-L2_S26_L001_R1_001
miRNA-seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Kidney_tissue_wise_diff_expr.csv


title: whole_blood_tropical_ambient_d0_F [MA0050_7_11]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330108

value: tropical


title: Colony 127 Nurse Day 26 Replicate 1 #2

description:
Library name: Sample 78
All samples were prepared together using an in-house TagSeq library preparation.

value: WT


title: Colony 137 Forager Day 7 Replicate 2 #2

description:
Library name: Sample 83
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse miRNA-seq Heart WT 1655

description:
Library name: 220100000049-E04_22Jan49-E04-L7_S26_L002_R1_001
miRNA-seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L007-L008 = lane 7-8. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male. Batch 2 comprises samples that had to be redone because of low sequencing depth (E04, A02) or were missing entirely (F04)
mirna_Heart_tissue_wise_diff_expr.csv

source_name: Heart

value: Heart

value: whole Heart tissue


title: whole_blood_temperate_30C_d3_M [MA0050_7_15]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310268


title: whole_blood_tropical_ambient_d0_M [MA0050_7_9]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330341


title: mouse miRNA-seq Heart Ftsj1_DF 1647

description:
Library name: 22Jan49-F03-L2_S23_L001_R1_001
miRNA-seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Heart_tissue_wise_diff_expr.csv


title: Spleen, CD23+ B cell, WT mb1, 0h naïve, H2AK119Ub, biol rep 3

value: WT (mb1-cre+)

value: unstimulated


title: Colony 137 Forager Day 7 Replicate 1

description:
Library name: Sample 81
All samples were prepared together using an in-house TagSeq library preparation.

value: Whole bee


title: whole_blood_temperate_24C_d0_F [MA0050_7_12]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310881


title: Spleen, CD23+ B cell, Xist mb1 cKO, 0h naïve, H2AK119Ub, biol rep 3

value: Spleen

value: Xist fl/fl ; mb1-cre+


title: mouse miRNA-seq Heart WT 1646

description:
Library name: 22Jan49-H02-L2_S28_L001_R1_001
miRNA-seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Heart_tissue_wise_diff_expr.csv


title: Spleen, CD23+ B cell, WT mb1, 0h naïve, H2AK119Ub, biol rep 2

value: Female


title: Spleen, CD23+ B cell, Xist mb1 cKO, 0h naïve, H2AK119Ub, biol rep 1

value: CD23+ B cell


title: Spleen, CD23+ B cell, WT mb1, 24h stimulated, H2AK119Ub, biol rep 2

value: stimulated with CpG for 24 hours


title: whole_blood_temperate_30C_d3_M [MA0050_7_7]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201312473

value: temperate


title: mouse miRNA-seq Heart Ftsj1_DF 1656

description:
Library name: 22Jan49-E01-L2_S17_L001_R1_001
miRNA-seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Heart_tissue_wise_diff_expr.csv

value: male


title: whole_blood_temperate_24C_d0_F [MA0050_7_8]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410513


title: Colony 127 Forager Day 26 Replicate 3

description:
Library name: Sample 76
All samples were prepared together using an in-house TagSeq library preparation.

value: untreated


title: Colony 127 Nurse Day 26 Replicate 1

description:
Library name: Sample 77
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse miRNA-seq Brain WT 1655

description:
Library name: 22Jan49-E02-L2_S18_L001_R1_001
miRNA-seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Brain_tissue_wise_diff_expr.csv

source_name: Brain

value: Brain

value: whole Brain tissue


title: Spleen, CD23+ B cell, WT mb1, 24h stimulated, H2AK119Ub, biol rep 1


title: Colony 127 Forager Day 26 Replicate 2

description:
Library name: Sample 75
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse miRNA-seq Heart Ftsj1_DF 1654

description:
Library name: 22Jan49-C03-L2_S11_L001_R1_001
miRNA-seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Heart_tissue_wise_diff_expr.csv

value: 4 months old


title: whole_blood_temperate_30C_d18_M [MA0050_7_6]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201411107


title: Spleen, CD23+ B cell, WT mb1, 24h stimulated, H2AK119Ub, biol rep 3


title: mouse miRNA-seq Brain WT 1653

description:
Library name: 22Jan49-C01-L2_S9_L001_R1_001
miRNA-seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Brain_tissue_wise_diff_expr.csv

value: WT


title: Spleen, CD23+ B cell, WT mb1, 0h naïve, H2AK119Ub, biol rep 1


title: Colony 127 Forager Day 26 Replicate 1 #2

description:
Library name: Sample 74
All samples were prepared together using an in-house TagSeq library preparation.


title: whole_blood_temperate_30C_d18_M [MA0050_7_5]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201312473


title: Colony 127 Nurse Day 7 Replicate 3

description:
Library name: Sample 72
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse miRNA-seq Brain Ftsj1_DF 1654

description:
Library name: 22Jan49-G01-L2_S24_L001_R1_001
miRNA-seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Brain_tissue_wise_diff_expr.csv


title: Colony 127 Forager Day 26 Replicate 1

description:
Library name: Sample 73
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, Xist mb1 cKO, 24h stimulated, H3K27me3, biol rep 3


title: Spleen, CD23+ B cell, Xist mb1 cKO, 24h stimulated, H3K27me3, biol rep 4


title: Colony 127 Nurse Day 7 Replicate 1 #2

description:
Library name: Sample 70
All samples were prepared together using an in-house TagSeq library preparation.


title: Colony 127 Nurse Day 7 Replicate 2

description:
Library name: Sample 71
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse miRNA-seq Brain Ftsj1_DF 1647

description:
Library name: 22Jan49-B02-L2_S6_L001_R1_001
miRNA-seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Brain_tissue_wise_diff_expr.csv


title: mouse miRNA-seq Brain WT 1646

description:
Library name: 22Jan49-D04-L2_S16_L001_R1_001
miRNA-seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Brain_tissue_wise_diff_expr.csv


title: Spleen, CD23+ B cell, Xist mb1 cKO, 24h stimulated, H3K27me3, biol rep 1


title: mouse miRNA-seq Brain Ftsj1_DF 1656

description:
Library name: 22Jan49-H03-L2_S29_L001_R1_001
miRNA-seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Brain_tissue_wise_diff_expr.csv


title: whole_blood_temperate_24C_d0_M [MA0050_7_4]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201411301


title: whole_blood_temperate_30C_d18_F [MA0050_7_3]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201316043

value: female


title: whole_blood_temperate_30C_d3_M [MA0050_7_1]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410594


title: whole_blood_tropical_ambient_d0_F [MA0050_6_96]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430136

value: tropical


title: whole_blood_temperate_30C_d3_M [MA0050_7_10]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310243


title: mouse degradome seq Spleen WT 0045

description:
Library name: 221000001050-DS26_22Oct1050-DL026_S26_L001_R1_001
Degradome seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male

data_processing:
Samples sequenced across 2 flowcells are concatenated
Samples are mapped to the mouse genome GRCm39 using NextGenMap (v0.5.5)
Genes are counted using featureCounts (subread-2.0.3) with the full Ensembl annotation (v108).
DESeq2 is used organ-wise to perform differential expression analysis
Assembly: GRCm39, annotation version 108
Supplementary files format and content: DESeq2 output of each experiment as csv-file

extract_protocol:
Tissues were extracted and frozen on dry ice. A bead mill (Retsch, Düsseldorf, Germany) was used to pulverize the tissue. RNA was subsequently extracted from the tissue powder using a phenol-based extraction protocol (PeqGold TRIFAST, VWR) according to the manufacturer's protocol. RNA integrity was visualized using a Bioalalyzer (Agilent, Santa Clara, CA, USA)
The protocol was adapted from Li et al (doi.org/10.1186/s13007-019-0524-7) but using oligo nucleotides compatible with NEBNext® Multiplex Oligos for Illumina (NEB, Ipswich, MA, USA). Poly(A) RNA was isolated from 5 µg total RNA using magnetic beads (NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEB, Ipschwich, MA, USA). Uncapped RNA was then ligated to an adapter and reverse transcribed using a poly(A) binding primer. After second strand synthesis and purification, the double stranded fragments were digested with EcoP15I and purified before a double stranded adapter was ligated to the fragment containing the EcoP15I recognition site. After purification and amplification these fragments were prepared for standard Illumina single-read sequencing using a small RNA sequencing protocol.

value: male. 4 months old

value: whole Spleen tissue


title: mouse degradome seq Spleen WT 0003

description:
Library name: 221000001050-DS31_22Oct1050-DL031_S31_L001_R1_001
Degradome seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: mouse degradome seq Spleen WT 0064

description:
Library name: 221000001050-DS28_22Oct1050-DL028_S28_L001_R1_001
Degradome seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: Spleen, CD23+ B cell, Xist mb1 cKO, 24h stimulated, H3K27me3, biol rep 2


title: whole_blood_tropical_ambient_d0_F [MA0050_6_95]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430258


title: Colony 127 Nurse Day 7 Replicate 1

description:
Library name: Sample 69
All samples were prepared together using an in-house TagSeq library preparation.

value: Whole bee


title: Colony 127 Forager Day 7 Replicate 3

description:
Library name: Sample 68
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, Xist mb1 cKO, 0h naive, H3K27me3, biol rep 5

value: Spleen


title: mouse miRNA-seq Heart WT 1653

description:
Library name: 22Jan49-C02-L2_S10_L001_R1_001
miRNA-seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male.
mirna_Heart_tissue_wise_diff_expr.csv

value: Heart

value: whole Heart tissue


title: Negative control

description:
Library name: Sample 66
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, Xist mb1 cKO, 0h naïve, H3K27me3, biol rep 3

value: Female

value: CD23+ B cell

value: Xist fl/fl ; mb1-cre+

value: unstimulated


title: whole_blood_temperate_30C_d18_M [MA0050_7_2]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201314565

value: temperate

value: male


title: Colony 127 Forager Day 7 Replicate 2

description:
Library name: Sample 67
All samples were prepared together using an in-house TagSeq library preparation.

value: untreated


title: Colony 127 Forager Day 7 Replicate 1

description:
Library name: Sample 65
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse degradome seq Spleen Ftsj1_DF 0063

description:
Library name: 221000001050-DS27_22Oct1050-DL027_S27_L001_R1_001
Degradome seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: mouse degradome seq Spleen Ftsj1_DF 0044

description:
Library name: 221000001050-DS25_22Oct1050-DL025_S25_L001_R1_001
Degradome seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: Spleen, CD23+ B cell, Xist mb1 cKO, 0h naïve, H3K27me3, biol rep 4


title: whole_blood_temperate_24C_d0_F [MA0050_6_91]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315547


title: Spleen, CD23+ B cell, Xist mb1 cKO, 0h naïve, H3K27me3, biol rep 2


title: whole_blood_temperate_30C_d18_M [MA0050_6_90]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310950


title: Spleen, CD23+ B cell, WT mb1, 24h stimulated, H3K27me3, biol rep 2

value: WT (mb1-cre+)

value: stimulated with CpG for 24 hours


title: mouse degradome seq Spleen Ftsj1_DF 0004

description:
Library name: 221000001050-DS32_22Oct1050-DL032_S32_L001_R1_001
Degradome seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: mouse degradome seq Spleen WT 0001

description:
Library name: 221000001050-DS29_22Oct1050-DL029_S29_L001_R1_001
Degradome seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male

value: WT


title: Colony 122 Nurse Day 26 Replicate 3

description:
Library name: Sample 64
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, Xist mb1 cKO, 0h naïve, H3K27me3, biol rep 1


title: whole_blood_tropical_ambient_d0_M [MA0050_6_92]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330120

value: tropical


title: whole_blood_tropical_ambient_d0_F [MA0050_6_93]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430096

value: female


title: Spleen, CD23+ B cell, WT mb1, 24h stimulated, H3K27me3, biol rep 4


title: Colony 122 Nurse Day 26 Replicate 2 #2

description:
Library name: Sample 63
All samples were prepared together using an in-house TagSeq library preparation.


title: Colony 122 Nurse Day 26 Replicate 2

description:
Library name: Sample 62
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, WT mb1, 24h stimulated, H3K27me3, biol rep 3


title: Spleen, CD23+ B cell, WT mb1, 24h stimulated, H3K27me3, biol rep 1


title: mouse degradome seq Liver WT 1655

description:
Library name: 221000001050-DS11_22Oct1050-DL011_S11_L001_R1_001
Degradome seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male

value: Liver

value: male. 4 months old

value: whole Liver tissue


title: mouse degradome seq Spleen Ftsj1_DF 0002

description:
Library name: 221000001050-DS30_22Oct1050-DL030_S30_L001_R1_001
Degradome seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male

value: Spleen

value: whole Spleen tissue


title: whole_blood_temperate_24C_d0_M [MA0050_6_89]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315305


title: Colony 122 Nurse Day 26 Replicate 1

description:
Library name: Sample 61
All samples were prepared together using an in-house TagSeq library preparation.

value: Whole bee


title: whole_blood_temperate_30C_d18_M [MA0050_6_94]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311654


title: Colony 122 Forager Day 26 Replicate 3

description:
Library name: Sample 60
All samples were prepared together using an in-house TagSeq library preparation.


title: whole_blood_temperate_30C_d18_F [MA0050_6_88]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311487


title: Spleen, CD23+ B cell, WT mb1, 0h naïve, H3K27me3, biol rep 3

value: Female

value: CD23+ B cell


title: Colony 122 Forager Day 26 Replicate 2 #2

description:
Library name: Sample 59
All samples were prepared together using an in-house TagSeq library preparation.


title: whole_blood_tropical_ambient_d0_F [MA0050_6_87]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331044


title: mouse degradome seq Liver WT 1653

description:
Library name: 221000001050-DS9_22Oct1050-DL009_S9_L001_R1_001
Degradome seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: Spleen, CD23+ B cell, WT mb1, 0h naïve, H3K27me3, biol rep 4

value: unstimulated


title: Spleen, CD23+ B cell, WT mb1, 0h naïve, H3K27me3, biol rep 2


title: whole_blood_temperate_30C_d18_F [MA0050_6_86]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313125

value: temperate


title: mouse degradome seq Liver WT 1646

description:
Library name: 221000001050-DS7_22Oct1050-DL007_S7_L001_R1_001
Degradome seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: mouse degradome seq Liver Ftsj1_DF 1656

description:
Library name: 221000001050-DS12_22Oct1050-DL012_S12_L001_R1_001
Degradome seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: Spleen, CD23+ B cell, WT mb1, 0h naïve, H3K27me3, biol rep 1


title: Colony 122 Forager Day 26 Replicate 2

description:
Library name: Sample 58
All samples were prepared together using an in-house TagSeq library preparation.


title: whole_blood_temperate_30C_d3_F [MA0050_6_84]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310275


title: Colony 122 Forager Day 26 Replicate 1

description:
Library name: Sample 57
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse degradome seq Liver Ftsj1_DF 1654

description:
Library name: 221000001050-DS10_22Oct1050-DL010_S10_L001_R1_001
Degradome seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: Colony 122 Nurse Day 7 Replicate 3

description:
Library name: Sample 56
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, F1, 24h stimulated, Ring1b, biol rep 3

data_processing:
Adaptors were removed using Trimmomatic v0.32
N-masked mm10 genome was created using SNPsplit v0.5.0 (C57Bl/6j N-masked Castaneus) and used to generate Bowtie2 indexes
Reads were aligned to N-masked genome using Bowtie2 v2.3.4.1 with parameters [-q --local --very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant --phred33 -I 10 -X 1000]
Duplicates were removed using Picard MarkDuplicates v1.141
Reads mapped to regions from the ENCODE blacklist were removed
Allele-specific BAM files were then generated using SNPsplit v0.5.0 with option [--paired]
CPM normalized bigwig files were generated using deepTools v3.5.1 bamCoverage with options [--effectiveGenomeSize 2652783500 --normalizeUsing CPM --ignoreForNormalization chrX]
mean CPM normalized bigwig files were generated using the WiggleTools v1.0 mean function for each group of biological replicates followed by bedGraphToBigWig v4.0
Assembly: mm10
Supplementary files format and content: CPM normalized bigwig files for each sample
Supplementary files format and content: mean CPM normalized bigwig files for each group of biological replicates
Library strategy: CUT&RUN

growth_protocol: Splenic CD23+ B cells were isolated using biotin anti-mouse CD23 Antibody (Cat #101604, Biolegend) then subjected to CUT&RUN, or stimulated with 1uM CpG for 12 or 24 hours followed by CUT&RUN

extract_protocol:
Cells were collected at respective timepoint and immobilized on concanavalin A-coated beads in Wash Buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 1x Protease Inhibitor Cocktail). 3ug (H3K27me3, H3K27ac, H3K9me3, IgG), 1.5ug  (H2AK119Ub), or 3:50 dilution (Suz12, Ring1B) of antibody was incubated with immobilized cells at 4°C for 5 hours with rotation in Antibody Buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 1x PIC, 0.05% Digitonin, 2mM EDTA). Cells were washed then incubated with pA-MNase fusion protein at 4°C for 1 hour with rotation in Digitonin Wash Buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 1x PIC, 0.05% Digitonin). Digestion was performed in Digitonin Wash Buffer at 0°C for 30 minutes by adding CaCl2 to 2mM. The digestion was stopped by adding one volume of 2X STOP Buffer (340mM NaCl, 20mM EDTA, 4mM EGTA, 0.02% Digitonin, 50ug/mL RNase A, 50ug/mL Linear Acrylamide, 2pg/mL Yeast Spike-In DNA). Chromatin was released from cells by shaking beads at 300rpm at 37°C for 10 minutes. The supernatant was incubated at 70°C for 10 min with SDS to 0.1% and 50ug of Proteinase K. DNA was then isolated with phenol:chloroform:isoamyl alcohol followed by precipitation with ammonium acetate.
Libraries were constructed with 1.5ng (H3K27me3, H3K27ac, H2AK119Ub, IgG) or 5ng (H3K9me3) of CUT&RUN DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturor's protocol

value: F1 mus x cast


title: mouse degradome seq Kidney WT 1655

description:
Library name: 221000001050-DS17_22Oct1050-DL017_S17_L001_R1_001
Degradome seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male

value: Kidney

value: whole Kidney tissue


title: mouse degradome seq Liver Ftsj1_DF 1647

description:
Library name: 221000001050-DS8_22Oct1050-DL008_S8_L001_R1_001
Degradome seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: whole_blood_temperate_24C_d0_F [MA0050_6_85]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410591


title: Colony 122 Nurse Day 7 Replicate 2 #2

description:
Library name: Sample 55
All samples were prepared together using an in-house TagSeq library preparation.

value: untreated


title: Spleen, CD23+ B cell, F1, 24h stimulated, IgG

value: IgG

value: stimulated with CpG for 24 hours


title: Colony 122 Nurse Day 7 Replicate 2

description:
Library name: Sample 54
All samples were prepared together using an in-house TagSeq library preparation.

value: WT


title: whole_blood_temperate_24C_d0_M [MA0050_6_83]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315559

value: male


title: whole_blood_tropical_ambient_d0_F [MA0050_6_82]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330982

value: tropical

value: female


title: mouse degradome seq Kidney WT 1653

description:
Library name: 221000001050-DS15_22Oct1050-DL015_S15_L001_R1_001
Degradome seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male

value: male. 4 months old


title: mouse degradome seq Kidney WT 1646

description:
Library name: 221000001050-DS13_22Oct1050-DL013_S13_L001_R1_001
Degradome seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: Spleen, CD23+ B cell, F1, 24h stimulated, Ring1b, biol rep 1

value: Spleen


title: whole_blood_temperate_30C_d3_F [MA0050_6_81]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201314540


title: Spleen, CD23+ B cell, F1, 24h stimulated, Ring1b, biol rep 2


title: mouse degradome seq Kidney Ftsj1_DF 1656

description:
Library name: 221000001050-DS18_22Oct1050-DL018_S18_L001_R1_001
Degradome seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: whole_blood_tropical_ambient_d0_F [MA0050_6_80]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331360


title: Spleen, CD23+ B cell, F1, 12h stimulated, Ring1b, biol rep 1

value: stimulated with CpG for 12 hours


title: Colony 122 Nurse Day 7 Replicate 1

description:
Library name: Sample 53
All samples were prepared together using an in-house TagSeq library preparation.

value: Whole bee


title: Colony 122 Forager Day 7 Replicate 3

description:
Library name: Sample 52
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, F1, 12h stimulated, Ring1b, biol rep 3

value: Female

value: CD23+ B cell


title: whole_blood_temperate_30C_d18_M [MA0050_6_79]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313946

value: temperate


title: mouse degradome seq Heart WT 1655

description:
Library name: 221000001050-DS23_22Oct1050-DL023_S23_L001_R1_001
Degradome seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male

value: Heart

value: whole Heart tissue


title: Spleen, CD23+ B cell, F1, 0h naïve, Ring1b, biol rep 2

value: F1 mus x cast

value: unstimulated


title: Colony 122 Forager Day 7 Replicate 2

description:
Library name: Sample 50
All samples were prepared together using an in-house TagSeq library preparation.

value: untreated


title: Spleen, CD23+ B cell, F1, 0h naïve, Ring1b, biol rep 3


title: Colony 122 Forager Day 7 Replicate 2 #2

description:
Library name: Sample 51
All samples were prepared together using an in-house TagSeq library preparation.


title: whole_blood_tropical_ambient_d0_M [MA0050_6_78]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430293


title: mouse degradome seq Kidney Ftsj1_DF 1654

description:
Library name: 221000001050-DS16_22Oct1050-DL016_S16_L001_R1_001
Degradome seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male

value: Kidney

value: whole Kidney tissue


title: Colony 115 Nurse Day 26 Replicate 3

description:
Library name: Sample 47
All samples were prepared together using an in-house TagSeq library preparation.

value: WT


title: Colony 115 Nurse Day 26 Replicate 1

description:
Library name: Sample 48
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, F1, 12h stimulated, Ring1b, biol rep 2


title: whole_blood_temperate_30C_d18_M [MA0050_6_77]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201316135

value: male


title: mouse degradome seq Kidney Ftsj1_DF 1647

description:
Library name: 221000001050-DS14_22Oct1050-DL014_S14_L001_R1_001
Degradome seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: mouse degradome seq Heart WT 1646

description:
Library name: 221000001050-DS19_22Oct1050-DL019_S19_L001_R1_001
Degradome seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: mouse degradome seq Heart Ftsj1_DF 1656

description:
Library name: 221000001050-DS24_22Oct1050-DL024_S24_L001_R1_001
Degradome seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: Spleen, CD23+ B cell, F1, 0h naïve, Ring1b, biol rep 1


title: Colony 122 Forager Day 7 Replicate 1

description:
Library name: Sample 49
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse degradome seq Heart WT 1653

description:
Library name: 221000001050-DS21_22Oct1050-DL021_S21_L001_R1_001
Degradome seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: Colony 115 Nurse Day 26 Replicate 2 #2

description:
Library name: Sample 46
All samples were prepared together using an in-house TagSeq library preparation.


title: whole_blood_temperate_30C_d3_M [MA0050_6_76]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310235


title: whole_blood_temperate_30C_d3_F [MA0050_6_74]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315299

value: female


title: whole_blood_tropical_ambient_d0_M [MA0050_6_75]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331131

value: tropical


title: Spleen, CD23+ B cell, F1, 24h stimulated, Suz12, biol rep 3

value: Spleen

value: stimulated with CpG for 24 hours


title: Spleen, CD23+ B cell, F1, 24h stimulated, Suz12, biol rep 2


title: whole_blood_tropical_ambient_d0_M [MA0050_6_73]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430089


title: Colony 115 Nurse Day 26 Replicate 2

description:
Library name: Sample 45
All samples were prepared together using an in-house TagSeq library preparation.

value: Whole bee


title: mouse degradome seq Heart Ftsj1_DF 1647

description:
Library name: 221000001050-DS20_22Oct1050-DL020_S20_L001_R1_001
Degradome seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male

value: male. 4 months old


title: Colony 115 Forager Day 26 Replicate 1

description:
Library name: Sample 44
All samples were prepared together using an in-house TagSeq library preparation.


title: whole_blood_tropical_ambient_d0_M [MA0050_6_72]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330340


title: Spleen, CD23+ B cell, F1, 24h stimulated, Suz12, biol rep 1

value: Female

value: CD23+ B cell


title: mouse degradome seq Brain WT 1655

description:
Library name: 221000001050-DS5_22Oct1050-DL005_S5_L001_R1_001
Degradome seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male

value: Brain

value: whole Brain tissue


title: Spleen, CD23+ B cell, F1, 12h stimulated, Suz12, biol rep 3

value: F1 mus x cast

value: stimulated with CpG for 12 hours


title: mouse degradome seq Brain WT 1653

description:
Library name: 221000001050-DS3_22Oct1050-DL003_S3_L001_R1_001
Degradome seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: whole_blood_temperate_30C_d3_M [MA0050_6_69]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201411300

value: temperate


title: mouse degradome seq Brain WT 1646

description:
Library name: 221000001050-DS1_22Oct1050-DL001_S1_L001_R1_001
Degradome seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: whole_blood_tropical_ambient_d0_F [MA0050_6_70]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331331


title: Spleen, CD23+ B cell, F1, 0h naïve, Suz12, biol rep 3

value: unstimulated


title: Spleen, CD23+ B cell, F1, 12h stimulated, Suz12, biol rep 2


title: mouse degradome seq Heart Ftsj1_DF 1654

description:
Library name: 221000001050-DS22_22Oct1050-DL022_S22_L001_R1_001
Degradome seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male

value: Heart

value: whole Heart tissue


title: Colony 115 Forager Day 26 Replicate 2

description:
Library name: Sample 41
All samples were prepared together using an in-house TagSeq library preparation.

value: WT

value: untreated


title: Spleen, CD23+ B cell, F1, 0h naïve, Suz12, biol rep 2


title: whole_blood_tropical_ambient_d0_M [MA0050_6_68]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430530

value: tropical

value: male


title: Spleen, CD23+ B cell, F1, 12h stimulated, Suz12, biol rep 1

value: Spleen


title: Colony 115 Forager Day 26 Replicate 3

description:
Library name: Sample 43
All samples were prepared together using an in-house TagSeq library preparation.

value: Whole bee


title: Colony 115 Nurse Day 7 Replicate 3

description:
Library name: Sample 39
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse degradome seq Brain Ftsj1_DF 1654

description:
Library name: 221000001050-DS4_22Oct1050-DL004_S4_L001_R1_001
Degradome seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male

value: male. 4 months old


title: whole_blood_temperate_30C_d3_F [MA0050_6_71]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315552

value: female


title: mouse degradome seq Brain Ftsj1_DF 1656

description:
Library name: 221000001050-DS6_22Oct1050-DL006_S6_L001_R1_001
Degradome seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: Colony 115 Forager Day 26 Replicate 2 #2

description:
Library name: Sample 42
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse degradome seq Brain Ftsj1_DF 1647

description:
Library name: 221000001050-DS2_22Oct1050-DL002_S2_L001_R1_001
Degradome seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L001-L002 = lane 1-2. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. For spleen, not enough material from the original mice was available. Spleen samples from 4 other pairs of brothers (0044+0045, 0063+0064, 0001+0002+0003+0004) was used. All mice are male


title: whole_blood_temperate_30C_d18_F [MA0050_6_67]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410591


title: Colony 115 Nurse Day 7 Replicate 2 #2

description:
Library name: Sample 38
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, F1, 0h naïve, Suz12, biol rep 1

value: Female

value: CD23+ B cell


title: Colony 115 Nurse Day 7 Replicate 1

description:
Library name: Sample 40
All samples were prepared together using an in-house TagSeq library preparation.


title: whole_blood_temperate_30C_d3_M [MA0050_6_66]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313207


title: Colony 115 Nurse Day 7 Replicate 2

description:
Library name: Sample 37
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse rRNA-depleted total-RNA seq Spleen WT 1655

description:
Library name: 22Jan49-D01-L3_S43_L003_R1_001
rRNA-depleted total-RNA seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

data_processing:
Samples sequenced across 2 flowcells are concatenated
Samples are mapped to the mouse genome GRCm39 using NextGenMap (v0.5.5)
For the poly-A data genes are counted using featureCounts (subread-2.0.3) with the full Ensembl annotation (v108). The rRNA-depletion total RNA seq data is counted four times, using the Ensembl annotation filtered to gene_biotype “lncRNA”, “snRNA”, and “snoRNA” and the RNAcentral annotation filtered to “tRNA”.
Four each respective dataset, DESeq2 is used organ-wise to perform differential expression analysis
Assembly: GRCm39, annotation version 108
Supplementary files format and content: DESeq2 output of each experiment as csv-file. As differential expression was done individually for each ncRNA type, 4 output files are created for the rRNA-depleted total RNA seq data.

extract_protocol:
Tissues were extracted and frozen on dry ice. A bead mill (Retsch, Düsseldorf, Germany) was used to pulverize the tissue. RNA was subsequently extracted from the tissue powder using PeqGold TRIFAST, a phenol-based extraction protocol, (VWR, Germany) according to the manufacturer's protocol. RNA integrity was visualized using a Bioanalyzer (Agilent, Santa Clara, CA, USA)
Each sample was prepared for library construction separately. The 60 libraries were prepared using the (30x) Illumina stranded mRNA Prep and (30x) Illumina stranded total RNA Prep (Illumina, San Diego, CA, USA) according to the manufacturer's recommendations

value: whole Spleen tissue


title: mouse rRNA-depleted total-RNA seq Spleen WT 1653

description:
Library name: 22Jan49-H01-L3_S58_L003_R1_001
rRNA-depleted total-RNA seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Spleen, CD23+ B cell, F1, 24h stimulated, H3K29me3, biol rep 4

value: F1 mus x cast

value: stimulated with CpG for 24 hours


title: whole_blood_temperate_24C_d0_M [MA0050_6_63]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313137

value: temperate


title: mouse rRNA-depleted total-RNA seq Spleen WT 1646

description:
Library name: 22Jan49-A04-L3_S34_L003_R1_001
rRNA-depleted total-RNA seq of whole Spleen tissue from WT mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Colony 115 Forager Day 7 Replicate 1

description:
Library name: Sample 36
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, F1, 24h stimulated, H3K29me3, biol rep 2


title: Colony 115 Forager Day 7 Replicate 3

description:
Library name: Sample 35
All samples were prepared together using an in-house TagSeq library preparation.


title: whole_blood_temperate_24C_d0_M [MA0050_6_61]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201316135


title: Spleen, CD23+ B cell, F1, 24h stimulated, H3K29me3, biol rep 3


title: Colony 115 Forager Day 7 Replicate 2

description:
Library name: Sample 33
All samples were prepared together using an in-house TagSeq library preparation.


title: whole_blood_temperate_24C_d0_F [MA0050_6_64]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310262


title: Spleen, CD23+ B cell, F1, 24h stimulated, H3K27ac, biol rep 3


title: mouse rRNA-depleted total-RNA seq Liver WT 1655

description:
Library name: 22Jan49-D03-L3_S45_L003_R1_001
rRNA-depleted total-RNA seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Liver

value: whole Liver tissue


title: Colony 115 Forager Day 7 Replicate 2 #2

description:
Library name: Sample 34
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse rRNA-depleted total-RNA seq Spleen Ftsj1_DF 1656

description:
Library name: 22Jan49-E03-L3_S49_L003_R1_001
rRNA-depleted total-RNA seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: mouse rRNA-depleted total-RNA seq Spleen Ftsj1_DF 1647

description:
Library name: 22Jan49-A03-L3_S33_L003_R1_001
rRNA-depleted total-RNA seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: whole_blood_tropical_ambient_d0_F [MA0050_6_60]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331521


title: Spleen, CD23+ B cell, F1, 24h stimulated, H3K29me3, biol rep 1


title: mouse rRNA-depleted total-RNA seq Liver WT 1653

description:
Library name: 22Jan49-F04-L3_S54_L003_R1_001
rRNA-depleted total-RNA seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: whole_blood_temperate_30C_d18_M [MA0050_6_65]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315282


title: whole_blood_temperate_30C_d18_M [MA0050_6_62]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313854


title: Colony 109 Nurse Day 26 Replicate 3

description:
Library name: Sample 31
All samples were prepared together using an in-house TagSeq library preparation.


title: Colony 109 Nurse Day 26 Replicate 3 #2

description:
Library name: Sample 32
All samples were prepared together using an in-house TagSeq library preparation.


title: Colony 109 Nurse Day 26 Replicate 2

description:
Library name: Sample 30
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, F1, 12h stimulated, H3K29me3, biol rep 2

value: stimulated with CpG for 12 hours


title: mouse rRNA-depleted total-RNA seq Spleen Ftsj1_DF 1654

description:
Library name: 22Jan49-D02-L3_S44_L003_R1_001
rRNA-depleted total-RNA seq of whole Spleen tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: whole_blood_temperate_24C_d0_F [MA0050_6_59]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410517


title: Spleen, CD23+ B cell, F1, 12h stimulated, H3K29me3, biol rep 3


title: Spleen, CD23+ B cell, F1, 12h stimulated, H3K29me3, biol rep 1


title: mouse rRNA-depleted total-RNA seq Liver Ftsj1_DF 1656

description:
Library name: 22Jan49-G02-L3_S56_L003_R1_001
rRNA-depleted total-RNA seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: whole_blood_temperate_30C_d18_F [MA0050_6_57]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311711


title: whole_blood_temperate_30C_d18_M [MA0050_6_58]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313877


title: whole_blood_temperate_24C_d0_F [MA0050_6_56]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313240


title: mouse rRNA-depleted total-RNA seq Liver WT 1646

description:
Library name: 22Jan49-A01-L3_S31_L003_R1_001
rRNA-depleted total-RNA seq of whole Liver tissue from WT mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: WT


title: mouse rRNA-depleted total-RNA seq Liver Ftsj1_DF 1654

description:
Library name: 22Jan49-B04-L3_S38_L003_R1_001
rRNA-depleted total-RNA seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: whole_blood_temperate_24C_d0_F [MA0050_6_54]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201411262


title: Spleen, CD23+ B cell, F1, 12h stimulated, H3K29me3, biol rep 4


title: Colony 109 Forager Day 26 Replicate 3

description:
Library name: Sample 27
All samples were prepared together using an in-house TagSeq library preparation.

value: untreated


title: Spleen, CD23+ B cell, F1, 0h naïve, H3K29me3, biol rep 3

value: unstimulated


title: mouse rRNA-depleted total-RNA seq Liver Ftsj1_DF 1647

description:
Library name: 22Jan49-F01-L3_S51_L003_R1_001
rRNA-depleted total-RNA seq of whole Liver tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Colony 109 Nurse Day 26 Replicate 1

description:
Library name: Sample 29
All samples were prepared together using an in-house TagSeq library preparation.


title: Colony 109 Forager Day 26 Replicate 3 #2

description:
Library name: Sample 28
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, F1, 0h naïve, H3K29me3, biol rep 1


title: whole_blood_temperate_30C_d18_F [MA0050_6_53]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313228


title: Colony 109 Forager Day 26 Replicate 2

description:
Library name: Sample 26
All samples were prepared together using an in-house TagSeq library preparation.


title: whole_blood_temperate_24C_d0_F [MA0050_6_55]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310878


title: Colony 109 Nurse Day 7 Replicate 3 #2

description:
Library name: Sample 24
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, F1, 0h naïve, H3K29me3, biol rep 4


title: Spleen, CD23+ B cell, F1, 0h naïve, H3K29me3, biol rep 2


title: whole_blood_temperate_30C_d3_F [MA0050_6_52]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313915


title: whole_blood_temperate_24C_d0_F [MA0050_6_51]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310893


title: mouse rRNA-depleted total-RNA seq Kidney WT 1655

description:
Library name: 22Jan49-G03-L3_S57_L003_R1_001
rRNA-depleted total-RNA seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Kidney

value: whole Kidney tissue


title: Colony 109 Nurse Day 7 Replicate 3

description:
Library name: Sample 23
All samples were prepared together using an in-house TagSeq library preparation.

value: Whole bee


title: Colony 109 Forager Day 26 Replicate 1

description:
Library name: Sample 25
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, F1, 24h stimulated, H2AK119Ub, biol rep 4

value: Spleen


title: whole_blood_temperate_30C_d18_M [MA0050_6_50]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311729

value: male


title: mouse rRNA-depleted total-RNA seq Kidney WT 1653

description:
Library name: 22Jan49-B03-L3_S37_L003_R1_001
rRNA-depleted total-RNA seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: male. 4 months old


title: mouse rRNA-depleted total-RNA seq Kidney Ftsj1_DF 1656

description:
Library name: 22Jan49-C04-L3_S42_L003_R1_001
rRNA-depleted total-RNA seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Colony 109 Nurse Day 7 Replicate 1

description:
Library name: Sample 21
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, F1, 24h stimulated, H2AK119Ub, biol rep 5

value: Female

value: CD23+ B cell


title: whole_blood_temperate_24C_d0_F [MA0050_6_49]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201316131

value: female


title: Spleen, CD23+ B cell, F1, 24h stimulated, H2AK119Ub, biol rep 3

value: F1 mus x cast

value: stimulated with CpG for 24 hours


title: mouse rRNA-depleted total-RNA seq Kidney WT 1646

description:
Library name: 22Jan49-A02-L3_S32_L003_R1_001
rRNA-depleted total-RNA seq of whole Kidney tissue from WT mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Spleen, CD23+ B cell, F1, 24h stimulated, H2AK119Ub, biol rep 2


title: Colony 109 Nurse Day 7 Replicate 2

description:
Library name: Sample 22
All samples were prepared together using an in-house TagSeq library preparation.


title: Colony 109 Forager Day 7 Replicate 3

description:
Library name: Sample 19
All samples were prepared together using an in-house TagSeq library preparation.


title: Colony 109 Forager Day 7 Replicate 2

description:
Library name: Sample 18
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse rRNA-depleted total-RNA seq Kidney Ftsj1_DF 1654

description:
Library name: 22Jan49-B01-L3_S35_L003_R1_001
rRNA-depleted total-RNA seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Colony 109 Forager Day 7 Replicate 3 #2

description:
Library name: Sample 20
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, F1, 12h stimulated, H2AK119Ub, biol rep 3


title: TCR_Z007

first: Hu

last: Zeng

state: MN

address: 209 Third Ave SW

department: Rheumatology

institute: Mayo Clinic

description:
Library name: Sample59
immune-related adverse event (irAE)

data_processing:
Cell type annotation was conducted using the Azimuth package with the Human PBMC reference dataset.
To refine cell type classifications, we manually reviewed cluster-specific gene markers identified by Immunopipe and further annotated subpopulations of CD8 T cells. Gene set enrichment analysis was performed using the clusterProfiler package in R.
Additionally, ANOVA test was applied to compare gene expression scores across patient groups for selected genes involved in the CD8 T cell cytotoxicity pathway.
Assembly: GRCh38
Supplementary files format and content: vdj_filtered_contig_annotations.csv

organism: Homo sapiens

source_name: PBMC

growth_protocol: Blood samples were collected into sodium heparin tubes, and plasma was collected after centrifuging at 4 °C, 1300 rpm for 10 mins.

extract_protocol:
Specifically, 13 mL Ficoll-Paque™ PLUS density gradient media (GE Healthcare, Cat# 17-1440-02) were added to the bottom of 30 mL diluted peripheral blood, and centrifuged at 4 °C, 400 g for 25 min with the acceleration and deceleration at lower speed. The PBMC layer was collected and washed with wash buffer (1×PBS + 10 mM HEPES + 0.1% BSA + 2 mM EDTA), and PBMCs were aliquoted and cryopreserved in a liquid nitrogen tank.
FASTQ files generated from the Gene Expression and Feature Barcode libraries were processed using the 10x Genomics Cell Ranger multi pipeline to create expression matrices for downstream analysis.
Integrated single-cell analysis of gene expression and T cell receptor data was performed using the Immunopipe package.

treatment_protocol: Peripheral blood mononuclear cells were isolated from the peripheral blood using Ficoll-Paque gradient centrifugation.

value: PBMC

tag: sample group

value: immune-related adverse event (irAE)


title: mouse rRNA-depleted total-RNA seq Kidney Ftsj1_DF 1647

description:
Library name: 22Jan49-F02-L3_S52_L003_R1_001
rRNA-depleted total-RNA seq of whole Kidney tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

tag: cell line


title: mouse rRNA-depleted total-RNA seq Heart WT 1655

description:
Library name: 22Jan49-E04-L3_S50_L003_R1_001
rRNA-depleted total-RNA seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Heart

value: whole Heart tissue

tag: genotype


title: Spleen, CD23+ B cell, F1, 12h stimulated, H2AK119Ub, biol rep 2

tag: treatment

value: stimulated with CpG for 12 hours


title: Spleen, CD23+ B cell, F1, 24h stimulated, H2AK119Ub, biol rep 1

tag: tissue


title: Spleen, CD23+ B cell, F1, 12h stimulated, H2AK119Ub, biol rep 1

tag: Sex


title: whole_blood_temperate_24C_d0_F [MA0050_6_48]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315215

value: temperate


title: mouse rRNA-depleted total-RNA seq Heart WT 1646

description:
Library name: 22Jan49-H02-L3_S59_L003_R1_001
rRNA-depleted total-RNA seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: WT


title: TCR_TZM035

description:
Library name: Sample58
rheumatoid arthritis control (RAC)

value: rheumatoid arthritis control (RAC)


title: mouse rRNA-depleted total-RNA seq Heart WT 1653

description:
Library name: 22Jan49-C02-L3_S40_L003_R1_001
rRNA-depleted total-RNA seq of whole Heart tissue from WT mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: TCR_TZ001

description:
Library name: Sample57
immune-related adverse event (irAE)


title: Colony 109 Forager Day 7 Replicate 1

description:
Library name: Sample 17
All samples were prepared together using an in-house TagSeq library preparation.

value: Whole bee

value: untreated


title: TCR_RA12

description:
Library name: Sample56
rheumatoid arthritis control (RAC)


title: TCR_irAE13

description:
Library name: Sample55
immune-related adverse event (irAE)


title: Spleen, CD23+ B cell, F1, 0h naïve, H2AK119Ub, biol rep 3

value: Spleen

value: unstimulated


title: Colony 107 Nurse Day 26 Replicate 3 #2

description:
Library name: Sample 16
All samples were prepared together using an in-house TagSeq library preparation.


title: Colony 107 Nurse Day 26 Replicate 2

description:
Library name: Sample 14
All samples were prepared together using an in-house TagSeq library preparation.


title: TCR_irAE04

description:
Library name: Sample54
immune-related adverse event (irAE)


title: Colony 107 Nurse Day 26 Replicate 1

description:
Library name: Sample 13
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse rRNA-depleted total-RNA seq Heart Ftsj1_DF 1647

description:
Library name: 22Jan49-F03-L3_S53_L003_R1_001
rRNA-depleted total-RNA seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: male. 4 months old


title: Spleen, CD23+ B cell, F1, 0h naïve, H2AK119Ub, biol rep 2

value: Female

value: CD23+ B cell


title: TCR_ICI31

description:
Library name: Sample53
ICI control (ICI)

value: ICI control (ICI)


title: Spleen, CD23+ B cell, F1, 24h stimulated, H3K27me3, biol rep 4

value: F1 mus x cast

value: stimulated with CpG for 24 hours


title: mouse rRNA-depleted total-RNA seq Brain WT 1653

description:
Library name: 22Jan49-C01-L3_S39_L003_R1_001
rRNA-depleted total-RNA seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Brain

value: whole Brain tissue


title: Spleen, CD23+ B cell, F1, 0h naïve, H2AK119Ub, biol rep 1


title: mouse rRNA-depleted total-RNA seq Brain WT 1655

description:
Library name: 22Jan49-E02-L3_S48_L003_R1_001
rRNA-depleted total-RNA seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Colony 107 Forager Day 26 Replicate 3 #2

description:
Library name: Sample 12
All samples were prepared together using an in-house TagSeq library preparation.


title: Spleen, CD23+ B cell, F1, 0h naïve, H2AK119Ub, biol rep 4


title: mouse rRNA-depleted total-RNA seq Heart Ftsj1_DF 1656

description:
Library name: 22Jan49-E01-L3_S47_L003_R1_001
rRNA-depleted total-RNA seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male

value: Heart

value: whole Heart tissue


title: Spleen, CD23+ B cell, F1, 24h stimulated, H3K27me3, biol rep 3


title: Colony 107 Nurse Day 26 Replicate 3

description:
Library name: Sample 15
All samples were prepared together using an in-house TagSeq library preparation.


title: mouse rRNA-depleted total-RNA seq Brain WT 1646

description:
Library name: 22Jan49-D04-L3_S46_L003_R1_001
rRNA-depleted total-RNA seq of whole Brain tissue from WT mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: mouse rRNA-depleted total-RNA seq Heart Ftsj1_DF 1654

description:
Library name: 22Jan49-C03-L3_S41_L003_R1_001
rRNA-depleted total-RNA seq of whole Heart tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Colony 107 Forager Day 26 Replicate 3

description:
Library name: Sample 11
All samples were prepared together using an in-house TagSeq library preparation.


title: TCR_H052

description:
Library name: Sample51
healthy control (HC)

value: PBMC

value: healthy control (HC)


title: mouse rRNA-depleted total-RNA seq Brain Ftsj1_DF 1656

description:
Library name: 22Jan49-H03-L3_S60_L003_R1_001
rRNA-depleted total-RNA seq of whole Brain tissue from Ftsj1_DF mice. R1 = forward, R2 = reverse, L003-L004 = lane 3-4. 1653, 1654, 1655, 1656 are brothers, 1646 and 1647 as well. All mice are male


title: Spleen, CD23+ B cell, F1, 24h stimulated, H3K27me3, biol rep 2


title: TCR_H039

description:
Library name: Sample50
healthy control (HC)