title: whole_blood_temperate_24C_d0_M [MA0050_8_46]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315304

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

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.

value: male


title: Ripk2 KO, Biol rep 3, M90T

status: Public on Mar 17 2026

type: SRA

city: Toronto

first: Stephen

middle: E

last: Girardin

state: ON

address: 1 King's College Cir

country: Canada

institute: University of Toronto

description: Library name: KO_RIP2_3_M90T_RNA_08_23_23

library_source: transcriptomic

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

molecule: total RNA

organism: Mus musculus

source_name: Primary Ileal Organoids

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

tag: cell type

value: Primary Ileal Organoids

tag: genotype

value: Nlrc4-/- Ripk2-/-

tag: treatment

value: M90T Shigella

tag: batch


title: Human primary NK cells, TGFBR2 gene knock-out and CAR gene knock-in , Dexamethasone treated, rep 2

city: Seoul

first: Mihue

last: Jang

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

department: Medicinal Materials Research Center, Biomedical Research Division

country: South Korea

institute: Korea Institute of Science and Technology

description: Library name: KI Dex 2

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

organism: Homo sapiens

source_name: Human promary NK cells

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

tag: cell line

value: Human primary NK cells

value: NK cell

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

value: Dexamethasone

value: Batch 2


title: Ripk2 KO, Biol rep 2, TSB

description: Library name: 2_KO_Rip2_TSB_RNA_08_23

value: TSB Control


title: whole_blood_temperate_30C_d18_F [MA0050_8_45]

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 FR17MAG201310241

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

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.

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

tag: experimental facility

value: temperate

tag: gender

value: female

tag: breeding batch

tag: condition

tag: wash batch

tag: analysis serial


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

description: Library name: KI Dex 1

value: Batch 1


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

description: Library name: KI 2

value: control


title: NC210219_HNDS0059-01_A_wt

city: Boston

first: Madison

middle: Rose

last: Glass

state: MA

address: 3 Blackfan St

department: Neurobiology

country: USA

institute: Boston Children's Hospital

description: Library name: IonCode_0111

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

source_name: induced neurons

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

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

treatment_protocol: no treatment

tag: tissue

value: induced neurons


title: NC210219_HNDS0022-01_D_wt

description: Library name: IonCode_0110


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

description: Library name: KO 1

value: TGFBR2 knock-out


title: Ripk2 KO, Biol rep 2, M90T Supernantant

description: Library name: 2_KO_Rip2_M9S_RNA_08_23

value: Sterile M90T Supernatant


title: whole_blood_temperate_30C_d3_M [MA0050_8_43]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315283

source_name: whole blood,3 days at 30 degrees

value: male


title: Ripk2 KO, Biol rep 2, M90T

description: Library name: 2_KO_Rip2_M90T_RNA_08_23

value: Primary Ileal Organoids


title: Human primary NK cells, Dexamethasone treated, rep 2

description: Library name: WT Dex 2

value: WT


title: NC201116_HNDS0059-01_C_mut

description: Library name: IonCode_0108


title: NC210219_HNDS0022-01_A_mut

description: Library name: IonCode_0109


title: Human primary NK cells, Dexamethasone treated, rep 1

description: Library name: WT Dex 1


title: whole_blood_temperate_30C_d3_F [MA0050_8_42]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313204


title: Ripk2 KO, Biol rep 1, TSB

description: Library name: 1_KO_Rip2_TSB_RNA_08_23

value: Nlrc4-/- Ripk2-/-


title: whole_blood_temperate_24C_d0_M [MA0050_8_41]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201311720

source_name: whole blood,24 degrees


title: Human primary NK cells, rep 2

description: Library name: WT 2

value: Human primary NK cells


title: NC201116_HNDS0059-01_A_wt

description: Library name: IonCode_0107


title: Ripk2 KO, Biol rep 1, M90T Supernantant

description: Library name: 1_KO_Rip2_M9S_RNA_08_23


title: Human primary NK cells, rep 1

description: Library name: WT 1

value: NK cell


title: NC201116_HNDS0022-01_D_wt

description: Library name: IonCode_0106


title: whole_blood_tropical_ambient_d0_M [MA0050_8_38]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430131

source_name: whole blood,ambient

value: tropical


title: whole_blood_temperate_30C_d18_M [MA0050_8_40]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310235


title: HCT26-1T, GSK126+PY-60, duplicate 1

city: Ariake

first: Ryoji

last: Yao

state: Tokyo

country: Japan

institute: Cancer Institute, JFCR

description:
20231016R-HCT26-1T-GSK10-PY10-3_S7_R1.fastq.gz
row_counts_GSKPY.csv

data_processing:
Quantification were carried out using Salmon.
Transcript-level abundance estimation was perfomed using Tximport with the argument, countFromAbundance .
Assembly: gencode.v30.transcripts
Supplementary files format and content: column separated value file includes row counts for each Sample

source_name: colorectal cancer

extract_protocol:
Organoids were colected and signle cells were prepared in TrypLE.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LT Sample Prep Kit following manufacturer's protocols.

value: colorectal cancer

value: organoid


title: whole_blood_temperate_24C_d0_M [MA0050_8_37]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310900


title: NC201116_HNDS0022-01_A_mut

description: Library name: IonCode_0105


title: whole_blood_tropical_ambient_d0_M [MA0050_8_44]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331210


title: NC200908_HNDS0059-01_C_mut

description: Library name: IonCode_0104


title: whole_blood_temperate_30C_d18_M [MA0050_8_39]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201314806


title: Ripk2 KO, Biol rep 1, Uninfected

description: Library name: 1_KO_Rip2_Ui_RNA_08_23

value: Uninfected Control


title: NC200908_HNDS0059-01_A_wt

description: Library name: IonCode_0103


title: Ripk2 KO, Biol rep 1, M90T

description: Library name: 1_KO_Rip2_M90T_RNA_08_23

value: M90T Shigella


title: forebrain, E18 KO, 4 hours after last saline injection rep 6

city: Warsaw

first: Laboratory

last: of Sequencing

state: mazowieckie

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology PAS

description:
Library name: Sample 18
KO_saline_6

data_processing:
Quality control of reads was performed using FastQC (v. 0.11.9). Adapter and quality trimming was performed using cutadapt (v. 3.4) and TrimGalore (v. 0.6.7), respectively. TrimGalore quality parameter was set to 25. Alignment of reads to the murine reference genome (GRCm39) was performed using STAR (v. 2.7.9a) with default settings. The GTF annotation file used was from the 105 Ensembl release.
Assembly: GRCm39
Supplementary files format and content: matrix with ensembl gene IDs and log2(FPKM+1) normalized counts

source_name: forebrain

extract_protocol:
Total RNA was isolated from the fetal brain using the RNeasy Mini Kit (#74104, Qiagen, Hilden, Germany).
Strand-specific polyA enriched RNA libraries were prepared using the KAPA Stranded mRNA Sample Preparation Kit according to the manufacturer’s protocol (Kapa Biosystems, MA, USA).

value: forebrain

value: KO

value: saline


title: whole_blood_temperate_24C_d0_M [MA0050_8_36]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313246

value: temperate


title: NC200908_HNDS0022-01_D_wt

description: Library name: IonCode_0102

value: induced neurons

value: control


title: HCT26-1T, GSK126, duplicate 1

description:
20231016R-HCT26-1T-GSK10-PY0-3_S5_R1.fastq.gz
row_counts_GSKPY.csv


title: whole_blood_tropical_ambient_d0_F [MA0050_8_35]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331746

value: female


title: HCT26-1T, GSK126, duplicate 2

description:
20231016R-HCT26-1T-GSK10-PY0-4_S6_R1.fastq.gz
row_counts_GSKPY.csv


title: HCT26-1T, PY-60, duplicate 1

description:
20231016R-HCT26-1T-GSK0-PY10-3_S3_R1.fastq.gz
row_counts_GSKPY.csv


title: HCT26-1T, GSK126+PY-60, duplicate 2

description:
20231016R-HCT26-1T-GSK10-PY10-4_S8_R1.fastq.gz
row_counts_GSKPY.csv


title: whole_blood_temperate_30C_d18_M [MA0050_8_34]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311643

value: male


title: forebrain, E18 KO, 4 hours after last saline injection rep 3

description:
Library name: Sample 15
KO_saline_3


title: forebrain, E18 KO, 4 hours after last saline injection rep 5

description:
Library name: Sample 17
KO_saline_5


title: forebrain, E18 KO, 4 hours after last saline injection rep 2

description:
Library name: Sample 14
KO_saline_2


title: forebrain, E18 KO, 4 hours after last saline injection rep 4

description:
Library name: Sample 16
KO_saline_4


title: whole_blood_temperate_30C_d3_M [MA0050_8_33]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311720


title: whole_blood_temperate_30C_d3_F [MA0050_8_32]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310774


title: HCT26-1T, PY-60, duplicate 2

description:
20231016R-HCT26-1T-GSK0-PY10-4_S4_R1.fastq.gz
row_counts_GSKPY.csv


title: GBM_tumor07

city: Bonn

first: Michael

last: Holzel

address: Sigmund-Freud Str. 25

department: Institute of Clinical Chemistry and Clinical Pharmacology

country: Germany

institute: University Hospital Bonn

description: Primary glioblastoma tissue obtained at surgical resection and processed as FFPE

hyb_protocol: Slides were incubated overnight at 50 °C with the Xenium Human Brain Panel (266 genes) together with 100 custom-designed add-on probes. After hybridization, slides were washed to remove unbound probes. Hybridized probe ends were ligated to form circular DNA templates, followed by rolling circle amplification to generate localized signal amplification products. Nuclei were stained with DAPI.

scan_protocol: Slides were loaded into the Xenium Analyzer and processed using cyclic rounds of fluorescent probe hybridization and imaging to acquire spatially resolved transcriptomic data.

data_processing: Spatial transcriptomics data were processed and visualized using Xenium Explorer (version 4.1.0, 10x Genomics). Cell-type and pathway signatures were defined a priori based on curated gene sets derived from established literature. For each spatial feature, log-normalized expression values of the genes within a given signature were averaged to obtain a composite signature score.

label: Xenium probe set

source_name: Bran

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: FFPE blocks from both samples were sectioned at 5 µm and prepared for spatial transcriptomics using the Xenium In Situ platform (10x Genomics). Sections were mounted within the defined sample area and processed following the Tissue Preparation Guide (CG000578, 10x Genomics).

value: Bran

tag: tissue preservation method

value: FFPE

tag: disease

value: Glioblastoma

value: Primary glioblastoma


title: forebrain, E18 WT, 4 hours after last LPS injection rep 6

description:
Library name: Sample 12
WT_LPS_6

value: WT

value: LPS


title: HCT26-1T, control, duplicate 2

description:
20231016R-HCT26-1T-GSK0-PY0-4_S2_R1.fastq.gz
row_counts_GSKPY.csv

value: colorectal cancer

value: organoid


title: GBM1_organoid_brain_slice

description: Patient-derived glioblastoma organoid cultured on brain slice and processed as FFPE

source_name: Brain

value: Brain


title: whole_blood_temperate_30C_d3_M [MA0050_8_29]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313135


title: NC200908_HNDS0022-01_A_mut

description: Library name: IonCode_0101


title: Spleen, CD23+ B cell, Xist tat KO DNMT1i, 24h stim, H2AK119Ub, biol rep 2

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

description: Library name: ub_ko_dnmt_24h_2

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 were immediately subjected to CUT&RUN. Stimulated samples were treated with 80ug TAT-cre for 45 minutes, incubated for 24 hours with 1uM CpG in combination with 6µM UNC1999 (Cat # ab146152, Abcam), 0.75µM 6-Thioguanine (Cat # A4882-100MG, Millipore Sigma), or 0.0006% DMSO, then subjected to 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) 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

tag: Sex

value: Female

value: CD23+ B cell

value: Xist fl/fl

value: stimulated with 1uM CpG and 0.75uM 6-Thioguanine for 24 hours

tag: antibody


title: HCT26-1T, control, duplicate 1

description:
20231016R-HCT26-1T-GSK0-PY0-3_S1_R1.fastq.gz
row_counts_GSKPY.csv


title: MOLM-13 cells, ShTICAM1#2_2

city: suzhou

first: Wenjuan

last: Ma

state: Jiang su

address: 199 Ren'ai Rd

department: Hematology Center Cyrus Tang medical institute

country: China

institute: Soochow University

data_processing:
Sample QC. Select the corresponding testing methods for quality inspection according to the requirements of samples and products.
mRNA Isolation. A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.
mRNA Fragmentation, cDNA Synthesis
End Repair, Add A and Adaptor Ligation
The PCR reaction system and program are configured and set up to amplify the product.Library QC
Assembly: GCF_000001405.25_GRCh37.p13
Supplementary files format and content: core_table_gene.xls.gz includes raw counts for each sample

source_name: Peripheral Blood

growth_protocol: MOLM-13 cells were cultured in 1640 medium in a 37° incubator containing 5% CO2

extract_protocol:
RNA was harvested using Rneasy mini kit(tian gen).500ng of total RNA was used for the consyruction of sequencing libraries
RNA libaary for RNA-seq were prepared use DNBSEQ platform

treatment_protocol: Scrambled and shTICAM1 sequence were delivered with lentiviral vectors into MOLM-13 cells.

value: Peripheral Blood

value: Acute myeloid leukemia cells


title: forebrain, E18 WT, 4 hours after last LPS injection rep 5

description:
Library name: Sample 11
WT_LPS_5

value: forebrain


title: forebrain, E18 KO, 4 hours after last saline injection rep 1

description:
Library name: Sample 13
KO_saline_1

value: KO

value: saline


title: whole_blood_temperate_30C_d3_F [MA0050_8_30]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201314801

value: temperate

value: female


title: MOLM-13 cells, ShTICAM1#2_1


title: MOLM-13 cells, ShTICAM1#3_3


title: whole_blood_temperate_30C_d3_F [MA0050_8_28]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201410592


title: forebrain, E18 WT, 4 hours after last LPS injection rep 2

description:
Library name: Sample 8
WT_LPS_2

value: WT


title: whole_blood_temperate_30C_d18_M [MA0050_8_31]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313851

value: male


title: MOLM-13 cells, ShTICAM1#1_3


title: Spleen, CD23+ B cell, Xist tat KO DNMT1i, 24h stim, H2AK119Ub, biol rep 1

description: Library name: ub_ko_dnmt_24h_1


title: Spleen, CD23+ B cell, Xist tat KO PRC2i, 24h stim, H2AK119Ub, biol rep 2

description: Library name: ub_ko_prc2_24h_2

value: stimulated with 1uM CpG and 6uM UNC1999 for 24 hours


title: Xenium_lung

city: New Haven

first: Rong

last: Fan

state: CT

address: 55 prospect street

institute: Yale University

hyb_protocol: 5,000 genes and 27 custom sgRNAs were included in this analysis. Gene panel probe hybridization occurred overnight for 18 hours at 50C. Slides were washed the next day to remove unbound probes. Ligase was added to circularize the paired ends of bound probes (2 hours at 37C) followed by enzymatic rolling circle amplification (2 hours at 30C). Slides were washed in TE buffer before background fluorescence was chemically quenched.

scan_protocol: Imaging processing, decoding, quality score generation, and DAPI-based cell segmentation was automatically performed by the Xenium Analyzer system.

data_processing: Xenium onboard analysis and R using Seurat packages.

source_name: Mouse lung

extract_protocol: tissue preparation protocol: Tissue sections were cut at a thickness of 7 microns and placed onto a xenium slide followed by fixation and permbealization

value: Mouse lung

value: FFPE

value: NSG


title: forebrain, E18 WT, 4 hours after last LPS injection rep 3

description:
Library name: Sample 9
WT_LPS_3

value: LPS


title: whole_blood_temperate_24C_d0_F [MA0050_8_27]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201314801


title: forebrain, E18 WT, 4 hours after last LPS injection rep 1

description:
Library name: Sample 7
WT_LPS_1


title: MOLM-13 cells, ShTICAM1#1_2


title: Spleen, CD23+ B cell, Xist tat KO DNMT1i, 24h stim, H2AK119Ub, biol rep 3

description: Library name: ub_ko_dnmt_24h_3

value: Spleen

value: Female

value: CD23+ B cell


title: Spleen, CD23+ B cell, Xist tat KO PRC2i, 24h stim, H2AK119Ub, biol rep 3

description: Library name: ub_ko_prc2_24h_3

value: Xist fl/fl


title: forebrain, E18 WT, 4 hours after last saline injection rep 6

description:
Library name: Sample 6
WT_saline_6


title: Spleen, CD23+ B cell, Xist tat KO PRC2i, 24h stim, H2AK119Ub, biol rep 1

description: Library name: ub_ko_prc2_24h_1


title: Spleen, CD23+ B cell, Xist tat KO DMSO, 24h stim, H2AK119Ub, biol rep 3

description: Library name: ub_ko_dmso_24h_3

value: stimulated with 1uM CpG and 0.0006% DMSO for 24 hours


title: forebrain, E18 WT, 4 hours after last saline injection rep 5

description:
Library name: Sample 5
WT_saline_5

value: forebrain


title: whole_blood_tropical_ambient_d0_F [MA0050_8_24]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430093

value: tropical


title: forebrain, E18 WT, 4 hours after last saline injection rep 4

description:
Library name: Sample 4
WT_saline_4

value: saline


title: forebrain, E18 WT, 4 hours after last LPS injection rep 4

description:
Library name: Sample 10
WT_LPS_4


title: MOLM-13 cells, ShTICAM1#1_1

value: Peripheral Blood

value: Acute myeloid leukemia cells


title: Spleen, CD23+ B cell, Xist tat KO DMSO, 24h stim, H2AK119Ub, biol rep 2

description: Library name: ub_ko_dmso_24h_2


title: whole_blood_temperate_30C_d3_F [MA0050_8_26]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315277

value: temperate

value: female


title: MOLM-13 cells, Scramble 3

value: Scramble


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

description: Library name: ub_ko_0h_3

value: unstimulated


title: MOLM-13 cells, Scramble 2


title: whole_blood_temperate_30C_d18_M [MA0050_8_22]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313248

value: male


title: forebrain, E18 WT, 4 hours after last saline injection rep 2

description:
Library name: Sample 2
WT_saline_2

value: WT


title: whole_blood_temperate_30C_d3_M [MA0050_8_23]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311718


title: forebrain, E18 WT, 4 hours after last saline injection rep 3

description:
Library name: Sample 3
WT_saline_3


title: whole_blood_temperate_30C_d3_F [MA0050_8_21]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311487


title: whole_blood_tropical_ambient_d0_M [MA0050_8_25]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331337


title: very young leaf, glabrous, rep 1

city: Saskatoon

first: Dwayne

last: Hegedus

state: SK

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

description:
Library name: 6-110-1
DH6_110_1 - TPM

data_processing:
Paired-end sequencing (2×150 bp) was done by LC Sciences (Houston, USA) on an Illumina Novaseq™ 6000. Libraries from three biological replicates (single leaves) were made for each line
Reads were filtered for adapters and quality using CutAdapt 1.9
RNAseq analysis using CLC Genomics Workbench version 25, using B. napus DH12075 genome version 4DH.2025 as a reference
PCA for RNAseq - excluded 6-47-2 and 6-110-2 as they did not cluster well and the reads showed signs of RNA degradation
Differential Expression in Two Groups using CLC genomics workbench version 25
Filter for FDR <=0.05 AND fold change >= the absolute value of 2.0
Assembly: DH12075.4DH.2025 (which will be submitted by Dr. Isobel Parkin soon)
Supplementary files format and content: Ms Excel file containing TPM and statistics for every B. napus gene

molecule: polyA RNA

organism: Brassica napus

source_name: One very young 3rd leaf

growth_protocol: individual seeds were planted in soil-less potting mix in 5 cm X 5 cm X 5 cm wells in 4 X 8 well arrays and placed in a growth cabinet under controlled conditions (16 hr day/8 hr night - supplemented with halogen lighting, day/night  temperature of 20-22°C and 75 % relative humidity)

extract_protocol:
Total RNA was extracted from very early third leaves of DH6-47 and DH6-110 using the RNeasy Trizol reagent (Qiagen) following the manufacturer's procedure
To generate cDNA libraries for sequencing, 10 mg of total RNA with a RIN quality higher than 7 as assessed using a Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) was subjected to poly-A mRNA selection using poly-T oligo magnetic beads (Invitrogen). cDNA libraries were prepared by Thermo Fisher Scientific (Waltham, USA) with an average insert size of 300±50 bp for the paired-end libraries

value: One very young 3rd leaf


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

description: Library name: ub_ko_0h_1

value: Spleen


title: forebrain, E18 WT, 4 hours after last saline injection rep 1

description:
Library name: Sample 1
WT_saline_1


title: very young leaf, glabrous, rep 3

description:
Library name: 6-110-3
DH6_110_3 - TPM


title: whole_blood_temperate_24C_d0_F [MA0050_8_19]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201312426


title: very young leaf, glabrous, rep 2

description: Library name: 6-110-2


title: whole_blood_temperate_30C_d3_F [MA0050_8_20]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201314558


title: MOLM-13 cells, Scramble 1


title: D568

city: Baltimore

first: Elena

last: MacFarlane

state: Maryland

address: 733 N Broadway St

department: Department of Genetic Medicine

institute: Johns Hopkins

description: Library name: Sample 29

data_processing:
Illumina’s CASAVA 1.8.4 was used to convert BCL files to FASTQ files using default parameters.  Rsem-1.3.0 was used for running the alignments and generating gene and transcript expression levels. The “rsem-calculate-expression” module was used with the following options: star, star-gzipped-read-file, calc-ci, star-output-genome-bam, paired-end, and forward-prob 0.
Assembly: Mm39
Supplementary files format and content: rsem file including FPKM and TPM values for each sample

source_name: Aorta

extract_protocol:
Between 11am and 1pm EST, the aorta was perfused with 5mL room temperature 1x PBS 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 placed into a screw cap tube containing 700uL TRIzol (ThermoFisher Scientific 15596018) plus 4-6 3mm zirconium (X) beads and flash frozen in liquid nitrogen. The tubes were then stored at -80°C until further processing. Within a treatment group (N = 3), aortas were randomized to determine processing order. Aortas were processed in batches containing 1 aorta per treatment group (total aortas per batch N = 10). Then, RNA was extracted using the PureLink RNA Mini Kit (Invitrogen 12-183-018A) according to the manufacturer’s instructions with the following modifications. For the “Homogenization” section of the protocol: The aortas were thawed on wet ice and homogenized using the FastPrep-24 5G bead beating grinder and lysis system using the following settings: 5 cycles of 4.5m/sec for 30sec with 300sec pause time using Lysing Matrix A at 1mg. Then 200uL chloroform (Fisher Scientific 02-002-590) was added and shaken vigorously for 15sec then incubated at room temperature for 3min. Samples were then spun at 4°C for 15min at 12,000xg. During the “Binding, Washing, and Elution of RNA” section of the protocol: 350uL of ice cold 70% ethanol was used in step 1 and only 350uL of Wash Buffer I was used in step 6. After step 7, 80uL of DNase I (70uL buffer RDD + 10uL DNase I) from RNase-Free DNase set (Qiagen 79254) was added to the column and incubated at room temperature for 15min. Step 6 was then repeated. Samples were eluted into 100uL of nuclease free water and spun down once in step 14, then they were stored at -80°C. Samples were submitted on wet ice to the Sidney Kimmel Comprehensive Cancer Center Experimental and Computational Genomics Core at Johns Hopkins for QC using the Agilent 2100 BioAnalyzer and cDNA synthesis.
Briefly, the TruSeq Stranded Total RNA Library Kit was used according to manufacturer’s instructions to generate barcoded samples. The library was sequenced on the NovaSeq6000 S4 (150bp PE), targeting 50K reads/sample.

treatment_protocol: Hydralazine treated mice were given 32mg/kg/day hydralazine in drinking water starting at birth until 30 days of age or 60 days of age when tissue was harvested. Mice treated with hydralazine and bicalutamide combination therapy were given 32mg/kg/day hydralazine in the drinking water from birth to P60; at P21 they also received 50mg/kg/day of bicalutamide in medicated chow until 60 days of age when tissue was harvested. Mice treated with hydralazine and spironolactone combination therapy were given 32mg/kg/day hydralazine in the drinking water from birth to P60; at P21 they also received 100mg/kg/day of spironolactone in medicated chow until 60 days of age when tissue was harvested. Untreated controls remained untreated throughout the experiment.

value: Aorta

value: Het

value: Hydral


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

description: Library name: ub_ko_0h_2

value: Female

value: CD23+ B cell

value: Xist fl/fl


title: Spleen, CD23+ B cell, Xist tat KO DMSO, 24h stim, H2AK119Ub, biol rep 1

description: Library name: ub_ko_dmso_24h_1

value: stimulated with 1uM CpG and 0.0006% DMSO for 24 hours


title: very young leaf, hairy, rep 2

description: Library name: 6-47-2


title: whole_blood_tropical_ambient_d0_M [MA0050_8_18]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330324

value: tropical


title: D620

description: Library name: Sample 30

value: HB


title: whole_blood_temperate_30C_d3_F [MA0050_8_16]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201312425

value: temperate


title: very young leaf, hairy, rep 1

description:
Library name: 6-47-1
DH6_47_1 - TPM


title: Spleen, CD23+ B cell, WT tat DNMT1i, 24h stim, H2AK119Ub, biol rep 1

description: Library name: ub_wt_dnmt_24h_1

value: stimulated with 1uM CpG and 0.75uM 6-Thioguanine for 24 hours


title: Spleen, CD23+ B cell, WT tat DNMT1i, 24h stim, H2AK119Ub, biol rep 3

description: Library name: ub_wt_dnmt_24h_3


title: D565

description: Library name: Sample 28


title: Spleen, CD23+ B cell, WT tat DNMT1i, 24h stim, H2AK119Ub, biol rep 2

description: Library name: ub_wt_dnmt_24h_2


title: D533

description: Library name: Sample 26


title: very young leaf, hairy, rep 3

description:
Library name: 6-47-3
DH6_47_3 - TPM


title: whole_blood_temperate_24C_d0_F [MA0050_8_17]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313871

value: female


title: Spleen, CD23+ B cell, WT tat PRC2i, 24h stim, H2AK119Ub, biol rep 3

description: Library name: ub_wt_prc2_24h_3

value: stimulated with 1uM CpG and 6uM UNC1999 for 24 hours


title: D534

description: Library name: Sample 27


title: D532

description: Library name: Sample 25


title: Primary mouse granulosa cells, Veh treatment,PA, rep2_SMAD3tagged

city: Houston

first: Martin

middle: M

last: Matzuk

state: TX

address: One Baylor Plaza

department: Pathology and Immunolodgy

institute: Baylor College of Medicine

description: Library name: Sample44

data_processing:
Data processing for CUT&RUN dataset largely follows the previously published pipeline with minor modifications. In short, after demultiplexing and quality control, clean reads were mapped to the mouse genome mm10 and the E. coli genome U00096.3 (for Spike-in) by Bowtie2. Uniquely mapped reads were kept for the Spike-in normalization. The normalization was done by multiplying primary genome coverage by a scale factor (100000 / fragments mapped to the E. coli genome). CUT&RUN peaks were called using SECAR with the default parameters. Track visualization was done by bedGraphToBigWig, and Integrative Genomics Viewer was used for visualization. Common peaks between replicates were identified with the 'mergePeaks' function in HOMER v4.1179 . For RNA-seq, alignment and quantification were done using STAR v2.7.11b again mouse genome mm1082. Aligned reads were assigned to genes with featureCounts v2.1.1. Count matrices were analyzed in R with DESeq2 v1.48.2.
Assembly: mm10
Supplementary files format and content: NormCount_GDF9-Veh.csv is the normalized CPM for all the RNA-seq sample included. The processed peak files are generated by SECAR with default settings.
Library strategy: CUT&Run

source_name: Ovary

growth_protocol: Cultering media for primary mouse granulosa cells

extract_protocol:
For CUT&RUN experiments, approximately 55,000 cells were used for each reaction. Concanavalin A-coated magnetic beads (Bangs Laboratories, BP531) were conjugated to the cells, and the resulting bead–cell complexes were resuspended in 100 ul of Antibody Buffer per reaction. Immunoprecipitation was initiated by adding 1 ug of the indicated antibodies: IgG control (Sigma, I5006), anti-HA (EpiCypher, 13-2010), anti-PA (Fujifilm, NZ-1), or anti-SMAD2 (Abcam, ab33875). After overnight incubation at 4 C, the bead-cell complexes were washed and subsequently incubated with pAG-MNase (EpiCypher, 15-1016) at room temperature for 10 minutes. bead-cell-pAG-MNase complexes were washed and chromatin digestion was initiated by adding 1 ul of 100 mM CaCl2 to each reaction, followed by incubation at 4 C for 2 hours. Reactions were terminated by adding 50 ul of Stop Buffer and incubating at 37 C for 10 minutes. The supernatant was collected, and DNA was purified by phenol–chloroform extraction and ethanol precipitation. For RNA experiments, total RNA from mouse granulosa cells was extracted using QIAGEN RNeasy kit (QIAGEN, Cat 74104) following the manufacturer’s protocol.
For Cut and Run experiments, sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England BioLabs, E7645) according to the manufacturer’s instructions, and paired-end 150 bp sequencing was performed. For RNA-seq experiments, NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760S, E7490S) with 500 ng input RNA following the manufacturer’s protocol.

treatment_protocol: Mouse GDF9 was treated for 4 hours

value: Ovary

value: Primary granulosa cells

value: Granulosa cells

value: vehicle


title: Primary mouse granulosa cells, Veh treatment,PA, rep1_SMAD3tagged

description: Library name: Sample43


title: whole_blood_temperate_30C_d3_F [MA0050_8_15]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201411265


title: Primary mouse granulosa cells, Veh treatment,IgG, rep2_SMAD3tagged

description: Library name: Sample42


title: Spleen, CD23+ B cell, WT tat PRC2i, 24h stim, H2AK119Ub, biol rep 1

description: Library name: ub_wt_prc2_24h_1

value: Spleen

value: WT


title: D531

description: Library name: Sample 24

value: Aorta

value: Het

value: Hydral


title: whole_blood_tropical_ambient_d0_F [MA0050_8_13]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330157


title: Spleen, CD23+ B cell, WT tat DMSO, 24h stim, H2AK119Ub, biol rep 3

description: Library name: ub_wt_dmso_24h_3

value: Female

value: CD23+ B cell


title: D509

description: Library name: Sample 23


title: Primary mouse granulosa cells, Veh treatment,IgG, rep1_SMAD3tagged

description: Library name: Sample41


title: Spleen, CD23+ B cell, WT tat PRC2i, 24h stim, H2AK119Ub, biol rep 2

description: Library name: ub_wt_prc2_24h_2


title: whole_blood_temperate_24C_d0_M [MA0050_8_11]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310950

value: male


title: Primary mouse granulosa cells, Veh treatment,SMAD4, rep2_SMAD3tagged

description: Library name: Sample40


title: D446

description: Library name: Sample 22


title: Primary mouse granulosa cells, Veh treatment,SMAD4, rep1_SMAD3tagged

description: Library name: Sample39


title: D413

description: Library name: Sample 21


title: Spleen, CD23+ B cell, WT tat DMSO, 24h stim, H2AK119Ub, biol rep 2

description: Library name: ub_wt_dmso_24h_2

value: stimulated with 1uM CpG and 0.0006% DMSO for 24 hours


title: D411

description: Library name: Sample 20


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

description: Library name: ub_wt_0h_3

value: unstimulated


title: whole_blood_temperate_24C_d0_F [MA0050_8_9]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410726

value: temperate


title: D409

description: Library name: Sample 19

value: HB


title: whole_blood_temperate_30C_d18_M [MA0050_8_12]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315557


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

description: Library name: ub_wt_0h_2


title: Spleen, CD23+ B cell, WT tat DMSO, 24h stim, H2AK119Ub, biol rep 1

description: Library name: ub_wt_dmso_24h_1


title: whole_blood_temperate_24C_d0_M [MA0050_8_10]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201314563


title: whole_blood_temperate_30C_d18_M [MA0050_8_8]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313229


title: Primary mouse granulosa cells, Veh treatment,H3K27ac, rep2_SMAD3tagged

description: Library name: Sample36


title: D399

description: Library name: Sample 17


title: whole_blood_temperate_30C_d18_F [MA0050_8_7]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310892

value: female


title: D400

description: Library name: Sample 18


title: whole_blood_temperate_30C_d18_M [MA0050_8_14]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201316038


title: whole_blood_temperate_30C_d3_F [MA0050_8_6]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311725


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

description: Library name: ub_wt_0h_1


title: Primary mouse granulosa cells, Veh treatment,SMAD2, rep1_SMAD3tagged

description: Library name: Sample37

value: Ovary


title: whole_blood_temperate_24C_d0_F [MA0050_8_5]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201312469


title: Primary mouse granulosa cells, Veh treatment,H3K27ac, rep1_SMAD3tagged

description: Library name: Sample35

value: Primary granulosa cells


title: Primary mouse granulosa cells, Veh treatment,SMAD2, rep2_SMAD3tagged

description: Library name: Sample38

value: Granulosa cells


title: Primary mouse granulosa cells, GDF9 treatment, PA, rep2_SMAD3tagged

description: Library name: Sample34

value: mouse GDF9


title: Spleen, CD23+ B cell, Xist tat KO DNMT1i, 24h stim, H3K27me3, biol rep 1

description: Library name: me3_ko_dnmt_24h_1

value: Spleen

value: Xist fl/fl

value: stimulated with 1uM CpG and 0.75uM 6-Thioguanine for 24 hours


title: Spleen, CD23+ B cell, Xist tat KO DNMT1i, 24h stim, H3K27me3, biol rep 2

description: Library name: me3_ko_dnmt_24h_2


title: D361

description: Library name: Sample 16

value: Aorta

value: Het


title: D1459

description: Library name: Sample 15

value: Untx


title: whole_blood_temperate_30C_d18_M [MA0050_8_3]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313874


title: Primary mouse granulosa cells, GDF9 treatment,IgG, rep2_SMAD3tagged

description: Library name: Sample32


title: Spleen, CD23+ B cell, Xist tat KO DNMT1i, 24h stim, H3K27me3, biol rep 3

description: Library name: me3_ko_dnmt_24h_3

value: Female

value: CD23+ B cell


title: Spleen, CD23+ B cell, Xist tat KO PRC2i, 24h stim, H3K27me3, biol rep 3

description: Library name: me3_ko_prc2_24h_3

value: stimulated with 1uM CpG and 6uM UNC1999 for 24 hours


title: whole_blood_tropical_ambient_d0_M [MA0050_8_4]

description: #N/A!

value: tropical

value: male


title: Primary mouse granulosa cells, GDF9 treatment,IgG, rep1_SMAD3tagged

description: Library name: Sample31


title: D1458

description: Library name: Sample 14

value: WT


title: Spleen, CD23+ B cell, Xist tat KO PRC2i, 24h stim, H3K27me3, biol rep 2

description: Library name: me3_ko_prc2_24h_2


title: D1449

description: Library name: Sample 13


title: whole_blood_temperate_24C_d0_M [MA0050_8_2]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201312473

value: temperate


title: Primary mouse granulosa cells, GDF9 treatment,PA, rep1_SMAD3tagged

description: Library name: Sample33

value: Ovary


title: Spleen, CD23+ B cell, Xist tat KO PRC2i, 24h stim, H3K27me3, biol rep 1

description: Library name: me3_ko_prc2_24h_1


title: Primary mouse granulosa cells, GDF9 treatment,SMAD4, rep2_SMAD3tagged

description: Library name: Sample30

value: Primary granulosa cells


title: Primary mouse granulosa cells, GDF9 treatment,SMAD4, rep1_SMAD3tagged

description: Library name: Sample29

value: Granulosa cells


title: whole_blood_temperate_30C_d18_F [MA0050_7_96]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310030

value: female


title: D1448

description: Library name: Sample 12


title: D1441

description: Library name: Sample 11


title: Spleen, CD23+ B cell, Xist tat KO DMSO, 24h stim, H3K27me3, biol rep 2

description: Library name: me3_ko_dmso_24h_2

value: Spleen

value: stimulated with 1uM CpG and 0.0006% DMSO for 24 hours


title: Primary mouse granulosa cells, GDF9 treatment,SMAD2, rep2_SMAD3tagged

description: Library name: Sample28

value: mouse GDF9


title: Spleen, CD23+ B cell, Xist tat KO DMSO, 24h stim, H3K27me3, biol rep 1

description: Library name: me3_ko_dmso_24h_1

value: Xist fl/fl


title: whole_blood_temperate_30C_d18_F [MA0050_7_95]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310878


title: D1202

description: Library name: Sample 9

value: Aorta

value: Het

value: HS


title: D1440

description: Library name: Sample 10

value: Untx


title: Primary mouse granulosa cells, GDF9 treatment,SMAD2, rep1_SMAD3tagged

description: Library name: Sample27


title: whole_blood_temperate_30C_d3_F [MA0050_8_1]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201411221


title: D1188

description: Library name: Sample 8


title: whole_blood_tropical_ambient_d0_M [MA0050_7_94]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331687


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

description: Library name: me3_ko_0h_2

value: Female

value: CD23+ B cell

value: unstimulated


title: D1165

description: Library name: Sample 7


title: whole_blood_tropical_ambient_d0_F [MA0050_7_92]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331045

value: tropical


title: Primary mouse granulosa cells, GDF9 treatment,H3K27ac, rep1_SMAD3tagged

description: Library name: Sample25


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

description: Library name: me3_ko_0h_3


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

description: Library name: me3_ko_0h_1


title: Primary mouse granulosa cells, Veh treatment rep2

description: Library name: Sample4

data_processing:
Data processing for CUT&RUN dataset largely follows the previously published pipeline with minor modifications. In short, after demultiplexing and quality control, clean reads were mapped to the mouse genome mm10 and the E. coli genome U00096.3 (for Spike-in) by Bowtie2. Uniquely mapped reads were kept for the Spike-in normalization. The normalization was done by multiplying primary genome coverage by a scale factor (100000 / fragments mapped to the E. coli genome). CUT&RUN peaks were called using SECAR with the default parameters. Track visualization was done by bedGraphToBigWig, and Integrative Genomics Viewer was used for visualization. Common peaks between replicates were identified with the 'mergePeaks' function in HOMER v4.1179 . For RNA-seq, alignment and quantification were done using STAR v2.7.11b again mouse genome mm1082. Aligned reads were assigned to genes with featureCounts v2.1.1. Count matrices were analyzed in R with DESeq2 v1.48.2.
Assembly: mm10
Supplementary files format and content: NormCount_GDF9-Veh.csv is the normalized CPM for all the RNA-seq sample included. The processed peak files are generated by SECAR with default settings.

value: vehicle


title: D1162

description: Library name: Sample 5

value: WT


title: whole_blood_temperate_30C_d18_M [MA0050_7_93]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313207

value: temperate

value: male


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

description: Library name: me3_ko_dmso_24h_3


title: whole_blood_temperate_30C_d3_F [MA0050_7_91]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201311727

value: female


title: Primary mouse granulosa cells, GDF9 treatment,H3K27ac, rep2_SMAD3tagged

description: Library name: Sample26

value: Ovary

value: Primary granulosa cells

value: Granulosa cells


title: D1161

description: Library name: Sample 4


title: whole_blood_temperate_30C_d3_F [MA0050_7_90]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315211


title: Spleen, CD23+ B cell, WT tat DNMT1i, 24h stim, H3K27me3, biol rep 1

description: Library name: me3_wt_dnmt_24h_1

value: Spleen

value: stimulated with 1uM CpG and 0.75uM 6-Thioguanine for 24 hours


title: Spleen, CD23+ B cell, WT tat DNMT1i, 24h stim, H3K27me3, biol rep 2

description: Library name: me3_wt_dnmt_24h_2


title: whole_blood_temperate_24C_d0_F [MA0050_7_89]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201310774


title: Primary mouse granulosa cells, GDF9 treatment rep1

description: Library name: Sample1

value: mouse GDF9


title: Spleen, CD23+ B cell, WT tat DNMT1i, 24h stim, H3K27me3, biol rep 3

description: Library name: me3_wt_dnmt_24h_3


title: D1123

description: Library name: Sample 2

value: Aorta


title: Primary mouse granulosa cells, Veh treatment rep1

description: Library name: Sample3


title: D1152

description: Library name: Sample 3

value: Het

value: HS


title: RNAPII-mut mESCs, RNAseq 7 days 2i, replicate 2

city: Madrid

first: Maria

last: Gomez

address: Nicolas Cabrera, 1

country: Spain

institute: CBMSO(CSIC/UAM)

description: Library name: RNAseq_RNAPIImut_d7_rep2

data_processing:
Alignment against mm10 genome using STAR (Dobin et al., 2013) with standard parameters.
BigWig files were generated with bamCoverage function from depTools.
Assembly: mm10
Supplementary files format and content: csv file includes raw read counts for each sample
Supplementary files format and content: bw

source_name: mESCs

growth_protocol: WT and RNAPII-mut E14 Mouse Embryonic Stem Cells (mESCs) were grown in DMEM (Invitrogen) supplemented with 10% fetalbovine serum (Gibco), 1x non-essential aminoacids, 1 mM sodium pyruvate, 2 mM L-glutamine (Gibco), 50 µM β-mercaptoethanol (ThermoFisher), 100 U/mL penicillin (Invitrogen), 100 μg/mL streptomycin (Invitrogen) and 1000 U/mL LIF (Leukaemia Inhibitory Factor, ESGRO) at 37ºC and 5% CO2 on a fibroblast-free surface coated on 0.1% gelatine (Sigma).

extract_protocol:
Cells were resuspended in TRIzol (ThermoFisher) following manufacturer's instructions and total RNA was isolated by isopropanol precipitation. RNA samples were treated with DNAse using Kit TURBO DNA-freeTM (Invitrogen) following manufacturer’s instructions.
Libraries were generated by DNBSeq (Illumina) at BGI Tech Solutions.

treatment_protocol: Naive pluripotency state was obtained by adding 1 µM  PD0325901 (MEK inhibitor; StemMACS Miltenyi Biotec, #130-103-923) and 3 µM CHIR99021 (GSK3 inhibitor; StemMACS Miltenyi Biotec, #130-103-926) to this medium for 0, 1, 2, and 7 days.

value: mESCs

value: slow/slow

value: serum+Lif+2i (7 days)


title: whole_blood_temperate_30C_d3_F [MA0050_7_88]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315300


title: D1122

description: Library name: Sample 1

value: Untx


title: RNAPII-mut mESCs, RNAseq 7 days 2i, replicate 1

description: Library name: RNAseq_RNAPIImut_d7_rep1


title: Spleen, CD23+ B cell, WT tat PRC2i, 24h stim, H3K27me3, biol rep 3

description: Library name: me3_wt_prc2_24h_3

value: Female

value: CD23+ B cell

value: WT

value: stimulated with 1uM CpG and 6uM UNC1999 for 24 hours


title: whole_blood_temperate_30C_d3_M [MA0050_7_86]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310900

value: temperate

value: male


title: RNAPII-mut mESCs, RNAseq 2 days 2i, replicate 2

description: Library name: RNAseq_RNAPIImut_d2_rep2

value: serum+Lif+2i (2 days)


title: whole_blood_temperate_30C_d18_F [MA0050_7_85]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310230

value: female


title: whole_blood_temperate_24C_d0_F [MA0050_7_87]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315211


title: Spleen, CD23+ B cell, WT tat PRC2i, 24h stim, H3K27me3, biol rep 1

description: Library name: me3_wt_prc2_24h_1

value: Spleen


title: D1163

description: Library name: Sample 6


title: Spleen, CD23+ B cell, WT tat PRC2i, 24h stim, H3K27me3, biol rep 2

description: Library name: me3_wt_prc2_24h_2


title: Primary mouse granulosa cells, GDF9 treatment rep2

description: Library name: Sample2

value: Ovary

value: Primary granulosa cells

value: Granulosa cells

value: mouse GDF9


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

description: Library name: me3_wt_dmso_24h_3

value: stimulated with 1uM CpG and 0.0006% DMSO for 24 hours


title: whole_blood_temperate_30C_d18_F [MA0050_7_84]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201410593


title: RNAPII-mut mESCs, RNAseq 1 days 2i, replicate 3

description: Library name: RNAseq_RNAPIImut_d1_rep3

value: mESCs

value: slow/slow

value: serum+Lif+2i (1 day)


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

description: Library name: me3_wt_dmso_24h_2

value: Female


title: RNAPII-mut mESCs, RNAseq 2 days 2i, replicate 1

description: Library name: RNAseq_RNAPIImut_d2_rep1


title: WT:ARG1CKO Tumor CD11C+ CKO1

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

description:
Library name: 24
27_WT-ARG1CKO_Tumor_raw

data_processing:
Sequenced reads were first QC’d using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK) and mapped to the reference genome (UCSCmm10) using Spliced Transcripts Alignment to a Reference (STAR 2.7.10a). Evaluation of sequencing data was performed by determining the number of reads that fall into different annotated regions of the reference genome using bamUtils (v.0.4.17). Uniquely mapped reads were assigned to mm10 reGene genes using featureCounts (subread v.2.0.3). Low-quality mapped reads were excluded.
Assembly: mm10
Supplementary files format and content: Excel file with Raw read counts

source_name: lung

growth_protocol: in-vivo mixed bone marrow chimera with B16 tumor

extract_protocol:
RNA extraction was performed using the QIAGEN micro RNA extraction kit
Library was constructed using the Clontech SMART-seq v4+Nextera XT protocol

value: lung

value: CD11C+ IM

value: B16 tumor


title: WT:ARG1CKO Tumor CD11C+ CKO2

description:
Library name: 25
28_WT-ARG1CKO_Tumor_raw


title: WT:ARG1CKO Tumor CD11C- CKO 3

description:
Library name: 23
25_WT-ARG1CKO_Tumor_raw

value: CD11C- IM


title: whole_blood_temperate_30C_d3_F [MA0050_7_82]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310775

value: temperate


title: RNAPII-mut mESCs, RNAseq 1 days 2i, replicate 2

description: Library name: RNAseq_RNAPIImut_d1_rep2


title: WT:ARG1CKO Tumor CD11C- CKO 1

description:
Library name: 21
23_WT-ARG1CKO_Tumor_raw


title: whole_blood_temperate_30C_d3_M [MA0050_7_83]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315558

value: male


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

description: Library name: me3_wt_0h_3

value: CD23+ B cell

value: WT

value: unstimulated


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

description: Library name: me3_wt_dmso_24h_1

value: Spleen


title: whole_blood_temperate_24C_d0_M [MA0050_7_81]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201314806


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

description: Library name: me3_wt_0h_1


title: whole_blood_temperate_24C_d0_F [MA0050_7_79]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313238

value: female


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

description: Library name: me3_wt_0h_2


title: WT mESCs, RNAseq 7 days 2i, replicate 2

description: Library name: RNAseq_WT_d7_rep2

value: serum+Lif+2i (7 days)


title: Spleen, CD23+ B cell, F1, 24h stimulated, 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 Bismark indexes
Reads were aligned to N-masked genome using Bismark v0.22.3 with parameters [--un --nucleotide_coverage --ambiguous]
Non-bisulfite converted reads were removed using Bismark v0.22.3 filter_non_conversion with parameters [-p --minimum_count 5 --percentage_cutoff 50]
Duplicates were removed using Bismark v0.22.3 deduplicate_bismark
Allele-specific BAM files were generated using SNPsplit v0.5.0 with options [--paired --bisulfite]
Methylation calls were extracted using Bismark v0.22.3 bismark_methylation_extractor with parameters [--ignore 4 --ignore_r2 10 -p --bedGraph --gzip]
Biological replicates for each timepoint were combined using R package methylKit v1.18.0 unite
Assembly: mm10
Supplementary files format and content: bedGraph of percent DNA methylation

growth_protocol: Splenic CD23+ B cells were isolated using biotin anti-mouse CD23 Antibody (Cat #101604, Biolegend) then collected for DNA extraction, or stimulated with 1uM CpG for 24 hours and collected for DNA extraction

extract_protocol:
Genomic DNA was extracted using phenol:chloroform:isoamyl alcohol followed by precipitation with ammonium acetate
Libraries were constructed with 1.5ng of genomic DNA spiked with 0.1% Unmethylated Lambda DNA (D152A, Promega) using NEBNext Ultra II DNA Library Prep Kit for Illumina. Libraries were bisulfite converted following adaptor ligation using the EZ DNA Methylation-Gold Kit (Cat # D5005, Zymo Research)

value: F1 mus x cast

value: stimulated with CpG for 24 hours


title: RNAPII-mut mESCs, RNAseq 0 days 2i, replicate 2

description: Library name: RNAseq_RNAPIImut_d0_rep2

value: mESCs

value: slow/slow

value: serum+Lif


title: WT:ARG1CKO Tumor CD11C+ WT3

description:
Library name: 20
22_WT-ARG1CKO_Tumor_raw

value: lung


title: whole_blood_temperate_24C_d0_M [MA0050_7_77]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201315558

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


title: whole_blood_tropical_ambient_d0_F [MA0050_7_78]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330515

value: tropical


title: WT:ARG1CKO Tumor CD11C- WT2

description:
Library name: 16
18_WT-ARG1CKO_Tumor_raw

value: B16 tumor


title: WT:ARG1CKO Tumor CD11C+ WT2

description:
Library name: 19
21_WT-ARG1CKO_Tumor_raw

value: CD11C+ IM


title: WT mESCs, RNAseq 7 days 2i, replicate 1

description: Library name: RNAseq_WT_d7_rep1


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

value: Female


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


title: WT:ARG1CKO TumorCD11C- WT3

description:
Library name: 17
19_WT-ARG1CKO_Tumor_raw

value: CD11C- IM


title: whole_blood_temperate_24C_d0_F [MA0050_7_80]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313845

value: temperate


title: WT mESCs, RNAseq 2 days 2i, replicate 2

description: Library name: RNAseq_WT_d2_rep2

value: WT

value: serum+Lif+2i (2 days)


title: whole_blood_tropical_ambient_d0_F [MA0050_7_76]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430323


title: WT:ARG1CKO Tumor CD11C- WT1

description:
Library name: 15
17_WT-ARG1CKO_Tumor_raw


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

value: Spleen

value: CD23+ B cell

value: unstimulated


title: whole_blood_temperate_24C_d0_F [MA0050_7_75]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313228

value: female


title: WT:ARG1CKO Tumor CD11C+WT1

description:
Library name: 18
20_WT-ARG1CKO_Tumor_raw


title: WT:IL9RKO Tumor CD11C+ KO3

description:
Library name: 14
16_WT-IL9RKO_Tumor_raw


title: WT:ARG1CKO Tumor CD11C- CKO2

description:
Library name: 22
24_WT-ARG1CKO_Tumor_raw


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

value: F1 mus x cast


title: whole_blood_temperate_24C_d0_F [MA0050_7_74]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313933


title: WT mESCs, RNAseq 1 days 2i, replicate 2

description: Library name: RNAseq_WT_d1_rep2

value: mESCs

value: serum+Lif+2i (1 day)


title: WT mESCs, RNAseq 1 days 2i, replicate 1

description: Library name: RNAseq_WT_d1_rep1


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


title: whole_blood_temperate_30C_d3_F [MA0050_7_73]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313869


title: Spleen, CD23+ B cell, F1 EPZ6438 7 days, 0h naïve, H3K27me3, biol rep 3

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
Library strategy: CUT&RUN

growth_protocol: Splenic CD23+ B cells were isolated using biotin anti-mouse CD23 Antibody (Cat #101604, Biolegend)

extract_protocol:
Cells were collected and immobilized on concanavalin A-coated beads in Wash Buffer (20mM HEPES, 150mM NaCl, 0.5mM Spermidine, 1x Protease Inhibitor Cocktail). 3ug of H3K27me3 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

tag: treatment mouse

value: EPZ6438 for 7 days

tag: treatment cells


title: WT:IL9RKO Tumor CD11C+ KO2

description:
Library name: 13
15_WT-IL9RKO_Tumor_raw

value: lung

tag: cell type

tag: genotype


title: WT mESCs, RNAseq 0 days 2i, replicate 2

description: Library name: RNAseq_WT_d0_rep2

tag: treatment

value: serum+Lif


title: WT mESCs, RNAseq 0 days 2i, replicate 1

description: Library name: RNAseq_WT_d0_rep1


title: Spleen, CD23+ B cell, Ezh2 CD1 cre cKO, 0h naïve, H3K27me3, biol rep 2

value: Ezh2 fl/fl ; CD19-cre+


title: whole_blood_temperate_24C_d0_M [MA0050_7_70]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201313874

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.

value: male


title: E17.5 mutant, ATAC

city: San Francisco

first: Erica

state: CA

address: 555 Mission Bay Blvd. South, Box 3118

institute: University of California, San Francisco

description: Library name: Mt_E17-5_ATAC

library_source: genomic single cell

data_processing:
Raw sequencing reads were processed using the 10x Genomics Cell Ranger Arc (v2.0.2) pipeline. Reads were aligned with cellranger-arc count to the mm10 mouse reference genome.
Assembly: mm10 mouse reference genome
Supplementary files format and content: atac_fragments.tsv.gz, filtered_feature_bc_matrix.h5

source_name: Lung

extract_protocol:
Live CD45- TER119- lung cells were isolated by FACS from mutant and littermate control mice at E14.5 and E17.5. Multiome samples were prepared following the 10x Genomics protocol [CG000366 Rev D]. Briefly, 50,000-100,000 sorted cells were incubated in 0.1X Lysis Buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.001% Digitonin, 1% BSA, 1 mM DTT, 1 U/μL RNase inhibitor in nuclease-free water) on ice for 3 min. The samples were washed three times with Wash Buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1 mM DTT, 1 U/μL RNase inhibitor in nuclease-free water), then resuspended in Diluted Nuclei Buffer prior to library preparation.
Libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit.

value: Lung

value: Whole Lung (CD45- TER119-)

tag: library type

value: ATAC


title: WT mESCs, RNAseq 2 days 2i, replicate 1

description: Library name: RNAseq_WT_d2_rep1

value: WT


title: RNAPII-mut mESCs, RNAseq 1 days 2i, replicate 1

description: Library name: RNAseq_RNAPIImut_d1_rep1

value: slow/slow


title: whole_blood_temperate_30C_d18_F [MA0050_7_72]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310775

source_name: whole blood,18 days at 30 degrees

tag: experimental facility

value: temperate


title: E17.5 control, ATAC

description: Library name: Ctrl_E17-5_ATAC


title: RNAPII-mut mESCs, RNAseq 0 days 2i, replicate 1

description: Library name: RNAseq_RNAPIImut_d0_rep1


title: WT:IL9RKO Tumor CD11C- KO3

description:
Library name: 11
13_WT-IL9RKO_Tumor_raw

value: CD11C- IM

value: B16 tumor

tag: batch


title: Spleen, CD23+ B cell, F1 EPZ6438 6 days, 0h naïve, H3K27me3, biol rep 2

value: Spleen

value: Female

value: CD23+ B cell

value: EPZ6438 for 6 days

value: unstimulated


title: Spleen, CD23+ B cell, F1 DMSO, 0h naïve, H3K27me3, biol rep 1

value: F1 mus x cast

value: DMSO for 7 days


title: WT:IL9RKO Tumor CD11C+ KO1

description:
Library name: 12
14_WT-IL9RKO_Tumor_raw

value: lung

value: CD11C+ IM


title: Spleen, CD23+ B cell, WT CD19 cre, 0h naïve, H3K27me3, biol rep 2

value: WT (CD19-cre+)


title: Spleen, CD23+ B cell, WT CD19 cre, 0h naïve, H3K27me3, biol rep 1


title: whole_blood_temperate_30C_d3_F [MA0050_7_71]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313126

source_name: whole blood,3 days at 30 degrees

tag: gender

value: female

tag: breeding batch


title: E17.5 mutant, GEX

description: Library name: Mt_E17-5_RNA

library_source: transcriptomic single cell

value: Lung

value: Whole Lung (CD45- TER119-)

value: mRNA


title: WT:IL9RKO Tumor CD11C- KO1

description:
Library name: 9
11_WT-IL9RKO_Tumor_raw


title: WT:IL9RKO Tumor CD11C+ WT 2

description:
Library name: 8
9_WT-IL9RKO_Tumor_raw

value: WT


title: WT:IL9RKO Tumor CD11C- KO2

description:
Library name: 10
12_WT-IL9RKO_Tumor_raw

value: CD11C- IM


title: E14.5 mutant, ATAC

description: Library name: Mt_E14-5_ATAC

value: ATAC


title: whole_blood_tropical_ambient_d0_F [MA0050_7_68]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331761

value: tropical

tag: condition

tag: wash batch


title: whole_blood_tropical_ambient_d0_M [MA0050_7_67]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330326

value: male

tag: analysis serial


title: whole_blood_tropical_ambient_d0_M [MA0050_7_69]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430347


title: whole_blood_tropical_ambient_d0_F [MA0050_7_65]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331343


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

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

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

tag: tissue

value: Spleen

value: Female

value: CD23+ B cell

value: Xist fl/fl

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


title: WT:IL9RKO Tumor CD11C- WT 1

description:
Library name: 5
5_WT-IL9RKO_Tumor_raw

value: lung

value: B16 tumor


title: E17.5 control, GEX

description: Library name: Ctrl_E17-5_RNA


title: WT:IL9RKO Tumor CD11C- WT 2

description:
Library name: 6
6_WT-IL9RKO_Tumor_raw


title: Spleen, CD23+ B cell, Ezh2 CD19 cre cKO, 0h naïve, H3K27me3, biol rep 1

value: Ezh2 fl/fl ; CD19-cre+

value: unstimulated


title: whole_blood_tropical_ambient_d0_M [MA0050_7_66]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430261


title: WT:IL9RKO naïve IL9RKO 1

description:
Library name: 4
4_WT-IL9RKO_naive_raw

value: Total macrophage

value: naïve


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


title: E14.5 mutant, GEX

description: Library name: Mt_E14-5_RNA

value: Lung

value: Whole Lung (CD45- TER119-)

value: mRNA


title: WT:IL9RKO naïve WT 1

description:
Library name: 3
3_WT-IL9RKO_naive_raw

value: WT


title: WT:IL9RKO Tumor CD11C+ WT 1

description:
Library name: 7
8_WT-IL9RKO_Tumor_raw

value: CD11C+ IM


title: E14.5 control, GEX

description: Library name: Ctrl_E14-5_RNA


title: whole_blood_temperate_30C_d3_F [MA0050_7_64]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310029

value: temperate

value: female


title: E14.5 control, ATAC

description: Library name: Ctrl_E14-5_ATAC

value: ATAC


title: WT:ARG1 naïve ARG1 CKO 1

description:
Library name: 2
2_WT-ARG1_naive_raw


title: whole_blood_temperate_24C_d0_F [MA0050_7_63]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410692

source_name: whole blood,24 degrees


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

value: Spleen

value: Female

value: CD23+ B cell


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

value: Xist fl/fl

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


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


title: E17.5 control

description:
Library name: Ctrl_E17-5
10x Genomics

data_processing:
Sequencing reads from each single-cell RNA-seq (scRNA-seq) sample were preprocessed, aligned, and quantified using the CellRanger pipeline (version 8.0.1, 10x Genomics) with the mm10 mouse reference genome (refdata-gex-mm10-2020-A, 10x Genomics).
Assembly: mm10 mouse reference genome (refdata-gex-mm10-2020-A, 10x Genomics)
Supplementary files format and content: matrix files

extract_protocol:
Lungs were isolated from E14.5 SftpcCre/+; Lats1f/f; Lats2f/f and littermate control embryos and dissociated with collagenase type IV and dispase for 30-50 minutes at 37°C. After washing with 1x PBS, cells were resuspended in freezing media (90% FBS/10% DMSO) and stored at -80°C overnight, then transferred to liquid nitrogen for long-term storage. On the day of scRNA-seq, cells were thawed and washed with 20% fetal bovine serum (FBS)/Leibovitz' L-15 media. Samples were incubated with eFluor 450 anti-CD45 and eFluor 450 anti-TER119 antibodies at 4°C for 30 min. The samples were sorted by FACS to remove dead cells, and CD45- TER119- cells were collected and resuspended in 0.04% BSA/PBS prior to scRNA-seq library preparation.
Libraries were prepared using 10x Genomics Chromium GEM-X Universal 3' Gene Expression Kit (v4).


title: whole_blood_temperate_24C_d0_F [MA0050_7_59]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201410515


title: E14.5 control

description:
Library name: Ctrl_E14-5
10x Genomics


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


title: WT:ARG1 naïve WT 1

description:
Library name: 1
1_WT-ARG1_naive_raw

value: lung


title: Primary mouse granulosa cells, Veh treatment, HA, rep2_SMAD2tagged

description: Library name: Sample24

value: Ovary

tag: cell line

value: Primary granulosa cells

value: Granulosa cells

value: vehicle


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

tag: Sex

value: unstimulated


title: E17.5 mutant

description:
Library name: Mt_E17-5
10x Genomics

value: Lung

value: Whole Lung (CD45- TER119-)


title: K443GA

city: Bunkyo-ku

first: Junya

last: Arai

address: Clinical reserch center A #422 7-3-1 Hongo

institute: University of Tokyo

description: Library name: Sample11

data_processing:
RaNA (https://ranaseq.eu/contact)
Read count extraction and normalization were performed with RaNa website.
Assembly: mm10
Supplementary files format and content: Tab-delimited tsv file included raw counts for each samples.

source_name: gastric mucosa at corpus

extract_protocol:
RNA was harvested using the Nucleospin RNA kit (takara-bio).
RNA libraries for RNA sequence were prepared using TruSeq Stranded mRNA Library Prep kit.

value: gastric mucosa at corpus


title: whole_blood_temperate_30C_d18_F [MA0050_7_62]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201315547

value: temperate


title: K422GA

description: Library name: Sample10


title: whole_blood_tropical_ambient_d0_M [MA0050_7_60]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331534

source_name: whole blood,ambient

value: tropical

value: male


title: E14.5 mutant

description:
Library name: Mt_E14-5
10x Genomics


title: whole_blood_tropical_ambient_d0_M [MA0050_7_58]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330318


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

value: Spleen

value: WT

tag: antibody


title: K279G

description: Library name: Sample6

value: GIF-DTR


title: K420GA

description: Library name: Sample9


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

value: Female

value: CD23+ B cell


title: Primary mouse granulosa cells, Veh treatment,HA, rep1_SMAD2tagged

description: Library name: Sample23


title: whole_blood_temperate_30C_d3_M [MA0050_7_56]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201316036


title: whole_blood_tropical_ambient_d0_F [MA0050_7_61]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331218

value: female


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


title: Primary mouse granulosa cells, Veh treatment,IgG, rep1_SMAD2tagged

description: Library name: Sample21

value: Ovary


title: K445G

description: Library name: Sample7


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


title: Primary mouse granulosa cells, Veh treatment,IgG, rep2_SMAD2tagged

description: Library name: Sample22

value: Primary granulosa cells


title: K448A

description: Library name: Sample5


title: whole_blood_temperate_30C_d18_F [MA0050_7_55]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311727


title: K446G

description: Library name: Sample8


title: whole_blood_temperate_30C_d18_F [MA0050_7_57]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201312469


title: whole_blood_temperate_24C_d0_M [MA0050_7_54]

description: Gene expression in blood in temperate facility at 24 degrees for individual FR17MAG201312474


title: Primary mouse granulosa cells, Veh treatment,SMAD3, rep2_SMAD2tagged

description: Library name: Sample20

value: Granulosa cells


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

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


title: whole_blood_tropical_ambient_d0_F [MA0050_7_53]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331751


title: Primary mouse granulosa cells, Veh treatment,SMAD3, rep1_SMAD2tagged

description: Library name: Sample19

value: vehicle


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

value: Xist fl/fl


title: K442A

description: Library name: Sample3


title: Primary mouse granulosa cells, Veh treatment,SMAD2, rep2_SMAD2tagged

description: Library name: Sample18


title: Control 2

description: Library name: Sample2


title: Primary mouse granulosa cells, Veh treatment,SMAD2, rep1_SMAD2tagged

description: Library name: Sample17


title: whole_blood_temperate_30C_d3_F [MA0050_7_50]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315551


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


title: whole_blood_temperate_30C_d18_M [MA0050_7_51]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201311718


title: whole_blood_temperate_30C_d3_M [MA0050_1_88_h2]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310913


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

value: unstimulated


title: Primary mouse granulosa cells, Veh treatment,H3K27ac, rep2_SMAD2tagged

description: Library name: Sample16


title: Control 1

description: Library name: Sample1

value: gastric mucosa at corpus


title: Primary mouse granulosa cells, GDF9 treatment,HA, rep2_SMAD2tagged

description: Library name: Sample14

value: mouse GDF9


title: whole_blood_temperate_30C_d3_M [MA0050_7_48]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201314565

value: temperate


title: K447A

description: Library name: Sample4


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


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


title: Primary mouse granulosa cells, Veh treatment,H3K27ac, rep1_SMAD2tagged

description: Library name: Sample15


title: VEDS Fludro, rep3

first: Tyler

middle: J

last: Creamer

address: 733 N Broadway

department: Genetic Medicine

institute: Johns Hopkins University

description: Library name: D3855

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

source_name: Fludrocortisone treated VEDS

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.

value: descending thoracic aorta

value: Male

tag: strain

tag: age

value: 60 days

value: Fludrocortisone


title: VEDS Fludro, rep2

description: Library name: D3706


title: whole_blood_temperate_30C_d18_F [MA0050_7_52]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313238


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

value: Spleen

value: Female

tag: cell type

value: WT


title: Primary mouse granulosa cells, GDF9 treatment,IgG, rep2_SMAD2tagged

description: Library name: Sample12

value: Ovary

tag: genotype


title: VEDS Fine, rep3

description: Library name: D3830

source_name: Finerenone treated VEDS

tag: treatment

value: Finerenone


title: whole_blood_temperate_30C_d3_M [MA0050_7_46]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201310272

value: male


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

value: CD23+ B cell

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


title: whole_blood_tropical_ambient_d0_F [MA0050_7_47]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331701

value: tropical

value: female


title: Primary mouse granulosa cells, GDF9 treatment,HA, rep1_SMAD2tagged

description: Library name: Sample13

value: Primary granulosa cells

value: Granulosa cells


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

value: Xist fl/fl

value: unstimulated


title: whole_blood_tropical_ambient_d0_F [MA0050_7_45]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DW201430125


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


title: Primary mouse granulosa cells, GDF9 treatment,IgG, rep1_SMAD2tagged

description: Library name: Sample11

value: mouse GDF9


title: VEDS Fludro, rep1

description: Library name: D3805

value: descending thoracic aorta

value: Male

value: 60 days


title: VEDS Fine, rep2

description: Library name: D3773


title: Primary mouse granulosa cells, GDF9 treatment,SMAD3, rep2_SMAD2tagged

description: Library name: Sample10


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

value: Spleen

value: Female


title: VEDS Spiro, rep3

description: Library name: D3784

source_name: Spironolactone treated VEDS

value: Spironolactone


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

source_name: Spleen

value: WT


title: whole_blood_temperate_30C_d18_F [MA0050_7_44]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201310029

value: temperate


title: whole_blood_tropical_ambient_d0_M [MA0050_7_42]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331358

value: male


title: VEDS Fine, rep1

description: Library name: D3772

value: Finerenone


title: VEDS Spiro, rep1

description: Library name: D3779


title: whole_blood_temperate_30C_d3_M [MA0050_7_43]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201313205


title: Primary mouse granulosa cells, GDF9 treatment,SMAD2, rep2_SMAD2tagged

description: Library name: Sample8

value: Ovary


title: VEDS Spiro, rep2

description: Library name: D3780


title: whole_blood_temperate_30C_d18_M [MA0050_7_41]

description: Gene expression in blood after heat stress at 30 degrees during 18 days for individual FR17MAG201313232


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

value: CD23+ B cell


title: Primary mouse granulosa cells, GDF9 treatment,SMAD2, rep1_SMAD2tagged

description: Library name: Sample7

value: Primary granulosa cells


title: VEDS Bical, rep3

description: Library name: D3736

source_name: Bicalutamide treated VEDS

value: Bicalutamide


title: VEDS Bical, rep2

description: Library name: D3800


title: Primary mouse granulosa cells, GDF9 treatment,H3K27ac, rep2_SMAD2tagged

description: Library name: Sample6

value: Granulosa cells


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

value: Xist fl/fl

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


title: whole_blood_tropical_ambient_d0_M [MA0050_7_39]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201330343

value: tropical


title: Primary mouse granulosa cells, GDF9 treatment,SMAD3, rep1_SMAD2tagged

description: Library name: Sample9

value: mouse GDF9


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

value: unstimulated


title: VEDS Bical, rep1

description: Library name: D3775

value: descending thoracic aorta

value: Male

value: 60 days


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

value: Spleen

value: Female


title: Primary mouse granulosa cells, GDF9 treatment,H3K27ac, rep1_SMAD2tagged

description: Library name: Sample5


title: whole_blood_temperate_30C_d3_M [MA0050_7_40]

description: Gene expression in blood after heat stress at 30 degrees during 3 days for individual FR17MAG201315305

value: temperate

value: male


title: whole_blood_tropical_ambient_d0_M [MA0050_7_38]

description: Gene expression in blood in tropical facility at ambient temperature for individual FR971DU201331592


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