title: Oocytes isolated from encapsulated follicles cultured in Blebbistatin - replicate 4

description:
Library name: OO_Blebb_4
Column name in salmon.merged.gene_counts_OO.txt: OO_Blebb_4

value: Blebb


title: OM3_H3K4me1

status: Public on Oct 15 2025

type: SRA

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

description: Library name: OM3_H3K4me1

library_source: genomic

data_processing:
Illumina sequencing reads were de-multiplexed, trimmed to remove adapter sequences, and checked for quality using fastqc ad multiqc.
Reads were aligned to the mouse reference genome (assembly GRCm38/mm10) using Bowtie/2-2.4.2.
Aligned reads were filtered to retain alignments with a minimum mapping quality of 2 using samtools/1.9. Reads mapping to Encyclopedia of DNA Elements (ENCODE) blacklist regions were removed using intersect function in bedtools/2.30.0.
RPKM normalized bigWig files were generated using the bamCoverage function in deepTools/3.5.0.
Broad peaks were called using MACS/2.2.7.1. Differential peak analysis was performed using DiffBind/3.2.6. ROSE (Rank Ordering of Super-Enhancers) algorithm was used to classify enhancers.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig coverage files
Library strategy: CUT&Run

molecule: genomic DNA

organism: Mus musculus

source_name: muscle

extract_protocol:
CUT&RUN was performed to profile enhancer histone modifications H3K4me1 and H3K27ac from young, old and geriatric MuSCs following guidelines in the CUTANA CUT&RUN Protocol (EpiCypher). Briefly, MuSCs were pelleted, and resuspended in wash buffer. ~10,000 cells per sample were bound to activated Concanavalin A beads (Bangs Laboratories). The bead-bound cells were incubated with antibody in wash buffer supplemented with 2 mM EDTA and 0.01% digitonin overnight at 4ºC, digitonin was added to permeabilize cells for antibody binding in situ. After washing with 0.01% digitonin in wash buffer, CUTANA® pAG-MNase (1:20) was added to each sample and incubated at RT for 10 mins to allow binding to antibody-labeled chromatin. Samples were then equilibrated on ice water for 5 mins. 2 mM CaCl2 was added to each sample to activate MNase and cleave antibody-bound chromatin. After 2 h of incubation with CaCl2 at 4ºC, reactions were stopped by adding 33 µL stop buffer to degrade RNA and release DNA fragments. DNA was purified using the Monarch DNA Cleanup Kit (NEB) following manufacturer's instructions and the concentration of CUT&RUN-enriched DNA was determined using the Qubit fluorometer with a DNA high sensitivity kit.
~2 ng of purified DNA was used to prepare libraries using NEBNext Ultra II library preparation kit with unique dual index PCR primers (NEB). The library concentrations were determined using Qubit fluorometer with a DNA high sensitivity kit. Library quality and quantity were confirmed on a BioAnalyzer (Agilent) high sensitivity DNA chip. Equimolar amounts of each library were combined, and the pooled library was further quantified using a NEBNext Library Quant Kit (NEB). The CUT&RUN libraries were subjected to paired-end sequencing with on the NextSeq 2000 platform using a P2 100 cycle kit (Illumina).

tag: tissue

value: muscle

tag: cell type

value: FISC/MuSC

tag: genotype


title: YM2_H3K4me1

description: Library name: YM2_H3K4me1


title: GF3_ATAC

description: Library name: GF3_ATAC

data_processing:
ATAC-seq data was processed by the Encyclopedia of DNA Elements (ENCODE) pipeline (https://www.encodeproject.org/atac-seq/). Briefly, Illumina sequencing reads were de-multiplexed, trimmed to remove adapter sequences, and checked for quality using fastqc ad multiqc.
Reads were aligned to the mouse reference genome (assembly GRCm38/mm10) using Bowtie/2-2.2.9.
Mapped reads were then filtered to remove low-quality and duplicate reads using Picard/2.10.6.
RPKM normalized bigWig files were generated using the bamCoverage function in deepTools/3.5.0.
DiffBind/3.2.6 to identify differential peaks.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig coverage files

extract_protocol:
ATAC-seq wash buffer was added to thaw cryopreserved FISCs (~60,000 cells each sample) and pelleted by centrifugation at 500g for 5 min at 4 °C. The pellet was resuspended in 50 μl of ice-cold ATAC-seq lysis buffer and incubated on ice for 3 min. The cell lysate was added with 1 ml of ATAC-seq wash buffer followed by centrifugation at 500g for 10 min at 4°C. The cell pellet was resuspended in transposition mix including 2.5 μl of Tagment DNA enzyme 1 (Illumina), 0.1% Tween 20, and 0.01% digitonin and incubated at 37°C for 30 min on thermomixer at 1000 rpm.
The transposed DNA fragments were PCR-amplified using NEBNext Ultra II Q5 2× Master Mix (NEB). The sample was purified using the DNA Clean and Concentrator-5 Kit (Zymo). The library quality and quantity were verified using the high sensitivity DNA kit on a 2100 Bioanalyzer (Agilent) and qPCR with NEBNext Library Quant kit (NEB) respectively. The ATAC libraries were subjected to 50 bp paired end sequencing on a NextSeq 2000 platform using a P2 100-cycle kit (Illumina).


title: Oocytes isolated from encapsulated follicles cultured in Blebbistatin - replicate 3

city: Singapore

first: Chii Jou

last: Chan

address: 5A Engineering Drive 1

department: Mechanobiology Institute

country: Singapore

institute: National University of Singapore

description:
Library name: OO_Blebb_3
Column name in salmon.merged.gene_counts_OO.txt: OO_Blebb_3

library_source: transcriptomic

data_processing:
Raw FASTQ files were processed using the nf-core/rnaseq pipeline, a standardized and reproducible bioinformatics workflow built using Nextflow.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

source_name: Ovarian follicle

growth_protocol: Isolated ovarian follicles were encapsulated in alginate and grown for three days in MEM-αGlutamax + 10% fetal bovine serum (FBS) +1% PenStrep, supplemented with 1X Insulin-Transferrin-Selenium (ITS) and 50 mIU/ml Follicle Stimulating Hormone (FSH) under different treatments

extract_protocol:
We identified encapsulated follicles in the different culture conditions that grew beyond 180 µm and removed the alginate from them. Immediately after retrieval, the follicles were mechanically separated into oocytes and granulosa cells (GCs) within 5–10 minutes. While 1-2 oocytes were pooled together, a few hundred GCs were pooled into one sample set respectively. This was repeated individually for the different conditions to maintain similar levels of harvested RNA in each case. Each set of samples was promptly transferred into lysis buffer from the RNeasy Plus Micro Kit (Qiagen) and stored at –80 °C until RNA isolation. To minimize technical variability, RNA extraction was performed simultaneously for all biological replicates after the completion of all experiments.  Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen), following the manufacturer's instructions, and eluted in RNase-free water before being stored at –80 °C.
Sequence-ready libraries were prepared following the manufacturer’s instructions. Each sample utilized 8 µL of total RNA for cDNA synthesis, with cDNA amplification performed over 15 PCR cycles. Libraries were indexed using the NEBNext Multiplex Oligos for Illumina (NEB, E6440L)

treatment_protocol: The three treatments are control, Blebbistatin added to the medium (Blebb, 20 µM), and dextran added to the medium (Dex, 10 kPa)

value: Ovarian follicle

tag: cell line

value: primary cells

value: Oocyte

value: WT

tag: treatment

tag: time

value: Day 3


title: YM1_H3K4me1

description: Library name: YM1_H3K4me1


title: Oocytes isolated from encapsulated follicles cultured in Blebbistatin - replicate 2

description:
Library name: OO_Blebb_2
Column name in salmon.merged.gene_counts_OO.txt: OO_Blebb_2


title: GF1_ATAC

description: Library name: GF1_ATAC


title: Endometrial cells, P+7, 882

city: Hangzhou

first: Jiucheng

last: Chen

state: Zhejiang

address: No.866 Yuhangtang Road

country: China

institute: Zhejiang University

description: Library name: ERA210718

data_processing:
Use the fastp tool for quality control of sequencing data. Remove sequences with the following low-quality criteria: Sequences with unknown bases numbering 5 or more. Sequences with a length less than 75bp. Sequences with an average base quality value less than 15. The resulting data after this step is termed Clean Data.
Use the sortmerna tool to align the Clean Data against a ribosomal database. Exclude sequences that align to the ribosomal database. The data obtained after this step is termed de-rRNA Clean Data.
Use the STAR tool to align the de-rRNA Clean Data to the reference genome.
Use the RSeQC tool to assess the quality of the alignment results from STAR.
Use the featureCounts tool to quantify gene expression from the alignment results. Use the edgeR tool for differential gene expression analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited rawcount files for each samples
Supplementary files format and content: tab-delimited FPKM files for each samples

organism: Homo sapiens

source_name: endometrium tissue

growth_protocol: All endometrial biopsy samples were obtained with disposable uterine-cavity tissue-suction tubes (Runting), and all the collected samples were stored in All protect Tissue Reagent (QIAGEN). The samples were transported to our laboratory on ice packs and stored at -80°C before processing.

extract_protocol:
RNA was extracted from endometrial tissue using RNAprep Pure Tissue Kit (DP341; Tiangen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using a KAPA Stranded RNA-Seq Library Preparation Kit (KR0934, KAPA Biosystems), following the manufacturer’s instructions.

treatment_protocol: The estradiol administration of all patients was started from the second day of menstruation with 4 mg estradiol valerate (Progynova; Bayer, Leverkusen, Germany) per day. When endometrial thickness was at least 7 mm and endogenous progesterone level was less than 1.5 ng/ml, 90 mg progesterone sustained-release vaginal gel (Crinone; Merck-Serono, Darmstadt, Germany) was applied transvaginally per day. The initial day of progesterone administration was recognized as “P+0” and endometrial biopsies were respectively taken on days P+3, P+5, and P+7 for each patient by a dedicated physician.

value: endometrium tissue


title: GF2_ATAC

description: Library name: GF2_ATAC


title: Endometrial cells, P+3, 883

description: Library name: ERA2101292


title: Endometrial cells, P+5, 881

description: Library name: ERA210733


title: GF2_H3K4me1

description: Library name: GF2_H3K4me1


title: GM4_ATAC

description: Library name: GM4_ATAC


title: Oocytes isolated from encapsulated follicles cultured in Blebbistatin - replicate 1

description:
Library name: OO_Blebb_1
Column name in salmon.merged.gene_counts_OO.txt: OO_Blebb_1


title: GM2_ATAC

description: Library name: GM2_ATAC


title: Endometrial cells, P+3, 880

description: Library name: ERA210671


title: GM1_ATAC

description: Library name: GM1_ATAC


title: Granulosa cells isolated from encapsulated follicles cultured in 10 kPa dextran - replicate 4

description:
Library name: GC_Dex_4
Column name in salmon.merged.gene_counts_GC.txt: GC_Dex_4

value: Granulosa cells

value: 10 kPa


title: Endometrial cells, P+5, 879

description: Library name: ERA210816


title: OF4_ATAC

description: Library name: OF4_ATAC


title: OF2_ATAC

description: Library name: OF2_ATAC


title: OM4_ATAC

description: Library name: OM4_ATAC


title: Granulosa cells isolated from encapsulated follicles cultured in 10 kPa dextran - replicate 2

description:
Library name: GC_Dex_2
Column name in salmon.merged.gene_counts_GC.txt: GC_Dex_2


title: Endometrial cells, P+3, 878

description: Library name: ERA210835


title: OF1_ATAC

description: Library name: OF1_ATAC


title: Granulosa cells isolated from encapsulated follicles cultured in 10 kPa dextran - replicate 3

description:
Library name: GC_Dex_3
Column name in salmon.merged.gene_counts_GC.txt: GC_Dex_3


title: Endometrial cells, P+7, 877

description: Library name: ERA210996


title: OM1_ATAC

description: Library name: OM1_ATAC


title: OM2_ATAC

description: Library name: OM2_ATAC


title: GM3_ATAC

description: Library name: GM3_ATAC


title: YF4_ATAC

description: Library name: YF4_ATAC


title: Granulosa cells isolated from encapsulated follicles cultured in 10 kPa dextran - replicate 1

description:
Library name: GC_Dex_1
Column name in salmon.merged.gene_counts_GC.txt: GC_Dex_1


title: Granulosa cells isolated from encapsulated follicles cultured in control - replicate 4

description:
Library name: GC_Ctrl_4
Column name in salmon.merged.gene_counts_GC.txt: GC_Ctrl_4

value: Control


title: Endometrial cells, P+7, 874

description: Library name: ERA210464


title: Endometrial cells, P+5, 876

description: Library name: ERA210984


title: YF3_ATAC

description: Library name: YF3_ATAC


title: Endometrial cells, P+3, 875

description: Library name: ERA210924


title: YM4_ATAC

description: Library name: YM4_ATAC


title: YF1_ATAC

description: Library name: YF1_ATAC


title: Granulosa cells isolated from encapsulated follicles cultured in control - replicate 2

description:
Library name: GC_Ctrl_2
Column name in salmon.merged.gene_counts_GC.txt: GC_Ctrl_2


title: YF2_ATAC

description: Library name: YF2_ATAC


title: Endometrial cells, P+5, 873

description: Library name: ERA210447


title: OF3_ATAC

description: Library name: OF3_ATAC


title: YM2_ATAC

description: Library name: YM2_ATAC


title: Granulosa cells isolated from encapsulated follicles cultured in control - replicate 1

description:
Library name: GC_Ctrl_1
Column name in salmon.merged.gene_counts_GC.txt: GC_Ctrl_1


title: Endometrial cells, P+3, 872

description: Library name: ERA210499


title: YM1_ATAC

description: Library name: YM1_ATAC


title: Endometrial cells, P+7, 871

description: Library name: ERA210524


title: MuSCs,L2A-Pax7CreER, 4 dpi, rep3

city: Barcelona

first: Ignacio

last: Ramirez Pardo

state: Barcelona

address: Carrer del Doctor Aiguader, 88, Ciutat Vella

department: Department of Medicine and Life Sciences

country: Spain

institute: Universitat Pompeu Fabra

description:
Library name: Sample_S23_KO_4__IgnacioRamirez_RNA_Seq_SMARTER
S23_KO_4

data_processing:
FASTQC (quality control)
STAR (mapping)
RSEM (counts normalization and expression matrix construction)
limma (differential gene expression)
Assembly: mm39
Supplementary files format and content: expression matrix with samples as columns and genes as rows

growth_protocol: FACS buffer (PBS 1X, P/S 1%, Goat Serum 1%)

extract_protocol:
SMART-Seq® v4 Ultra® Low Input RNA
SMART-Seq® v4 Ultra® Low Input RNA

treatment_protocol: For injured muscles, we did intramuscular injection of 50uL of cardiotoxin (CTX) 10uM

value: primary

value: muscle stem cells

value: 4 dpi

tag: batch


title: Granulosa cells isolated from encapsulated follicles cultured in Blebbistatin - replicate 3

description:
Library name: GC_Blebb_3
Column name in salmon.merged.gene_counts_GC.txt: GC_Blebb_3


title: Granulosa cells isolated from encapsulated follicles cultured in control - replicate 3

description:
Library name: GC_Ctrl_3
Column name in salmon.merged.gene_counts_GC.txt: GC_Ctrl_3


title: MuSCs,L2A-Pax7CreER, 4 dpi, rep2

description:
Library name: Sample_S22_KO_4__IgnacioRamirez_RNA_Seq_SMARTER
S22_KO_4


title: MuSCs,L2A-Pax7CreER, 4 dpi, rep4

description:
Library name: Sample_S24_KO_4__IgnacioRamirez_RNA_Seq_SMARTER
S24_KO_4


title: Endometrial cells, P+5, 870

description: Library name: ERA210502


title: Granulosa cells isolated from encapsulated follicles cultured in Blebbistatin - replicate 2

description:
Library name: GC_Blebb_2
Column name in salmon.merged.gene_counts_GC.txt: GC_Blebb_2


title: MuSCs,L2A-Pax7CreER, 4 dpi, rep1

description:
Library name: Sample_S21_KO_4__IgnacioRamirez_RNA_Seq_SMARTER
S21_KO_4


title: MuSCs,L2A-WT, 4 dpi, rep4

description:
Library name: Sample_S20_Wt_4__IgnacioRamirez_RNA_Seq_SMARTER
S20_Wt_4


title: Endometrial cells, P+7, 868

description: Library name: ERA210045


title: MuSCs,L2A-WT, 4 dpi, rep2

description:
Library name: Sample_S18_Wt_4__IgnacioRamirez_RNA_Seq_SMARTER
S18_Wt_4


title: Ctrl12

city: Los Angeles

first: Yuichiro

last: Itoh

state: California

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

description: Library name: 9

data_processing:
Sequencing was performed on NovaSeq (paired end 2x50) at the UCLA Technology Center for Genomics and Bioinformatics core facility. Statistical analyses and production of figures were performed in R (R Core Team, 2024, http://www.R-project.org/). Qualities of raw sequence data were examined using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and Trimmomatic (9) was used for cleaning. R package “QuasR” was used for the read alignment to the mouse genome (mm10). Differentially binding sites were identified with R package “csaw” (13). False discovery rate of 0.1 and more than 4 fold of difference were used as the threshold of differentially binding sites.
Assembly: mm10
Supplementary files format and content: Wig files
Library strategy: CUT&Run

source_name: spinal cord

extract_protocol:
Frozen tissues were homogenized with ice-cold Dounce homogenizer in 4 ml of freshly made low sucrose buffer (LSB) [15 mM Tris-HCl (pH 7.4, Invitrogen), 25 mM KCl (Fisher scientific), 5 mM MgCl2 (Fisher Scientific), 1 mM DTT (Sigma-Aldrich), 1 tablet / 20 ml of EDTA-free proteinase inhibitors (Thermo Scientific), 0.5 mM  Spermidine (Sigma-Aldrich), 0.15 mM Spermine (Sigma-Aldrich), 250 mM Sucrose (Sigma-Aldrich)]. After the homogenization, Nonidet P-40 (Roche) was added to make final 0.1% Nonidet P-40, and mix. The homogenates were filtered through a 70 µm filter, followed by a 40 µm filter. The filtered homogenates were transferred to 2 tubes and centrifuged at 600×g, 4 degrees for 10 min, then the pellet was resuspended in 0.5 ml (per tube) of wash buffer (WB) [15 mM Tris-HCl (pH 7.4, Invitrogen), 25 mM KCl (Fisher scientific), 5 mM MgCl2 (Fisher Scientific), 1 mM DTT (Sigma-Aldrich), 1 tablet / 20 ml of EDTA-free proteinase inhibitors (Thermo Scientific), 0.5 mM  Spermidine (Sigma-Aldrich), 0.15 mM Spermine (Sigma-Aldrich), 250 mM Sucrose (Sigma-Aldrich), 0.1% Nonidet P-40]. Add 0.9 ml (per tube) of Sucrose Cushion Buffer [15 mM Tris-HCl (pH 7.4, Invitrogen), 25 mM KCl (Fisher scientific), 5 mM MgCl2 (Fisher Scientific), 1 mM DTT (Sigma-Aldrich), 1 tablet / 20 ml of EDTA-free proteinase inhibitors (Thermo Scientific), 0.5 mM  Spermidine (Sigma-Aldrich), 0.15 mM Spermine (Sigma-Aldrich), 1.2 M Sucrose (Sigma-Aldrich)] to the suspension, and gently mix. Carefully overlay this mixture (1.4 ml) on top of the 0.5 ml of Sucrose Cushion Buffer, and centrifuged at 13,000×g, 4 degrees for 45 min. Discard the supernatant, and the pellet was resuspended in total 1 ml of WB. Washed and resuspended GFP-Trap® Magnetic Particles M-270 (Protein Tech) were added, and the mixture were incubated at 4 degrees for 1 hour with continuous rotation. After the removal of the supernatant, the magnetic beads were washed in WB, for three times. After removing the WB, CUT&RUN was performed as described in the user manual (Cell Signaling, 86652S), with UTX (D3Q1I) Rabbit mAb (Cell Signaling, 33510S) and Rabbit (DA1E) mAb IgG XP Isotype Control (Cell Signaling, 66362).
Sequence library was made using Zymo-Seq™ SPLAT DNA Library Kit (Zymo Research).

value: spinal cord

tag: Sex

value: Female

value: microglia

tag: disease

value: healthy normal

tag: strain

tag: antibody

value: CUT&RUN Seq using anti-IgG


title: MuSCs,L2A-WT, 4 dpi, rep3

description:
Library name: Sample_S19_Wt_4__IgnacioRamirez_RNA_Seq_SMARTER
S19_Wt_4

value: muscle


title: YM3_ATAC

description: Library name: YM3_ATAC

value: FISC/MuSC


title: MuSCs,L2A-Pax7CreER, 1 dpi, rep3

description:
Library name: Sample_S15_KO_1__IgnacioRamirez_RNA_Seq_SMARTER
S15_KO_1

value: 1 dpi


title: Endometrial cells, P+3, 869

description: Library name: ERA210933


title: Granulosa cells isolated from encapsulated follicles cultured in Blebbistatin - replicate 1

description:
Library name: GC_Blebb_1
Column name in salmon.merged.gene_counts_GC.txt: GC_Blebb_1

value: Ovarian follicle

value: primary cells

value: WT

value: Blebb


title: MuSCs,L2A-Pax7CreER, 1 dpi, rep4

description:
Library name: Sample_S16_KO_1__IgnacioRamirez_RNA_Seq_SMARTER
S16_KO_1


title: Ctrl7

description: Library name: 8


title: Endometrial cells, P+5, 867

description: Library name: ERA210384

value: endometrium tissue


title: OM3_ATAC

description: Library name: OM3_ATAC


title: MuSCs,L2A-Pax7CreER, 1 dpi, rep2

description:
Library name: Sample_S14_KO_1__IgnacioRamirez_RNA_Seq_SMARTER
S14_KO_1


title: Granulosa cells isolated from encapsulated follicles cultured in Blebbistatin - replicate 4

description:
Library name: GC_Blebb_4
Column name in salmon.merged.gene_counts_GC.txt: GC_Blebb_4

value: Granulosa cells

value: Day 3


title: MuSCs,L2A-WT, 1 dpi, rep4

description:
Library name: Sample_S12_Wt_1__IgnacioRamirez_RNA_Seq_SMARTER
S12_Wt_1

value: primary

value: muscle stem cells


title: MuSCs,L2A-WT, 4 dpi, rep1

description:
Library name: Sample_S17_Wt_4__IgnacioRamirez_RNA_Seq_SMARTER
S17_Wt_4

value: 4 dpi


title: NL2

description: Library name: 6

value: spinal cord

value: Female

value: CUT&RUN Seq using anti-Kdm6a


title: Endometrial cells, P+7, 866

description: Library name: ERA210558


title: MuSCs,L2A-WT, 1 dpi, rep3

description:
Library name: Sample_S11_Wt_1__IgnacioRamirez_RNA_Seq_SMARTER
S11_Wt_1


title: MuSCs,L2A-Pax7CreER, uninjured (0), rep4

description:
Library name: Sample_S8_KO_0__IgnacioRamirez_RNA_Seq_SMARTER
S8_KO_0

value: uninjured


title: NL3

description: Library name: 7

value: microglia

value: healthy normal


title: Endometrial cells, P+5, 865

description: Library name: ERA210395


title: MuSCs,L2A-WT, 1 dpi, rep2

description:
Library name: Sample_S10_Wt_1__IgnacioRamirez_RNA_Seq_SMARTER
S10_Wt_1

value: muscle

value: 1 dpi


title: WT9

description:
Library name: 11
microglia RNA isolated from Tmem119-Cre:RiboTag mice

data_processing:
Data quality check was done on Illumina SAV. De-multiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.
Qualities of raw sequence data were examined using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and Trimmomatic (Bolger et al., 2014) was used for cleaning.
R package “QuasR” (Gaidatzis et al., 2015) was used for the read alignment to the mouse genome (mm10) followed by counting at the gene level.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts

extract_protocol:
RNAs were isolated using the Direct-zol™ RNA Microprep kit (Zymo Research).
The RNA sequencing library was made using KAPA Stranded RNA-Seq Kit (Kapa Biosystems) which consists of mRNA enrichment, cDNA generation, end repair, A-tailing, adaptor ligation, strand selection, and PCR amplification.

value: wildtype


title: Endometrial cells, P+3, 864

description: Library name: ERA210365


title: NL1

description: Library name: 5


title: MuSCs,L2A-Pax7CreER, uninjured (0), rep2

description:
Library name: Sample_S6_KO_0__IgnacioRamirez_RNA_Seq_SMARTER
S6_KO_0


title: WT8

description:
Library name: 10
microglia RNA isolated from Tmem119-Cre:RiboTag mice


title: Endometrial cells, P+7, 863

description: Library name: ERA210167


title: MuSCs,L2A-Pax7CreER, uninjured (0), rep1

description:
Library name: Sample_S5_KO_0__IgnacioRamirez_RNA_Seq_SMARTER
S5_KO_0


title: MuSCs,L2A-Pax7CreER, 1 dpi, rep1

description:
Library name: Sample_S13_KO_1__IgnacioRamirez_RNA_Seq_SMARTER
S13_KO_1


title: MuSCs,L2A-WT, uninjured (0), rep4

description:
Library name: Sample_S4_Wt_0__IgnacioRamirez_RNA_Seq_SMARTER
S4_Wt_0


title: Endometrial cells, P+5, 862

description: Library name: ERA210162


title: MuSCs,L2A-Pax7CreER, uninjured (0), rep3

description:
Library name: Sample_S7_KO_0__IgnacioRamirez_RNA_Seq_SMARTER
S7_KO_0


title: Endometrial cells, P+3, 861

description: Library name: ERA210103


title: MuSCs,L2A-WT, uninjured (0), rep2

description:
Library name: Sample_S2_Wt_0__IgnacioRamirez_RNA_Seq_SMARTER
S2_Wt_0


title: Endometrial cells, P+7, 860

description: Library name: ERA210148


title: MuSCs,L2A-WT, uninjured (0), rep3

description:
Library name: Sample_S3_Wt_0__IgnacioRamirez_RNA_Seq_SMARTER
S3_Wt_0


title: WT17

description:
Library name: 9
microglia RNA isolated from Tmem119-Cre:RiboTag mice


title: MuSCs, L2A-WT, uninjured (0), rep1

description:
Library name: Sample_S1_Wt_0__IgnacioRamirez_RNA_Seq_SMARTER
S1_Wt_0


title: MuSCs,L2A-WT, 1 dpi, rep1

description:
Library name: Sample_S9_Wt_1__IgnacioRamirez_RNA_Seq_SMARTER
S9_Wt_1


title: WT16

description:
Library name: 8
microglia RNA isolated from Tmem119-Cre:RiboTag mice


title: Endometrial cells, P+5, 859

description: Library name: ERA210156


title: CD8_TILs_WildType3

city: Tampa

first: Dongliang

last: Du

address: 111 Magnolia

institute: Moffitt

data_processing:
Sequenced reads were aligned to mm10 genome using STAR. Htseq_count was used for read count.
Assembly: mm10
Supplementary files format and content: tab-deliminited text file containing read count for each sample

source_name: B16F10 subcutaneous tumor

extract_protocol:
CD4+ and CD8+ tumor infiltrating T lynphocytes were isolated from B16F10 subcutaneuos tumors from WT and Sirt2KO mice (n = 4 per group). Total RNAs were extracted using the RNeasy Micro Kit (Qiagen; cat. #74004) according to the manufacturer’s instructions.
Extracted RNAs were quantitated with the Qubit Fluorometer (ThermoFisher Scientific, Waltham, MA) and screened for quality on the Agilent TapeStation 4200 using the high-sensitivity RNA ScreenTape (Agilent Technologies, Santa Clara, CA). The samples were then processed for RNA-sequencing using the Takara SMARTer Stranded Total RNA-seq Kit v2 Pico Input Mammalian kit (Takara Bio USA Inc., San Jose, CA). Briefly, one ng of RNA was used to generate cDNA and a strand-specific ribosomal RNA-depleted library following the manufacturer’s protocol. Quality control steps were performed, including TapeStation size assessment and quantification using the Kapa Library Quantification Kit (Roche, Wilmington, MA). The final libraries were then normalized, denatured, and sequenced on the Illumina NextSeq 2000 sequencer with the P3-200 cycle reagent kit to generate at least 60 million 100-base read pairs per sample (Illumina, Inc., San Diego, CA).

value: B16F10 subcutaneous tumor

value: Tumor infiltrating T lymphocytes

value: CD8 T cells

value: Wild type


title: Endometrial cells, P+3, 858

description: Library name: ERA210164

value: endometrium tissue


title: CD8_TILs_WildType1


title: CD8_TILs_Sirt2KO4


title: Endometrial cells, P+7, 857

description: Library name: ERA210145


title: WT13

description:
Library name: 6
microglia RNA isolated from Tmem119-Cre:RiboTag mice


title: CD8_TILs_Sirt2KO1


title: CD8_TILs_Sirt2KO3


title: cKO7

description:
Library name: 5
microglia RNA isolated from Tmem119-Cre:RiboTag mice

value: Kdm6a cKO


title: CD8_TILs_Sirt2KO2


title: CD4_TILs_WildType4

value: CD4 T cells


title: Endometrial cells, P+5, 856

description: Library name: ERA210146


title: Endometrial cells, P+3, 855

description: Library name: ERA210155


title: CD4_TILs_WildType3


title: cKO5

description:
Library name: 3
microglia RNA isolated from Tmem119-Cre:RiboTag mice


title: cKO4

description:
Library name: 2
microglia RNA isolated from Tmem119-Cre:RiboTag mice


title: CD4_TILs_WildType2


title: Endometrial cells, P+7, 854

description: Library name: ERA19A186


title: CD4_TILs_Sirt2KO3


title: CD4_TILs_WildType1


title: Endometrial cells, P+5, 853

description: Library name: ERA19A180


title: cKO2

description:
Library name: 1
microglia RNA isolated from Tmem119-Cre:RiboTag mice


title: CD4_TILs_Sirt2KO4


title: CD8_TILs_WildType2


title: CD4_TILs_Sirt2KO2


title: Endometrial cells, P+3, 852

description: Library name: ERA19A185


title: CD4_TILs_Sirt2KO1


title: WT15

description:
Library name: 7
microglia RNA isolated from Tmem119-Cre:RiboTag mice


title: cKO6

description:
Library name: 4
microglia RNA isolated from Tmem119-Cre:RiboTag mice


title: Endometrial cells, P+7, 851

description: Library name: ERA210132


title: BAP1KO_2

city: nicosia

first: PHILIPPOS

last: DEMETRIOU

state: nicosia

address: Nicandrou Papamina Avenue, 15, Strovolos

country: Cyprus

institute: THE CENTER FOR THE STUDY OF HEMATOLOGICAL AND OTHER MALIGNANCIES

description:
Library name: Sample 5
column name in All samples_counts.xls: BAP1KO_2

data_processing:
BlueBee Genomics Platform
Assembly: GRCh38
Supplementary files format and content: xls includes unique counts for each sample

source_name: cell line

extract_protocol:
Total RNA was extracted using the MagCore triXact RNA Kit (Cat.no. 631) as per manufacturer’s recommendations. 500ng max of total RNA was used for the construction of the libraries
Libraries were prepared from the extracted total RNA using the QuantSeq 3’mRNA-Seq V2 Library Prep Kit-FWD (Lexogen; 192.96)

value: cell line

value: Jurkat E6-1

value: immune cell

value: BAP1 knockout


title: Male Wild-type Mouse 1

city: Rostock

first: Robert

last: Jaster

address: Ernst-Heydemann-Str. 6

department: Dept. of Medicine, Div. of Gastroenterology

country: Germany

institute: Rostock University Medical Center

description: Library name: Bach2_WT_3_m

data_processing:
Data processing was performed by Novogene (Cambridge, UK).
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website. Use HISAT2 (2.2.1) to build the index of the reference genome, and use HISAT2 to align paired-end clean reads to the reference genome. HISAT2 can use the gene model annotation file to create splice-aware alignments, providing better alignment accuracy compared to other non-splice alignment tools.
FeatureCounts (2.0.6) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions was performed using the DESeq2Rpackage (1.42.0). The resulting P-values were adjusted using the Benjamini and Hochberg's approach for controlling the error discovery rate. The threshold of significant differential expression: padj <= 0.05 & |log2(foldchange)| >= 1
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts and fpkm for each sample
Supplementary files format and content: MS Excel file includes raw counts and fpkm for each sample

source_name: male, 18 weeks old

extract_protocol:
Total RNA was isolated from homogenized pancreatic tissue by the guanidinium thiocyanate/phenol method according to Sparmann et al. (Sparmann G, Jäschke A, Loehr M, Liebe S, Emmrich J. Tissue homogenization as a key step in extracting RNA from human and rat pancreatic tissue. Biotechniques 1997; 22(3):408-10, 412.). Total RNA was quantified by spectrophotometry (NanoDrop 1000, Thermo Fisher Scientific, Waltham, MA, United States), and their integrity was checked using the Agilent Bioanalyzer 2100 with an RNA Nano chip kit (Agilent Technologies, Waldbronn, Germany). Afterwards, the samples were transferred to Novogene (Cambridge, UK) for further processing.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: Pancreas

value: C57BL/6N-Bach2tm1b(EUCOMM)Wtsi/leg mice (EMMA ID EM:09104)

value: male

tag: age

value: 18 weeks


title: BAP1KO_3

description:
Library name: Sample 6
column name in All samples_counts.xls: BAP1KO_3


title: Female Wild-type Mouse 2

description: Library name: Bach2_WT_2_f

source_name: female, 18 weeks old

value: female


title: BAP1KO_1

description:
Library name: Sample 4
column name in All samples_counts.xls: BAP1KO_1


title: Endometrial cells, P+5, 850

description: Library name: ERA200315


title: Wildtype_1

description:
Library name: Sample 1
column name in All samples_counts.xls: WT_1


title: Wildtype_2

description:
Library name: Sample 2
column name in All samples_counts.xls: WT_2


title: Endometrial cells, P+3, 849

description: Library name: ERA200329


title: Wildtype_3

description:
Library name: Sample 3
column name in All samples_counts.xls: WT_3


title: Endometrial cells, P+7, 848

description: Library name: ERA200332


title: Endometrial cells, P+5, 847

description: Library name: ERA200308


title: UMSCC47 cells, radiation (4Gy, 24hr) 3

city: Cincinnati

first: Julianna

last: Korns

state: OH

address: 3100 Eden Avenue

institute: University of Cincinnati

description:
Library name: UMSCC47 Radiation 3
Column name in UMSCC47 Vehicle.Radiation.xlsx: radiation.3

data_processing:
The quality control of raw and aligned reads was performed using FastQC, RNA-SeQC, and summarized using MultQC software. Differentially expressed genes were identified based on the FDR-adjusted p-values obtained by fitting a generalized linear model based on negative-binomial distribution of read counts as implemented in the edgeR Bioconductor package. The functional characteristics of DEGs were studied by Gene Set Enrichment Analysis (GSEA) as implemented in the R package fgsea. Gene sets analyzed included hallmark gene sets in MSigDb.
Assembly: hg38
Supplementary files format and content: xlsx processed files include FPKM values for each replicate

growth_protocol: HN5 and UMSCC47 cells were cultured in DMEM containing 10% FBS, 1% sodium pyruvate, 1% non-essential amino acids, 1% L-glutamine, and 1% penicillin-streptomycin. Cells were maintained at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using a Qiagen RNA Isolation kit.
RNA libraries for RNA-seq were prepared using a NEBNext Ultra II Directional RNA Library Prep kit (New England BioLabs).

value: head and neck squamous cell carcinoma

value: radiation (4Gy, 24hr)


title: UMSCC47 cells, onvansertib and radiation 2

description:
Library name: UMSCC47 OnvRad 2
Column name in UMSCC47 Vehicle.OnvRad.xlsx: onvrad.2

value: onvansertib (25nM, 24hr) and radiation (4Gy, 24hr)


title: Male Knockout Mouse 2

description: Library name: Bach2_KO_4_m

value: knockout


title: UMSCC47 cells, radiation (4Gy, 24hr) 2

description:
Library name: UMSCC47 Radiation 2
Column name in UMSCC47 Vehicle.Radiation.xlsx: radiation.2


title: Endometrial cells, P+3, 846

description: Library name: ERA200313


title: Female Wild-type Mouse 1

description: Library name: Bach2_WT_1_f

value: wildtype


title: UMSCC47 cells, radiation (4Gy, 24hr) 1

description:
Library name: UMSCC47 Radiation 1
Column name in UMSCC47 Vehicle.Radiation.xlsx: radiation.1


title: Male Knockout Mouse 1

description: Library name: Bach2_KO_3_m


title: UMSCC47 cells, onvansertib and radiation 3

description:
Library name: UMSCC47 OnvRad 3
Column name in UMSCC47 Vehicle.OnvRad.xlsx: onvrad.3


title: UMSCC47 cells, onvansertib (25nM, 24hr) 3

description:
Library name: UMSCC47 Onvansertib 3
Column name in UMSCC47 Vehicle.Onvanserib.xlsx: onvansertib.3

value: onvnsertib (25nM, 24hr)


title: Female Knockout Mouse 2

description: Library name: Bach2_KO_2_f


title: Male Wild-type Mouse 2

description: Library name: Bach2_WT_4_m


title: Endometrial cells, P+7, 845

description: Library name: ERA200336

value: endometrium tissue


title: CD8_TILs_WildType4

value: B16F10 subcutaneous tumor

value: Tumor infiltrating T lymphocytes

value: CD8 T cells

value: Wild type


title: UMSCC47 cells, onvansertib and radiation 1

description:
Library name: UMSCC47 OnvRad 1
Column name in UMSCC47 Vehicle.OnvRad.xlsx: onvrad.1


title: UMSCC47 cells, onvansertib (25nM, 24hr) 2

description:
Library name: UMSCC47 Onvansertib 2
Column name in UMSCC47 Vehicle.Onvanserib.xlsx: onvansertib.2


title: Female Knockout Mouse 1

description: Library name: Bach2_KO_1_f


title: Endometrial cells, P+5, 844

description: Library name: ERA200324


title: UMSCC47 cells, onvansertib (25nM, 24hr) 1

description:
Library name: UMSCC47 Onvansertib 1
Column name in UMSCC47 Vehicle.Onvanserib.xlsx: onvansertib.1


title: UMSCC47 cells, vehicle 3

description:
Library name: UMSCC47 Vehicle 3
Column name in all processed data files: vehicle.3

value: vehicle


title: Met_EAE_6

description: microglia RNA isolated from Tmem119-Cre:RiboTag mice

extract_protocol:
RNAs were isolated using the Direct-zol™ RNA MiniPrep Plus kit (Zymo Research).
The RNA sequencing library was made using KAPA Stranded RNA-Seq Kit (Kapa Biosystems) which consists of mRNA enrichment, cDNA generation, end repair, A-tailing, adaptor ligation, strand selection, and PCR amplification.

value: spinal cord

value: microglia

value: WT

value: EAE

value: Metformin


title: UMSCC47 cells, vehicle 1

description:
Library name: UMSCC47 Vehicle 1
Column name in all processed data files: vehicle.1

value: head and neck squamous cell carcinoma


title: HN5 cells, onvansertib and radiation 3

description:
Library name: HN5 OnvRad 3
Column name in HN5 Vehicle.OnvRad.xlsx: onvrad.3


title: Met_EAE_5

value: female


title: UMSCC47 cells, vehicle 2

description:
Library name: UMSCC47 Vehicle 2
Column name in all processed data files: vehicle.2


title: Endometrial cells, P+7, 842

description: Library name: ERA0173


title: HN5 cells, onvansertib and radiation 2

description:
Library name: HN5 OnvRad 2
Column name in HN5 Vehicle.OnvRad.xlsx: onvrad.2

value: onvansertib (25nM, 24hr) and radiation (4Gy, 24hr)


title: HN5 cells, radiation (4Gy, 24hr) 3

description:
Library name: HN5 Radiation 3
Column name in HN5 Vehicle.Radiation.xlsx: radiation.3

value: radiation (4Gy, 24hr)


title: HN5 cells, onvansertib and radiation 1

description:
Library name: HN5 OnvRad 1
Column name in HN5 Vehicle.OnvRad.xlsx: onvrad.1


title: Met_EAE_21


title: HN5 cells, radiation (4Gy, 24hr) 2

description:
Library name: HN5 Radiation 2
Column name in HN5 Vehicle.Radiation.xlsx: radiation.2


title: Met_EAE_14


title: Endometrial cells, P+3, 840

description: Library name: ERA0165


title: HN5 cells, onvansertib (25nM, 24hr) 3

description:
Library name: HN5 Onvansertib 3
Column name in HN5 Vehicle.Onvanserib.xlsx: onvansertib.3


title: HN5 cells, radiation (4Gy, 24hr) 1

description:
Library name: HN5 Radiation 1
Column name in HN5 Vehicle.Radiation.xlsx: radiation.1


title: Met_EAE_13


title: Endometrial cells, P+5, 839

description: Library name: ERA0282


title: HN5 cells, onvansertib (25nM, 24hr) 2

description:
Library name: HN5 Onvansertib 2
Column name in HN5 Vehicle.Onvanserib.xlsx: onvansertib.2


title: HN5 cells, vehicle 3

description:
Library name: HN5 Vehicle 3
Column name in all processed data files: vehicle.3


title: HN5 cells, onvansertib (25nM, 24hr) 1

description:
Library name: HN5 Onvansertib 1
Column name in HN5 Vehicle.Onvanserib.xlsx: onvansertib.1


title: HN5 cells, vehicle 2

description:
Library name: HN5 Vehicle 2
Column name in all processed data files: vehicle.2


title: Endometrial cells, P+3, 838

description: Library name: ERA0224


title: Ctrl_Healthy_4

value: Healthy

value: Control


title: Endometrial cells,p7,126

description: Library name: ERA0126

value: endometrium tissue


title: HN5 cells, vehicle 1

description:
Library name: HN5 Vehicle 1
Column name in all processed data files: vehicle.1


title: Endometrial cells, P+3, 843

description: Library name: ERA200318


title: Ctrl_Healthy_3


title: Endometrial cells,p5,125

description: Library name: ERA0125


title: hTERT RPE-1 cells, XIST deletion, clone 2B4

city: Vancouver

first: Carolyn

last: Brown

address: 2350 Health Sciences Mall

country: Canada

institute: University of British Columbia

description:
Library name: XISTdel_2B4
XISTAC2B4

data_processing:
Fastq files were aligned to the hg38 genome using STAR 2.7.9a. Samtools 1.15.1 was used to obtain sorted bam files filtered for uniquely mapped reads.
Seqmonk 1.48.1 (Babraham Bioinformatics) was used to generate PCA plots, calculate reads per kilobase per million mapped reads (RPKM), and perform differential gene expression analysis with DEseq2. DEGs have a p < 0.05 after Benjamimi and Hochberg correction with the application of independent filtering. NCBI RefSeq gene track was used in Seqmonk.
Fastq files from GSE65830, GSE164595 and GSE192931 were downloaded from GEO and processed using the same bioinformatic protocol as our hTERT RPE-1 samples.
Allelic gene expression analysis was done by pooling fastq files of biological replicates and aligning them to hg38 masked at SNP sites that are reported to be heterozygous on chrX in hTERT RPE-1. Only uniquely mapped reads were used. Bcftools mpileup was used to perform read count at each SNP and generate a list of candidate genes with ≥ 10 reads (Xa + Xi) and ≥ 5 reads at each SNP. Allelic expression of candidate genes was confirmed by manual counting of reads overlapping the SNP sites on IGV.
Assembly: hg38
Supplementary files format and content: tab-delimited text file with RPKMs for each sample

source_name: hTERT RPE-1

growth_protocol: hTERT RPE-1 cells were cultured in DMEM/F-12 supplemented with 10% v/v fetal bovine serum with 5% CO2 at 37C.

extract_protocol:
RNA samples were extracted using RNAeasy plus kit (Qiagen) and sent to School of Biomedical Engineering sequencing core at UBC for quality control, library preps and sequencing.
Qualifying samples were prepped using Illumina Stranded mRNA prep with standard protocol. Paired-end equencing was performed on Illumina NextSeq2000 (59bp x 59bp reads), with a read depth of 30 million reads per sample.

treatment_protocol: hTERT RPE-1 cells were transfected using Lipofectamine 3000 reagent with equimolar amounts of the guide plasmid (pSPgRNA, Addgene #47108); the guide/Cas9 plasmid (pSpCas9(BB)-2A-Puro (PX459) V2.0, Addgene #62988); and the Cas9 plasmid with Neomycin selectable marker (pSpCas9(BB)-2A-Neo, Addgene #127762). The cells were treated with 750 ug/ml geneticin for 2 days approximately 18 hours after transfection.

value: hTERT RPE-1

value: female immortalized retinal pigmented epithelial cells

value: XIST KO

value: CRISPR-mediated XIST deletion


title: Ctrl_Healthy_20


title: hTERT RPE-1 cells, XIST deletion, clone 1B3

description:
Library name: XISTdel_1B3
XISTAC1B3


title: Endometrial cells, P+5, 841

description: Library name: ERA0167


title: Met_EAE_22


title: hTERT RPE-1 cells, XIST deletion, clone 2B2

description:
Library name: XISTdel_2B2
XISTAC2B2


title: hTERT RPE-1 cells, XIST deletion, clone 1A5

description:
Library name: XISTdel_1A5
XISTAC1A5


title: Ctrl_Healthy_19


title: Endometrial cells,p7,123

description: Library name: ERA0123


title: Ctrl_Healthy_12


title: hTERT RPE-1 cells, wild-type, biological replicate 1

description:
Library name: WT_rep1
WT1


title: hTERT RPE-1 cells, wild-type, biological replicate 2

description:
Library name: WT_rep2
WT2


title: Endometrial cells,p5,122

description: Library name: ERA0122


title: Ctrl_Healthy_11


title: D19 PPs, LN411, 24hr, Rep2

city: København N

first: Adam Kappel

last: Rump

address: Blegdamsvej 3

department: DanStem

country: Denmark

institute: University of Copenhagen

data_processing:
Reads were mapped using STAR v2.7.2d with the --quantMode GeneCounts option and gencode.v32 annotations.
Differential expression was analyzed using DESeq2_1.34.0.
Assembly: hg38
Supplementary files format and content: tab-delimited file containing results of differential expression analysis for all genes and time points (LN411 vs FN).

molecule: polyA RNA

growth_protocol: SA121-derived NGN3-GFP cells were differentiated into pancreatic progenitor cells (Day 19) following a previously established protocol (Ameri et al., Cell Reports, 2017)

extract_protocol:
RNA was harvested using the RNeasy micro kit (Qiagen).
Library was constructed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (Bionordika) and NEBNext Ultra II RNA Library Prep Kit for Illumina (Bionordika)

treatment_protocol: All samples were harvested using accutase and reseeded in wells of a 24-well plate pre-coated with indicated ECM and harvested at indicated time points.

value: ESC-derived pancreatic progenitor cells

tag: time point


title: hTERT RPE-1 cells, wild-type, biological replicate 3

description:
Library name: WT_rep3
WT3


title: D19 PPs, LN411, 24hr, Rep3


title: Ctrl_EAE_9

value: spinal cord


title: D19 PPs, LN411, 24hr, Rep1


title: D19 PPs, LN411, 6hr, Rep3


title: Endometrial cells,p7,120

description: Library name: ERA0120


title: D19 PPs, LN411, 6hr, Rep2


title: D19 PPs, LN411, 6hr, Rep1


title: Ctrl_EAE_2

value: microglia


title: Endometrial cells,p5,119

description: Library name: ERA0119


title: D19 PPs, LN411, 3hr, Rep3


title: Ctrl_EAE_17

value: WT


title: D19 PPs, LN411, 3hr, Rep1


title: Endometrial cells,p3,124

description: Library name: ERA0124


title: D19 PPs, FN, 24hr, Rep3

value: FN


title: Ctrl_EAE_18

value: EAE


title: Endometrial cells,p7,117

description: Library name: ERA0117


title: Endometrial cells,p3,118

description: Library name: ERA0118


title: D19 PPs, FN, 24hr, Rep1


title: Endometrial cells,p5,116

description: Library name: ERA0116


title: Ctrl_EAE_1


title: Endometrial cells,p3,121

description: Library name: ERA0121


title: Endometrial cells,p3,115

description: Library name: ERA0115


title: D19 PPs, FN, 6hr, Rep3


title: D19 PPs, FN, 6hr, Rep2


title: Foxj1+, 28dpi, rep1, GEX

city: Stockholm

first: Margherita

last: Zamboni

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

description: Library name: FT_U_28dpi_GEX

library_source: transcriptomic single cell

data_processing:
Raw reads from the Illumina sequencing runs were processed using cellranger-arc standard pipeline (v2.0.2, 10X Genomics), and mapped to the mm10 reference genome, which was supplemented with tdTomato DNA sequence to record expression of the fluorescent reporter in the transgenic line. Raw reads from the MGI sequencing runs were obtained in fastq format, with R2 and the indexes in a single R2 file. For demultiplexing, we first split the R2 file and reverse-complemented the index reads using a custom script, and then demultiplexed by sample using deML (v1.1.4). Subsequently, cellranger-arc count function was used to individually map fastq files of each sample to the reference genome. Following read alignment, we obtained gene expression matrices and fragment files for the transcriptomic and epigenomic modalities, respectively. These sets of data were first pre-processed and filtered separately, prior to integration for multimodal downstream analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated feature matrices

source_name: Spinal cord

extract_protocol:
Fresh spinal cords were microdissected and cleared of the meninges. We obtained 5 mm segments of tissue around the injury epicenter, or at the same rostrocaudal level in uninjured animals. Nuclei from WT mice were isolated with the Chromium Nuclei Isolation Kit (10X Genomics, PN-1000493). These were, subsequently, stained with fluorescently conjugated antibodies against NeuN (1:500) or Sox10 (1:200) for 1h on ice, and with 7AAD (1:50), prior to sorting on BD FACS Influx sorter with a 100 μm nozzle. We used the transgenic line Foxj1-tdTomato to enrich for ependymal cells.We  digested the tissue to obtain single cell suspensions. Briefly, we used papain as digestion enzyme and a GentleMacs Dissociator (Miltenyi) to triturate the samples according to specifications provided in the Miltenyi’s Adult Brain Dissociation protocol. Whole cells were, then, sorted based on expression of the fluorescent reporters and collected in sorting buffer containing 1% BSA for subsequent nuclei isolation (performed according to 10x protocol CG000124 Rev F).
Sequencing-ready libraries were prepared following the Chromium Next GEM Single Cell Multiome protocol (10X Genomics, CG000338 Rev F) and sequenced in an Illumina NextSeq or an MGI machine.

value: Spinal cord

value: tdTomato+


title: D19 PPs, FN, 3hr, Rep2


title: D19 PPs, FN, 3hr, Rep1


title: Endometrial cells,p5,114

description: Library name: ERA0114


title: D19 PPs, FN, 3hr, Rep3


title: Endometrial cells,p3,113

description: Library name: ERA0113


title: Hd-rR,non-feeding,8dph-6

city: SHizuoka-shi

first: Taijun

last: Myosho

state: Shizuoka-ken

country: Japan

institute: University of Shizuoka

description: myosho_312_FKDL230363916-1A_22CNYFLT3_L1

data_processing:
Only Read 1 reads were used to quantify gene expression. Read 1 reads were processed with fastp (version 0.21.0) (Chen et al., 2018) using the following parameters: trim_poly_x -w 20 --adapter_sequence = 5'-AGATCGGAAGAGCACACGTCTGAACTCCAGTCA-3' --adapter_sequence_r2 = 5'-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-3' -l 31. The trimmed reads were mapped to the medaka reference sequences of O. latipes (ASM223467v1.cdna.all.fa) using BWAmem (version 0.7.17-r1188) (Li and Durbin, 2009) with default parameters. The read count for each gene was calculated for salmon using l IU, specifying the library type (version v0.12.0) (Patro et al., 2017). The sum of the read counts per gene was calculated using R software (version 4.4.0) (R Core Team, 2017). Log2 reads per million (log2RPM) were calculated using the “NormalizeData” function in the Seurat (version 5.0.0) (Hao et al., 2024) package with default parameters, except for scale.factor = 106. Principal component analysis (PCA) was conducted using “ScaleData”, “FindVariableFeatures”, and “RunPCA” functions with default parameters. Based on the weights of each gene along PC1, the 100 genes with the largest absolute weights between normal and starved fish were selected.genes with the 100 largest absolute weights that exhibited differential expression between normal and starved fish were selected. Using biomaRt (version 2.56.1) (Durinck et al., 2009), and GO.db (version 3.17.0), Gene Ontology (GO) enrichment analysis of biological processes for the selected genes was conducted with the “fisher.test” and “p.adjust” functions using the following parameters: alternative = "less" and method = "fdr".
Assembly: the medaka reference sequences of O. latipes (ASM223467v1.cdna.all.fa)
Supplementary files format and content: excel files include raw counts and sanple information

organism: Oryzias latipes

source_name: Hd-rR

extract_protocol:
For RNA extraction, the fry were anesthetized by administering 0.1% 2-phenoxyethanol (ethylene glycol monophenyl ether; Fujifilm Wako, Tokyo, Japan) in dechlorinated water. The fry were stored in RNAlater reagent (Ambion, Austin, TX, USA) at 4 °C until RNA extraction. Whole-body specimens of the NIES-R and Hd-rR strains were used for total RNA extraction, performed using the NucleoSpin RNA kit (TaKaRa, Shiga, Japan) according to the manufacturer’s instructions.
RNA-Seq library preparation was conducted using the Lasy-Seq ver. 1.1 protocol (https://sites.google.com/view/lasy-seq/) (Kamitani et al., 2019; Kashima et al., 2020). Total RNA (180 ng) was reverse transcribed using an RT primer with an index and SuperScript IV reverse transcriptase (Thermo Fisher Scientific, Waltham, MA, USA). All RT mixtures were pooled and purified using an equal volume of KAPA HyperPure Beads (F. Hoffmann-La Roche, Ltd., Basel, Switzerland) following the manufacturer’s instructions. Second-strand synthesis was performed on the pooled samples using RNase H (5 U/μL, Enzymatics, Beverly, MA, USA) and DNA polymerase I (10 U/μL, Enzymatics, Beverly, MA, USA). To minimize carryover of large amounts of rRNAs, the mixture underwent RNase T1 treatment (Thermo Fisher Scientific, Waltham, MA, USA). Purification was conducted with a 0.8× volume of KAPA HyperPure Beads. Fragmentation, end-repair, and A-tailing were performed using 5× WGS Fragmentation Mix (Enzymatics, Beverly, MA, USA). The adapter for Lasy-Seq was ligated using 5× Ligation Mix (Enzymatics, Beverly, MA, USA), and the adapter-ligated DNA was purified twice with 0.8× volume of KAPA HyperPure Beads. After optimizing the PCR cycles for library amplification via qPCR using EvaGreen (20× in water; Biotium, Fremont, CA, USA) and the AriaMx Real-Time PCR System (Agilent Technologies, Santa Clara, CA, USA), the library was amplified using KAPA HiFi HotStart ReadyMix (F. Hoffmann-La Roche, Ltd., Basel, Switzerland) on a MiniAmp Thermal Cycler (Applied Biosystems, Waltham, MA, USA). The amplified library was purified using equal volumes of KAPA HyperPure Beads. Subsequently, 1 μL of the library was electrophoresed using a Bioanalyzer 2100 with an Agilent High Sensitivity DNA kit (Agilent Technologies, Santa Clara, CA, USA) to assess quality. Sequencing of 150-bp paired-end reads was performed using NovaSeq X Plus (Illumina, San Diego, CA, USA).

value: Hd-rR

tag: developmental stage

value: 8 dph

value: non-feeding


title: Hd-rR,non-feeding,8dph-4

description: myosho_310_FKDL230363916-1A_22CNYFLT3_L1


title: Foxj1+, 1dpi, rep1, GEX

description: Library name: FT_1dpi_1_GEX


title: Hd-rR,non-feeding,8dph-5

description: myosho_311_FKDL230363916-1A_22CNYFLT3_L1


title: Endometrial cells,p7,112

description: Library name: ERA0112


title: D19 PPs, FN, 24hr, Rep2


title: Ctrl_EAE_10

description: microglia RNA isolated from Tmem119-Cre:RiboTag mice

value: female

value: Control


title: Endometrial cells,p5,111

description: Library name: ERA0111

value: endometrium tissue


title: NeuN-/Sox10-, 28dpi, rep1, GEX

description: Library name: DEPL_28dpi_1_GEX


title: Foxj1+, Uninjured, rep1, GEX

description: Library name: FT_U_1_GEX


title: Hd-rR,non-feeding,8dph-1

description: myosho_307_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,non-feeding,8dph-2

description: myosho_308_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,non-feeding,8dph-3

description: myosho_309_FKDL230363916-1A_22CNYFLT3_L1


title: Endometrial cells,p3,110

description: Library name: ERA0110


title: Hd-rR,non-feeding,6dph-6

description: myosho_306_FKDL230363916-1A_22CNYFLT3_L1

value: 6 dph


title: D19 PPs, FN, 6hr, Rep1


title: NeuN-/Sox10-, 7dpi, rep1, GEX

description: Library name: DEPL_7dpi_1_GEX


title: Hd-rR,non-feeding,6dph-5

description: myosho_305_FKDL230363916-1A_22CNYFLT3_L1


title: D19 PPs, LN411, 3hr, Rep2


title: Input.Dex24h.0

city: Basel

first: Mohamed

last: Bentires-Alj

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

description:
Library name: sample17
InputDex24h_S18

data_processing:
Paired-end reads were aligned to the UCSC hg38 genome using bowtie2, version 2.4.2, with parameters “--maxins 2000” (the maximum fragment length for valid paired-end alignments), “--no-mixed, --no-discordant, --local” (allowing for only paired, concordant and local alignments). Duplicate reads were marked using MarkDuplicates from Picard, version 3.0.0., The resulting BAM files were sorted and indexed with samtools version 1.20., and used for peak calling with macs2, version 2.2.9.1. The parameters “—nomodel, —shift 0, —keep-dup all, —format BAMPE” were used. The qvalue cutoff of significant enrichment of the signal above control sample was 0.05. All “—treatment” samples were analysed by macs2 together in one run. The list of called peaks was cleaned from those identified in mitochondria, chrX and chrY, and ENCODE blacklist regions. The subsequent analysis was performed in R. Detected peaks were further filtered according to their enrichement above the signal from the input samples and only peaks with log-enrichment higher than 2 in at least one sample were kept. Altogether, 20,280 peaks were identified.
Assembly: hg38
Supplementary files format and content: bed files with genomic locations of the called peaks per group
Supplementary files format and content: raw_counts_ChIPseq.csv: raw counts in called peaks across the data set, feature_annotation_ChIPseq.csv: annotation of the peaks

growth_protocol: 2.5% Charcoal stripped FCS, phenol red free DMEM medium (Gibco)

extract_protocol:
Cells were wash with ice-cold PBS (2x), Fixed in FA 1.5% for 10 min. Tris-Glycine buffer was added for 1 minute and cells were washed ice cold PBS (2x). Cells were lysed and sonicated (Diagenode bioruptor) in order to get DNA fragments of 300-800pb. IP was performed overnight using anti-GR or ER antibodies, in IP buffer, ytRNA and from 15 ug of chromatin quantified by Qubit. Protein-A coated magnetic beads were added the next day for 4 h. Pulled-down DNA was washed multiple times, extracted in SDS based buffer and incubated at 65°C for reverse crosslinking. DNA was treated with RNase A and proteinase K, and purified using Zymo ChIP DNA Clean & Concentrator kit. DNA concentration was assessed using Qubit.
NEBNext Ultra II DNA #E7645S kit

treatment_protocol: Dexamethasone (700 nM) or vehicle, for 1h or 24h

value: breast cancer cell line

value: Dexamethasone


title: Hd-rR,non-feeding,6dph-3

description: myosho_303_FKDL230363916-1A_22CNYFLT3_L1


title: Foxj1+, 7dpi, rep1, GEX

description: Library name: FT_7dpi_1_GEX


title: NeuN-/Sox10-, 1dpi, rep1, GEX

description: Library name: DEPL_1dpi_1_GEX


title: Hd-rR,non-feeding,6dph-2

description: myosho_302_FKDL230363916-1A_22CNYFLT3_L1


title: Input.Dex1h.0

description:
Library name: sample16
InputDex1h_S17


title: Input.ctr.0

description:
Library name: sample15
Inputcontrol_S16

value: Vehicle


title: Hd-rR,non-feeding,4dph-6

description: myosho_296_FKDL230363916-1A_22CNYFLT3_L1

value: 4 dph


title: Hd-rR,non-feeding,6dph-1

description: myosho_301_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,non-feeding,4dph-5

description: myosho_295_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,non-feeding,4dph-4

description: myosho_294_FKDL230363916-1A_22CNYFLT3_L1


title: Unsorted, 3dpi, rep1, GEX

description: Library name: 3dpi_1_GEX


title: Hd-rR,non-feeding,4dph-3

description: myosho_293_FKDL230363916-1A_22CNYFLT3_L1


title: GR.Dex1h.3

description:
Library name: sample13
bed files of called peaks, counts in peaks and peak annotation
GRDex1hrep3_S14
GR.Dex1h_filtered.bed


title: NeuN-/Sox10-, Uninjured, rep1, GEX

description: Library name: DEPL_U_1_GEX


title: ER.Dex24h.3

description:
Library name: sample14
bed files of called peaks, counts in peaks and peak annotation
ERDex24hrep3_S15
ER.Dex24h_filtered.bed


title: NeuN-/Sox10-, 3dpi, rep1, GEX

description: Library name: DEPL_3dpi_1_GEX


title: Hd-rR,non-feeding,2dph-5

description: myosho_289_FKDL230363916-1A_22CNYFLT3_L1

value: 2 dph


title: ER.Dex1h.3

description:
Library name: sample12
bed files of called peaks, counts in peaks and peak annotation
ERDex1hrep3_S13
ER.Dex1h_filtered.bed


title: Hd-rR,non-feeding,6dph-4

description: myosho_304_FKDL230363916-1A_22CNYFLT3_L1


title: GR.ctr.3

description:
Library name: sample11
bed files of called peaks, counts in peaks and peak annotation
GRControlrep3_S12
GR.ctr_filtered.bed


title: Hd-rR,non-feeding,2dph-4

description: myosho_288_FKDL230363916-1A_22CNYFLT3_L1


title: Foxj1+, 1dpi, rep1, ATAC

description: Library name: FT_1dpi_1_ATAC

library_source: genomic single cell


title: Foxj1+, 28dpi, rep1, ATAC

description: Library name: FT_U_28dpi_ATAC


title: ER.ctr.3

description:
Library name: sample10
bed files of called peaks, counts in peaks and peak annotation
ERControlrep3_S11
ER.ctr_filtered.bed


title: Foxj1+, Uninjured, rep1, ATAC

description: Library name: FT_U_1_ATAC


title: Hd-rR,non-feeding,2dph-3

description: myosho_287_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,non-feeding,2dph-6

description: myosho_290_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,non-feeding,2dph-1

description: myosho_285_FKDL230363916-1A_22CNYFLT3_L1


title: ER.Dex24h.2

description:
Library name: sample9
bed files of called peaks, counts in peaks and peak annotation
ERDex24hrep2_S10
ER.Dex24h_filtered.bed


title: Hd-rR,feeding,8dph-6

description: myosho_284_FKDL230363916-1A_22CNYFLT3_L1

value: feeding


title: GR.Dex1h.2

description:
Library name: sample8
bed files of called peaks, counts in peaks and peak annotation
GRDex1hrep2_S9
GR.Dex1h_filtered.bed


title: NeuN-/Sox10-, 28dpi, rep1, ATAC

description: Library name: DEPL_28dpi_1_ATAC

value: WT


title: Hd-rR,non-feeding,4dph-2

description: myosho_292_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,feeding,8dph-5

description: myosho_283_FKDL230363916-1A_22CNYFLT3_L1


title: NeuN-/Sox10-, 7dpi, rep1, ATAC

description: Library name: DEPL_7dpi_1_ATAC


title: Hd-rR,feeding,8dph-1

description: myosho_279_FKDL230363916-1A_22CNYFLT3_L1


title: ER.Dex1h.2

description:
Library name: sample7
bed files of called peaks, counts in peaks and peak annotation
ERDex1hrep2_S8
ER.Dex1h_filtered.bed


title: Hd-rR,non-feeding,4dph-1

description: myosho_291_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,feeding,8dph-3

description: myosho_281_FKDL230363916-1A_22CNYFLT3_L1


title: Foxj1+, 7dpi, rep1, ATAC

description: Library name: FT_7dpi_1_ATAC


title: NeuN-/Sox10-, 3dpi, rep1, ATAC

description: Library name: DEPL_3dpi_1_ATAC


title: Hd-rR,feeding,8dph-2

description: myosho_280_FKDL230363916-1A_22CNYFLT3_L1


title: GR.ctr.2

description:
Library name: sample6
bed files of called peaks, counts in peaks and peak annotation
GRControlrep2_S7
GR.ctr_filtered.bed


title: Hd-rR,feeding,6dph-4

description: myosho_276_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,non-feeding,2dph-2

description: myosho_286_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,feeding,6dph-6

description: myosho_278_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,feeding,6dph-5

description: myosho_277_FKDL230363916-1A_22CNYFLT3_L1


title: ER.ctr.2

description:
Library name: sample5
bed files of called peaks, counts in peaks and peak annotation
ERControlrep2_S6
ER.ctr_filtered.bed


title: NeuN-/Sox10-, Uninjured, rep1, ATAC

description: Library name: DEPL_U_1_ATAC


title: Hd-rR,feeding,6dph-2

description: myosho_274_FKDL230363916-1A_22CNYFLT3_L1


title: GR.Dex1h.1

description:
Library name: sample4
bed files of called peaks, counts in peaks and peak annotation
GRDex1hrep1_S4
GR.Dex1h_filtered.bed


title: Hd-rR,feeding,6dph-3

description: myosho_275_FKDL230363916-1A_22CNYFLT3_L1


title: Unsorted, 3dpi, rep1, ATAC

description: Library name: 3dpi_1_ATAC


title: Hd-rR,feeding,6dph-1

description: myosho_273_FKDL230363916-1A_22CNYFLT3_L1


title: ER.Dex1h.1

description:
Library name: sample3
bed files of called peaks, counts in peaks and peak annotation
ERDex1hrep1_S3
ER.Dex1h_filtered.bed


title: Hd-rR,feeding,4dph-5

description: myosho_271_FKDL230363916-1A_22CNYFLT3_L1


title: Cut&Tag, SOX9, 1dpi, F

description:
Library name: SOX9_1dpi_f
Ad2.14

data_processing:
Raw reads were obtained in fastq format, with R2 and the indexes in a single R2 file. For demultiplexing, we first split the R2 file and reverse-complemented the index reads using a custom script, and then demultiplexed by sample using deML (v1.1.4). Subsequently, samples were mapped to the reference genome with bowtie2 (2.5.4). Duplicates were removed with picard (3.4.0) and peak called using SEACR (1.3).
Assembly: mm10
Supplementary files format and content: Fragment files
Library strategy: CUT&Tag

extract_protocol:
Spinal cords were microdissected and cleared of the meninges. We obtained 5 mm segments of tissue around the injury epicenter, or at the same rostrocaudal level in uninjured animals. Nuclei from WT mice were isolated with the Chromium Nuclei Isolation Kit (10X Genomics, PN-1000493) and sorted on BD FACS Influx sorter with a 100 μm nozzle, based on 7AAD (1h on ice, 1:50) staining.
A total of 150,000 nuclei from each sample were used to perform CUT&Tag. Nuclei were incubated overnight at 4°C with Sox9 antibody (1:100 dilution; Sigma AB5535) in antibody buffer. 20% of the nuclei per sample were set aside as secondary-only controls and underwent all other steps in parallel. After washing, nuclei were incubated for 1 hour with guinea pig anti-rabbit secondary antibody (1:50 dilution; Novus Biologicals, NBP1-72763) in dig-wash buffer. After washing, samples were incubated with loaded pA-Tn5 transposase (1:100 dilution; C01070001) and subsequently tagmented for 1 hour at 37°C. After the reaction was stopped, DNA was purified using MinElute Reaction cleanup kit (Qiagen 28204) and directly used for PCR amplification and indexing for 15 cycles using NEBnext High Fidelity master mix (NEB, M0541). Samples were then sequenced on an MGI G99 sequencer using paired-end reads according to manufacturer’s protocols.


title: Hd-rR,feeding,4dph-6

description: myosho_272_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,feeding,8dph-4

description: myosho_282_FKDL230363916-1A_22CNYFLT3_L1


title: GR.ctr.1

description:
Library name: sample2
bed files of called peaks, counts in peaks and peak annotation
GRControlrep1_S2
GR.ctr_filtered.bed


title: Cut&Tag, SOX9, 1dpi, M

description:
Library name: SOX9_1dpi_m
Ad2.13

value: male


title: Hd-rR,feeding,4dph-4

description: myosho_270_FKDL230363916-1A_22CNYFLT3_L1


title: Cut&Tag, SOX9, Uninjured, F

description:
Library name: SOX9_U_f
Ad2.11

value: Spinal cord


title: ER.ctr.1

description:
Library name: sample1
bed files of called peaks, counts in peaks and peak annotation
ERControlrep1_S1
ER.ctr_filtered.bed


title: Hd-rR,feeding,4dph-1

description: myosho_267_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,feeding,4dph-2

description: myosho_268_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,feeding,2dph-6

description: myosho_266_FKDL230363916-1A_22CNYFLT3_L1


title: NeuN-/Sox10-, 1dpi, rep1, ATAC

description: Library name: DEPL_1dpi_1_ATAC


title: Cut&Tag, SOX9, Uninjured, M

description:
Library name: SOX9_U_m
Ad2.10


title: Hd-rR,feeding,2dph-5

description: myosho_265_FKDL230363916-1A_22CNYFLT3_L1


title: Y537S_Ctr_24h.3

description:
Library name: sample23
raw gene counts and separate gene annotation file
Y537SCTRL24h4_S23

data_processing:
Reads were aligned to the human genome (UCSC version hg38AnalysisSet) with STAR, version 2.7.11, using the multi-map settings outFilterMultimapNmax = 10 (maximal number of multiple alignments allowed for a read) and outSAMmultNmax = 1 (maximal number of SAM lines for each mapped read). The output was sorted and indexed with SAMtools, version 1.11. Duplicate reads were marked using MarkDuplicates from Picard, version 3.0.0. Strand-specific coverage tracks per sample were generated by tiling the genome in 20-bp windows and counting overlapping reads in each window using the bamCount function from the Bioconductor package bamsignals (Bioconductor version 3.18). The rsubread::featureCounts function was used to count the number of reads (5'ends) overlapping with the exons of each gene assuming an exon union model
Assembly: hg38
Supplementary files format and content: raw_counts_RNAseq.csv contains raw count per gene (rows) and sample (columns)
Supplementary files format and content: feature_annotation_RNAseq.csv contains gene annotation

extract_protocol:
Qiagen Rneasy Mini Kit for RNA extraction
Illumina TruSeq Stranded mRNA Library Preparation Kit

treatment_protocol: Dexamethasone (700 nM) or vehicle, for 8h or 24h


title: Y537S_Dex_24h.3

description:
Library name: sample24
raw gene counts and separate gene annotation file
Y537SDEX24h4_S24


title: Y537S_Dex_8h.3

description:
Library name: sample22
raw gene counts and separate gene annotation file
Y537SDEX8h4_S22


title: Hd-rR,feeding,2dph-4

description: myosho_264_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,feeding,2dph-3

description: myosho_263_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,feeding,2dph-2

description: myosho_262_FKDL230363916-1A_22CNYFLT3_L1


title: Cut&Tag, Control, 1dpi, M

description:
Library name: CTRL_1dpi_m
Ad2.7


title: Y537S_Ctr_8h.3

description:
Library name: sample21
raw gene counts and separate gene annotation file
Y537SCTRL8h4_S21


title: Hd-rR,feeding,0dph-6

description: myosho_260_FKDL230363916-1A_22CNYFLT3_L1

value: 0 dph


title: Hd-rR,feeding,2dph-1

description: myosho_261_FKDL230363916-1A_22CNYFLT3_L1

value: Hd-rR


title: Cut&Tag, Control, 1dpi, F

description:
Library name: CTRL_1dpi_f
Ad2.9


title: Cut&Tag, Control, Uninjured, F

description:
Library name: CTRL_U_f
Ad2.3


title: Hd-rR,feeding,0dph-5

description: myosho_259_FKDL230363916-1A_22CNYFLT3_L1


title: Hd-rR,feeding,4dph-3

description: myosho_269_FKDL230363916-1A_22CNYFLT3_L1


title: Cut&Tag, Control, Uninjured, M

description:
Library name: CTRL_U_m
Ad2.2


title: Hd-rR,feeding,0dph-3

description: myosho_257_FKDL230363916-1A_22CNYFLT3_L1


title: Y537S_Ctr_24h.2

description:
Library name: sample19
raw gene counts and separate gene annotation file
Y537SCTRL24h2_S19


title: Hd-rR,feeding,0dph-1

description: myosho_255_FKDL230363916-1A_22CNYFLT3_L1


title: Y537S_Dex_8h.2

description:
Library name: sample18
raw gene counts and separate gene annotation file
Y537SDEX8h2_S18


title: A. cahirinus skin, DMBA/TPA treated, R3

city: Rochester

first: Francesco

last: Morandini

state: NY

address: 402 Hutchison Hall

institute: University of Rochester

description:
Library name: AcoDT3
counts_aco_dt.tsv

data_processing:
Trimming: TrimGalore!
Alignment:Hisat2
Counting: featureCounts
Assembly: Mouse: GRCm39, Acomys: https://doi.org/10.5281/zenodo.7761277
Supplementary files format and content: csv files with unnormalized counts

organism: Acomys cahirinus

source_name: Skin

extract_protocol:
Purelink RNA extraction kit, according to manufacturer instructions
Stranded mRNA library

value: Skin

value: DMBA/TPA


title: Y537S_Ctr_8h.2

description:
Library name: sample17
raw gene counts and separate gene annotation file
Y537SCTRL8h2_S17


title: A. cahirinus skin, DMBA/TPA treated, R4

description:
Library name: AcoDT4
counts_aco_dt.tsv


title: NIES-R,non-feeding,8dph-5

description: myosho_253_FKDL230363916-1A_22CNYFLT3_L1

source_name: NIES-R

value: NIES-R

value: 8 dph

value: non-feeding


title: NIES-R,non-feeding,8dph-6

description: myosho_254_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,non-feeding,8dph-4

description: myosho_252_FKDL230363916-1A_22CNYFLT3_L1


title: Y537S_Dex_24h.1

description:
Library name: sample16
raw gene counts and separate gene annotation file
Y537SDEX24h1_S16


title: NIES-R,non-feeding,8dph-3

description: myosho_251_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,non-feeding,8dph-2

description: myosho_250_FKDL230363916-1A_22CNYFLT3_L1


title: A. cahirinus skin, DMBA/TPA treated, R1

description:
Library name: AcoDT1
counts_aco_dt.tsv


title: NIES-R,non-feeding,8dph-1

description: myosho_249_FKDL230363916-1A_22CNYFLT3_L1


title: Y537S_Ctr_24h.1

description:
Library name: sample15
raw gene counts and separate gene annotation file
Y537SCTRL24h1_S15


title: A. cahirinus skin, DMBA/TPA treated, R2

description:
Library name: AcoDT2
counts_aco_dt.tsv


title: NIES-R,non-feeding,6dph-6

description: myosho_248_FKDL230363916-1A_22CNYFLT3_L1

value: 6 dph


title: Y537S_Dex_24h.2

description:
Library name: sample20
raw gene counts and separate gene annotation file
Y537SDEX24h2_S20

value: breast cancer cell line


title: NIES-R,non-feeding,6dph-5

description: myosho_247_FKDL230363916-1A_22CNYFLT3_L1


title: A. cahirinus skin, untreated, R3

description:
Library name: AcoCtrl3
counts_aco_dt.tsv

value: Untreated


title: Hd-rR,feeding,0dph-4

description: myosho_258_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,non-feeding,6dph-4

description: myosho_246_FKDL230363916-1A_22CNYFLT3_L1


title: Y537S_Dex_8h.1

description:
Library name: sample14
raw gene counts and separate gene annotation file
Y537SDEX8h1_S14

value: Dexamethasone


title: Hd-rR,feeding,0dph-2

description: myosho_256_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,non-feeding,6dph-2

description: myosho_244_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,non-feeding,6dph-3

description: myosho_245_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,non-feeding,6dph-1

description: myosho_243_FKDL230363916-1A_22CNYFLT3_L1


title: Y537S_Ctr_8h.1

description:
Library name: sample13
raw gene counts and separate gene annotation file
Y537SCTRL8h1_S13

value: Vehicle


title: A. cahirinus skin, untreated, R2

description:
Library name: AcoCtrl2
counts_aco_dt.tsv


title: NIES-R,non-feeding,4dph-6

description: myosho_242_FKDL230363916-1A_22CNYFLT3_L1

value: 4 dph


title: D538G_Dex_24h.3

description:
Library name: sample12
raw gene counts and separate gene annotation file
D538GDEX24h4_S12


title: NIES-R,non-feeding,4dph-5

description: myosho_241_FKDL230363916-1A_22CNYFLT3_L1


title: D538G_Ctr_24h.3

description:
Library name: sample11
raw gene counts and separate gene annotation file
D538GCTRL24h4_S11


title: NIES-R,non-feeding,4dph-4

description: myosho_240_FKDL230363916-1A_22CNYFLT3_L1


title: A. cahirinus skin, untreated, R1

description:
Library name: AcoCtrl1
counts_aco_dt.tsv


title: NIES-R,non-feeding,4dph-3

description: myosho_239_FKDL230363916-1A_22CNYFLT3_L1


title: A. cahirinus fibroblasts, 20 gy, 12d, R4

description:
Library name: ACO_12d_ASM11_20Gy
counts_aco_irrad.tsv

source_name: Primary skin fibroblasts

value: Primary skin fibroblasts

value: 20 gy

tag: timepoint


title: D538G_Dex_8h.3

description:
Library name: sample10
raw gene counts and separate gene annotation file
D538GDEX8h4_S10


title: NIES-R,non-feeding,4dph-2

description: myosho_238_FKDL230363916-1A_22CNYFLT3_L1


title: A. cahirinus fibroblasts, 10 gy, 12d, R4

description:
Library name: ACO_12d_ASM11_10Gy
counts_aco_irrad.tsv

value: 10 gy


title: NIES-R,non-feeding,4dph-1

description: myosho_237_FKDL230363916-1A_22CNYFLT3_L1


title: A. cahirinus fibroblasts, untreated, 12d, R4

description:
Library name: ACO_12d_ASM11_Con
counts_aco_irrad.tsv


title: A. cahirinus skin, untreated, R4

description:
Library name: AcoCtrl4
counts_aco_dt.tsv


title: NIES-R,non-feeding,2dph-6

description: myosho_236_FKDL230363916-1A_22CNYFLT3_L1

value: 2 dph


title: NIES-R,non-feeding,2dph-5

description: myosho_235_FKDL230363916-1A_22CNYFLT3_L1


title: D538G_Ctr_8h.3

description:
Library name: sample9
raw gene counts and separate gene annotation file
D538GCTRL8h4_S9


title: D538G_Dex_24h.2

description:
Library name: sample8
raw gene counts and separate gene annotation file
D538GDEX24h3_S8


title: A. cahirinus fibroblasts, untreated passaged, 12d, R4

description:
Library name: ACO_12d_ASM11_ConP
counts_aco_irrad.tsv

value: Untreated passaged


title: NIES-R,non-feeding,2dph-3

description: myosho_233_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,non-feeding,2dph-2

description: myosho_232_FKDL230363916-1A_22CNYFLT3_L1


title: A. cahirinus fibroblasts, 20 gy, 12d, R3

description:
Library name: ACO_12d_ASM10_20Gy
counts_aco_irrad.tsv


title: NIES-R,non-feeding,2dph-1

description: myosho_231_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,non-feeding,2dph-4

description: myosho_234_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,feeding,8dph-6

description: myosho_230_FKDL230363916-1A_22CNYFLT3_L1

value: feeding


title: NIES-R,feeding,8dph-5

description: myosho_229_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,feeding,8dph-4

description: myosho_228_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,feeding,8dph-3

description: myosho_227_FKDL230363916-1A_22CNYFLT3_L1


title: D538G_Dex_8h.2

description:
Library name: sample6
raw gene counts and separate gene annotation file
D538GDEX8h3_S6


title: A. cahirinus fibroblasts, untreated passaged, 12d, R3

description:
Library name: ACO_12d_ASM10_ConP
counts_aco_irrad.tsv


title: D538G_Ctr_8h.2

description:
Library name: sample5
raw gene counts and separate gene annotation file
D538GCTRL8h3_S5


title: NIES-R,feeding,8dph-2

description: myosho_226_FKDL230363916-1A_22CNYFLT3_L1


title: A. cahirinus fibroblasts, 10 gy, 12d, R3

description:
Library name: ACO_12d_ASM10_10Gy
counts_aco_irrad.tsv


title: A. cahirinus fibroblasts, untreated, 12d, R3

description:
Library name: ACO_12d_ASM10_Con
counts_aco_irrad.tsv


title: D538G_Ctr_24h.1

description:
Library name: sample3
raw gene counts and separate gene annotation file
D538GCTRL24h2_S3


title: NIES-R,feeding,8dph-1

description: myosho_225_FKDL230363916-1A_22CNYFLT3_L1


title: D538G_Dex_24h.1

description:
Library name: sample4
raw gene counts and separate gene annotation file
D538GDEX24h2_S4


title: NIES-R,feeding,6dph-5

description: myosho_223_FKDL230363916-1A_22CNYFLT3_L1


title: D538G_Dex_8h.1

description:
Library name: sample2
raw gene counts and separate gene annotation file
D538GDEX8h2_S2


title: NIES-R,feeding,6dph-4

description: myosho_222_FKDL230363916-1A_22CNYFLT3_L1


title: A. cahirinus fibroblasts, 20 gy, 12d, R2

description:
Library name: ACO_12d_ASM9_20Gy
counts_aco_irrad.tsv


title: NIES-R,feeding,6dph-3

description: myosho_221_FKDL230363916-1A_22CNYFLT3_L1


title: A. cahirinus fibroblasts, 10 gy, 12d, R2

description:
Library name: ACO_12d_ASM9_10Gy
counts_aco_irrad.tsv


title: D538G_Ctr_8h.1

description:
Library name: sample1
raw gene counts and separate gene annotation file
D538GCTRL8h2_S1


title: D538G_Ctr_24h.2

description:
Library name: sample7
raw gene counts and separate gene annotation file
D538GCTRL24h3_S7


title: A. cahirinus fibroblasts, untreated, 12d, R2

description:
Library name: ACO_12d_ASM9_Con
counts_aco_irrad.tsv


title: CRC17 RNA

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

country: Netherlands

institute: AUMC

data_processing:
Adapter sequences were removed using cutadapt
Trimmed sequences were mapped to the human genome (GRCh38) with STAR 2.7.10a using GENCODE v43
Gene counts were determined during the STAR mapping procedure with the ‘–quantMode GeneCounts’ setting
Gene counts were normalised to log2 transformed TPM values.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: Primary Tumor

extract_protocol:
SEC with the Automated Fraction Collector (AFC-V1, Izon) was performed to isolate vesicles from 2-3 ml of plasma of each patient using 2 qEV original / 70 nm gen 2 columns (IZON) per plasma sample. Using a buffer volume of 2.70 ml, and a fraction volume of 0.5 ml, the particles of interest were collected in fractions 3 and 4 (between 1 and 2 ml of the Purified Collection Volume (PCV)). Both fractions of the 2 isolations were pooled, resulting in a volume of 2 ml per plasma. 1 ml of the vesicle isolate was concentrated with an Amicon Ultra-2 Centrifugal Filter Unit (Millipore) to 250 µl. Total RNA from the EVs was isolated using the miRNeasy serum/plasma kit (QIAgen) according to the manufacturers' protocol with minor adjustments.
mRNA libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara Bio Inc.) according to the manufacturers' protocol, including ribosomal cDNA depletion

tag: disease state

value: CRC

value: Primary Tumor


title: NIES-R,feeding,6dph-2

description: myosho_220_FKDL230363916-1A_22CNYFLT3_L1

value: NIES-R


title: NIES-R,feeding,6dph-1

description: myosho_219_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,feeding,4dph-6

description: myosho_218_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,feeding,4dph-5

description: myosho_217_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,feeding,4dph-4

description: myosho_216_FKDL230363916-1A_22CNYFLT3_L1


title: A. cahirinus fibroblasts, 20 gy, 12d, R1

description:
Library name: ACO_12d_ASM8_20Gy
counts_aco_irrad.tsv


title: NIES-R,feeding,6dph-6

description: myosho_224_FKDL230363916-1A_22CNYFLT3_L1


title: CRC14 RNA


title: A. cahirinus fibroblasts, 10 gy, 12d, R1

description:
Library name: ACO_12d_ASM8_10Gy
counts_aco_irrad.tsv


title: NIES-R,feeding,4dph-2

description: myosho_214_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,feeding,2dph-6

description: myosho_212_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,feeding,4dph-1

description: myosho_213_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,feeding,4dph-3

description: myosho_215_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,feeding,2dph-5

description: myosho_211_FKDL230363916-1A_22CNYFLT3_L1


title: CRC13 RNA


title: NIES-R,feeding,2dph-4

description: myosho_210_FKDL230363916-1A_22CNYFLT3_L1


title: A. cahirinus fibroblasts, untreated passaged, 12d, R1

description:
Library name: ACO_12d_ASM8_ConP
counts_aco_irrad.tsv


title: A. cahirinus fibroblasts, untreated, 12d, R1

description:
Library name: ACO_12d_ASM8_Con
counts_aco_irrad.tsv


title: NIES-R,feeding,2dph-2

description: myosho_208_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,feeding,2dph-3

description: myosho_209_FKDL230363916-1A_22CNYFLT3_L1


title: A. cahirinus fibroblasts, 20 gy, 24h, R4

description:
Library name: ACO_24h_ASM11_20Gy
counts_aco_irrad.tsv


title: NIES-R,feeding,2dph-1

description: myosho_207_FKDL230363916-1A_22CNYFLT3_L1


title: CRC12 RNA


title: CRC11 RNA


title: NIES-R,feeding,0dph-6

description: myosho_206_FKDL230363916-1A_22CNYFLT3_L1

value: 0 dph


title: CRC10 RNA


title: CRC16 RNA


title: A. cahirinus fibroblasts, untreated passaged, 12d, R2

description:
Library name: ACO_12d_ASM9_ConP
counts_aco_irrad.tsv


title: NIES-R,feeding,0dph-5

description: myosho_205_FKDL230363916-1A_22CNYFLT3_L1


title: NIES-R,feeding,0dph-4

description: myosho_204_FKDL230363916-1A_22CNYFLT3_L1


title: A. cahirinus fibroblasts, untreated, 24h, R4

description:
Library name: ACO_24h_ASM11_Con
counts_aco_irrad.tsv


title: NIES-R,feeding,0dph-3

description: myosho_203_FKDL230363916-1A_22CNYFLT3_L1


title: CRC15 RNA


title: CRC09 RNA


title: NIES-R,feeding,0dph-2

description: myosho_202_FKDL230363916-1A_22CNYFLT3_L1


title: CRC08 RNA


title: NIES-R,feeding,0dph-1

description: myosho_201_FKDL230363916-1A_22CNYFLT3_L1


title: A. cahirinus fibroblasts, 20 gy, 24h, R3

description:
Library name: ACO_24h_ASM10_20Gy
counts_aco_irrad.tsv


title: A. cahirinus fibroblasts, 10 gy, 24h, R3

description:
Library name: ACO_24h_ASM10_10Gy
counts_aco_irrad.tsv


title: Pulpitis_3

city: Guangzhou

first: Zhongchun

last: Tong

address: Lingyuan West Road 56#

department: Hosiptal of Stomatology

institute: Sun Yat- Sen University

data_processing:
The Seurat package was used to normalise data, dimensionality reduction, clustering, differential expression.
Gene Ontology (GO) enrichment analysis of marker genes was implemented by the clusterProfiler R package, in which gene length bias was corrected.
We used cluster Profiler R package to test the statistical enrichment of markergenes in KEGG pathways.
CellChat was used to compare cell-cell communication and infer ligand–receptor interactions in the young and aged dental pulp groups
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Dental Pulp

extract_protocol:
RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2 reagent kit (10× Genomics) according to the manufacturer’s instructions.
Raw reads were demultiplexed and mapped to the reference genome by 10× Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat

value: Dental Pulp

value: pulpitis


title: CRC07 RNA


title: Pulpitis_2


title: CRC06 RNA


title: CRC05 RNA


title: Day 7 injured WT mouse ear 3 treated with Rosemary

city: philadelphia

first: Emmanuel

last: Rapp Reyes

address: 421 curie boulevard brb 1039

institute: University of Pennsylvania

description: Library name: Rose 2L

data_processing:
Fastq files were aligned to the GRCm39 reference genome using STAR_2.4.0 in basic 2-pass mode using the Encode options as specified in the manual. Resulting BAM files were turned into a count matrix using the featureCounts program. Normalization by fragments per kilobase per million mapped fragments (FPKM) counts and differentially expressed transcripts were generated using the R packages edgeR and Limma, respectively.
Assembly: GRCm39/mm39
Supplementary files format and content: FPKM in .xlsx file

source_name: Mouse ear wound

extract_protocol:
RNA was isolated using an RNeasy kit (74106, QIAGEN).
The RNA-seq libraries were made using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7760S, New England Biolabs) and NEBNext Multiplex Oligos for Illumina (E6609S, New England Biolabs)

value: Mouse ear wound

value: Mouse ear

value: WT

value: Rosemary cream


title: Day 7 injured WT mouse ear 4 treated with Rosemary

description: Library name: Rose 2R


title: A. cahirinus fibroblasts, untreated, 24h, R3

description:
Library name: ACO_24h_ASM10_Con
counts_aco_irrad.tsv

value: Untreated


title: Day 7 injured WT mouse ear 1 treated with Rosemary

description: Library name: Rose 1L


title: A. cahirinus fibroblasts, 10 gy, 24h, R4

description:
Library name: ACO_24h_ASM11_10Gy
counts_aco_irrad.tsv

value: Primary skin fibroblasts


title: Pulpitis_1


title: A. cahirinus fibroblasts, 20 gy, 24h, R2

description:
Library name: ACO_24h_ASM9_20Gy
counts_aco_irrad.tsv

value: 20 gy


title: Day 7 injured WT mouse ear 2 treated with Rosemary

description: Library name: Rose 1R


title: CRC04 RNA


title: Day 7 injured WT mouse ear 3 treated with cetaphil

description: Library name: Ceta 2L

value: Vehicle control cream (cetaphil + DMSO)


title: A. cahirinus fibroblasts, 10 gy, 24h, R2

description:
Library name: ACO_24h_ASM9_10Gy
counts_aco_irrad.tsv

value: 10 gy


title: CRC03 RNA


title: Day 7 injured WT mouse ear 2 treated with cetaphil

description: Library name: Ceta 1R


title: Day 7 injured WT mouse ear 1 treated with cetaphil

description: Library name: Ceta 1L


title: Day 7 injured WT mouse ear 4 treated with cetaphil

description: Library name: Ceta 2R


title: A. cahirinus fibroblasts, untreated, 24h, R2

description:
Library name: ACO_24h_ASM9_Con
counts_aco_irrad.tsv


title: CRC02 RNA


title: Gag-SRSF5-rep4

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: MO

address: 660 S. Euclid Avenue, Campus Box 8230

institute: Washington University School of Medicine

data_processing:
RNA-seq reads were aligned to the human genome (hg19) or to corresponding viral genomes, with up to 1 mismatches allowed using the Bowtie algorithm.
FeatureCounts was used to summarize and count mapped RNA-seq reads for genomic features.
Assembly: hg19 and NL4-3
Supplementary files format and content: Counts files showing summarization of reads (i.e. chromosomal locations and counts).

growth_protocol: 293T cells grown in 6-well dishes were transfected with 2 μg of the indicated PR- NL4-3-derived proviral plasmids using polyethylenimine (PolySciences).

extract_protocol:
Trizol extraction
TruSeq Stranded Total RNA Sample Prep Kit (Illumina) was used to generate libraries following manufacturer's protocol.

treatment_protocol: No treatments

value: cell line

value: 293T cells transfected


title: A. cahirinus fibroblasts, 20 gy, 24h, R1

description:
Library name: ACO_24h_ASM8_20Gy
counts_aco_irrad.tsv


title: CRC01 RNA

value: CRC


title: Gag-NCx3-rep4


title: Gag-SRSF4-rep4


title: A. cahirinus fibroblasts, untreated, 24h, R1

description:
Library name: ACO_24h_ASM8_Con
counts_aco_irrad.tsv


title: CRC17 miRNA

data_processing:
Data processing and UMI correction was done using sRNAbench. (Aparicio-Puerta E, Gómez-Martín C, Giannoukakos S, Medina JM, Scheepbouwer C, García-Moreno A, Carmona-Saez P, Fromm B, Pegtel M, Keller A, Marchal JA, Hackenberg M. sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms. Nucleic Acids Res. 2022 Jul 5;50(W1):W710-W717. doi: 10.1093/nar/gkac363. PMID: 35556129; PMCID: PMC9252802.)
Counts were normalised to log2 transformed CPM values.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes CPM values for each sample

extract_protocol:
SEC with the Automated Fraction Collector (AFC-V1, Izon) was performed to isolate vesicles from 2-3 ml of plasma of each patient using 2 qEV original / 70 nm gen 2 columns (IZON) per plasma sample. Using a buffer volume of 2.70 ml, and a fraction volume of 0.5 ml, the particles of interest were collected in fractions 3 and 4 (between 1 and 2 ml of the Purified Collection Volume (PCV)). Both fractions of the 2 isolations were pooled, resulting in a volume of 2 ml per plasma. 1 ml of the vesicle isolate was concentrated with an Amicon Ultra-2 Centrifugal Filter Unit (Millipore) to 250 µl. Total RNA from the EVs was isolated using the miRNeasy serum/plasma kit (QIAgen) according to the manufacturers' protocol with minor adjustments.
Small RNA libraries were prepared using the costum IsoSeek protocol described in the STAR protocol. (van Eijndhoven, M.A.J., Scheepbouwer, C., Aparicio-Puerta, E., Hackenberg, M., and Pegtel, D.M. (2023). IsoSeek for unbiased and UMI-informed sequencing of miRNAs from low input samples at single-nucleotide resolution. STAR Protoc 4, 102645. 10.1016/j.xpro.2023.102645.)

value: Primary Tumor


title: Gag-NCx2-rep4


title: CRC16 miRNA


title: Gag-dNC-rep4

value: Gag-dNC


title: Gag-hnRNP F-rep4

value: Gag-hnRNP F


title: WT male V2

city: Portland

first: Gabriela

last: Elizondo

state: OR

address: 3222 SW Research Drive

institute: OHSU

description: Library name: Sample 11

data_processing:
Illumina Bcl2Fastq package
Analysis was performed using Galaxy. DE analysis used the DESeq2.
Pathview was used for identification of relevant up- and down-represented KEGG metabolic pathways.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: text file of normalized DEseq2 counts median of ratios

source_name: heart ventricle

extract_protocol:
RNA extracted from fresh tissue  using Rneasy Fibrous Tissue Mini (QIAGEN) protocol.
RNA was converted into cDNA and sequenced on the NovaSeq 6000

treatment_protocol: no treatment

value: heart ventricle

value: male


title: Gag-hnRNP K-rep4

value: Gag-hnRNP K


title: WT male V1

description: Library name: Sample 12


title: Gag-dNC-NC-rep4

value: Gag-dNC-NC


title: Gag-CNBP7-rep4

value: WT


title: WT male V3

description: Library name: Sample 10


title: Gag-hnRNP A1-rep4

value: Gag-hnRNP A1


title: Gag-CNBP5-rep4


title: CRC14 miRNA


title: Gag-CNBP6-rep4


title: WT fem V3

description: Library name: Sample 9

value: female


title: CRC13 miRNA


title: Gag-CNBP4-rep4


title: CRC12 miRNA


title: WT fem V2

description: Library name: Sample 8


title: Gag-SRSF1-rep4


title: Gag-CNBP2-rep4


title: A. cahirinus fibroblasts, 10 gy, 24h, R1

description:
Library name: ACO_24h_ASM8_10Gy
counts_aco_irrad.tsv

value: Primary skin fibroblasts


title: Gag-CNBP3-rep4


title: Gag-bZIP-rep4

value: Gag-bZIP


title: CRC15 miRNA


title: WT fem V1

description: Library name: Sample 7


title: CRC11 miRNA


title: Gag-SRSF5-rep3


title: WT-Gag-rep4

value: WT-Gag


title: CRC10 miRNA


title: LCHADD male V3

description: Library name: Sample 6

value: LCHADD


title: LCHADD male V1

description: Library name: Sample 5


title: Gag-dNC-rep3

value: cell line


title: LCHADD male V2

description: Library name: Sample 4


title: Gag-dNC-NC-rep3

value: 293T cells transfected


title: CRC09 miRNA

value: CRC


title: Gag-CNBP7-rep3


title: Gag-CNBP5-rep3


title: CRC07 miRNA

value: Primary Tumor


title: Gag-CNBP6-rep3


title: LCHADD fem V2

description: Library name: Sample 2


title: Gag-CNBP3-rep3


title: CRC08 miRNA


title: CRC03 miRNA


title: Gag-SRSF1-rep2


title: Gag-SRSF5-rep2


title: LCHADD fem V3

description: Library name: Sample 3


title: CRC06 miRNA


title: CRC05 miRNA


title: Gag-CNBP2-rep3


title: Gag-NCx3-rep2


title: CRC04 miRNA


title: Gag-hnRNP K-rep2


title: Gag-SRSF4-rep2


title: Gag-NCx2-rep2


title: Gag-hnRNP A1-rep2


title: Gag-CNBP4-rep3


title: CRC02 miRNA


title: LCHADD fem V1

description: Library name: Sample 1


title: Gag-hnRNP F-rep2


title: PyMT_PCBP1_KO(2)

city: Charleston

first: Cécile

last: Fréreux

state: SC

address: 173 Ashley Avenue

institute: Medical University of South Carolina

description:
Library name: Sample 4
Chromium Single Cell 3' (v3.1 Chemistry, 10x Genomics)

data_processing:
Raw sequencing data were processed with Cell Ranger (v7.0.0)66. Cellranger mkfastq command was used to demultiplex the different samples and cellranger count command was used to generate gene – cell expression matrices. Downstream analysis was performed in R with Seurat (v4.1.0) and customized R scripts. Data from four different samples were merged into a single dataset. For quality control, cells with > 200 genes, < 10000 UMIs, and < 5% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0)68 for a resultant expression matrix with 16,568 genes and 37,801 cells. Prior to integration, the data was normalized and scaled using Seurat’s implementation of SCTransform69, regressing out variables of number of UMIs, percent of mitochondrial expression, and cell cycling scores (determined using Seurat’s CellCycleScoring function). The data was integrated via Seurat, using Canonical Correlation Analysis (CCA) to find anchors for integration of the samples. After integration, PCA was used to cluster all cells, using 30 principal components. Batch correction was also performed using Harmony (v0.1.1). Cluster markers were identified via the package Presto (https://github.com/immunogenomics/presto) using a Wilcoxon Rank Sum test.
Assembly: GRCm39
Supplementary files format and content: CellBender-filtered count matrices (.h5) and combined Seurat analysis object (.rds)

source_name: Mammary tumor

extract_protocol:
Sized-matched mammary tumors from PyMT PCBP1+/+ and PyMT PCBP1–/– females were collected and flash frozen in liquid nitrogen. Tissues were chopped and cell membrane were lysed in NP40 lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 1mM DTT, 0.1% NP40, 1U/µL RNAse inhibitor) using a mini bead mill and crude nuclei suspensions were filtered through 70 µm strainers. Nuclei were spun, resuspended in pre-chilled 1% BSA PBS, stained with 10µg/mL 7AAD, and positive nuclei were collected by FACS in 1% BSA PBS.
Single-nucleus suspensions were prepared from mammary tumors, evaluated for quality (Cellometer, Nexelom Bioscience), and adjusted to 1,000 nuclei/µL. Libraries were generated using the Chromium Next GEM Single Cell 3′ Library & Gel Bead Kit v3.1 (10x Genomics, Cat. no. CG000315) according to the manufacturer’s protocol. Nuclei were loaded onto a Chromium Next GEM Chip G and partitioned on a Chromium Controller (10x Genomics). Barcoded cDNA was amplified and converted into gene expression libraries following the Chromium Next GEM Single Cell 3′ protocol. Libraries were sequenced on an Illumina NovaSeq 6000 S4 flow cell (2 × 150 bp, ~300 million paired-end reads per library) at the VANTAGE facility (Vanderbilt University Medical Center).

value: Mammary tumor

value: PCBP1 KO


title: Gag-CNBP7-rep2


title: PyMT_PCBP1_WT(1)

description:
Library name: Sample 1
Chromium Single Cell 3' (v3.1 Chemistry, 10x Genomics)


title: SW1116 rep2 RNA

description: SW1116 rep2

growth_protocol: Cells were cultured in DMEM/F12  supplemented with 10% v/v fetal bovine serum and 50 units/mL of penicillin/streptomycin. Cells were maintained at 37 °C in humidified air containing 5% CO2.

extract_protocol:
Ultrafiltration was performed prior to SEC. SEC with the Automated Fraction Collector (AFC-V1, Izon) was performed to isolate vesicles using 2 qEV original / 70 nm gen 2 columns (IZON) per sample. Using a buffer volume of 2.70 ml, and a fraction volume of 0.5 ml, the particles of interest were collected in fractions 3 and 4 (between 1 and 2 ml of the Purified Collection Volume (PCV)). Both fractions of the 2 isolations were pooled, resulting in a volume of 2 ml per sample. 1 ml of the vesicle isolate was concentrated with an Amicon Ultra-2 Centrifugal Filter Unit (Millipore) to 250 µl. Total RNA from the EVs was isolated using the miRNeasy serum/plasma kit (QIAgen) according to the manufacturers' protocol with minor adjustments.
mRNA libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara Bio Inc.) according to the manufacturers' protocol, including ribosomal cDNA depletion


title: PyMT_PCBP1_KO(1)

description:
Library name: Sample 3
Chromium Single Cell 3' (v3.1 Chemistry, 10x Genomics)


title: Gag-dNC-NC-rep2


title: SW1116 rep1 RNA

description: SW1116 rep1


title: Sample 11_PyMT_PCBP1_WT(5)

description: Library name: Sample 11

data_processing:
Read quality was assessed with FastQC and reads were aligned with Bowtie2. Differential expression analysis was performed in Partek Flow using the Gene Specific Analysis algorithm.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes normalized CPM for each sample

extract_protocol:
RNA was extracted by Trizol/phenol chloroform and analyzed for quality (RIN) by a Bioanalyzer (Agilent 2100)
Libraries were generated by the Medical University of South Carolina core facility using a poly(A)-enrichment mRNA-seq protocol (Illumina-compatible stranded mRNA library preparation) according to the manufacturer’s instructions


title: Gag-CNBP5-rep2


title: PyMT_PCBP1_WT(2)

description:
Library name: Sample 2
Chromium Single Cell 3' (v3.1 Chemistry, 10x Genomics)


title: Sample 9_PyMT_PCBP1_WT(3)

description: Library name: Sample 9


title: Gag-CNBP3-rep2


title: MDST8 rep2 RNA

description: MDST8 rep2


title: Gag-CNBP2-rep2