title: starved cells, mated for 24 hours, 2 hours after refeeding rep2

city: Bryan

first: GEOFFREY

last: KAPLER

state: TX

address: 4209B Medical Research Education Building II

institute: Texas A&M University

data_processing:
After sequencing, adapters and low quality reads were removed by Trimmomatic, paired reads with concordant mappings were aligned to the Tetrahymena genome  by HISAT2, the abundance of these transcripts in each sample was computed using StringTie.
Assembly: Tetrahymena genome (SB210, 2021 version, TGD)
Supplementary files format and content: tab-delimited text files include count values for each Sample

organism: Tetrahymena thermophila

source_name: CU428 and CU427

growth_protocol: CU428 and CU427 strains (1.5 L) were grown to ~1x10e5 cells/ml in 2% PPYS/1000 U/ml pen-strep (Sigma Aldrich)  at 30˙C.

extract_protocol:
For RNA isolation, cell pellets were resuspended in 1 ml RNAlater and placed at 4˙C overnight. RNAlater was removed and RNA prepared using the Qiagen RNeasy kit with additional DNAse digestion on the column.
10 ug of total RNA were used to make cDNA library was prepared using Illumina RNA-seq Prep Kit (Illumina).

treatment_protocol: Two samples of vegetative growing cells (CU428) were starved for 43 hours. Two samples of vegetative growing cells (CU428) were starved for 43 hours, then refeeded with 2% PPYS/1000 U/ml pen-strep (Sigma Aldrich)  at 30˙C, cells were collected 2 hours after refeeding. Two samples of vegetative growing cells (CU428 and CU427, different mating types) were starved for 19 hours, then mated for 24 hours, refeeded with 2% PPYS/1000 U/ml pen-strep (Sigma Aldrich)  at 30˙C, cells were collected 2 hours after refeeding.

value: CU428 and CU427

value: vegetative growing cells

value: WT

value: starved, mated, refeeded


title: HEL_DOT1L-ko_DMSO_rep1

status: Public on Jul 29 2025

type: SRA

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

description: Library name: HEL_DOT1L-ko_DMSO_rep1

library_source: transcriptomic

data_processing:
Data processing and analysis was perfomed in a Galaxy environment (version: 24.2.3) hosted at Hannover Medical School, Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation
FASTQ files were trimmed using "fastp" (0.23.4) (default mode)
Trimmed paired-end reads were aligned to the human reference genome GRCh38/hg38 using RNA STAR (2.7.11a).
genome-coverage (generation of bigwig wiles) was conducted using "bamcoverage" (default mode)
Mapped reads were quantified using featureCounts (2.0.3) against the corresponding GTF annotation file.
Differential gene expression analysis was carried out using DESeq2 (2.11.40.8), and genes with an adjusted p-value < 0.05 and a fold change >2 were considered significantly differentially expressed.
Assembly: hg38
Supplementary files format and content: .bigwig file encoding coverage data for visualization in genome browser for all samples
Supplementary files format and content: .txt files containing normalized gene counts for HEL cells and MPN-BP1 primary patient cells
Supplementary files format and content: .xlsx file contains differentiall expression analysis (DESeq2 output) for HEL cells (all comparisons)
Supplementary files format and content: . Txt file  contains differentiall expression analysis (DESeq2 output) for MPN-BP1 primary patient cells (DOT1L-shRNA vs. scr control)

molecule: polyA RNA

organism: Homo sapiens

source_name: hematopoietic

growth_protocol: The human MPN-BP cell line HEL was grown in RPMI+10%FBS+5%Pen/Strep (Gibco) at 5% CO2 and 37°C. Primary MPN-BP patient cells were cultured in fully-supplemented human methylcellulose medium (H4034 Optimum)

extract_protocol:
RNA was extracted using the RNeasy Mini kit (Qiagen) accoding to the manufacturer's instructions
Poly-A tail selection and library preparation were performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module and the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA).

treatment_protocol: Drug treatment of HEL cells was performed using the LSD1-inhibitor Bomedemstat at a concentration of 150nM for 24h or 5d. DOT1L-knockouts in HEL cells were performed using the CRISPR-Cas9 system by stable expression of Cas9 and the sgRNA construct and continous selection with blasticidin (10µg/ml) and puromycin (1µg/ml). RNAi-mediated knockdown of DOT1L in primary human MPN-BP cell was performed by stable expression of a commercial shRNA construct (Sigma, Mission shRNAs) and continous selection with puromycine (1µg/ml).

tag: tissue

value: hematopoietic

tag: cell line

value: HEL

tag: cell type

value: blast-phase MPN (MPN-BP)

tag: genotype

value: JAK2-V617F / TP53-loss

tag: treatment

value: DMSO

tag: batch


title: A204, anlotinib resistant, replicate 1

city: Sutton

first: Paul

middle: H

last: Huang

address: 15 Cotswold Road

country: United Kingdom

institute: The Institute of Cancer Research

description:
Library name: A204AnloR_n1
Column name in gene_fpkm.txt: A204AnloR_n1

data_processing:
Adapter trimming and low-quality sequence removal was performed using trimmomatic
Mapping to hg38 reference genome was performed using HISAT2
Read count quantification was undertaken using featureCounts
Raw count normalisation and fpkm generation was undertaken using edgeR
Assembly: hg38
Supplementary files format and content: Tab-delimited text file contains FPKM values per sample

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen) according to manufacturer's instructions.
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. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: Anlotinib


title: starved cells, mated for 24 hours, 2 hours after refeeding rep1

country: USA

molecule: total RNA


title: HEL_DOT1L-ko_DMSO_rep2

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

description: Library name: HEL_DOT1L-ko_DMSO_rep2


title: A204, regorafenib resistant, replicate 1

description:
Library name: A204_RegR_n1
Column name in gene_fpkm.txt: A204_RegR_n1

value: Regorafenib


title: A204, regorafenib resistant, replicate 2

description:
Library name: A204_RegR_n2
Column name in gene_fpkm.txt: A204_RegR_n2


title: HEL_DOT1L-ko_Bomedemstat_5d_rep1

description: Library name: HEL_DOT1L-ko_Bomedemstat_5d_rep1


title: Exp.5_patient_MPN-BP5_DOT1L-ChIP

description: Library name: Exp.5_patient_MPN-BP5_DOT1L-ChIP

library_source: genomic

data_processing:
Data processing and analysis was perfomed in a Galaxy environment (version: 24.2.3) hosted at Hannover Medical School, Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation
FASTQ files were trimmed using "fastp" (0.23.4) (default mode)
Trimmed paired-end reads were aligned to the human reference genome hg19 using Bowtie2 (2.5.3).
Read counts were obtained using bedtools multicov (2.30.0), and coverage tracks were generated using bamCoverage (3.5.4) for visualization in IGV (2.17.4).
Duplicates were removed using macs2 filterdup (2.2.9.1) and peaks were called with macs2 callpeak (2.2.9.1)
Assembly: hg19
Supplementary files format and content: .bigwig file encoding coverage data for visualization in genome browser for all samples
Supplementary files format and content: .bed files containing the peak calling results for each ChIP sample

molecule: genomic DNA

growth_protocol: The human MPN-BP cell lines HEL and SET2 were grown in RPMI+10%FBS+5%Pen/Strep (Gibco) at 5% CO2 and 37°C. Primary MPN-BP patient cells were cultured in fully-supplemented human methylcellulose medium (H4034 Optimum)

extract_protocol:
Cells were double cross-linked with 50 µL/mL of 40 mM disuccinimidyl glutarate (DSG) for 30 minutes and 2% formaldehyde solution for 10 minutes. The reaction was quenched by adding 200 µL of 1.25 M glycine and 100 µL of 1 M Tris-HCl per mL of suspension. Cells were pelleted by centrifugation (1400 rpm, 5 min). Cells were lysed in 1 mL of Cytoplasmic Lysis Buffer (20 mM Tris-HCl pH 7.5, 300 mM NaCl, 2 mM EDTA, 0.5% NP-40, 1% Triton X-100; freshly supplemented with 1 mM PMSF and cOmplete™ Protease Inhibitor Cocktail). Nuclei were extracted by applying 10–15 strokes with a pre-chilled Dounce homogenizer. The nuclear pellet was resuspended in Sonication Buffer (10 mM Tris-HCl pH 8.1, 100 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.5% N-lauroylsarcosine, 0.1% SDS; freshly supplemented with 1 mM PMSF and cOmplete™ Protease Inhibitor Cocktail). Chromatin was sonicated to an average fragment size of 200–600 bp using a Covaris ME220 Focused-ultrasonicator. For immunoprecipitation, 5 µg of antibody per IP were used. Beads were then resuspended in Wash Buffer (50 mM HEPES pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% sodium deoxycholate; freshly supplemented with 1 mM PMSF) and washed six times with 800 µL Wash Buffer by gentle inversion for 2 minutes per wash, followed by a final wash with 1 mL of 1x TE buffer. Chromatin was eluted in 150 µL Elution Buffer and decrosslinked at 65°C overnight.
Library preparation for Illumina sequencing was performed using the NEBNext Ultra II DNA Library Prep Kit, following the manufacturer's instructions. Libraries were purified with 0.9× AmpureXP beads

treatment_protocol: DOT1L-knockouts in HEL cells were performed using the CRISPR-Cas9 system by stable expression of Cas9 and the sgRNA construct and continous selection with blasticidin (10µg/ml) and puromycin (1µg/ml).

value: primary MPN-BP patient bone marrow

tag: chip antibody

value: anti-DOT1L, CST, clone:D1W4Z, cat:77087S


title: Col0_HS_Rep1

city: Columbia

first: Ron

last: Mittler

state: Missouri

address: University of Missouri,1201 Rollins St

department: Division of Plant Science and Technology

institute: University of Missouri - Columbia

data_processing:
Sequencing was performed by Novogene, Inc.
Bioinformatic analysis was performed by Joshi Lab in University of Missouri
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence. Subsequently, the processed reads were mapped to the Arabidopsis thaliana TAIR10.57 version whole genome using Hisat2 V2.2.1.
Assembly: Arabidopsis thaliana TAIR10.54
Supplementary files format and content: Matrix table FPKM values for all samples

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis thaliana wild-type (Col0), and mutants of bHLH35  gene plants were subjected to salt stress (S; 50mM), high light stress (HL; 700 µE), heat stress (HS; 33 °C) and different combinations of these three stresses (S+HL, S+HS, HL+HS, S+HL+HS). Sterilized seeds of above-mentioned genotypes were germinated on ½ MS (murashige and Skoog media) with or without salt, at 21°C temperature and 150 µE light intensity. 7 days old seedling were subjected to HL and HS for 3 days (in combinations mentioned above) to determine the impact of stresses on survival. Seedlings for control were grown on ½ MS media without salt at 21°C temperature and 150 µE light intensity. To study the transcriptomic response of Arabidopsis genotypes, 7 days old seedling growing on ½ MS with or without salt were exposed to HS and HL stress (in combinations mentioned above) for 1.5 hrs.

extract_protocol:
Total RNA from the seedlings were isolated using Qiagen RNeasy® Plant Mini Kit.
RNA libraries for sequencing were prepared using standard Illumina protocols.

value: Seedlings

value: Columbia 0

value: Heat stress


title: Myobacterium tuberculosis, UNT, 0 hrs, Biological Replicate 2, Plate Control

city: Boston

first: Bree

last: Aldridge

state: Massachusetts

address: 136 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University

data_processing:
Reads were aligned to GCF_000350205.1 using BWA. Aligned reads were then sorted and indexed with samtools (v1.9) using the commands “samtools sort -l 0” and “samtools index”. Gene-level counts were obtained from the sorted, genome-mapped reads using the python-based package HTSeq (v0.13.5).
Assembly: GCF_000350205.1
Supplementary files format and content: tab-deliminated text file of raw counts for each Mycobacterium tuberculosis Erdman locus tag

organism: Mycobacterium tuberculosis

source_name: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

growth_protocol: Mtb strain Erdman with plasmid pMV306hsp+LuxG13 were adapted to a cholesterol in-vitro growth condition prior to drug exposure and RNA extraction. Briefly, Mtb were first cultured in standard growth medium consisting of 7H9 broth, (ThermoFisher; DF0713-17-9), 0.2% glycerol, 10% OADC (0.5g/L oleic acid, 50g/L albumin, 20g/L dextrose and 0.04g/L catalase), and 0.05% Tween-80 and then subcultured at least once prior to cholesterol adaptation. Once the bacterial cultures reached an OD600nm ~0.5, the cultures were diluted to an OD600nm of 0.05 in cholesterol growth medium consisting of 7H9 powder (4.7g/L), fatty acid-free BSA (0.5g/L), NaCl (100mM) and tyloxapol (0.05%). Cultures were then subcultured once more in the same media after reaching mid-log phase (OD600nm ∼0.5-0.7). Then, the cultures were subcultured to 0.05 OD in 50ml conical tubes containing the cholesterol growth media and their respective drug. All cultures were buffered with 100 mM 3-(N-morpholino)propanesulfonic acid at pH 7.

extract_protocol:
Drug-treated cultures and untreated controls were then harvested by centrifugation at timepoints 4, and 24 hours post drug treatment. To halt transcriptional responses during the RNA extraction process, GTC buffer was added to the cultures and they were washed twice in GTC buffer. The resulting pellets were stored in Eppendorf tubes containing ~1ml of GTC buffer (4M guanidinium thiocyanate) + 0.5% sarcosyl, 25 mM sodium citrate and 0.1M beta-mercaptoethanol. Samples were stored in aerosol tight O-ring caps at -80°C until RNA extractions were performed. On the day of extraction, the frozen GTC treated pellets were thawed at 37 degrees, harvested by centrifugation, resuspended in prewarmed triazole and transferred to 2ml O-ring tubes containing sterile zirconia beads. The triazole mixture was then bead beaten twice followed by the addition of chloroform and vigorous shaking for one minute. The samples were then centrifuged, and the aqueous layer was removed and placed in Qiagen RNeasy columns for RNA cleanup. Genomic DNA was removed from all samples through a DNAse digest on the columns prior to elution in pre-warmed RNase free water. The resulting RNA was then removed from the BSL-3 facility. Concentration and quality of RNA (260nm/280nm absorbance) was assessed using a nanodrop spectrophotometer and stored at -80°C until sample submission.
Samples were submitted to the Broad Institute MOCP for sequencing, where they performed QC, library preparation, ribodepletion and paired-end sequencing on the Illumina NovaSeq 6000 following a modified version of the RNAtag-Seq method.

treatment_protocol: Cultures were treated with 1x the IC90 of the drug. Cells were then harvested by centrifugation at timepoints 4, and 24 hours post drug treatment.

tag: time point

value: 0 hrs

value: UNT


title: starved cells, 2 hours after refeeding rep2

value: vegetative growing cells

value: starved, refeeded


title: HEL_NTC_Bomedemstat_24h_rep1

description: Library name: HEL_NTC_Bomedemstat_24h_rep1


title: Col0_Control_Rep1

value: No treatment


title: HEL_DOT1L-ko_Bomedemstat_5d_rep3

description: Library name: HEL_DOT1L-ko_Bomedemstat_5d_rep3

value: hematopoietic


title: A204, sitravatinib resistant, replicate 2

description:
Library name: A204_SitR_n2
Column name in gene_fpkm.txt: A204_SitR_n2

value: Sitravatinib


title: Myobacterium tuberculosis, UNT, 4 hrs, Biological Replicate 2

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs


title: Exp.5_patient_MPN-BP5_LSD1-ChIP

description: Library name: Exp.5_patient_MPN-BP5_LSD1-ChIP

value: blast-phase MPN (MPN-BP)

value: JAK2-V617F / TP53-loss

value: anti-LSD1, Abcam, clone:EPR6825, cat:ab129195


title: HEL_DOT1L-ko_Bomedemstat_24h_rep1

description: Library name: HEL_DOT1L-ko_Bomedemstat_24h_rep1

value: HEL


title: A204, pazopanib resistant, replicate 2

description:
Library name: A204_PazR_n2
Column name in gene_fpkm.txt: A204_Pazr_n2

value: Pazopanib


title: Myobacterium tuberculosis, RIF, 4 hrs, Biological Replicate 2

value: RIF


title: A204, pazopanib resistant, replicate 1

description:
Library name: A204_PazR_n1
Column name in gene_fpkm.txt: A204_PazR_n1


title: Exp.5_patient_MPN-BP5_input-chromatin

description: Library name: Exp.5_patient_MPN-BP5_input-chromatin

value: primary MPN-BP patient bone marrow


title: Myobacterium tuberculosis, PZA, 4 hrs, Biological Replicate 2

value: PZA


title: Cells starved for 43 hours rep2

value: WT

value: starved


title: A204, parental, replicate 1

description:
Library name: A204_n1
Column name in gene_fpkm.txt: A204_n1


title: Myobacterium tuberculosis, RFP, 4 hrs, Biological Replicate 2

value: RFP


title: Cells starved for 43 hours rep1

value: vegetative growing cells


title: Myobacterium tuberculosis, PRE, 4 hrs, Biological Replicate 2

value: PRE


title: Exp.5_patient_MPN-BP4_DOT1L-ChIP

description: Library name: Exp.5_patient_MPN-BP4_DOT1L-ChIP

value: hematopoietic

value: anti-DOT1L, CST, clone:D1W4Z, cat:77087S


title: Exp.5_patient_MPN-BP4_LSD1-ChIP

description: Library name: Exp.5_patient_MPN-BP4_LSD1-ChIP


title: A204, parental, replicate 2

description:
Library name: A204_n2
Column name in gene_fpkm.txt: A204_n2


title: HepG2, sh2TUG1_3

city: Bangkok

first: Thammachanok

last: Boonto

address: 254 Phaya Thai Rd, Khwaeng Wang Mai, Pathum Wan

department: Biochemistry

country: Thailand

institute: Faculty of Medicine, Chulalongkorn University

data_processing:
Clean data with high quality, each sample had a Q-score no less than Q30, was obtained by filtering Raw data, which removes adapter sequence and reads with low quality. HISAT2 and StringTie was applied to assemble the mapped reads. In this project, GSEA software (UC San Diego and Broad Institute) was utillized to explore the differentailly expressed gene set/pathway between each group.
Assembly: Homo_sapiens.GRCh38_release95.genome.fa.
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

growth_protocol: HCC cell line HepG2 was purchased from the American Type Culture Collection (ATCC) and maintained maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with low glucose containing 10% fetal bovine serum (FBS), 1% L-glutamine, 1% antibiotic-antimycotic (Gibco™, Thermo Fisher Scientific), and 0.1 % primocin at 37 °C with 5% CO2 in a humidified atmosphere

extract_protocol:
total RNA was extracted from HepG2 cell using RNeasy mini kit (Qiagen). 1 µg of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations.

value: Epithelial-like cell

value: TUG1 knockdown


title: HepG2, sh2TUG1_2


title: Myobacterium tuberculosis, LIN, 4 hrs, Biological Replicate 2

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs

value: LIN


title: Exp.5_patient_MPN-BP2_DOT1L-ChIP

description: Library name: Exp.5_patient_MPN-BP2_DOT1L-ChIP

value: blast-phase MPN (MPN-BP)

value: JAK2-V617F / TP53-loss


title: HepG2, sh2TUG1_1


title: Exp.5_patient_MPN-BP4_input-chromatin

description: Library name: Exp.5_patient_MPN-BP4_input-chromatin


title: Myobacterium tuberculosis, MOX, 4 hrs, Biological Replicate 2

value: MOX


title: Myobacterium tuberculosis, INH, 4 hrs, Biological Replicate 2

value: INH


title: Exp.5_patient_MPN-BP2_LSD1-ChIP

description: Library name: Exp.5_patient_MPN-BP2_LSD1-ChIP

value: primary MPN-BP patient bone marrow

value: anti-LSD1, Abcam, clone:EPR6825, cat:ab129195


title: HepG2, sh1TUG1_3


title: Exp.5_patient_MPN-BP2_input-chromatin

description: Library name: Exp.5_patient_MPN-BP2_input-chromatin


title: starved cells, 2 hours after refeeding rep1

value: WT

value: starved, refeeded


title: Myobacterium tuberculosis, ETH, 4 hrs, Biological Replicate 2

value: ETH


title: Day 10 TFSEM (~E8.5), a single TFSEM

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description: Library name: TFSEM_E8_5-1EMB

library_source: transcriptomic single cell

data_processing:
Demultiplexing was done with bcl-convert
Alignment and quantification of single cell features was done with cellranger/9.0.0 counts
Suerat/5.0.0 R/4.3.1 package was used for the rest of the analysis:
Cells with under 3000 expressing genes, over 8000 expressing genes or over 10% mitochondrial gene expression were filtered out for the rest of the analysis. Genes that are expressed in less than 3 cells were filtered out.
Sample were log-normalization using a scale-factor of 10,000. The top 2,000 variable genes were identified by the variance stabilizing transformation method and subsequently scaled and centered.  UMAP dimensional reduction was performed on the first 10 dimensions in all samples. Clusters were detected using Seurat FindClusters function, with resolution parameter 0.1.
Clusters were annotated with a combination of manual examination of known cell type gene markers, along with statistical analysis of the top significant genes that are expressed in each cluster, using FindAllMarkers() Seurat function.
Assembly: mm10
Supplementary files format and content: CellRanger 10X output, including genes, cells (barcodes) and counts. Can be read by R Seurat package.

organism: Mus musculus

source_name: Whole E8.5 TFSEM

extract_protocol:
RNA extracted according to 10x Genomics Chromium v4 Dual Index system kit instructions
10x Genomics Chromium v4 Dual Index system (5000 cell target cell recovery)

value: Whole E8.5 TFSEM

value: V6.5 tdTomato-CDX2

value: mouse Embryonic Stem Cells


title: HepG2, sh1TUG1_2

value: Epithelial-like cell


title: Uninfected WT control  mice

first: Bumsuk

last: Hahm

state: MO

address: NW301C Medical Sciences Building

department: Surgery-Research

institute: University of Missouri

description:
Library name: Sample 1
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v8.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: GRCm39-2024-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

growth_protocol: LCMV Cl 13 virus were amplifed in BHK cell lines and harvested virus from culture supernatant were stored at -80 freezer.

extract_protocol:
Bone marrows were collected from uninfected WT and LCMV Cl 13-infected WT and Sphk2–/– mice at 3 dpi. Bone marrow cells were isolated as mentioned above with little modification in the isolation and suspension buffer. Cells were passed through a 40 µM cell strainer twice to remove debris and aggregates. Total bone marrow cell suspensions were resuspended in PBS+0.04% BSA buffer. Finally, 1×106 cells/ml with >85% viable bone marrow cell suspensions were prepared and immediately handed over to the university DNA core facility for scRNA-seq.
Libraries were constructed by following the manufacturer’s protocol with reagents supplied in 10× Genomics Chromium Next GEM Single Cell 3′ Kit v3.1.  Briefly, cell suspension concentration and viability were measured with a Cellometer K2 (Revvity) stained with an acridine orange/propidium iodine dye mix (Invitrogen).  Subsequently, cell suspension (targeting 10,000 cells) combined with reverse transcription master mix was loaded on a Chromium Next GEM chip G along with gel beads and partitioning oil to generate gel emulsions (GEMs).  GEMs were then transferred to a PCR strip tube, followed by the reverse transcription, which was performed on a Veriti thermal cycler (Applied Biosystems) at 53°C for 45 minutes.  cDNA was amplified for 11 cycles and purified using AxyPrep MagPCR Clean-up beads (Axygen).  cDNA fragmentation, end-repair, A-tailing and ligation of sequencing adaptors were performed according to the manufacture’s specifications.  Library concentration was measured with a Qubit HS DNA kit (Invitrogen) and fragment size was measured on a 5200 Fragment Analyzer (Agilent).  Libraries were pooled and sequenced on a NovaSeq X (Illumina) to generate 50,000 reads per cell with a sequencing configuration of 28 base pair (bp) on read 1 and 100 bp on read 2.

treatment_protocol: LCMV Cl13 Infection

value: Bone marrow

value: Neutrophils

value: WT mice

value: No treatment


title: LCMV Cl 13 Infected Sphk2-/- mice

description:
Library name: Sample 3
10x Genomics

value: Sphk2-/- mice

value: LCMV Cl 13


title: LCMV Cl 13 Infected WT mice

description:
Library name: Sample 2
10x Genomics


title: Exp.5_patient_MPN-BP1_DOT1L-ChIP

description: Library name: Exp.5_patient_MPN-BP1_DOT1L-ChIP

value: hematopoietic

value: blast-phase MPN (MPN-BP)

value: JAK2-V617F / TP53-loss

value: anti-DOT1L, CST, clone:D1W4Z, cat:77087S


title: Day 10 TFSEM (~E8.5), 5 pooled TFSEMs,  biological replicate 3

description: Library name: TFSEM_E8_5-5EMB


title: Day 10 TFSEM (~E8.5), 5 pooled TFSEMs, technical replicate 2

description: Library name: TFSEM_E8_5_V2


title: HepG2, sh1TUG1_1

value: TUG1 knockdown


title: Myobacterium tuberculosis, CLZ, 4 hrs, Biological Replicate 2

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs

value: CLZ


title: Exp.5_patient_MPN-BP1_LSD1-ChIP

description: Library name: Exp.5_patient_MPN-BP1_LSD1-ChIP

value: primary MPN-BP patient bone marrow

value: anti-LSD1, Abcam, clone:EPR6825, cat:ab129195


title: HepG2, shControl_3

value: Epithelial-like cell

value: WT


title: Day 10 TFSEM (~E8.5), 5 pooled TFSEMs, replicate 1

description: Library name: TFSEM_E8_5

value: Whole E8.5 TFSEM

value: V6.5 tdTomato-CDX2

value: mouse Embryonic Stem Cells


title: Myobacterium tuberculosis, UNT, 0 hrs, Biological Replicate 2

value: 0 hrs

value: UNT


title: Day 8 TFSEM (~E7.5)

description: Library name: TFSEM_E7_5

source_name: Whole E7.5 TFSEM

value: Whole E7.5 TFSEM


title: Exp.5_patient_MPN-BP1_input-chromatin

description: Library name: Exp.5_patient_MPN-BP1_input-chromatin

value: hematopoietic

value: blast-phase MPN (MPN-BP)


title: HepG2, shControl_2


title: HepG2, shControl_1


title: Myobacterium tuberculosis, UNT, 24 hrs, Biological Replicate 1

value: 24 hrs


title: Exp.4_HEL_NTC_LSD1-ChIP

description: Library name: Exp.4_HEL_NTC_LSD1-ChIP

value: HEL

value: JAK2-V617F / TP53-loss


title: E7.5 natural embryo

description: Library name: InUtero_E7_5

source_name: Whole E7.5 Embryo

value: Whole E7.5 Embryo


title: 9B_del3_SINrep_Gal4 Replicate3

city: Stockholm

first: Neus

last: Visa

address: Svante Arrhenius väg 20c

country: Sweden

institute: Stockholm University

data_processing:
nf-core/ATAC-Seq Workflow
Assembly: dm6
Supplementary files format and content: bigWig; output from nf-core pipeline

organism: Drosophila melanogaster

source_name: third instar larva brain

growth_protocol: All fly stocks were reared on instant potato mash–agar food in mixed female/male populations at 25°C, 60% relative humidity and a 12-hour light/12h-hour dark cycle.

extract_protocol:
Tagementation reaction from 5 brains of third instar larvae was performed according to Dhall et al (2023)
All the samples consist of biological triplicates. Libraries were sequenced on NextSeq 2000 P3 (100 cycles) sequencer obtaining paired-end reads (2 x 61bp).

value: third instar larva brain

value: delta9B3; Act>SIN


title: Myobacterium tuberculosis, RFP, 24 hrs, Biological Replicate 1

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: RFP


title: Exp.4_HEL_NTC_input_chromatin

description: Library name: Exp.4_HEL_NTC_input_chromatin


title: Exp.4_HEL_DOT1L-ko_LSD1-ChIP

description: Library name: Exp.4_HEL_DOT1L-ko_LSD1-ChIP

value: anti-LSD1, Abcam, clone:EPR6825, cat:ab129195


title: Myobacterium tuberculosis, BDQ, 4 hrs, Biological Replicate 2

value: 4 hrs

value: BDQ


title: Myobacterium tuberculosis, RIF, 24 hrs, Biological Replicate 1

value: RIF


title: mouse cells after 96h of protocol (MLMM)

description: Library name: D_96h

data_processing:
Demultiplexing was done with bcl-convert
Alignment and quantification of single cell features was done with cellranger/9.0.0 counts
Suerat/5.0.0 R/4.3.1 package was used for the rest of the analysis:
Cells with under 3000 expressing genes, over 8000 expressing genes or over 10% mitochondrial gene expression were filtered out for the rest of the analysis. Genes that are expressed in less than 3 cells were filtered out. For AC sample, due to deep-sequencing, filtering criteria were as following: Cells with under 5000 expressing genes, over 10000 expressing genes or over 10% mitochondrial gene expression were filtered out for the rest of the analysis. Genes that are expressed in less than 3 cells were filtered out.
Sample were log-normalization using a scale-factor of 10,000. The top 2,000 variable genes were identified by the variance stabilizing transformation method and subsequently scaled and centered.  UMAP dimensional reduction was performed on the first 10 dimensions in all samples. Clusters were detected using Seurat FindClusters function, with resolution parameter 0.1.
Clusters were annotated with a combination of manual examination of known cell type gene markers, along with statistical analysis of the top significant genes that are expressed in each cluster, using FindAllMarkers() Seurat function.
Assembly: mm10
Supplementary files format and content: raw counts matrix file (csv), after filtering of cells and genes. Saved from Seurat object
Supplementary files format and content: Cell metadata file (csv), saved from Seurat object.

source_name: cell culture

value: cell culture

value: mouse Embryonic Stem Cells

value: MLMM

value: polyA RNA


title: 9B_del1_SINrep_Gal4 Replicate3

value: delta9B1; Act>SIN


title: Exp.3_MOLM13_input-chromatin

description: Library name: Exp.3_MOLM13_input-chromatin

value: hematopoietic

value: blast-phase MPN (MPN-BP)


title: SINrep_Gal4 Replicate3

value: +; Act>SIN


title: Exp.3_MOLM13_H3K79me2-ChIP

description: Library name: Exp.3_MOLM13_H3K79me2-ChIP

value: JAK2-V617F / TP53-loss

value: anti-H3K79me2, CST, clone:D15E8, cat:5427S


title: mouse cells after 48h of protocol (MLPM2)

description: Library name: C_48h


title: Myobacterium tuberculosis, PZA, 24 hrs, Biological Replicate 1

value: 24 hrs

value: PZA


title: Myobacterium tuberculosis, PRE, 24 hrs, Biological Replicate 1

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: PRE


title: mouse ESCs treated with 2i/LIF

description: Library name: A_2iLIF


title: mouse cells after 24h of protocol (MLPM1)

description: Library name: B_24h


title: 9B_del3_SINrep Replicate3

value: third instar larva brain

value: delta9B3; SIN


title: Myobacterium tuberculosis, MOX, 24 hrs, Biological Replicate 1

value: MOX


title: Exp.3_MOLM13_DOT1L-ChIP

description: Library name: Exp.3_MOLM13_DOT1L-ChIP

value: anti-DOT1L, CST, clone:D1W4Z, cat:77087S


title: mouse cells in AC media conditions, passage 12

description: Library name: AC_P12

value: cell culture

value: mouse Embryonic Stem Cells

value: AC


title: C57BL/6J mouse ovary, hypobaric hypoxia (6500m), miRNA-seq, PU3

city: Lanzhou

first: mengwen

last: Jiao

state: Gansu

address: No. 333, Nanbinhe Road, Qilihe District

department: Department of Reproductive Center

country: China

institute: The 940th Hospital of Joint Logistic Support Force of Chinese People's Liberation Army

description:
Library name: PU3
Fifteen female C57BL/6J mice (6-8 weeks old) were hormonally synchronized via oral gavage administration of levonorgestrel (0.1 mg/kg) and ethinylestradiol (0.02 mg/kg), then exposed to hypobaric hypoxia (simulated 5000 m altitude) for 17 consecutive days.Ovarian tissues were harvested for RNA sequencing to investigate the circRNA-mediated competitive endogenous RNA (ceRNA) regulatory network in hypoxia-induced ovarian injury.
PU3 Expression

data_processing:
Raw reads were filtered to remove adapter contamination, poly-N, and low-quality reads using internal BGI pipelines. Clean reads were then aligned to the Mus musculus reference genome (GRCm38.p6) using Bowtie2. miRNA expression levels were quantified, and differential expression analysis was performed using DESeq2.
Assembly: GRCm38.p6 (GCF_000001635.26)
Supplementary files format and content: XLS files contain FPKM values for each sample (based on GRCm38.p6 annotation).

source_name: Ovary

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.3 µg of total RNA was used for the construction of sequencing libraries.
Small RNA libraries were prepared using BGI's small RNA library construction protocol, including PAGE-based small RNA selection, adapter ligation, reverse transcription, and PCR amplification, followed by sequencing on the DNBSEQ platform (SE50).

value: Ovary

value: Ovarian cell

value: hypobaric hypoxia (simulated 6500m altitude, 8.1kPa O₂, 21 - 24℃, 50% humidity, 24h continuous hypoxia except 0.5h/2d for feeding, 12h/12h light - dark)


title: Myobacterium tuberculosis, LIN, 24 hrs, Biological Replicate 1

value: LIN


title: SINrep Replicate3

value: +; SIN


title: Exp.2_SET2_H3K79me2-ChIP_rep2

description: Library name: Exp.2_SET2_H3K79me2-ChIP_rep2

value: hematopoietic

value: blast-phase MPN (MPN-BP)

value: JAK2-V617F / TP53-loss

value: anti-H3K79me2, CST, clone:D15E8, cat:5427S


title: Myobacterium tuberculosis, INH, 24 hrs, Biological Replicate 1

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 24 hrs

value: INH


title: 9B_del3_SINrep_Gal4 Replicate2

value: third instar larva brain

value: delta9B3; Act>SIN


title: Myobacterium tuberculosis, ETH, 24 hrs, Biological Replicate 1

value: ETH


title: 9B_del1_SINrep_Gal4 Replicate2

value: delta9B1; Act>SIN


title: C57BL/6J mouse ovary, hypobaric hypoxia (6500m), miRNA-seq, PU1

description:
Library name: PU1
Fifteen female C57BL/6J mice (6-8 weeks old) were hormonally synchronized via oral gavage administration of levonorgestrel (0.1 mg/kg) and ethinylestradiol (0.02 mg/kg), then exposed to hypobaric hypoxia (simulated 5000 m altitude) for 15 consecutive days.Ovarian tissues were harvested for RNA sequencing to investigate the circRNA-mediated competitive endogenous RNA (ceRNA) regulatory network in hypoxia-induced ovarian injury.
PU1 Expression


title: C57BL/6J mouse ovary, hypobaric hypoxia (6500m), miRNA-seq, PU2

description:
Library name: PU2
Fifteen female C57BL/6J mice (6-8 weeks old) were hormonally synchronized via oral gavage administration of levonorgestrel (0.1 mg/kg) and ethinylestradiol (0.02 mg/kg), then exposed to hypobaric hypoxia (simulated 5000 m altitude) for 16 consecutive days.Ovarian tissues were harvested for RNA sequencing to investigate the circRNA-mediated competitive endogenous RNA (ceRNA) regulatory network in hypoxia-induced ovarian injury.
PU2 Expression


title: Exp.2_SET2_H3K79me2-ChIP_rep1

description: Library name: Exp.2_SET2_H3K79me2-ChIP_rep1


title: Myobacterium tuberculosis, CLZ, 24 hrs, Biological Replicate 1

value: CLZ


title: C57BL/6J mouse ovary, normal pressure (1500m), miRNA-seq, MP3

description:
Library name: MP3
Fifteen female C57BL/6J mice (6-8 weeks old) were synchronized by oral gavage administration of levonorgestrel and ethinylestradiol, then maintained under normoxic conditions in Lanzhou, China.All mice were housed continuously for 17 days.Ovarian tissues were collected for RNA-seq as the control group to analyze the circular RNA (circRNA)-mediated competitive endogenous RNA (ceRNA) network in hypoxia-induced ovarian injury.
MP3 Expression

value: Ovary

value: Normal pressure (Lanzhou local, ~1500m altitude, 17.8kPa O₂, 20 - 23℃, 12h/14h light - dark)


title: 9B_del1_SINrep Replicate3

value: delta9B1; SIN


title: Myobacterium tuberculosis, BDQ, 24 hrs, Biological Replicate 1

value: BDQ


title: Exp.2_SET2_input_chromatin

description: Library name: Exp.2_SET2_input_chromatin


title: Exp.2_SET2_DOT1L-ChIP_rep2

description: Library name: Exp.2_SET2_DOT1L-ChIP_rep2

value: anti-DOT1L, CST, clone:D1W4Z, cat:77087S


title: Exp.2_SET2_H3K4me1-ChIP_rep1

description: Library name: Exp.2_SET2_H3K4me1-ChIP_rep1

value: hematopoietic

value: anti-H3K4me1, Abcam, clone:EPR16597, cat:ab176877


title: C57BL/6J mouse ovary, normal pressure (1500m), miRNA-seq, MP2

description:
Library name: MP2
Fifteen female C57BL/6J mice (6-8 weeks old) were synchronized by oral gavage administration of levonorgestrel and ethinylestradiol, then maintained under normoxic conditions in Lanzhou, China.All mice were housed continuously for 16 days.Ovarian tissues were collected for RNA-seq as the control group to analyze the circular RNA (circRNA)-mediated competitive endogenous RNA (ceRNA) network in hypoxia-induced ovarian injury.
MP2 Expression

value: Ovarian cell

value: Normal pressure (Lanzhou local, ~1500m altitude, 17.8kPa O₂, 20 - 23℃, 12h/13h light - dark)


title: MPN-BP_patient_DOT1L-shRNA_rep1

description: Library name: MPN-BP_patient_DOT1L-shRNA_rep1

value: MPN-BP patient bone marrow

value: blast-phase MPN (MPN-BP)

value: JAK2-V617F / TP53-loss


title: 9B_del3_SINrep Replicate2

value: third instar larva brain

value: delta9B3; SIN


title: Exp.2_SET2_DOT1L-ChIP_rep1

description: Library name: Exp.2_SET2_DOT1L-ChIP_rep1


title: Myobacterium tuberculosis, UNT, 4 hrs, Biological Replicate 1

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs

value: UNT


title: 9B_del1_SINrep Replicate2


title: Myobacterium tuberculosis, UNT, 0 hrs, Biological Replicate 1

value: 0 hrs


title: C57BL/6J mouse ovary, hypobaric hypoxia (6500m), PU3

description:
Library name: PU3
Fifteen female C57BL/6J mice (6-8 weeks old) were hormonally synchronized via oral gavage administration of levonorgestrel (0.1 mg/kg) and ethinylestradiol (0.02 mg/kg), then exposed to hypobaric hypoxia (simulated 5000 m altitude) for 17 consecutive days.Ovarian tissues were harvested for RNA sequencing to investigate the circRNA-mediated competitive endogenous RNA (ceRNA) regulatory network in hypoxia-induced ovarian injury.

data_processing:
aw reads were filtered to remove adapter contamination, poly-N, and low-quality reads using internal BGI pipelines.
Clean reads were aligned to the mouse reference genome GRCm38.p6 using HISAT2.
Reads were also aligned to the reference transcriptome using Bowtie2 for gene quantification.
Expression levels were quantified using FPKM, and differentially expressed genes were identified with DESeq2.
Assembly: Genome Reference Consortium Mouse Build 38 patch 6
Supplementary files format and content: XLS files contain FPKM values for each sample (based on GRCm38.p6 annotation).

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1.3 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Ovary

tag: strain

value: hypobaric hypoxia (simulated 6500m altitude, 8.1kPa O₂, 21 - 24℃, 50% humidity, 24h continuous hypoxia except 0.5h/2d for feeding, 12h/12h light - dark)


title: C57BL/6J mouse ovary, normal pressure (1500m), miRNA-seq, MP1

description:
Library name: MP1
Fifteen female C57BL/6J mice (6-8 weeks old) were synchronized by oral gavage administration of levonorgestrel and ethinylestradiol, then maintained under normoxic conditions in Lanzhou, China.All mice were housed continuously for 15 days.Ovarian tissues were collected for RNA-seq as the control group to analyze the circular RNA (circRNA)-mediated competitive endogenous RNA (ceRNA) network in hypoxia-induced ovarian injury.
MP1 Expression

value: Normal pressure (Lanzhou local, ~1500m altitude, 17.8kPa O₂, 20 - 23℃, 12h/12h light - dark)


title: C57BL/6J mouse ovary, hypobaric hypoxia (6500m), PU2

description:
Library name: PU2
Fifteen female C57BL/6J mice (6-8 weeks old) were hormonally synchronized via oral gavage administration of levonorgestrel (0.1 mg/kg) and ethinylestradiol (0.02 mg/kg), then exposed to hypobaric hypoxia (simulated 5000 m altitude) for 16 consecutive days.Ovarian tissues were harvested for RNA sequencing to investigate the circRNA-mediated competitive endogenous RNA (ceRNA) regulatory network in hypoxia-induced ovarian injury.


title: Exp.2_SET2_H3K4me1-ChIP_rep2

description: Library name: Exp.2_SET2_H3K4me1-ChIP_rep2


title: Myobacterium tuberculosis, RIF, 4 hrs, Biological Replicate 1

value: RIF


title: 9B_del3_SINrep_Gal4 Replicate1

value: delta9B3; Act>SIN


title: SINrep Replicate2

value: +; SIN


title: C57BL/6J mouse ovary, hypobaric hypoxia (6500m), PU1

description:
Library name: PU1
Fifteen female C57BL/6J mice (6-8 weeks old) were hormonally synchronized via oral gavage administration of levonorgestrel (0.1 mg/kg) and ethinylestradiol (0.02 mg/kg), then exposed to hypobaric hypoxia (simulated 5000 m altitude) for 15 consecutive days.Ovarian tissues were harvested for RNA sequencing to investigate the circRNA-mediated competitive endogenous RNA (ceRNA) regulatory network in hypoxia-induced ovarian injury.

value: Ovarian cell


title: 9B_del1_SINrep_Gal4 Replicate1

value: delta9B1; Act>SIN


title: SINrep_Gal4 Replicate2

value: +; Act>SIN


title: Myobacterium tuberculosis, PZA, 4 hrs, Biological Replicate 1

value: PZA


title: SINrep_Gal4 Replicate1


title: Myobacterium tuberculosis, RFP, 4 hrs, Biological Replicate 1

value: RFP


title: Myobacterium tuberculosis, PRE, 4 hrs, Biological Replicate 1

value: PRE


title: C57BL/6J mouse ovary, normal pressure (1500m), MP2

description:
Library name: MP2
Fifteen female C57BL/6J mice (6-8 weeks old) were synchronized by oral gavage administration of levonorgestrel and ethinylestradiol, then maintained under normoxic conditions in Lanzhou, China.All mice were housed continuously for 16 days.Ovarian tissues were collected for RNA-seq as the control group to analyze the circular RNA (circRNA)-mediated competitive endogenous RNA (ceRNA) network in hypoxia-induced ovarian injury.

value: Normal pressure (Lanzhou local, ~1500m altitude, 17.8kPa O₂, 20 - 23℃, 12h/13h light - dark)


title: Exp.1_HEL_input_chromatin

description: Library name: Exp.1_HEL_input_chromatin

value: hematopoietic

value: HEL

value: blast-phase MPN (MPN-BP)

value: JAK2-V617F / TP53-loss


title: Myobacterium tuberculosis, MOX, 4 hrs, Biological Replicate 1

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs

value: MOX


title: 9B_del3_SINrep Replicate1

value: third instar larva brain

value: delta9B3; SIN


title: Exp.1_HEL_H3K79me2-ChIP-rep3

description: Library name: Exp.1_HEL_H3K79me2-ChIP-rep3

value: anti-H3K79me2, CST, clone:D15E8, cat:5427S


title: Exp.1_HEL_LSD1-ChIP-rep3

description: Library name: Exp.1_HEL_LSD1-ChIP-rep3

value: anti-LSD1, Abcam, clone:EPR6825, cat:ab129195


title: C57BL/6J mouse ovary, normal pressure (1500m), MP3

description:
Library name: MP3
Fifteen female C57BL/6J mice (6-8 weeks old) were synchronized by oral gavage administration of levonorgestrel and ethinylestradiol, then maintained under normoxic conditions in Lanzhou, China.All mice were housed continuously for 17 days.Ovarian tissues were collected for RNA-seq as the control group to analyze the circular RNA (circRNA)-mediated competitive endogenous RNA (ceRNA) network in hypoxia-induced ovarian injury.

value: Ovary

value: Ovarian cell

value: Normal pressure (Lanzhou local, ~1500m altitude, 17.8kPa O₂, 20 - 23℃, 12h/14h light - dark)


title: C57BL/6J mouse ovary, normal pressure (1500m), MP1

description:
Library name: MP1
Fifteen female C57BL/6J mice (6-8 weeks old) were synchronized by oral gavage administration of levonorgestrel and ethinylestradiol, then maintained under normoxic conditions in Lanzhou, China.All mice were housed continuously for 15 days.Ovarian tissues were collected for RNA-seq as the control group to analyze the circular RNA (circRNA)-mediated competitive endogenous RNA (ceRNA) network in hypoxia-induced ovarian injury.

value: Normal pressure (Lanzhou local, ~1500m altitude, 17.8kPa O₂, 20 - 23℃, 12h/12h light - dark)


title: 9B_del1_SINrep Replicate1

value: delta9B1; SIN


title: Vehicle under 11.1 mM glucose, scRNA-seq

city: Maebashi

first: Jun

last: Shirakawa

state: Gunma

address: 3-39-15, Showa-machi

department: Department of Diabetes and Metabolic Disorders

country: Japan

institute: Institute for Molecular and Cellular Regulation, Gunma University

description: 10x Genomics

data_processing:
The dimultiplexing, barcoded processing, gene counting were made using the Cell Ranger software (ver 6.0.2).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pancreatic islet cells

extract_protocol:
The islets were collected in microcentrifuge tubes, centrifuged at 100g for 1 minute, and washed with 1mL PBS. The islets were incubated in 700 μL Accutase for 5 minutes at 37℃, then gently pippeted 30 times using 1mL pippete. The reaction to disperse the islets was stopped by adding RPMI1640 containing 3.9 mM or 11.1 mM glucose, 30% FBS. The single-cell suspensions were centrifuged at 300g for 5 minutes, the supernatants were gently removed, then 1mL RPMI1640 containing 10% FBS and 3.9 mmol/LM or 11.1 mM glucose was added.
Approximately 10000 cells per sample were loaded onto a 10X Chromium Controller for GEM formation and cell barcoding using Next GEM Single Cell 30 v3.1 reagents. Barcoded single cells were subjected to cDNA synthesis and sequencing library construction using 10X Next GEM Single Cell 30 v3.1 reagents according to manufacturer’s instructions.

treatment_protocol: The islets were cultured for 24 hours in the presence or absence of 1 mM imeglimin under 3.9 mM or 11.1 mM glucose.

value: Pancreatic islet cells

value: Wild type

value: DMSO under 11.1 mM glucose


title: Imeglimin under 11.1 mM glucose, scRNA-seq

description: 10x Genomics

value: 1 mM imeglimin under 11.1 mM glucose


title: Exp.1_HEL_LSD1-ChIP-rep2

description: Library name: Exp.1_HEL_LSD1-ChIP-rep2

value: hematopoietic

value: HEL

value: blast-phase MPN (MPN-BP)

value: JAK2-V617F / TP53-loss


title: Myobacterium tuberculosis, LIN, 4 hrs, Biological Replicate 1

value: Mycobacterium tuberculosis Erdman with pMV306hsp+LuxG13

value: 4 hrs

value: LIN


title: Myobacterium tuberculosis, INH, 4 hrs, Biological Replicate 1

value: INH


title: Exp.1_HEL_H3K79me2-ChIP-rep1

description: Library name: Exp.1_HEL_H3K79me2-ChIP-rep1

value: anti-H3K79me2, CST, clone:D15E8, cat:5427S


title: Exp.1_HEL_H3K79me2-ChIP-rep2

description: Library name: Exp.1_HEL_H3K79me2-ChIP-rep2


title: WT-SINrepGAL4_REP2

data_processing:
nf-core/rnaseq Workflow
Assembly: dm6
Supplementary files format and content: raw count data in a .txt file

extract_protocol:
Third instar larval brains were dissected and RNA was extracted using TRIzol reagent (Life Technologies).
The siTOOLs riboPOOL kit was used for ribosomal RNA depletion. Paired-end strand-specific libraries were prepared using NEBNext Ultra II directional RNA library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.

value: third instar larva brain

value: +; Act>SIN


title: Exp.1_HEL_LSD1-ChIP-rep1

description: Library name: Exp.1_HEL_LSD1-ChIP-rep1

value: anti-LSD1, Abcam, clone:EPR6825, cat:ab129195


title: Imeglimin under 3.9 mM glucose, scRNA-seq

description: 10x Genomics

value: 1 mM imeglimin under 3.9 mM glucose


title: Exp.1_HEL_H3K4me1-ChIP-rep2

description: Library name: Exp.1_HEL_H3K4me1-ChIP-rep2

value: anti-H3K4me1, Abcam, clone:EPR16597, cat:ab176877


title: Myobacterium tuberculosis, ETH, 4 hrs, Biological Replicate 1

value: ETH


title: WT-SINrepGAL4_REP1


title: Exp.1_HEL_H3K4me1-ChIP-rep1

description: Library name: Exp.1_HEL_H3K4me1-ChIP-rep1


title: Myobacterium tuberculosis, CLZ, 4 hrs, Biological Replicate 1

value: CLZ


title: Exp.1_HEL_DOT1L-ChIP-rep3

description: Library name: Exp.1_HEL_DOT1L-ChIP-rep3

value: anti-DOT1L, CST, clone:D1W4Z, cat:77087S


title: Vehicle under 3.9 mM glucose, scRNA-seq

description: 10x Genomics

value: Pancreatic islet cells

value: Wild type

value: DMSO under 3.9 mM glucose


title: Myobacterium tuberculosis, BDQ, 4 hrs, Biological Replicate 1

value: BDQ


title: SINrep Replicate1

value: +; SIN


title: WT-SINrepGAL4_REP3


title: WT-SINrep_REP3


title: Sepsis16

city: fuzhou

first: siming

last: lin

state: fujian

address: 20 Chazhong Road

institute: The First Affiliated Hospital of Fujian Medical University

data_processing:
The raw data obtained from sequencing were filtered by SOAPnuke (v1.5.6), which filtered out 1) reads containing junctions (junction contamination); 2) reads with unknown base N content greater than 5%; and 3) low-quality reads (reads with the ratio of bases with quality value less than 15 to the total number of bases in the reads greater than 20% were considered as low-quality reads) to obtain clean data. reads), and clean data were obtained. Data were subsequently analyzed, mapped and mined using the Dr. Tom Multi-Organomics Data Mining System (https://biosys.bgi.com).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include RPKM values for each Samlpe

source_name: gastrocnemius muscle

growth_protocol: Male SPF-grade C57BL/6J mice, 3-4 mice per cage, were housed for 7 days in SPF conditions with appropriate humidity and temperature on a 12-hour light-dark cycle.Food and water were both available ad libitum.

extract_protocol:
RNA was harvested using Rneasy mini plus kit(Qiagen). 1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Qiagen mRNA-Seq library Prep Kit following manufacturer's protocols

treatment_protocol: The mice were randomly divided into sepsis and control groups. Mice in the sepsis group were injected intraperitoneally with a single dose of LPS at 10 mg/kg, whereas mice in the control group were replaced with an equal amount of saline. The mice were executed 18 h after LPS injection, respectively, and the gastrocnemius muscle was taken immediately. Gastrocnemius muscle tissues were collected from each group (sepsis group = 8 mice, control group = 7 mice) and then subjected to RNA sequencing.

value: gastrocnemius muscle

value: LPS


title: Exp.1_HEL_DOT1L-ChIP-rep2

description: Library name: Exp.1_HEL_DOT1L-ChIP-rep2

value: hematopoietic

value: HEL

value: blast-phase MPN (MPN-BP)

value: JAK2-V617F / TP53-loss


title: Sepsis15


title: Exp.1_HEL_DOT1L-ChIP-rep1

description: Library name: Exp.1_HEL_DOT1L-ChIP-rep1


title: Sepsis14


title: WT-SINrep_REP2

value: third instar larva brain


title: WT-SINrep_REP1


title: Sepsis13


title: infected day3, rep3

city: Chicago

first: Shabaana

middle: A

last: Khader

address: 5801 S Ellis Ave

institute: University of Chicago

description:
Library name: sample13
10X genomics

data_processing:
demultiplexing, alignment, raw gene expression matrices were by the Cell Ranger software (10x Genomics, version 6.1.1) available on the 10x website
Assembly: Macaca mulatta 10
Supplementary files format and content: tab seperated values files and matrix files

organism: Macaca mulatta

source_name: BAL Cells

extract_protocol:
Single-cell suspensions from BAL obtained at different time points were collected and cryopreserved in Cryostor-CS10 (Biolife Solutions, USA) at -70ºC and then used for single cell RNAlibrary preparation as per manufacturer's instructions (10x genomics).
10x 3' GEX

value: BAL Cells

value: Airway cells, Leukocytes

value: infected with sars-cov2

tag: time post_infection

value: day 3


title: Sepsis12


title: U39B-del3GAL4_REP2

value: {delta}9B3; Act>SIN


title: U39B-del3GAL4_REP3


title: infected day3, rep1

description:
Library name: sample11
10X genomics


title: infected day2, rep3

description:
Library name: sample10
10X genomics

value: day 2


title: Sepsis11


title: U39B-del3GAL4_REP1


title: infected day2, rep2

description:
Library name: sample9
10X genomics


title: infected day3, rep4

description:
Library name: sample14
10X genomics


title: Sepsis10


title: infected day2, rep1

description:
Library name: sample8
10X genomics


title: Sepsis09


title: U39B-del3_REP1

value: {delta}9B3; SIN


title: infected day1, rep4

description:
Library name: sample7
10X genomics

value: day 1


title: infected day3, rep2

description:
Library name: sample12
10X genomics


title: Control08

value: saline


title: U39B-del3_REP2


title: Control07


title: U39B-del1GAL4_REP3

value: {delta}9B1; Act>SIN


title: infected day1, rep3

description:
Library name: sample6
10X genomics


title: infected day1, rep2

description:
Library name: sample5
10X genomics


title: U39B-del1GAL4_REP1


title: U39B-del1GAL4_REP2


title: Control04

value: gastrocnemius muscle


title: heart_20m_rep1

type: RNA

city: Shanghai

first: Zheng

last: Kuai

address: No180 fenglin Road

institute: Zhongshan Hospital Fudan University

description: Gene expression in 20m mouse heart

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Gene Expression Microarrays (G2545A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: heart,20m, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using the One-Color Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Heart tissue was cryopulverized by the Biopulverizer（BIospec，Bartlesville，OK）. RNAs were isolated in TRIzol Reagent. RNA was quantified using a NanoDrop-1000 spectrophotometer

value: heart

tag: gender

value: male

tag: age


title: heart_20m_rep4

description: Gene expression in 20m mouse heart

source_name: heart,20m, replicate 4


title: Control03


title: heart_3m_rep4

description: Gene expression in 3m mouse heart

source_name: heart,3m, replicate 4


title: baseline, rep3

description:
Library name: sample3
10X genomics

value: day 0


title: heart_3m_rep3

description: Gene expression in 3m mouse heart

source_name: heart,3m, replicate 3


title: U39B-del1_REP3

value: {delta}9B1; SIN


title: heart_20m_rep3

description: Gene expression in 20m mouse heart

source_name: heart,20m, replicate 3


title: heart_3m_rep2

description: Gene expression in 3m mouse heart

source_name: heart,3m, replicate 2


title: heart_20m_rep2

description: Gene expression in 20m mouse heart

source_name: heart,20m, replicate 2


title: U39B-del3_REP3


title: heart_3m_rep1

description: Gene expression in 3m mouse heart

source_name: heart,3m, replicate 1


title: baseline, rep2

description:
Library name: sample2
10X genomics


title: Control02


title: U39B-del1_REP2


title: Control01


title: Control05


title: CAD_147

status: Public on Jul 28 2025

type: genomic

city: Miaoli County

middle: Wei-Che

last: Hsu

state: Taiwan

address: Zhunan: 35, Keyan Road, Zhunan Town

department: National Health Research Institutes

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: Using the Axiom Genome-Wide Array Plate technology platform provided by Thermo Fisher Scientific Inc.

data_processing:
Import the CEL files into Axiom Analysis Suite, using Best Practices Workflow from the recommendations of the Axiom Genotyping Solution-Data Analysis Guide. Annotation and library downloaded from Taiwan Biobank (https://www.biobank.org.tw/fd.php)
SNP ID: dbSNP_RS_ID and affy_snp_id; SNP Call: AA, AB, BB, and NoCall; SNP Annotation: Allele_A, Allele_B, Ref_Allele and Alt_Allele; SNP Quality: CR(Call Rate), ConversionType; SNP frequency: n_AA, n_AB, n_BB, n_NC and MinorAlleleFrequency.

label: biotin

source_name: peripheral white blood cells

label_protocol: The CAD group comprised individuals demonstrating angiographic evidence showing significant (>75%) coronary artery stenosis post-administration of intracoronary nitroglycerine (50-200 μg), individuals with a history of percutaneous coronary revascularization or individuals who had undergone coronary artery bypass grafting. The high-risk group consisted of individuals whose calculated 10-year and lifetime risk of atherosclerotic cardiovascular disease (ASCVD) equaled or exceeded 20% based on established criteria, but without any history of angina pectoris or myocardial infarction. The criteria for inclusion in the control group encompassed a number of factors, namely the absence of major systemic diseases, various specific fasting measurements including high-density lipoprotein (HDL) levels (>40 mg/dL for males, >50 mg/dL for females), fasting glucose levels (<100 mg/dL), fasting triglyceride (TG) levels (<150 mg/dL), systolic blood pressure (SBP) below 130 mmHg, diastolic blood pressure (DBP) below 85 mmHg, and a waist circumference below 80 cm for females or 90 cm for males.

growth_protocol: Peripheral venous blood was obtained after an overnight fast.

extract_protocol: After centrifugation, the plasma component of the blood was used for either immediate biochemistry analysis or for storage at -80o C for the subsequent measurements. Genomic DNA was then isolated from peripheral white blood cells using the phenol/chloroform DNA extraction method after lysis of red blood cells.

tag: disease state

value: CAD

value: female


title: baseline, rep1

description:
Library name: sample1
10X genomics

value: BAL Cells


title: heart_20m_rep5

description: Gene expression in 20m mouse heart

source_name: heart,20m, replicate 5


title: CAD_145

scan_protocol: Using the Axiom Genome-Wide Array Plate technology platform provided by Thermo Fisher Scientific Inc.


title: heart_3m_rep5

description: Gene expression in 3m mouse heart

source_name: heart,3m, replicate 5


title: CAD_144


title: CAD_141


title: CAD_142


title: CAD_140


title: CAD_138


title: Dicer1 +/- Stroma 3

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

description: TASD 227 (MEH138)

hyb_protocol: Amplified cDNA was prepared using the Ovation Pico WTA System V2 (#3302, Nugen)

scan_protocol: Affymetrix Titan scanner

data_processing: Data were imported into Partek Genome Suite 6.6, visualized by principal component analysis to check for consistency of samples and class variance; rma_values.allGenes.txt

source_name: Dicer1 +/- Stroma

label_protocol: standard Affymetrix protocol

extract_protocol:
Tissues were manually dissociated and then digested for 1 hour at 37°C in 2 U/mL Collagenase B (#11088831001, Roche)/Dispase II (#04942078001, Roche), 50 mM HEPES/KOH pH 7.4; 150 mM NaCl. Cells were then spun down and resuspended in 2X volume 10% fetal bovine serum (FBS) (#SH30910.03, GE Hyclone) in phosphate buffered saline (PBS) to inactive digestion enzymes, samples were sequentially filtered through 70 μm (#22363548, Fisher) and 40 μm (#22363547, Fisher) filters to yield single cell suspensions. Data was acquired on a FACS Aria Cellsorter (BD Biosciences) and analyzed using FACSDiva software. DAPI used as a live/dead cell marker.
RNA was isolated from sorted cell populations using a miRNEasy Micro Kit (#217084, Qiagen)

value: FACS purified PECAM1-;Tomato- stroma cells

value: Dicer1 +/-


title: CAD_143


title: Dicer1 +/- Stroma 1

description: TASD 178 (MEH129)


title: CAD_139


title: CAD_136


title: Dicer1 +/- Stroma 2

description: TASD 200 (MEH135)


title: U39B-del1_REP1

source_name: third instar larva brain

value: third instar larva brain


title: CAD_137


title: CAD_135


title: CAD_134


title: CAD_133


title: CAD_126


title: CAD_129


title: CAD_131


title: CAD_130


title: CAD_128


title: CAD_127


title: CAD_124


title: CAD_122


title: CAD_123


title: CAD_116


title: CAD_119


title: CAD_117


title: CAD_113


title: CAD_118


title: CAD_114


title: CAD_120


title: CAD_111


title: CAD_132


title: CAD_110


title: CAD_109


title: CAD_112


title: CAD_125


title: CAD_108


title: CAD_107


title: CAD_106


title: CAD_121


title: CAD_105


title: CAD_103


title: CAD_104


title: CAD_115


title: CAD_101


title: CAD_102


title: CAD_98


title: CAD_100


title: CAD_99


title: CAD_96


title: CAD_95


title: CAD_93


title: CAD_97


title: CAD_94


title: CAD_89


title: CAD_91


title: CAD_92


title: CAD_86


title: CAD_85


title: CAD_87


title: CAD_88


title: CAD_84


title: CAD_83


title: CAD_81


title: CAD_82


title: CAD_79


title: CAD_78


title: CAD_77


title: CAD_76


title: CAD_75


title: CAD_72


title: CAD_70


title: CAD_74


title: CAD_69


title: CAD_71


title: CAD_90


title: CAD_67


title: CAD_65


title: CAD_68


title: CAD_66


title: CAD_64


title: CAD_63


title: CAD_146


title: CAD_59


title: CAD_62


title: CAD_61


title: CAD_57


title: CAD_80


title: CAD_56


title: CAD_55


title: CAD_54


title: CAD_53


title: CAD_52


title: CAD_60


title: CAD_73


title: CAD_51


title: CAD_49


title: CAD_50


title: CAD_47


title: CAD_48


title: CAD_46


title: CAD_58


title: CAD_45


title: CAD_43


title: CAD_44


title: CAD_42


title: CAD_41


title: CAD_39


title: CAD_36


title: CAD_37


title: CAD_38


title: CAD_35


title: CAD_34


title: infected day1, rep1

description:
Library name: sample4
10X genomics

value: Airway cells, Leukocytes

value: infected with sars-cov2


title: CAD_33


title: CAD_32


title: CAD_31


title: CAD_28


title: CAD_27


title: CAD_29


title: CAD_26


title: CAD_30


title: CAD_23


title: CAD_22


title: CAD_25


title: CAD_24


title: CAD_21


title: CAD_20


title: CAD_19


title: CAD_40


title: CAD_17


title: CAD_18


title: CAD_16


title: CAD_15


title: CAD_13


title: CAD_14


title: CAD_12


title: CAD_11


title: CAD_9


title: CAD_10


title: CAD_8


title: CAD_7


title: CAD_4


title: CAD_6


title: CAD_5


title: CAD_2


title: CAD_3


title: High_Risk_361


title: CAD_1


title: High_Risk_362


title: High_Risk_360


title: High_Risk_359


title: High_Risk_358


title: High_Risk_355


title: High_Risk_357


title: High_Risk_354


title: High_Risk_356


title: High_Risk_351


title: High_Risk_363


title: High_Risk_353


title: High_Risk_352


title: High_Risk_350


title: High_Risk_349


title: High_Risk_346


title: High_Risk_347


title: High_Risk_348


title: High_Risk_345


title: High_Risk_343


title: High_Risk_344


title: High_Risk_342


title: High_Risk_340


title: High_Risk_338


title: High_Risk_337


title: High_Risk_336


title: High_Risk_333


title: High_Risk_334


title: High_Risk_335


title: High_Risk_332


title: High_Risk_331


title: High_Risk_328


title: High_Risk_327


title: High_Risk_326


title: High_Risk_329


title: High_Risk_325


title: High_Risk_322


title: High_Risk_320


title: High_Risk_323


title: High_Risk_321


title: High_Risk_317


title: High_Risk_316


title: High_Risk_324


title: High_Risk_341


title: High_Risk_315


title: High_Risk_312


title: High_Risk_311


title: High_Risk_314


title: High_Risk_319


title: High_Risk_330


title: High_Risk_308


title: High_Risk_306


title: High_Risk_307


title: High_Risk_305


title: High_Risk_318


title: High_Risk_301


title: High_Risk_302


title: High_Risk_303


title: High_Risk_300


title: High_Risk_304


title: High_Risk_299


title: High_Risk_298


title: High_Risk_292


title: High_Risk_313


title: High_Risk_291


title: High_Risk_290


title: High_Risk_310


title: High_Risk_295


title: High_Risk_287


title: High_Risk_309


title: High_Risk_293


title: High_Risk_288


title: High_Risk_296


title: High_Risk_285


title: High_Risk_294


title: High_Risk_289


title: High_Risk_284


title: High_Risk_283


title: High_Risk_297


title: High_Risk_339


title: High_Risk_282


title: High_Risk_276


title: High_Risk_278


title: High_Risk_277


title: High_Risk_279


title: High_Risk_274


title: High_Risk_286


title: High_Risk_268


title: High_Risk_273


title: High_Risk_272


title: High_Risk_271


title: High_Risk_269


title: High_Risk_267


title: High_Risk_266


title: High_Risk_265


title: High_Risk_270


title: High_Risk_259


title: High_Risk_264


title: High_Risk_260


title: High_Risk_262


title: High_Risk_258


title: High_Risk_280


title: High_Risk_255


title: High_Risk_256


title: High_Risk_257


title: High_Risk_254


title: High_Risk_275


title: High_Risk_253


title: High_Risk_281


title: High_Risk_251


title: High_Risk_249


title: High_Risk_263


title: High_Risk_250


title: High_Risk_252


title: High_Risk_247


title: High_Risk_261


title: High_Risk_246


title: High_Risk_245


title: High_Risk_244


title: High_Risk_241


title: High_Risk_240


title: High_Risk_242


title: High_Risk_239


title: High_Risk_237


title: High_Risk_235


title: High_Risk_236


title: High_Risk_232


title: High_Risk_234


title: High_Risk_231


title: High_Risk_243


title: High_Risk_229


title: High_Risk_248


title: High_Risk_228


title: High_Risk_227


title: High_Risk_223


title: High_Risk_224


title: High_Risk_219


title: High_Risk_218


title: High_Risk_233


title: High_Risk_217


title: High_Risk_216


title: High_Risk_238


title: High_Risk_215


title: High_Risk_213


title: High_Risk_226


title: High_Risk_212


title: High_Risk_214


title: High_Risk_211


title: High_Risk_210


title: High_Risk_208


title: High_Risk_207


title: High_Risk_205


title: High_Risk_203


title: High_Risk_201


title: High_Risk_204


title: High_Risk_200


title: High_Risk_202


title: High_Risk_221


title: High_Risk_199


title: High_Risk_197


title: High_Risk_195


title: High_Risk_196


title: High_Risk_194


title: High_Risk_209


title: High_Risk_192


title: High_Risk_191


title: High_Risk_206


title: High_Risk_193


title: High_Risk_185


title: High_Risk_188


title: High_Risk_190


title: High_Risk_183


title: High_Risk_187


title: High_Risk_182


title: High_Risk_189


title: High_Risk_181


title: High_Risk_177


title: High_Risk_179


title: High_Risk_230


title: High_Risk_198


title: High_Risk_178


title: High_Risk_176


title: High_Risk_175


title: High_Risk_184


title: High_Risk_174


title: High_Risk_173


title: High_Risk_186


title: High_Risk_172


title: High_Risk_171


title: High_Risk_168


title: High_Risk_169


title: High_Risk_167


title: High_Risk_180


title: High_Risk_170


title: High_Risk_225


title: High_Risk_165


title: High_Risk_164


title: High_Risk_161


title: High_Risk_156


title: High_Risk_162


title: High_Risk_155


title: High_Risk_157


title: High_Risk_159


title: High_Risk_154


title: High_Risk_158


title: High_Risk_160


title: High_Risk_152


title: High_Risk_153


title: High_Risk_150


title: High_Risk_149


title: High_Risk_151


title: High_Risk_148


title: High_Risk_166


title: High_Risk_147


title: High_Risk_146


title: High_Risk_145


title: High_Risk_163


title: High_Risk_142


title: High_Risk_140


title: High_Risk_144


title: High_Risk_141


title: High_Risk_143


title: High_Risk_138


title: High_Risk_139


title: High_Risk_137


title: High_Risk_134


title: High_Risk_136


title: High_Risk_132


title: High_Risk_133


title: High_Risk_131


title: High_Risk_130


title: High_Risk_129


title: High_Risk_127


title: High_Risk_126


title: High_Risk_128


title: High_Risk_125


title: High_Risk_124


title: High_Risk_123


title: High_Risk_121


title: High_Risk_118


title: High_Risk_120


title: High_Risk_117


title: High_Risk_119


title: High_Risk_116


title: High_Risk_115


title: High_Risk_135


title: High_Risk_112


title: High_Risk_110


title: High_Risk_113


title: High_Risk_111


title: High_Risk_122


title: High_Risk_108


title: High_Risk_107


title: High_Risk_106


title: High_Risk_105


title: High_Risk_103


title: High_Risk_102


title: High_Risk_101


title: High_Risk_100


title: High_Risk_99


title: High_Risk_104


title: High_Risk_98


title: High_Risk_114


title: High_Risk_96


title: High_Risk_97


title: High_Risk_92


title: High_Risk_93


title: High_Risk_94


title: High_Risk_95


title: High_Risk_109


title: High_Risk_91


title: High_Risk_88


title: High_Risk_90


title: High_Risk_86


title: High_Risk_85


title: High_Risk_87


title: High_Risk_89


title: High_Risk_83


title: High_Risk_82


title: High_Risk_81


title: High_Risk_80


title: High_Risk_78


title: High_Risk_77


title: High_Risk_75


title: High_Risk_73


title: High_Risk_76


title: High_Risk_74


title: High_Risk_72


title: High_Risk_70


title: High_Risk_69


title: High_Risk_71


title: High_Risk_67


title: High_Risk_68


title: High_Risk_84


title: High_Risk_64


title: High_Risk_65


title: High_Risk_66


title: High_Risk_79


title: High_Risk_62


title: High_Risk_59


title: High_Risk_58


title: High_Risk_57


title: High_Risk_55


title: High_Risk_60


title: High_Risk_54


title: High_Risk_63


title: High_Risk_220


title: High_Risk_52


title: High_Risk_61


title: High_Risk_53


title: High_Risk_51


title: High_Risk_56


title: High_Risk_48


title: High_Risk_222


title: High_Risk_50


title: High_Risk_49


title: High_Risk_47


title: High_Risk_46


title: High_Risk_43


title: High_Risk_44


title: High_Risk_41


title: High_Risk_42


title: High_Risk_45


title: High_Risk_38


title: High_Risk_40


title: High_Risk_39


title: High_Risk_35


title: High_Risk_36


title: High_Risk_34


title: High_Risk_33


title: High_Risk_32


title: High_Risk_30


title: High_Risk_28


title: High_Risk_31


title: High_Risk_25


title: High_Risk_29


title: High_Risk_21


title: High_Risk_22


title: High_Risk_20


title: High_Risk_19


title: High_Risk_27


title: High_Risk_26


title: High_Risk_18


title: High_Risk_17


title: High_Risk_24


title: High_Risk_37


title: High_Risk_12


title: High_Risk_9


title: High_Risk_15


title: High_Risk_10


title: High_Risk_8


title: High_Risk_16


title: High_Risk_7


title: High_Risk_14


title: High_Risk_13


title: High_Risk_4


title: High_Risk_23


title: High_Risk_6


title: High_Risk_5


title: High_Risk_3


title: High_Risk_1


title: High_Risk_11


title: Control_270

value: Control


title: Control_271


title: High_Risk_2


title: Control_268


title: Control_266


title: Control_267


title: Control_262


title: Control_265


title: Control_259


title: Control_263


title: Control_258


title: Control_257


title: Control_260


title: Control_255


title: Control_256


title: Control_252


title: Control_250


title: Control_254


title: Control_246


title: Control_248


title: Control_269


title: Control_261


title: Control_245


title: Control_243


title: Control_247


title: Control_242


title: Control_244


title: Control_240


title: Control_264


title: Control_253


title: Control_239


title: Control_251


title: Control_234


title: Control_249


title: Control_236


title: Control_233


title: Control_238


title: Control_237


title: Control_231


title: Control_232


title: Control_230


title: Control_228


title: Control_229


title: Control_226


title: Control_227


title: Control_225


title: Control_241


title: Control_224


title: Control_235


title: Control_223


title: Control_222


title: Control_220


title: Control_219


title: Control_218


title: Control_221


title: Control_217


title: Control_215


title: Control_214


title: Control_211


title: Control_213


title: Control_210


title: Control_209


title: Control_212


title: Control_206


title: Control_207


title: Control_205


title: Control_203


title: Control_204


title: Control_201


title: Control_200


title: Control_208


title: Control_198


title: Control_199


title: Control_197


title: Control_196


title: Control_194


title: Control_216


title: Control_195


title: Control_193


title: Control_188


title: Control_190


title: Control_189


title: Control_187


title: Control_185


title: Control_191


title: Control_184


title: Control_186


title: Control_178


title: Control_179


title: Control_183


title: Control_202


title: Control_181


title: Control_182


title: Control_176


title: Control_175


title: Control_174


title: Control_171


title: Control_170


title: Control_173


title: Control_192


title: Control_168


title: Control_169


title: Control_167


title: Control_180


title: Control_166


title: Control_177


title: Control_164


title: Control_165


title: Control_162


title: Control_161


title: Control_159


title: Control_172


title: Control_153


title: Control_163


title: Control_151


title: Control_150


title: Control_154


title: Control_152


title: Control_148


title: Control_157


title: Control_147


title: Control_146


title: Control_145


title: Control_141


title: Control_142


title: Control_144


title: Control_143


title: Control_160


title: Control_140


title: Control_139


title: Control_156


title: Control_138


title: Control_158


title: Control_137


title: Control_155


title: Control_136


title: Control_133


title: Control_132


title: Control_149


title: Control_131


title: Control_134


title: Control_129


title: Control_130


title: Control_128


title: Control_127


title: Control_126


title: Control_125


title: Control_124


title: Control_123


title: Control_122


title: Control_121


title: Control_116


title: Control_135


title: Control_119


title: Control_118


title: Control_115


title: Control_114


title: Control_113


title: Control_111


title: Control_109


title: Control_110


title: Control_112


title: Control_106


title: Control_107


title: Control_108


title: Control_105


title: Control_99


title: Control_102


title: Control_104


title: Control_103


title: Control_98


title: Control_101


title: Control_97


title: Control_117


title: Control_100


title: Control_95


title: Control_96


title: Control_93


title: Control_120


title: Control_91


title: Control_89


title: Control_94


title: Control_90


title: Control_88


title: Control_86


title: Control_87


title: Control_83


title: Control_84


title: Control_85


title: Control_82


title: Control_81


title: Control_79


title: Control_80


title: Control_78


title: Control_73


title: Control_74


title: Control_76


title: Control_92


title: Control_70


title: Control_69


title: Control_68


title: Control_66


title: Control_77


title: Control_64


title: Control_61


title: Control_71


title: Control_67


title: Control_58


title: Control_57


title: Control_63


title: Control_60


title: Control_56


title: Control_55


title: Control_53


title: Control_54


title: Control_51


title: Control_52


title: Control_72


title: Control_75


title: Control_50


title: Control_65


title: Control_62


title: Control_48


title: Control_46


title: Control_47


title: Control_42


title: Control_45


title: Control_43


title: Control_39


title: Control_40


title: Control_41


title: Control_37


title: Control_38


title: Control_32


title: Control_35


title: Control_34


title: Control_33


title: Control_30


title: Control_28


title: Control_29


title: Control_27


title: Control_31


title: Control_25


title: Control_26


title: Control_22


title: Control_24


title: Control_44


title: Control_21


title: Control_20


title: Control_36


title: Control_19


title: Control_17


title: Control_18


title: Control_16


title: Control_14


title: Control_15


title: Control_13


title: Control_12


title: Control_10


title: Control_11


title: Control_23


title: Control_7


title: Control_6


title: Control_8


title: Control_9


title: Control_59


title: Control_2


title: Control_5


title: Control_3


title: T4 pAP142 line 22.4.15 timepoint2 rep3

city: La Jolla

first: Allen

last: Mamerto

state: CA

address: 10010 N Torrey Pines Rd

department: Plant Molecular and Cellular Biology Laboratory

institute: Salk Institute for Biological Studies

description:
Library name: Atha_T4_pAP142_22.4.15_t2_rep3
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.

data_processing:
RNA-seq libraries were mapped to the Araport11 reference genome using hisat2(v2.2.1). The RNA-seq libraries were also quantified against the Araport11 primary transcriptome using salmon(v1.6.0). Initial characterization and DE analysis of the samples was performed with DEseq2(v1.44.0).
Assembly: Araport11
Supplementary files format and content: tab-delimited files with TPMs and read counts for transcript-level quantification.

source_name: pooled seedlings

extract_protocol:
All RNA extractions were done using the Direct-zol RNA Miniprep Kit (Zymo Research).
To prepare libraries for RNA-seq, the Illumina Stranded mRNA Library Prep Kit was used.

value: pooled seedlings


title: Control_1


title: T4 pAP142 line 22.4.15 timepoint2 rep2

description:
Library name: Atha_T4_pAP142_22.4.15_t2_rep2
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: Control_4


title: T4 pAP142 line 22.4.15 timepoint2 rep1

description:
Library name: Atha_T4_pAP142_22.4.15_t2_rep1
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T4 pAP142 line 22.4.15 timepoint1 rep2

description:
Library name: Atha_T4_pAP142_22.4.15_t1_rep2
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T4 pAP142 line 22.4.15 timepoint1 rep3

description:
Library name: Atha_T4_pAP142_22.4.15_t1_rep3
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T4 pAP141 line 25.12.63 timepoint1 rep3

description:
Library name: Atha_T4_pAP141_25.12.63_t1_rep3
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T4 pAP141 line 25.12.63 timepoint1 rep1

description:
Library name: Atha_T4_pAP141_25.12.63_t1_rep1
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T3 pAP146 line 17.11 (sibling control) rep3

description:
Library name: Atha_T3_pAP146_17.11_sibling_rep3
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.

source_name: leaves

value: leaves


title: T3 pAP146 line 17.11 (homozygous) rep3

description:
Library name: Atha_T3_pAP146_17.11_hom_rep3
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.

source_name: seedling

value: seedling


title: T3 pAP146 line 17.11 (sibling control) rep4

description:
Library name: Atha_T3_pAP146_17.11_sibling_rep4
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T4 pAP141 line 25.12.63 timepoint2 rep2

description:
Library name: Atha_T4_pAP141_25.12.63_t2_rep2
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T4 pAP141 line 25.12.63 timepoint1 rep2

description:
Library name: Atha_T4_pAP141_25.12.63_t1_rep2
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T4 pAP142 line 22.4.15 timepoint1 rep1

description:
Library name: Atha_T4_pAP142_22.4.15_t1_rep1
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T3 pAP146 line 17.11 (sibling control) rep2

description:
Library name: Atha_T3_pAP146_17.11_sibling_rep2
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: Col-0_146 rep4

description:
Library name: Atha_Col0_pAP146_rep4
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T4 pAP141 line 25.12.63 timepoint1 rep4

description:
Library name: Atha_T4_pAP141_25.12.63_t1_rep4
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T4 pAP141 line 25.12.63 timepoint2 rep1

description:
Library name: Atha_T4_pAP141_25.12.63_t2_rep1
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T3 pAP146 line 17.11 (sibling control) rep1

description:
Library name: Atha_T3_pAP146_17.11_sibling_rep1
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T3 pAP146 line 17.11 (heterozygous) rep1

description:
Library name: Atha_T3_pAP146_17.11_het_rep1
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: Col-0_146 rep1

description:
Library name: Atha_Col0_pAP146_rep1
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: Col-0_146 rep2

description:
Library name: Atha_Col0_pAP146_rep2
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T3 pAP146 line 17.11 (homozygous) rep4

description:
Library name: Atha_T3_pAP146_17.11_hom_rep4
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T3 pAP146 line 17.11 (homozygous) rep1

description:
Library name: Atha_T3_pAP146_17.11_hom_rep1
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: Col-0 timepoint2 rep2

description:
Library name: Atha_Col0_t2_rep2
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T3 pAP146 line 17.11 (homozygous) rep2

description:
Library name: Atha_T3_pAP146_17.11_hom_rep2
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T3 pAP146 line 17.11 (heterozygous) rep3

description:
Library name: Atha_T3_pAP146_17.11_het_rep3
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: Col-0 timepoint1 rep4

description:
Library name: Atha_Col0_t1_rep4
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: Col-0 timepoint2 rep1

description:
Library name: Atha_Col0_t2_rep1
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: T3 pAP146 line 17.11 (heterozygous) rep2

description:
Library name: Atha_T3_pAP146_17.11_het_rep2
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: Col-0 timepoint1 rep3

description:
Library name: Atha_Col0_t1_rep3
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: Col-0 timepoint1 rep2

description:
Library name: Atha_Col0_t1_rep2
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: Col-0_146 rep3

description:
Library name: Atha_Col0_pAP146_rep3
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: Col-0 timepoint1 rep1

description:
Library name: Atha_Col0_t1_rep1
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: Infected fruit, 6 days post harvest, S16

city: Davis

first: Barbara

last: Blanco-Ulate

state: California

address: One Shields Ave

department: Plant Sciences

institute: University of California Davis

data_processing:
Raw reads were quasi-mapped to a combined papaya and C. gloeosporioides and C. truncatum transcriptomes using Salmon (v.1.10.3)
Parameter set includes: “-l A”, “-p 8”, and the “--validateMappings --posBias --seqBias --gcBias” flags.
Count matrices were made from the Salmon output using the Bioconductor package tximport (Love et al., 2017)
Assembly: Carica papaya SunUp (SAMC462411), Colletotrichum gloeosporioides (GCF_011800055.1), Colletotrichum truncatum (GCA_014235925.2)
Supplementary files format and content: Processed data file contains read counts per sample, with each sample being listed on one column from column B-M, and gene IDs being listed on column A

organism: Carica papaya

source_name: fruit tissue

extract_protocol:
RNA was extracted from 1 g of ground tissue as described in Blanco-Ulate et al. (2013).
Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, CA).

value: fruit tissue

tag: natural anthracnose_infections

value: Colletotrichum gloeosporioides, Colletotrichum truncatum

tag: time

value: 6 days post harvest


title: Infected fruit, 5 days post harvest, S12

value: 5 days post harvest


title: Col-0 timepoint2 rep3

description:
Library name: Atha_Col0_t2_rep3
RNAseq libraries mapped with hisat2, quantified with salmon, and DE analysis with DEseq2.


title: Infected fruit, 6 days post harvest, S13


title: Infected fruit, 6 days post harvest, S14


title: Infected fruit, 5 days post harvest, S11


title: Infected fruit, 5 days post harvest, S10


title: Infected fruit, 5 days post harvest, S4


title: Infected fruit, 5 days post harvest, S3


title: Infected fruit, 6 days post harvest, S8


title: Infected fruit, 6 days post harvest, S6


title: Infected fruit, 6 days post harvest, S5


title: G217Bura5-DA dbcAMP C-2 (wt_10mM)

city: San Francisco

first: Mark

last: Voorhies

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

data_processing:
Transcript abundances were quantified based on version ucsf_hc.01_1.G217B of the Histoplasma G217B transcriptome (S5 Data of PMID:26177267). Relative abundances (reported as TPM values) and estimated counts (est_counts) of each transcript in each sample were estimated by alignment free comparison of k-mers between the reads and mRNA sequences using KALLISTO version 0.46.0. Further analysis was restricted to transcripts with TPM ≥ 10 in at least one sample.
Differentially expressed genes were identified by comparing replicate means for contrasts of interest using LIMMA version 3.30.8. Genes were considered significantly differentially expressed if they were statistically significant (at 5% FDR) with an effect size of at least 1.5x (absolute log2 fold change ≥ 0.585) for a given contrast.
For comparison with previous expression profiling, the above KALLISTO/LIMMA pipeline was applied to the reads from PMID:26177267 (SRA accession SRP058149) and LIMMA fit parameters were taken from S2 Data of PMID:31568523.
The results of the LIMMA analysis are in supplementary file Table_all_genes_2.cdt, an Excel-compatible tab-delimited text file conforming to JavaTreeView extended CDT format.  Each row is a transcript with the UNIQID column giving the systematic gene name from PMID:26177267.  Annotation columns are taken from S4 of PMID:35089059: NAME -- manually curated short gene name; Description; HcG217B_pred -- systematic name from the 9/21/2005 predicted gene set from Washington University; HcG217B_acc -- GenBank accession from GCA_017607445.1; HcG217B_rc -- repeat classification as in fig 4A of PMID:35089059.  ChIP-chip associations (RypX_chip columns) are taken from S2 of PMID:23935449 based on the HcG217B_pred column.  The p(X) columns give limma BH-adjusted p-values for differential expression in each contrast.  Class indicates the differential expression pattern and BGCOLOR gives class-specific hex color codes.  GWEIGHT is a place-holder column for JavaTreeView compatibility.  The final seven columns give the limma fit contrasts as log2(CPM ratio) values; viz., dbcAMP/ddw|1, CPT/ddw|1, and butyrate/ddw|1 give differential expression in response to treatment for samples in batch 1; d8/t=0|Rodriguez and Y/H|Gilmore give comparison contrasts from prior publications (PMID:26177267 and PMID:31568523); and (WT/SG1|2 and dbcAMP/ddw|2) give differential expression in reponse to treatment for samples in batch 2.
Assembly: Version ucsf_hc.01_1.G217B of the Hc G217B transcriptome (S5 Data of PMID:26177267)
Supplementary files format and content: tab-delimited text files include TPM and estimated count values for each sample

organism: Histoplasma ohiense

source_name: yeast cells

extract_protocol:
Total RNA was extracted from fungal cells using a Qiazol-based RNA extraction protocol. Frozen, resuspended pellets of cells were incubated at RT for 5 minutes to thaw. The lysate was subjected to bead beating (Mini-Beadbeater, Biospec Products, Bartlesville, OK) followed by a chloroform extraction. The aqueous phase was then transferred to an Epoch RNA column where the filter was washed with 3 M NaOAc (pH=5.5) and then with 10 mM TrisCl (pH=7.5) in 80% EtOH. DNase (Purelink, Invitrogen, Carlsbad, CA) treatment was used to remove any residual DNA, and the filters were washed again with NaOAc and TrisCl before eluting the RNA in nuclease-free water.  For each experiment, mRNA was extracted from an equal amount of total RNA (up to 20 μg) of each sample. Total RNA samples and were treated with rDNase I (Ambion). RNA quality was determined with a RNA 6000 Nano Bioanalyzer chip (Agilent Technologies, Santa Clara, CA). mRNA was purified using polyA selection with Oligo-dT Dynabeads (Thermo Fisher, Waltham, MA) as described in the manufacturer’s protocol. Ribosomal RNA depletion was confirmed with an RNA 6000 Nano Bioanalyzer chip.
Libraries for RNAseq were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA). Individual libraries were uniquely barcoded with NEBNext Multiplex Oligos for Illumina sequencing platform (New England Biolabs, Ipswich, MA). Average fragment size and presence of excess adapter was determined with High Sensitivity DNA Bioanalyzer chip from Agilent Technologies (Santa Clara, CA). Libraries had an average fragment length of 300 to 500 bp. The concentration of the individual libraries was quantified using the KAPA library quantification kit. A total of 5 ng of each library was pooled into each final libraries and run on a High Sensitivity DNA Bioanalyzer chip to determine the average fragment size of the final pooled samples. The final libraries were submitted to the UCSF Center for Advanced Technology for sequencing on an Illumina HiSeq 4000 sequencer.

treatment_protocol: Samples were prepared in two separate experiments. In the first experiment, Histoplasma G217Bura5 was grown in liquid HMM culture at 37°C for 2 passages. On the day of chemical addition, the culture was passaged into fresh HMM + GlcNAc at a final OD600 of 0.2, and 10 mM dbcAMP, 4 mM 8-CPT-cAMP, 5 mM of sodium butyrate, or filter-sterilized autoclaved water (vehicle control) were added to the appropriate cultures, with 3 biological replicates for each chemical. Cultures were returned to 37°C growth with shaking. 2 days after the addition of each chemical, a small volume of each culture was fixed by adding paraformaldehyde (final paraformaldehyde concentration 4% v/v), and 10 ml of each culture were harvested by filtration using Nalgene Rapid-Flow Sterile Disposable Bottle Top Filters with SFCA Membrane (Fisher 09-740-22G). Cells were scraped from the filter into tubes containing 1mL of Qiazol (Qiagen) and promptly flash-frozen in liquid nitrogen. In the second experiment, Histoplasma G217Bura5 or the SG1 mutant were grown in liquid HMM culture at 37°C for 2 passages. On the day of dbcAMP addition, the cultures were passaged into fresh HMM + GlcNAc at a final OD600 of 0.2, and 10 mM dbcAMP or filter-sterilized autoclaved water (vehicle control) were added to the appropriate cultures, with 3 biological replicates for each chemical-strain combination. The cultures were treated and samples were collected as described for the first experiment.

value: dbcAMP

tag: replicate

value: C

value: yeast cells


title: G217Bura5-DA dbcAMP B-2 (wt_10mM)

value: B


title: SG1 dbcAMP C-2 (SG1_10mM)


title: Infected fruit, 5 days post harvest, S2


title: SG1 dbcAMP B-2 (SG1_10mM)


title: SG1 dbcAMP A-2 (SG1_10mM)

value: A


title: SG1 dbcAMP B-2 (SG1_0mM)


title: G217Bura5-DA dbcAMP A-2 (wt_10mM)


title: SG1 dbcAMP C-2 (SG1_0mM)


title: G217Bura5-DA dbcAMP C-2 (wt_0mM)


title: G217Bura5-DA dbcAMP B-2 (wt_0mM)


title: G217Bura5-DA dbcAMP A-2 (wt_0mM)


title: G217Bura5-DA butyrate C-1 (butyrate5)

value: butyrate


title: G217Bura5-DA butyrate B-1 (butyrate5)


title: SG1 dbcAMP A-2 (SG1_0mM)


title: G217Bura5-DA butyrate A-1 (butyrate5)


title: G217Bura5-DA dbcAMP C-1 (dbcAMP10)


title: G217Bura5-DA dbcAMP A-1 (dbcAMP10)


title: G217Bura5-DA ddw C-1 (ddw)

value: ddw


title: G217Bura5-DA ddw B-1 (ddw)


title: G217Bura5-DA ddw A-1 (ddw)


title: E16.5M PGCs control  bisulfite-seq bio rep2

first: Jiangshan

last: Cong

address: No.130,Dongan Road

institute: Fudan University

description: Library name: Sample 26

data_processing:
Raw sequencing reads from WGBS were processed using the integrated methylpy software package. First, methylpy indexed the bisulfite-converted genome sequence, and alignment was conducted in paired-end mode using Bowtie2 as the alignment tool. Then, the call-methylation-state function within methylpy was used to calculate the methylation state of all cytosines across the genome, storing results in allc files. Finally, biological replicates from different samples were merged into a single allc file for further analysis.
Assembly: mm39
Supplementary files format and content: bigwig

source_name: PGCs

growth_protocol: Mice were maintained on a 12h light and 12h dark cycle in a constant temperature (20-25 ℃) and humidity levels (30-70%).

extract_protocol:
The EGFP-positive PGCs obtained through FACS were washed with PBS. DNA was isolated from the cells by using QIAamp® DNA Micro Kit (QIAGEN).
Genomic DNA was subjected to bisulfite conversion using EpiArt® DNA Methylation Bisulfite Kit (Vazyme) following the manufacturer’s instructions. Libraries for sequencing were prepared using 100ng-200ng of genomic DNA by EpiArt® DNA Methylation Library Kit. Libraries were purified for DNA fragments between 100bp-200bp. Library quality was assessed on the Agilent 5400 system (Agilent) and then amplified by PCR system.

treatment_protocol: STZ-induced intrauterine hyperglycemia mice at E3.5 of pregnancy by 120mg/kg STZ (Sigma).  A blood glucose level of more than 14 mM was used as the inclusion criterion for diabetes at E6.5 of pregnancy.

tag: Sex

value: male

tag: developmental stage

value: PGCs

value: WT

value: control group


title: E16.5M PGCs IUHG  bisulfite-seq bio rep3

description: Library name: Sample 30

value: STZ-induced


title: E16.5M PGCs IUHG  bisulfite-seq bio rep1

description: Library name: Sample 28