title: Early 2 cell stage embryos IgG Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg sperm derived rep 1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore with parameters (--quality 20 --nextera --stringency 3 )
Trimmed reads were then aligned to the mouse genome build mm10 using STAR (version 2.5.0a) with settings (--alignIntronMin 1 --alignIntronMax 1 --alignEndsType EndToEnd --alignMatesGapMax 1000 --outFilterMatchNminOverLread 0.85)
For allelic discrimination a SNP table of JF1 versus C57BL/6J mouse genome was acquired from (Takada, T., Ebata, T., Noguchi, H., Keane, T.M., Adams, D.J., Narita, T., Shin, I.T., Fujisawa, H., Toyoda, A., Abe, K. et al. (2013) The ancestor of extant Japanese fancy mice contributed to the mosaic genomes of classical inbred strains. Genome Res, 23, 1329-1338.). SNPs were injected into mm10 genome and alignment was done separately for C57BL/6J (R - reference paternal) and JF1 (A - alternative maternal) genomes. Allelic assignment for each read was done by comparing number of mismatches between alignments to each genome.
Aligned reads were deduplicated using SAMtools (version 1.10) with standard settings
Uniquely mapped reads were counted on genomic regions using the function qCount (mapqMin = 255L) from QuasR package (version 1.36.0).
Assembly: mm10
Supplementary files format and content: BigWig (.bw) processed files were generated from BAM files using the function qExportWig from QuasR package (version 1.36.0) with standard settings separately for maternal (files ending with XV_A.bw), paternal (XV_R.bw) and total alignments.
Library strategy: ATATA-Seq

source_name: 2 cell stage embryos

extract_protocol:
To obtain early embryos, 7-10-week-old JF1 female mice were injected intraperitoneally with HyperOva (Cosmo Bio, KYD-010-EX-X5) 63 hours pre collection and human chorionic gonadotropin (hCG, Chorulon MSD) 15 hours pre collection. Oviducts were dissected and oocytes from 2 animals were collected in 30 μl drops of HTF medium (EmbryoMax® Human Tubal Fluid Millipore, MR-070-D). Sperm was collected from 2 cauda epididymides in 50 μl drops of HTF medium. 2-5 μl of sperm sample was transferred to the oocyte drops and incubated for 3 hours at 37 °C. Zygotes with visible pronuclei washed 3 times in HTF medium and transferred to KSOM medium (Millipore, MR-106-D) and cultured in low oxygen chamber filled with the mixture gas (5% O2/ 5% CO2). Early 2 cell stage embryos were collected 22 hours post fertilization.
We fused N terminally the Tn5 transposase to two tandem IgG binding Z domains to specifically target the ZZ-Tn5 to antibody bound regions. Early 2 cell embryos (50 embryos per reaction) were incubated in 30 ul LIB buffer (20mM HEPES pH 7.5, 300mM NaCl, 0.5mM Spermidine, 0.05% Digitonin, 0.05% Triton X-100, 1X EDTA-free protease inhibitor cocktail) on ice for 10 mins for nuclei permeabilization. Active transposomes were generated by incubating ZZ-Tn5 (8μM) with Mosaic End double-stranded (MEDS) oligonucleotides (12μM) for 30 minutes at 37°C. Active transposomes (0.4 μM) were incubated with anti-H3K4me3 antibody or normal rabbit IgG (1μM) in LIB buffer for 30 minutes at 4°C with continuous mixing. Antibody- ZZ-transposomes complexes (final concentration 0.1 μM) were added to the embryo samples and incubated for 1 hour at 4°C with continuous mixing to allow targeting to the chromatin. Antibody- ZZ-transposomes were activated by addition of TAB buffer (20mM HEPES, 5%PEG6000, 7.5mM MgCl2, 300mM NaCl) and incubated for 1 hour at 37°C with continuous mixing. The tagmentation reaction was stopped with addition of Stop buffer (0.2% SDS, 10mM EDTA, 100ug/ml ProteinaseK) and incubated at 65°C for 15 minutes. DNA was purified by phenol-chloroform, ethanol precipitation and libraries were amplified for 16 cycles. Libraries were purified by 0.5X-1.5X volumes left-right side of Ampure XP DNA purification beads and sequenced in 50-bp single-end mode with HiSeq 2500 sequencing technology (Illumina), per the manufacturer’s recommendations.

value: 2 cell stage embryos

value: Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg

tag: chip antibody

value: rabbit IgG

value: early 2 cell stage embryos (22hpf)


title: 029_TRNA_S26

status: Public on Oct 22 2024

type: SRA

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

country: USA

institute: Mayo Clinic

library_source: transcriptomic

data_processing:
Data were processed using a previoulsy published method[https://pubmed.ncbi.nlm.nih.gov/24972667/]. In brief, reads were quality controlled using FASTQC. Reads were mapped against hg38 genome using STAR aligner. HT-Seq was utilized to analyzed the aligned reads and generate gene-wise counts using Ensemble version 78 transcriptome. Extracted read data was processed using edgeR software. Timmed means of M-values method was utilized to normalized reads that were provided in the file named "Grover-PIIBS-Normed-Counts.tsv".
Assembly: hg38
Supplementary files format and content: Grover-PIIBS-Normed-Counts.tsv; tab-delimited

molecule: total RNA

organism: Homo sapiens

source_name: Colon Muscle

extract_protocol:
mRNA was extracted using Trizol and stored in RNAlater.
mRNA library was constructed using Illumina TruSeq Stranded kit following manufacturer's recommendations.

tag: tissue

value: Colon Muscle

tag: cell type

value: Muscle

tag: genotype

value: PIIBS


title: Early 2 cell stage embryos IgG Dnmt3a f/+ ; Dnmt3b f/+ sperm derived  rep 1

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: maternal strain

tag: maternal genotype

value: wildtype

tag: paternal strain

tag: paternal genotype

tag: developmental stage


title: P21_brain_20um_H3K27ac_H3K27me3

city: Philadelphia

first: Liran

last: Mao

state: PA

address: 422 Curie Boulevard

department: Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
library strategy: nanobody-based Spatial CUT&Tag
For ATAC and CUT&Tag data, linkers 1 and 2 are used for targeted filtering of read 2, aligning utilizing BWA followed by sorting and indexing via Samtools to facilitate efficient data handling and retrieval. This reformatting process assigned genome sequences to the first read and incorporated barcodes A and B into the second read. We aligned these fastq files against mouse (GRCm38) reference genomes. The conversion produced tsv-like fragments files, enriched with spatial and genomic information through the integration of barcode pairs, facilitating comprehensive downstream analysis.   For RNA sequencing data, we refined read 2 to extract barcode A, barcode B, and the Unique Molecular Identifier (UMI). Using the Spatial Transcriptomics (ST) pipeline version 1.7.2, this processed data was mapped against the appropriate mouse (GRCm38) genome references. This step produced a gene matrix that captures both gene expression and spatial positioning data, encoded through the combination of barcodes A and B, enabling detailed spatial transcriptomic analysis.
Assembly: GRCm38
Supplementary files format and content: TSV files for downstream analysis. For CUT&Tag and ATAC-seq, the tsv file contains tissue location info (barcode A x barcode B) and fragments info on the genome.
Supplementary files format and content: For RNA-seq, Tab-delimited text files include counts for each pixels for each Sample.
Supplementary files format and content: The *spatial.tar.gz file is a compressed folder that stores spatial-related files including quality control (QC) images. These QC images are useful to confirm accurate fiducial alignment and tissue detection. Inside the folder, it contains tissue_lowres_image.png, scalefactors_json.json, and tissue_positions_list.csv. tissue_lowres_image.png is a downsampled version of the original, full-resolution light microscope image. scalefactors_json.json contains basic information about the pixel positions and sizes. tissue_positions_list.csv is a table with rows that correspond to pixels.

source_name: Mouse brain

extract_protocol:
The workflow of simultaneous profiling of chromatin accessibility or a panel of cell surface proteins with two histone modifications and gene expression on the same tissue cryosections is shown schematically in Fig. 1a and Extended Data Fig. 1a-b. For joint analysis of chromatin accessibility, two histone modifications, and transcriptome (Extended Data Fig. 1a, Methods), a frozen tissue section was first fixed with formaldehyde and in situ Tn5 transposition was performed to insert a unique barcoded ligation linker to the accessible DNA loci. The same tissue section was then incubated with two primary antibodies targeting different histone modifications simultaneously, such as the combination of H3K27me3 with H3K27ac or H3K4me3. Afterwards, species specific nanobody-Tn5 fusion proteins loaded with unique barcoded ligation linkers were added to enable the demultiplexing of different histone modification loci. Next, the tissue section was incubated with a biotinylated DNA adaptor containing a universal ligation linker and poly-T sequence that binds to the messenger RNA (mRNA) to perform in situ reverse transcription (RT). Next, barcodes A (A1-A50) and barcodes B (B1-B50) were sequentially flowed over the tissue using microchannels and were conjugated to the universal ligation liker via templated ligation, which formed a two-dimensional grid of spatially barcoded tissue pixels (n =2,500), allowing all of modalities from the same pixel share the same spatial barcodes. Finally, barcoded complementary DNA (cDNA) and genomic DNA (gDNA) fragments were released by reverse crosslinking. cDNAs were separated from gDNA by streptavidin beads. Sequencing libraries for cDNAs and gDNA were separately constructed. For co-profiling of protein, gene expression, and histone modifications (Extended Data Fig. 1b, Methods), the fixed frozen tissue section was first incubated with two primary antibodies targeting different histone modifications, followed by nanobody-Tn5 in situ transposition. The same tissue section was then labeled with a panel of barcoded poly-A-tailed oligo-conjugated antibodies, which recognize surface antigens. Next, in situ reverse transcript was performed using the Biotinylated poly-T RT primer to capture complimentary DNA of both poly-A-tailed oligo-conjugated antibodies and mRNA. The subsequent steps for spatial barcoding and library construction were similar to above discussed methods. The protein library and RNA library can be separated by SPRI bead purification.
Frozen tissue slides were thawed for 1 min at 37 °C. Tissue was fixed with formaldehyde (0.2%, with 0.05 U μl–1 RNase Inhibitor) for 5 min and quenched with 1.25 M glycine for a further 5 min. After fixation, tissue was washed twice with 1 ml of 0.5× DPBS-RI and cleaned with ddH2O. The sequential order for spatial multiple profiling is as follows: 1. ATAC-seq; 2. Nanobody-based CUT&Tag; 3. In situ reverse transcription; 4. Ligation of barcode A; 5. Ligation of barcode B; 6. Reverse crosslink; 7. gDNA and cDNA separation; 8. Library construction; 9. Library QC and sequencing.

value: Mouse brain


title: P21_brain_20um_RNA

data_processing:
library strategy: spatial-RNA-seq
For ATAC and CUT&Tag data, linkers 1 and 2 are used for targeted filtering of read 2, aligning utilizing BWA followed by sorting and indexing via Samtools to facilitate efficient data handling and retrieval. This reformatting process assigned genome sequences to the first read and incorporated barcodes A and B into the second read. We aligned these fastq files against mouse (GRCm38) reference genomes. The conversion produced tsv-like fragments files, enriched with spatial and genomic information through the integration of barcode pairs, facilitating comprehensive downstream analysis.   For RNA sequencing data, we refined read 2 to extract barcode A, barcode B, and the Unique Molecular Identifier (UMI). Using the Spatial Transcriptomics (ST) pipeline version 1.7.2, this processed data was mapped against the appropriate mouse (GRCm38) genome references. This step produced a gene matrix that captures both gene expression and spatial positioning data, encoded through the combination of barcodes A and B, enabling detailed spatial transcriptomic analysis.
Assembly: GRCm38
Supplementary files format and content: TSV files for downstream analysis. For CUT&Tag and ATAC-seq, the tsv file contains tissue location info (barcode A x barcode B) and fragments info on the genome.
Supplementary files format and content: For RNA-seq, Tab-delimited text files include counts for each pixels for each Sample.
Supplementary files format and content: The *spatial.tar.gz file is a compressed folder that stores spatial-related files including quality control (QC) images. These QC images are useful to confirm accurate fiducial alignment and tissue detection. Inside the folder, it contains tissue_lowres_image.png, scalefactors_json.json, and tissue_positions_list.csv. tissue_lowres_image.png is a downsampled version of the original, full-resolution light microscope image. scalefactors_json.json contains basic information about the pixel positions and sizes. tissue_positions_list.csv is a table with rows that correspond to pixels.

molecule: polyA RNA


title: 019_TRNA_S74


title: ME13_20um_protein

library_source: other

data_processing:
library strategy: spatial-CITE-seq
For ATAC and CUT&Tag data, linkers 1 and 2 are used for targeted filtering of read 2, aligning utilizing BWA followed by sorting and indexing via Samtools to facilitate efficient data handling and retrieval. This reformatting process assigned genome sequences to the first read and incorporated barcodes A and B into the second read. We aligned these fastq files against mouse (GRCm38) reference genomes. The conversion produced tsv-like fragments files, enriched with spatial and genomic information through the integration of barcode pairs, facilitating comprehensive downstream analysis.   For RNA sequencing data, we refined read 2 to extract barcode A, barcode B, and the Unique Molecular Identifier (UMI). Using the Spatial Transcriptomics (ST) pipeline version 1.7.2, this processed data was mapped against the appropriate mouse (GRCm38) genome references. This step produced a gene matrix that captures both gene expression and spatial positioning data, encoded through the combination of barcodes A and B, enabling detailed spatial transcriptomic analysis.
Assembly: GRCm38
Supplementary files format and content: TSV files for downstream analysis. For CUT&Tag and ATAC-seq, the tsv file contains tissue location info (barcode A x barcode B) and fragments info on the genome.
Supplementary files format and content: For RNA-seq, Tab-delimited text files include counts for each pixels for each Sample.
Supplementary files format and content: The *spatial.tar.gz file is a compressed folder that stores spatial-related files including quality control (QC) images. These QC images are useful to confirm accurate fiducial alignment and tissue detection. Inside the folder, it contains tissue_lowres_image.png, scalefactors_json.json, and tissue_positions_list.csv. tissue_lowres_image.png is a downsampled version of the original, full-resolution light microscope image. scalefactors_json.json contains basic information about the pixel positions and sizes. tissue_positions_list.csv is a table with rows that correspond to pixels.

molecule: protein

source_name: Embryo

value: Embryo


title: LNCaP-sgPRKCI_DMSO_EZH2

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

data_processing:
Quality control of raw sequencing reads was performed using FastQC
Low-quality reads were removed using Trimmomatic with a sliding window of 4bp and quality threshold of 15
Reads passing QC were aligned to GRCh38 using Bowtie2
BAM file creation, sorting, removal of PCR duplicates and indexing were performed using samtools
CUT&RUN peaks were called using MACS2 with IgG as the control for each set of data.
Assembly: Homo Sapiens - Human (GRCh38)
Supplementary files format and content: CUT&RUN signal (bigWig) called by MACS2 IgG as control

source_name: Prostate carcinoma

growth_protocol: LNCaP cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum, 1x glutamine, 1x pen/strep

extract_protocol:
The cells were incubated overnight with conA beads and specific antibodies including K-metstat internal control at 4C. Chromatin were digested using pAG-MNase for 15 minutes at RT. The fragmented DNA was column purified.
CUT&RUN libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for illumina. 5ng of CUT&RUN DNA were used to prepare the libraries using specific index primers and universal PCR primer and amplified for 14 cycles in a thermocycler. Post amplification, the libraries were size selected for 300-400bp using SPRIselect beads from NEB. The concentration and size of the libraries were measured using Qubit and Agilent High Sensitivity DNA kit respectively.

treatment_protocol: Enzalutamide 10 uM for 72 h.

value: Prostate carcinoma

tag: cell line

value: LNCaP

value: Epithelial

value: sgPRKCI

tag: treatment

value: DMSO 72 hours

tag: cut&run antibody

value: EZH2 (Epicypher, #13-2026)


title: LNCaP-sgPRKCI_DMSO_H3K4me3


title: 009_TRNA_S11


title: LNCaP-sgC_DMSO_EZH2

value: sgControl


title: Early 2 cell stage embryos H3K4me3 Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg sperm derived rep 3

value: 2 cell stage embryos


title: 049_TRNA_S12


title: LNCaP-sgC_DMSO_H3K4me3


title: ME13_20um_H3K4me3_H3K27me3


title: Early 2 cell stage embryos H3K4me3 Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg sperm derived rep 1

value: Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg


title: Early 2 cell stage embryos H3K4me3 Dnmt3a f/- ; Dnmt3b f/- ; Stra8-iCre tg sperm derived rep 2


title: SAMPLE12_hMSCs, Ru-LDH+H2O2-3

city: Chengdu

first: Mingru

last: Bai

address: Renmin Road No.14

country: China

institute: Sichuan University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug 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: bone

value: mesenchymal stem cells (hMSCs)


title: LNCaP-sgPRKCI_DMSO_IgG

value: IgG (Epicypher, #13-0042)


title: Early 2 cell stage embryos H3K4me3 Dnmt3a f/+ ; Dnmt3b f/+ sperm derived  rep 3

value: Dnmt3a f/+ ; Dnmt3b f/+

value: early 2 cell stage embryos (22hpf)


title: SAMPLE11_hMSCs, Ru-LDH+H2O2-2


title: LNCaP_sgC_DMSO_IgG


title: ME13_50um_3_ATAC_H3K4me3_H3K27me3


title: ME13_50um_2_H3K27me3_H3K27ac


title: Early 2 cell stage embryos H3K4me3 Dnmt3a f/+ ; Dnmt3b f/+ sperm derived  rep 2

value: wildtype


title: SAMPLE9_hMSCs, LDH+H2O2-3


title: SAMPLE10_hMSCs, Ru-LDH+H2O2-1


title: WT,24h,ChIP-seq

city: Wuhan

first: Xiangsong

last: Chen

state: Hubei

address: Bayi Road

institute: Wuhan university

data_processing:
For H4K16ac ChIP-Seq, clean reads were aligned to either the TAIR10 genome or the MSU7.0 genome using Bowtie2 v.2.3.5 (Langmead & Salzberg, 2012). The mapped reads were sorted, and duplicates were removed using SAMtools v.1.9 (Danecek et al., 2021). The spike-in reads were normalized by scale factor (At q30 mapped reads/Os q30 mapped reads). Peak locations were identified using Sicer (Zang et al., 2009) with parameters -fdr 0.001 -g 200 -w 200. We reanalyzed the published ChIP-Seq data of H3K9me2. Reads which removed adapters were aligned by Bowtie2 v.2.3.5 with the default parameters. The degree of heterochromatin was reflected by calculating the log2 ratio between H3K9me2 and H3 within each 100 kb. Z-scores were calculated for each bin by subtracting the mean log ratio from individual log ratios and dividing by the standard deviation.
Assembly: TAIR10
Supplementary files format and content: BigWig

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana

growth_protocol: A. thaliana plants were growth on 1/2X MS agar (0.6%) + 1% sucrose  at 22 degree under a 16-h-light/8-h-dark photoperiod.

extract_protocol:
Total 4 g of 18-d-old plants was used for each sample. Add c. 2 g of ground tissue to a 50 ml Falcon tube containing 25 ml nuclear isolation buffer (10 mM HEPES pH 8.0, 1 M sucrose, 5 mM KCl, 5 mM MgCl2, 5 mM EDTA, 0.6% Triton X-100, 0.4 mM PMSF, and 1 × Mini-Complete cocktail). Then, crosslinked with 1% formaldehyde for 20 min and used for chromatin extraction. After 15 min sonication (45 s on/15 s off, at high energy level) by Covaris S220 (Thermo Fisher, Shanghai, China) and centrifugation for 15 min at 12 000 g, the supernatant was incubated with 5 μg anti-H4K16ac antibody (PTM-122; PTM Bio, Hangzhou, China). Nipponbare rice nucleosomes were added as spike-in with 1 : 50 ratio. After one night, the supernatant was added 40 μl Protein A/G beads (SA032005; Smart Lifesciences, Changzhou, China) and incubated 2 h with rotation at 4°C. After extensive washing, immunoprecipitated chromatin was reverse-crosslinked and purified for sequencing.
For ChIP-Seq, DNA from chromatin immunoprecipitation was used to construct sequencing libraries following the protocol provided with Scale ssDNA-Seq Lib Prep Kit for Illumina V2 (RK20228; Abclonal) and sequenced on an Illumina NovaSeq 6000 instrument (Annoroad).

treatment_protocol: 18 day seedling were treated at 37 degrees for 24 hours

value: WT

value: 37 degrees heat shock for 24 hours

value: Arabidopsis thaliana


title: hd2bhd2c,24h,ChIP-seq

value: hd2b hd2c knockout


title: Early 2 cell stage embryos H3K4me3 Dnmt3a f/+ ; Dnmt3b f/+ sperm derived  rep 1


title: 004_TRNA_S59

value: Colon Muscle

value: Muscle

value: PIIBS


title: ME13_50um_1_H3K27me3_H3K27ac

value: Embryo


title: RA_7d, scRNAseq

city: St Louis

first: Jie

last: Shen

state: MO

address: 425 S. Euclid Ave

institute: Washington University in St Louis

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger pipeline (v7.0.1, https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/what-is-cell-ranger) was used to align reads, extract cell barcode and unique molecular identifier (UMI) counts, and generate feature-barcode matrices, after mapping to the mouse (mm10) reference genome, according to the standard workflow of 10x Genomics.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: fracture callus

extract_protocol: 10,000 cells for each sample were loaded in aim of preparing single-cell mRNA libraries for each group, barcoded, purified using Chromium Single Cell 3’ kit (v3.1 Chemistry, 10x Genomics Inc)

value: fracture callus

value: primary cells

tag: strain

value: wild-type

tag: age

value: 3 months old

value: K/BxN serum injection

tag: time point


title: SW620,control,rep1

city: Moscow

first: Alexander

middle: Petrovich

last: Rezvykh

address: Obninsk, Zvyozdnaya st. 15 - 130

country: Russia

institute: EIMB

data_processing:
read trimming (TrimGalore, version 0.6.4dev)
Read alignment (STAR, version 2.7.3a)
Read counting (featureCounts, version 2.0.5)
Assembly: hg38
Supplementary files format and content: Tab-separated files conatining gene identifyers in ENSEMBL format and corresponding number of reads spanning on exonic regions of each gene

source_name: Colorectal adenocarcinoma cells

growth_protocol: Colorectal adenocarcinoma cell lines SW620B8-mCherry and SW480-B8mCherry expressing fluorescent immunoproteasomes were obtained previously [Burov et al., 2021, Burov et al., 2024]. Cells were maintained in DMEM (Thermo Fisher Scientific, Paisley, Renfrewshire, Scotland, UK) supplemented with 10% fetal calf serum (FCS) (Hyclone, Logan, UT, USA), 100 U/mL of penicillin and 100 μg/mL of streptomycin. Cells were grown at 37°C and 5% CO2.

extract_protocol:
The 1-1.5x106 cells were used for the isolation of total RNA using Extract RNA reagent (Evrogen, Russia). At least two biological replicates were performed for each group. The RNA concentration was determined using the Qubit Fluorometer (Invitrogen, Waltham, MA, USA). The RNA quality was estimated by using the RNA 600 nano kit and Agilent BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). The RNA Integrity Number (RIN) of the RNA samples was either 8, or above. The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA), was used to prepare libraries for the RNA-seq in accordance with the manufacturer’s guidelines. Seventy-five bp single-end sequencing was performed using the Illumina NextSeq 500 platform (Illumina, San Diego, CA, USA).
75-bp single-end reads

treatment_protocol: SW620B8-mCherry cells were treated with 30, 60, 100, 250 and 500 µM of caffeine for 72h. To study the cumulative effect of caffeine SW620B8-mCherry cells were propagated in a medium containing 125 µM of caffeine for 28 days. Every 3-4 days, the cells were seeded into a fresh medium containing caffeine

value: Colorectal adenocarcinoma cells


title: hd2bhd2c,0h,ChIP-seq

value: normal


title: ME13_20um_RNA


title: SW620,control,rep2


title: RA_4d, scRNAseq

description: 10x Genomics


title: WT,0h,ChIP-seq


title: SAMPLE7_hMSCs, LDH+H2O2-1

value: bone

value: mesenchymal stem cells (hMSCs)


title: SAMPLE6_hMSCs, H2O2-3


title: SW620,caffeine-treated,rep2

value: Caffeine


title: Granulosa cells, Heat stressed, Treated, Biol Rep3

city: Guwahati

first: Jaya

last: Bharati

state: ASSAM

address: ICAR-NRC on Pig, Rani

department: Animal Physiology

country: India

institute: ICAR-National Research Centre on Pig, Guwahati, Assam

description:
GCT3
counts raw_all samples.txt
counts normalized_all samples.txt

data_processing:
Sequenced data were processed to generate FASTQ files. Paired-end raw sequence data quality check (QC) was conducted using FastQC (v.0.11.4) and Trim Galore was used for removing adapters and poor-quality sequences.
The trimmed sequenced reads were then mapped to the reference genome of Sus scrofa (pig) using splice aware alignment tool STAR. Feature specific expression counts were estimated using the Rsubread R package.
Low count features across samples were detected and removed with NOISeq R package. Expression counts normalization was performed with TMM method along with the estimation of significant differential features using NOISeq R package.
Significant differential features were obtained using cut-offs, probability value ≥ 0.95 and absolute log2(fold change) ≥ 1.
Assembly: Sscrofa11.1, INSDC Assembly GCA_000003025.6, Feb 2017
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample

organism: Sus scrofa

source_name: Ovarian Follicle

growth_protocol: Follicular fluid was aspirated from small healthy porcine ovarian follicles (size 3 mm to ≤ 6 mm) by aspiration using 18-gauge sterile needle and granulosa cells were collected by centrifuging follicular fluid at 1600×gfor 5 min. Granulosa cells settled at bottom, which was resuspended in cell culture media (DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin). Resuspended granulosa cells were then seeded in a T75 cell culture flask with cell culture media at 37 °C under 5% CO2in humidified air and cultured till cells attained 70 % confluency.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen) and concentrations of total RNA was measured with NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Qubit 4 Fluorometer (Thermo Fisher Scientific -IN). The RNA quality was assessed with the Tapestation 4200TM (Agilent Technologies, Santa Clara, US).
The initial input of 500 ng of QC passed RNA were used for construction of stranded mRNA-Seq libraries using KAPA mRNA HyperPrep Kitfollowing manufacturer protocol.
RNA-Seq: Illumina libraries were loaded onto Illumina NextSeq2000 to generate 40M, 2 X 150 bp reads/sample.

treatment_protocol: When granulosa cells reached the confluency of more than 70%; cell culture plates were then assigned to temperature 37 °C, non-heat stressed (control) group and 42 °C, heat stressed (treated) groups for 6 hours under 5% CO2in humidified air. The cells were harvested by trypsinization using 0.25% trypsin-EDTA and spent media were collected immediately for further analysis.

value: Ovarian Follicle

value: Granulosa cells

tag: stress

value: Heat stressed


title: SAMPLE8_hMSCs, LDH+H2O2-2


title: control_7d, scRNAseq

description: 10x Genomics

value: Vehicle


title: SW620,caffeine-treated,rep1


title: SAMPLE5_hMSCs, H2O2-2


title: SAMPLE4_hMSCs, H2O2-1


title: control_4d, scRNAseq

description: 10x Genomics


title: Granulosa cells, Heat stressed, Treated, Biol Rep1

description:
GCT1
counts raw_all samples.txt
counts normalized_all samples.txt


title: SW480,control,rep2


title: Granulosa cells, Heat stressed, Treated, Biol Rep2

description:
GCT2
counts raw_all samples.txt
counts normalized_all samples.txt


title: MOC7_homeostasis_Achillestendoncells

city: Boston

first: Mor

last: Grinstein

state: MA

address: 2114 Cambrisge street

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

data_processing:
For SMART-seq bulk RNA-seq samples, gene expression was quantified using Salmon (version 0.13.1) using the mm10 transcriptome (Ensembl 92, 2018-10-10). To identify differentially expressed genes in a pairwise manner, the statistical package DESeq2 (version 1.24.0) was utilized. Genes were classified as differentially expressed based on a 2-fold change in expression value and false discovery rates (FDR) below 0.05.
For single cell RNA-sequencing samples, raw demultiplexed fastq files were merged and trimmed using Trimmomatic. Trimmed reads were then aligned to the mm10 mouse genome build and processed using Cellranger. Raw feature-barcode matrices were analyzed downstream using Seurat and SCANPy to identify cell type clusters and cluster marker expression.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts for Salmon-aligned SMART-seq bulk samples (A1-A8)
Supplementary_files_format_and_content: TPM_SalmonSMARTSeq: Normalized counts for samples B10-C11
Supplementary_files_format_and_content: Raw cellranger output files for barcodes, features, and barcode-feature matrices

source_name: homeostasis

extract_protocol:
For SMART-seq samples: Fresh isolated tendons were collected from mouse forelimbs and hindlimbs or from injured Achilles tendons (10 dpi) and dissociated as described (Grinstein et al., 2019; Grinstein et al., 2018). The cells were sorted using BD FACSARIA II. CD31-APC, CD45-APC Cy7 cells were excluded. The Axin2TdTom and the Axin2- cells were sorted separately into 96-well plates into TCL buffer, 200-1000 cells of  Axin2TdTom / Axin2-  cells were sorted into each well, and stored at -80 ̊C.
For single cell RNA-sequencing samples: Achilles tendons were freshly isolated from 4 adult mice (3-4 months of age), 8 tendons total for homeostasis, and 3 tendons total from 3 adult mice (3-4 months of age) for 10 days post injury.  Tendons were dissociated as described (Grinstein et al., 2019; Grinstein et al., 2018). Cells were sorted using BD FACSARIA II. CD31-APC, CD45-APCCy7 and TER-119/Erythroid APC-Cy7 cells were excluded.  Immediately following FACS, cells were loaded to the 10X platform using Chromium next GEM single cells 3’ reagents kit V3.1.
SMART seq libraries were generated using the Nextera XT library prep kit (Illumina), pooled, and sequenced on NextSeq 500 sequencer, using 38 bp PE reads, and resulted in approximately 30 million 75 bp reads per sample. For 10x single cell sequencing, libraries were generated using the 10x V3 library kit and run on the 10x Chromium system. Libraries were sequenced on a Nextseq 500 and Novaseq 6000.

value: Achilles tendon cells

value: achilles

value: 3-5 months


title: SAMPLE3_hMSCs, Ctrl-3

value: Ctrl


title: Granulosa cells, Non-heat stressed, Control, Biol Rep2

description:
GCC2
counts raw_all samples.txt
counts normalized_all samples.txt

value: Non-heat stressed


title: SW480,caffeine-treated,rep2


title: small intestine epithelium, Tet3KO, scRNA-seq

city: Muenster

first: Marcos

middle: J.

last: Araúzo-Bravo

address: Rogentstrasse

department: Cell and Developmental Biology

country: Germany

institute: Max Planck Institute for Molecular Biomedicine

description: replicate 1

data_processing:
We used the alevin pipeline integrated with the salmon software (version salmon-0.14.1) to process the 10X-Chromium v3 droplet-based single-cell RNA sequencing data (scRNA-Seq).
We performed cell barcode (CB) detection, read mapping, unique molecular identifier (UMI) deduplication, gene count estimation, and cell barcode whitelisting.
Reads were aligned to the mouse GRCm38 reference genome, transcriptome and annotation downloaded from GENOME website, version 21, and annotated.
We used the --forceCells option of alevin set to 6000 for both WT (Wild Type) and KO populations’ scRNA-Seq data to specify the number of CB to consider for white-listing.
Standard procedures for filtering, variable gene selection, dimension reduction and clustering were performed using the Scanpy toolkit version 1.6.0.
Cells with fewer than 200 detected genes were excluded.
A gene was counted as expressed if it was detected in at least 3 cells.
Genes with too many total counts (>100,000) were also removed.
For each cell we computed the fraction of counts in mitochondrial genes vs. all genes and filtered out the cells with this fraction greater than 0.15.
The data matrix was total-count normalized (library-size corrected) to 10,000 reads per cell, so that counts became comparable among cells, and stabilized by computing the natural logarithm of one plus the counts for each cell
Each gene was scaled to unit variance and values exceeding standard deviation 10 were clipped.
Genome_build: mm10 mouse
Supplementary_files_format_and_content: Combined-6000cells-adata_raw_x.csv  (file include counts values for each sample; barcode-1 corresponds to Control, barcode-2 corresponds to Tet3KO)

growth_protocol:
Tet3 knockout ESCs were used to generate chimeric mice through aggregation with morula stage (C57BL6/J x C3H/HeJ)F1 embryos.
Male chimeric mice were crossed to CD1 females to screen for germ line transmission of the Tet3 knockout allele.
Finally, Tet3 heterozygous females were backcrossed with pure C57BL6/JRccHsd
males at least 5 generations to obtain an incipient congenic line (N5 or >95% C57BL6/JRccHsd).
Animals were housed in a controlled environment with a 12h light/dark cycle in open cages,
with access ad libitum to a standard chow diet and water.
Mice were time-mated and the presence of a vaginal plug was considered as embryonic day 0.5 (E0.5).
All experiments were performed on E18.5 with embryos obtained by caesarian section.
All animal experiments were performed in accordance with the animal care
guidelines of the European Union (2010/63/EU) prior approval of the
Spanish National Research Council Ethics Committee and the Regional Government competent authority.

extract_protocol:
Sorted E18.5 intestinal epithelial cells were fixed in 90% ice-cold methanol and stored at -80ºC until analysis.
Tet3 knockout and wild-type samples correspond to a pool of intestinal epithelial cells from two embryos each.
For analysis, cells were resuspended in 3x saline sodium citrate buffer containing 0.04% BSA,
1% SUPERase·In RNase Inhibitor (Invitrogen, AM2694) and 40mM DTT (Chen et al, 2018).
Single-indexed libraries were prepared using the Chromium Single Cell 3’ v3/v3.1 chemistry (10x Genomics) following the manufacturer’s instructions.
6,000 cells were used per sample. The generated libraries were sequenced on an Illumina Novaseq (Illumina)
system using the following transcript read lengths: 28bp for cell barcode and UMI, 8bp for sample index and 91bp for insert.
10,000 reads per cell were sequenced. scRNA-seq analysis was performed at Princess Margaret Genomics Centre (Toronto, Canada).

treatment_protocol:
A targeting vector introducing loxP sites around Tet3 exon 5
was constructed and electroporated into (C57BL6/J x C3H/HeJ)F1 embryonic stem cells (ESCs).
The construct also contained an FRT-flanked selection cassette coding for neomycin and thymidine kinase.
Individual neomycin-resistant ESC clones were screened for recombination in the proper genomic locus.
Next, FIAU-negative selection was used to select for clones that had
excised the thymidine kinase cassette after transient transfection of an Flp-coding plasmid.
Then, a Cre-coding plasmid was transiently transfected to excise the loxP-flanked exon 5
and single ESC clones were genotyped to confirm the excision.
Deletion of the floxed region results in a frame-shift that introduces a premature stop codon in exon 6,
triggering nonsense-mediated decay of the mutant transcript.

value: Tet3 knockout

value: small intestine epithelium


title: SAMPLE2_hMSCs, Ctrl-2


title: MOC6_10dayspostinjury_Achillestendoncells

source_name: 10 days post injury


title: small intestine epithelium, Control, scRNA-seq

description: replicate 1

source_name: Control

value: Control


title: SW480,control,rep1

value: Colorectal adenocarcinoma cells


title: Tissue Section 5, DLK1 Positive, F11

status: Public on Oct 21 2024

city: London

first: James

last: Pittaway

address: Charterhouse Square

department: Centre for Endocrinology

country: United Kingdom

institute: Queen Mary University of London

data_processing:
Fastq files were converted to DCC files using the Nanostring NGS Pipeline software.
DCC files were loaded into an R environment and a raw counts matrix generated using the GeoMxTools & NanoStringNCTools packages by following the recommended steps at:https://www.bioconductor.org/packages/release/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html
Assembly: As per Nanostring GeoMx protocol
Supplementary files format and content: Excel file with raw counts for each gene per sample
Library strategy: Spatial Transcriptomics

source_name: Adrenocortical carcinoma

extract_protocol:
As per Nanostring GeoMx extraction protocol
As per Nanostring GeoMx library construction protocol

value: Adrenocortical carcinoma


title: Tissue Section 5, DLK1 Positive, G01


title: Tissue Section 5, DLK1 Negative, F10


title: Tissue Section 5, DLK1 Positive, F07


title: Tissue Section 5, DLK1 Negative, F06


title: SAMPLE1_hMSCs, Ctrl-1

value: bone


title: Granulosa cells, Non-heat stressed, Control, Biol Rep1

description:
GCC1
counts raw_all samples.txt
counts normalized_all samples.txt


title: Tissue Section 5, DLK1 Positive, F05


title: Tissue Section 5, DLK1 Negative, F04


title: Tissue Section 5, DLK1 Positive, F09


title: 126_S49

value: Colon Muscle

value: Muscle

value: PIIBS


title: Tissue Section 5, DLK1 Negative, F02


title: Tissue Section 5, DLK1 Negative, F08


title: Granulosa cells, Non-heat stressed, Control, Biol Rep3

description:
GCC3
counts raw_all samples.txt
counts normalized_all samples.txt

value: Ovarian Follicle

value: Granulosa cells


title: Tissue Section 3, DLK1 Positive, E09


title: Tissue Section 5, DLK1 Positive, F03


title: Tissue Section 3, DLK1 Negative, F01


title: Tissue Section 3, DLK1 Positive, E07


title: Tissue Section 3, DLK1 Negative, E04


title: Tissue Section 3, DLK1 Negative, E10


title: Tissue Section 3, DLK1 Positive, E11


title: Tissue Section 3, DLK1 Positive, E12


title: Tissue Section 3, DLK1 Positive, E05


title: Tissue Section 5, DLK1 Negative, F12


title: Tissue Section 3, DLK1 Positive, E08


title: Tissue Section 3, DLK1 Negative, E03


title: Tissue Section 4, DLK1 Positive, E01


title: Tissue Section 4, DLK1 Negative, D08


title: Tissue Section 3, DLK1 Negative, E06


title: Tissue Section 4, DLK1 Negative, D04


title: Tissue Section 4, DLK1 Negative, D10


title: Tissue Section 4, DLK1 Positive, D09


title: Tissue Section 4, DLK1 Positive, D07


title: Tissue Section 4, DLK1 Negative, D02


title: Tissue Section 4, DLK1 Negative, D12


title: Tissue Section 4, DLK1 Positive, D03


title: Tissue Section 2, DLK1 Negative, C10


title: Tissue Section 2, DLK1 Positive, D01


title: Tissue Section 2, DLK1 Positive, C11


title: Tissue Section 2, DLK1 Negative, C12


title: Tissue Section 1, DLK1 Positive, C07


title: Tissue Section 3, DLK1 Negative, E02


title: Tissue Section 2, DLK1 Negative, C08


title: Tissue Section 2, DLK1 Positive, C09


title: Tissue Section 1, DLK1 Positive, C05


title: Tissue Section 1, DLK1 Negative, C06


title: Tissue Section 1, DLK1 Negative, C04


title: Tissue Section 1, DLK1 Positive, C03


title: Tissue Section 4, DLK1 Negative, D06


title: Tissue Section 2, DLK1 Negative, B12


title: Tissue Section 2, DLK1 Positive, B11


title: Tissue Section 4, DLK1 Positive, D11


title: Tissue Section 1, DLK1 Negative, C02


title: Tissue Section 2, DLK1 Positive, C01


title: Tissue Section 4, DLK1 Positive, D05


title: Tissue Section 2, DLK1 Negative, B10


title: Tissue Section 2, DLK1 Positive, B07


title: Tissue Section 2, DLK1 Positive, B05


title: Tissue Section 2, DLK1 Negative, B06


title: Tissue Section 2, DLK1 Negative, B08


title: Tissue Section 2, DLK1 Negative, B04


title: Tissue Section 2, DLK1 Positive, B09


title: SW480,caffeine-treated,rep1

value: Caffeine


title: Tissue Section 1, DLK1 Positive, B01


title: Tissue Section 1, DLK1 Positive, A11


title: Tissue Section 2, DLK1 Negative, B02


title: Tissue Section 1, DLK1 Negative, A08


title: Tissue Section 1, DLK1 Negative, A12


title: Tissue Section 1, DLK1 Negative, A10


title: Tissue Section 1, DLK1 Positive, A05


title: Tissue Section 2, DLK1 Positive, B03


title: Tissue Section 1, DLK1 Positive, A03


title: Tissue Section 1, DLK1 Negative, A02


title: Caco-2, differentiated, control, rep1

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

description: Differentiated Caco-2 cells without further treatment

data_processing:
Raw single-end FASTQ reads were trimmed using FASTX Toolkit 0.0.14 to remove library adapters and low-quality bases. The trimmed reads were then first aligned (using STAR 2.7.11a) to a list of tRNA/rRNA sequences to filter out tRNA/rRNA contaminants, and the remaining unmapped reads were aligned to the hg38 reference genome.
smORF counts were quantified from the aligned reads using HOMER analyzeRepeats, using a smORFs GTF file obtained from the pipeline described in Martinez et al (Martinez TF, Chu Q, Donaldson C, Tan D, Shokhirev MN, Saghatelian A: Accurate annotation of human protein-coding small open reading frames. Nat Chem Biol 2020, 16:458-468.).
Assembly: GRCh38.p13
Supplementary files format and content: A counts file generated using HOMER, where the first 8 columns contain annotation information such as feature (gene/smORF) ID and coordinates, and the remaining columns contain the counts of each feature

growth_protocol: Cells were seeded into larger format plates according to the following densities: CCD18-Co cells 3 x 106 cells/23mL in 15cm plate, CaCo2 cells 4.2 x 106 cells/10mL in 10cm plate, HCEC-1CT cells 5 x 106 cells/8.7mL in 10cm plate, PBMC 39 x 106 cells/39mL in T75 flask.

extract_protocol:
Cells were washed twice after treatment with ice cold PBS supplemented with 100ug/mL cycloheximide (CHX; Fisher Scientific, AAJ66004X) and snap frozen in liquid nitrogen and stored at -80°C. After thawing briefly on ice, the cells were lysed with 300uL of ice-cold lysis buffer (20mM Tris-HCl, pH 7.4, 150mM NaCl, 5mM MgCl2, 1% Triton X-100, 1mM DTT, 25U Turbo DNase (Thermofisher Cat# AM2238), and 100ug/mL CHX – added fresh) for 10 minutes with periodic vortexing and pipetting through an 18G needle to ensure the cells are dispersed. Cell lysates were clarified by centrifugation for 15,000g for 10 minutes at 4°C, flash frozen in liquid nitrogen, and stored in -80°C for up to 1 week.
Ribosome footprinting was carried out by digesting 50 ug of RNA in 300 uL lysate with 0.375 U/ug RNase I (Lucigen, N6901K) for 45 min at room temperature. Digestion reactions were quenched with 200 U Superase-In RNase I inhibitor (Thermo Fisher, AM2694) on ice. Following digestion, monosomes were purified from small RNA fragments using Micro-Spin S-400 HR columns (GE Life Sciences), and ribosome protected RNA fragments (RPFs) were extracted by acid phenol chloroform and isopropanol precipitation. Sequencing libraries were prepared as in McGlincy and Ingolia with some modifications. First, the RiboZero Mammalian Kit (Illumina) was used to deplete rRNA after RPF extraction and just prior to RPF size selection by gel extraction. Second, the Zymo clean & concentrator step after adaptor ligation is omitted and the reaction was carried over straight into reverse transcription. For the reverse transcription step to form cDNA, Episcript RT (Lucigen, ERT12910K) was used. Following reverse transcription, excess primer was degraded using Exonuclease I (Lucigen, X40520K) and the RNA templates were degraded using Hybridase (Lucigen, H39500). For the cDNA circularization step, CircLigase I (Lucigen, CL4111K) was used. PCR amplification was then carried out using Phusion Hot Start II High-Fidelity Master Mix (Thermo Fisher, F565L) for 9–12 cycles.

treatment_protocol: Cells were then either allowed or not allowed to differentiate, and then treated or not treated with following stimulants: lipid micelles, micelles without lipid.

value: differentiated, control


title: Tissue Section 1, DLK1 Positive, A07


title: IMR90_ATRX_KO_HIRA_KD_Rep1_ATACseq

city: Pittsburgh

first: Sarah

last: Hainer

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Raw fastq reads were trimmed to 25 bp
Reads mapped to the human T2T (chm13v2.0) genome using bowtie2 v2.4.5 allowing for 1 mismatch
Duplicates were removed using Picard v2.18.12
Reads were size-selected for nucleosome free region size fragments (1-100 bp)
Reads were processed in deepTools by using bamCoverage with options --normalizeUsing RPGC --effectiveGenomeSize 2725240337 --ignoreDuplicates -bs 1 to generate bigwig files used for making heatmaps
Assembly: chm13v2.0 (T2T)
Supplementary files format and content: RPGC normalized bigwigs
Supplementary files format and content: bed files converted from input bam files for qMotif and TelSeq analyses. Bed files used to calculate average genome coverage for manual normalization of telomere motif counts

growth_protocol: Cultured in Glutamax-DMEM supplemented with 10% fetal growth serum. Cells were cultured at normal oxygen conditions of 20% O2 and 7.5% CO2 at 37℃.

extract_protocol:
Cells were pelleted, washed with DPBS, and nuclei were extracted with a hypotonic buffer. Extracted nuclei were transposed for 30 minutes with Tn5 transposome in buffer containing digitonin, NP-40, and Tween-20.
ATAC-seq libraries were amplified by high-fidelity PCR with barcoded Nextera indices.

treatment_protocol: 72h shRNA knockdown of HIRA or NT (non-targeting shRNA) using Dharmafect

value: fibroblast

value: ATRX KO

value: ALT shHIRA


title: IMR90_ATRX_KO_HIRA_KD_Rep2_ATACseq


title: IMR90_ATRX_KO_conKD_Rep2_ATACseq

value: ALT NT


title: IMR90_ATRX_KO_conKD_Rep3_ATACseq


title: IMR90_ATRX_KO_conKD_Rep1_ATACseq


title: IMR90_ATRX_KO_HIRA_KD_Rep3_ATACseq


title: 7B9, DENV-2

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

description: 10x Genomics

data_processing:
Raw sequencing data (BCL files) were demultiplexed and coverted to fastq files using the CellRanger v6.1.1 mkfastq pipline (10x Genomics). Data qualty control, data filtering, cell barcode processing, UMI compression, 5' transcript alignment, and single-cell gene counting was performed using the CellRanger v6.1.1 count pipeline (10x Genomics).
Assembly: Human (GRCh38) with DENV-2 (NC 001474.2) added as an additional chromosome
Supplementary files format and content: Tab-separated values files and matrix files

source_name: cell line

extract_protocol:
Single-cell RNAseq libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) and the Chromium Single Cell Analyzer (10x Genomics). Indexed sequencing libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) according to the manufacture's protocol.
Library construction was performed according to the manufacturer's instructions (single cell 5' v2 protocol, 10x Genomics). In short, sequencing libraries were generated by 1) transcript fragmentation and end-repair, 2) post-fragmentation size-selection using SPRIselect beads, 3) Adaptor ligation and 4) sample index PCR and SPRIselect cleanup

treatment_protocol: The DENV-specific B cell line 7B9 was infected with DENV-2 for 24 hrs, washed, then incubated for and additional 24 hours prior to harvest and analysis by scRNAseq. A parallel uninfected/control culture was cultured and analyzed in a parallel fashion.

value: cell line

value: B cells


title: IMR90_HIRA_KD_Rep2_ATACseq

value: wild-type

value: Control shHIRA


title: IMR90_KD_Rep3_ATACseq

value: Control NT


title: IMR90_HIRA_KD_Rep3_ATACseq


title: 7B9, control

description: 10x Genomics


title: Tissue Section 1, DLK1 Negative, A06

value: Adrenocortical carcinoma


title: IMR90_KD_Rep1_ATACseq


title: IMR90_ATRX_KO_HIRA-KD_Rep3_CR_noab

data_processing:
Raw fastq files trimmed to 25bp
Reads mapped to human T2T genome assembly (chm13v2.0) using Bowtie2 v2.4.5 with a mismatch allowance parameter of 1 base to account for telomeric repeat sequence variation
Picard v2.18.12 used to remove duplicates
Low quality reads were removed (MAPQ <10)
Reads were size selected for 150-500bp fragments representative of histone sequences
Assembly: chm13v2.0 (T2T)
Supplementary files format and content: bed files used for manual genome sequencing coverage normalization of raw telomere motif counts
Supplementary files format and content: RPGC normalized bigwigs with CUT&RUN specific published blacklist regions read removal
Library strategy: CUT&RUN

extract_protocol:
Cells were pelleted, washed with DPBS, and nuclei were extracted following protocol described in Methods section of the publication. Extracted nuclei were bound to ConA lectin-coated beads, blocked with buffer containing EDTA to chelate any biological reactions, washed, and then incubated with either a primary antibody solution containing an anti-H3.3 antibody (Active Motif Cat: 91191, Lot: 25820004) or a no antibody negative control for 1hr at RT with rotation. Next, nuclei with bound primary antibody were incubated with pA/G-MNase for 30 minutes at room temperature with rotation.  pA/G-MNase activity was initiated by addition of calcium and digestion controlled with samples on ice water bath for 30minutes. Following digestion period, fragments were solubilized and used as input to the library build protocol to prepare deep sequencing libraries.
CUT&RUN libraries were amplified by high-fidelity PCR with barcoded NEB indices.

value: shHIRA


title: IMR90_ATRX_KO_HIRA-KD_Rep2_CR_noab


title: IMR90_KD_Rep2_ATACseq


title: IMR90_HIRA_KD_Rep1_ATACseq


title: IMR90_ATRX_KO_con-KD_Rep2_CR_noab


title: IMR90_ATRX_KO_con-KD_Rep3_CR_noab


title: IMR90_HIRA-KD_Rep3_CR_noab


title: IMR90_HIRA-KD_Rep2_CR_noab


title: IMR90_ATRX_KO_con-KD_Rep1_CR_noab


title: IMR90_HIRA-KD_Rep1_CR_noab


title: Tissue Section 1, DLK1 Positive, A09


title: IMR90_con-KD_Rep1_CR_noab


title: IMR90_con-KD_Rep3_CR_noab


title: Tissue Section 1, DLK1 Negative, A04


title: IMR90_ATRX_KO_HIRA-KD_Rep3_CR_H33


title: IMR90_ATRX_KO_HIRA-KD_Rep1_CR_H33


title: IMR90_ATRX_KO_HIRA-KD_Rep2_CR_H33


title: IMR90_HIRA-KD_Rep2_CR_H33


title: IMR90_HIRA-KD_Rep1_CR_H33


title: IMR90_ATRX_KO_con-KD_Rep3_CR_H33


title: IMR90_HIRA-KD_Rep3_CR_H33


title: IMR90_ATRX_KO_con-KD_Rep1_CR_H33


title: IMR90_ATRX_KO_con-KD_Rep2_CR_H33


title: IMR90_con-KD_Rep3_CR_H33


title: IMR90_ATRX_KO_HIRA-KD_Rep1_CR_noab


title: IMR90_con-KD_rep1_CR_H33


title: IMR90_con-KD_Rep2_CR_H33


title: R. tolerans, DMSO(Vehicle) Control, Replicate 3, early stationary phase

city: Princeton

first: Jack

last: Ganley

state: NJ

address: Frick Chemistry Laboratory, 333, Washington Road

institute: Princeton University

data_processing:
FASTQ data underwent quality control checks using FastQC
Adapter sequences were subsequently trimmed from reads using Trimmomatic v0.39 (parameters: -phred33, ILLUMINACLIP:adapters.fasta:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, MINLEN:36
The R. tolerans EL-164 genome was indexed using HISAT2 (parameters: paired-end reads: -1, -2, SAM output: -S alignment.sam), paired-end reads were aligned, mapped, indexed, and sorted using SAMtools (commands: view -b, sort, index), and quantification was performed using featureCounts v2.0.6 (parameters: -a GCF_028885395.1_ASM2888539v1_genomic.gtf, -t gene, -g gene_id, -s 2, -p, -B, -C, -Q 30, -F GTF)
Differential expression values were obtained using DESeq2 v1.38.0
Assembly: NCBI RefSeq assembly GCF_028885395.1
Supplementary files format and content: featureCount .txt files in tab-separated format

organism: Roseovarius tolerans

source_name: Roseovarius tolerans

growth_protocol: R. tolerans starter cultures were used to inoculate 25 mL of ½ YTSS liquid media in 125 mL flasks at a starting OD600 of 0.01 containing either 12.5 or 0 µM myricetin (1% DMSO for all) and grown at 30 ºC and 40 RPM. Growth curves were monitored by OD600 and 3 mL samples were collected in Rnase-free centrifuge tubes when cultures reached an OD600 of ~0.3 and ~0.75.

extract_protocol:
The samples were centrifuged, and the pellets were resuspended in 1 mL of RNAlaterTM stabilization solution (Thermo) and stored at 4 ºC for 24 hours. To isolate total RNA for RNA-seq, the samples were centrifuged, the RNAlaterTM solution was discarded, and total RNA was isolated using the Rneasy kit (QIAGEN). Any contaminating genomic DNA was removed by treating the total RNA with Dnase (TURBO Dnase Kit), per manufacturer’s instructions.
Strand-specific RNA-seq was performed by Azenta, which included quality control, an additional Dnase step to further remove residual contaminating genomic DNA, rRNA depletion, library preparation, and sequencing at 20 million paired end reads per sample

value: Roseovarius tolerans

value: DMSO (1 % vol, vehicle)


title: R. tolerans, Myricetin 12.5 µM, Replicate 3, early stationary phase

treatment_protocol: R. tolerans starter cultures were used to inoculate 25 mL of ½ YTSS liquid media in 125 mL flasks at a starting OD600 of 0.01 containing either 12.5 or 0 µM myricetin (1% DMSO for all) and grown at 30 ºC and 40 RPM. Growth curves were monitored by OD600 and 3 mL samples were collected in Rnase-free centrifuge tubes when cultures reached an OD600 of ~0.3 and ~0.75.

value: Myricetin (12.5 µM, 1% volume DMSO as vehicle)


title: R. tolerans, DMSO(Vehicle) Control, Replicate 3, exponential phase


title: R. tolerans, DMSO(Vehicle) Control, Replicate 1, exponential phase


title: R. tolerans, Myricetin 12.5 µM, Replicate 1, early stationary phase


title: R. tolerans, Myricetin 12.5 µM, Replicate 1, exponential phase


title: R. tolerans, Myricetin 12.5 µM, Replicate 2, early stationary phase


title: R. tolerans, DMSO(Vehicle) Control, Replicate 1, early stationary phase


title: R. tolerans, DMSO(Vehicle) Control, Replicate 2, early stationary phase


title: R. tolerans, DMSO(Vehicle) Control, Replicate 2, exponential phase


title: IMR90_con-KD_Rep2_CR_noab


title: ChIP-Seq WT spherules 8h Replicate 2 Figure4 WCE

city: San Francisco

first: Christina

last: Homer

state: CA

address: 513 Parnassus Ave, S472

institute: University of California, San Francisco

data_processing:
For ChIP-Seq: Reads were aligned to the Silveira genome22 using BWA version 0.7.17-r1188. Peaks were called using IP samples compared to control input samples with macs2 version 2.2.7.1, --mfold 5-60, with option –keep-dup set to all, and with the nomodel option selected and a manually set extension size of 197 for all samples based on estimated fragment size from bioanalyzer traces.
Assembly: Silveira genome (de Melo Teixeira et al 2022, PMID 35137016)
Supplementary files format and content: For ChIP-Seq: Processed data are MACS peaks output files.

organism: Coccidioides posadasii str. Silveira

source_name: liquid culture

growth_protocol: The wildtype Coccidioides posadasii strain Silveira (NR-48944) was used for growth experiments and as the background for the generation of the ryp1∆ mutant. All manipulation of live Coccidioides strains were performed in a biosafety level 3 facility. Standard spherulation conditions: polypropylene flasks containing Converse media were inoculated with 1 x 10^6/mL arthroconidia (unless otherwise stated) and placed at 39˚C, 10 % CO2, shaking at 120 rpm.  Where noted, spherulation was induced under the same conditions with different media: DMEM (UCSF Media Core) containing 20 % FBS (Corning) or RPMI (UCSF Media Core) containing 10 % FBS. For hyphal growth, polypropylene flasks containing Converse media were inoculated with 1 x 10^6 arthroconidia/mL and grown at 25˚C (Figures 2, S2) or room temperature (RT) (Figure 4, S4) shaking at 120 rpm. Experiments were performed in 1 L flasks with 330 mL Converse for wildtype and 500 mL flasks with 100 mL Converse for ryp1∆ mutant.Arthroconidia were generated on 2x GYE agar (2% Dextrose (Fisher), 1% Yeast extract (Gibco), 1.5% Bacto-Agar (BD)) + Penicillin/Streptomycin (100 U/ml penicillin and 100 g/ml streptomycin, UCSF Media Core) in T225 tissue culture flasks for 4-6 weeks at 30˚C, 25˚C, or 37˚C. Arthroconidia were then collected through scraping and washing as previously described (Mead et al 2020, PMID 32894648) and stocks were stored in PBS until use.

extract_protocol:
For ChIP-Seq: 50 mL of cultures were collected at start of the experiment (arthroconidia), and 8h, day 1, day2, and day 4 timepoints from spherule or hyphal growth induced as described above. Paired samples for RNA-seq (50mL initial culture for arthroconidia and 8h spherules/hyphae timepoints, then 10 mL of day 1, 2, and 4 spherules/hyphae) were also collected and processed as above. Cells were immediately crosslinked with 1 % formaldehyde (Neta Scientific) and incubated at RT for 20 min, mixing every 4 min. Crosslinking was then quenched with 125mM glycine (Fisher) and incubated for 5 min at RT, then frozen at -80˚C. Frozen samples were collected for all timepoints in the experiment prior to downstream processing. All following buffers were made using autoclaved ddH2O in baked glassware/DNA-free plastic tubes. Samples were thawed, pelleted, and washed twice with 25mL of TBS (20 mM Tris-HCl pH 7.5 (Fisher), 150mM NaCl (EMD)), centrifuging at 3000 x g for 5 min at 4˚C at each step. Pellets were resuspended in 700 µL of 4˚C lysis buffer (50mM HEPES (Fisher) / KOH (Fisher), 140 mM NaCl, 1 mM EDTA (Fisher), 1 % Triton X-100 (Acros Organics), 0.1 % sodium deoxycholate (Sigma), 2X Halt Protease Inhibitor Cocktail (ThermoFisher), 0.2X Halt Phosphatase Inhibitor Cocktail (ThermoFisher)). Cells were lysed by 8 x 1 min cycles of bead beating (0.5mm Zirconia/silica beads Biospec) at RT with 2 min rests on ice in between each cycle. Insoluble chromatin was pelleted by centrifugation at 8000rpm for 10 min, 4˚C and resuspended in 350 µL cold lysis buffer then sonicated (Diagenode Biorupter) for 15 cycles (30 seconds on, 30 seconds off). Cell debris was removed by centrifuged at 14000 rpm at 4˚C, yielding soluble chromatin fraction. 10 µL of input DNA was removed from the sample and placed in TE (10 mM Tris HCl pH 8.0, 1 mM EDTA) + 1 % SDS (Fisher). The remaining chromatin was immunoprecipitated (IP) with 5 µg of a polyclonal rabbit antibody against an epitope of Ryp1 (ID: 3878, Epitope: VYRELDKPFPPGEKKRAMKK, Bethyl laboratories) with rotation overnight at 4˚C. 50 µL of a 50% slurry of protein A dynabeads (Life technologies, washed 2x with cold TBS and 3x with cold lysis buffer) were added to each protein/antibody mixture and incubated an additional 3h at 4˚C with rotation. Beads were then pelleted on a magnetic rack and washed 2x with cold lysis buffer (without protease or phosphatase inhibitors), 2x with cold lysis buffer with 500 mM NaCl instead of 140 mM NaCl, 2x with cold wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl (Sigma), 0.5 % NP-40 (Fluka), 0.5 % sodium deoxycholate, 1 mM EDTA), 1x with cold TE. Bound protein/DNA complexes were eluted by adding 110 µL of elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS), vortexing, and incubating 10 min at 65˚C, mixing every 2 min. Samples placed on a magnet and 100 µL eluate was moved to a new tube. Then 150 µL TE + 0.65 % SDS was added to same beads, vortexed and placed back on the magnet, allowing 150 µL to be removed and combined with previous eluate for 250 µL for each sample. 1 µL of proteinase K (20 mg/mL, Qiagen) was added to these IP samples and previously-collected input samples and incubated at 65˚C overnight (approximately 16h). 2 ug of RNase A (Qiagen) was added to each sample, which was incubated at 37˚C for 1h. Samples were then purified using the Zymo ChIP DNA Clean and Concentrator kit.
For ChIP-Seq: . Libraries were prepared using NEBNext Ultra II DNA Library Prep kit, with an additional round of higher and lower size selection (calibrated to select for 150-350 bp fragment sizes) using homemade Serapure size selection beads. Library quality and adaptor dimer contamination was analyzed using Agilent High Sensitivity DNA Chip. Final library concentrations were measured using the Qubit High Sensitivity or Broad Range reagents depending on estimated library concentration by Agilent analysis of libraries. Libraries were pooled and final pool subjected to another round of size selection with homemade Serapure beads to remove remaining adaptor dimers.

treatment_protocol: No additional treatments aside from the differing growth conditions above.

value: fungal cell

value: WT

tag: morphology

value: spherules

tag: timepoint

tag: media

value: Converse

tag: figure of related microscopy data

tag: replicate


title: ChIP-Seq WT arthroconidia arthroconidia Replicate 3 Figure4 WCE

tag: cell type

tag: genotype

value: arthroconidia

value: PBS


title: ChIP-Seq WT arthroconidia arthroconidia Replicate 2 Figure4 WCE


title: ChIP-Seq WT arthroconidia arthroconidia Replicate 1 Figure4 WCE


title: R. tolerans, Myricetin 12.5 µM, Replicate 3, exponential phase


title: ChIP-Seq WT spherules 8h Replicate 3 Figure4 WCE


title: ChIP-Seq WT hyphae 8h Replicate 2 Figure4 WCE

value: hyphae


title: R. tolerans, Myricetin 12.5 µM, Replicate 2, exponential phase


title: ChIP-Seq WT hyphae 8h Replicate 3 Figure4 WCE


title: ChIP-Seq Ryp1 hyphae D1 Replicate 1 Figure4 WCE


title: ChIP-Seq WT hyphae 8h Replicate 1 Figure4 WCE


title: ChIP-Seq Ryp1 arthroconidia arthroconidia Replicate 2 Figure4 WCE


title: ChIP-Seq Ryp1 hyphae D1 Replicate 3 Figure4 WCE


title: ChIP-Seq Ryp1 hyphae D1 Replicate 2 Figure4 WCE


title: ChIP-Seq WT hyphae D4 Replicate 3 Figure4 WCE


title: ChIP-Seq WT spherules D4 Replicate 3 Figure4 WCE


title: ChIP-Seq WT spherules D4 Replicate 2 Figure4 WCE


title: ChIP-Seq Ryp1 arthroconidia arthroconidia Replicate 1 Figure4 WCE


title: ChIP-Seq WT spherules D4 Replicate 1 Figure4 WCE


title: ChIP-Seq Ryp1 spherules D1 Replicate 1 Figure4 WCE


title: ChIP-Seq WT hyphae D4 Replicate 1 Figure4 WCE


title: ChIP-Seq Ryp1 arthroconidia arthroconidia Replicate 3 Figure4 WCE


title: ChIP-Seq WT spherules D2 Replicate 3 Figure4 WCE


title: ChIP-Seq WT spherules D2 Replicate 1 Figure4 WCE


title: ChIP-Seq WT hyphae D2 Replicate 1 Figure4 WCE


title: ChIP-Seq WT spherules 8h Replicate 1 Figure4 WCE


title: ChIP-Seq WT hyphae D2 Replicate 3 Figure4 WCE


title: ChIP-Seq Ryp1 spherules D1 Replicate 3 Figure4 WCE


title: ChIP-Seq WT spherules D1 Replicate 2 Figure4 WCE


title: ChIP-Seq Ryp1 spherules D1 Replicate 2 Figure4 WCE


title: ChIP-Seq WT spherules D1 Replicate 3 Figure4 WCE


title: ChIP-Seq WT hyphae D2 Replicate 2 Figure4 WCE


title: ChIP-Seq WT hyphae D1 Replicate 3 Figure4 WCE


title: ChIP-Seq WT arthroconidia arthroconidia Replicate 1 Figure4


title: ChIP-Seq WT hyphae D1 Replicate 2 Figure4 WCE


title: ChIP-Seq WT hyphae D4 Replicate 2 Figure4 WCE


title: ChIP-Seq WT hyphae D1 Replicate 1 Figure4 WCE


title: ChIP-Seq WT spherules D2 Replicate 2 Figure4 WCE


title: ChIP-Seq WT spherules 8h Replicate 2 Figure4


title: ChIP-Seq WT spherules 8h Replicate 1 Figure4


title: ChIP-Seq WT spherules 8h Replicate 3 Figure4


title: ChIP-Seq WT hyphae 8h Replicate 1 Figure4


title: ChIP-Seq Ryp1 spherules D1 Replicate 3 Figure4


title: ChIP-Seq WT hyphae 8h Replicate 3 Figure4


title: ChIP-Seq WT arthroconidia arthroconidia Replicate 2 Figure4


title: ChIP-Seq Ryp1 spherules D1 Replicate 2 Figure4


title: ChIP-Seq Ryp1 hyphae D1 Replicate 1 Figure4


title: ChIP-Seq Ryp1 hyphae D1 Replicate 2 Figure4


title: ChIP-Seq WT spherules D1 Replicate 1 Figure4 WCE


title: ChIP-Seq Ryp1 arthroconidia arthroconidia Replicate 2 Figure4


title: ChIP-Seq Ryp1 arthroconidia arthroconidia Replicate 3 Figure4


title: ChIP-Seq Ryp1 arthroconidia arthroconidia Replicate 1 Figure4


title: ChIP-Seq WT spherules D4 Replicate 3 Figure4


title: ChIP-Seq Ryp1 hyphae D1 Replicate 3 Figure4


title: ChIP-Seq WT spherules D2 Replicate 2 Figure4


title: ChIP-Seq WT spherules D2 Replicate 3 Figure4


title: ChIP-Seq Ryp1 spherules D1 Replicate 1 Figure4


title: ChIP-Seq WT hyphae D4 Replicate 1 Figure4


title: ChIP-Seq WT arthroconidia arthroconidia Replicate 3 Figure4


title: ChIP-Seq WT spherules D4 Replicate 2 Figure4


title: ChIP-Seq WT hyphae D2 Replicate 2 Figure4


title: ChIP-Seq WT hyphae 8h Replicate 2 Figure4


title: ChIP-Seq WT hyphae D4 Replicate 3 Figure4


title: ChIP-Seq WT spherules D2 Replicate 1 Figure4


title: ChIP-Seq WT spherules D4 Replicate 1 Figure4


title: ChIP-Seq WT hyphae D2 Replicate 3 Figure4


title: ChIP-Seq WT hyphae D4 Replicate 2 Figure4


title: ChIP-Seq WT hyphae D2 Replicate 1 Figure4


title: ChIP-Seq WT hyphae D1 Replicate 2 Figure4


title: ChIP-Seq WT hyphae D1 Replicate 1 Figure4


title: ChIP-Seq WT spherules D1 Replicate 1 Figure4


title: ChIP-Seq WT hyphae D1 Replicate 3 Figure4


title: RNA-seq WT arthroconidia arthroconidia Replicate 1 Figure2

data_processing:
For RNA-Seq: Estimated counts of each transcript were calculated for each sample by alignment-free comparison against the predicted mRNA for the published Silveira genome (de Melo Teixeira et al 2022, PMID 35137016) using KALLISTO version 0.46.2 (Bray et al 2016, PMID 27043002).
Assembly: Silveira genome (de Melo Teixeira et al 2022, PMID 35137016)
Supplementary files format and content: For RNA-Seq: Processed data are Kallisto output files with estimated counts per gene.

growth_protocol: The wildtype Coccidioides posadasii strain Silveira (NR-48944) was used for growth experiments and as the background for the generation of the ryp1∆ mutant. All manipulation of live Coccidioides strains were performed in a biosafety level 3 facility. Standard spherulation conditions: polypropylene flasks containing Converse media were inoculated with 1 x 10^6/mL arthroconidia (unless otherwise stated) and placed at 39˚C, 10 % CO2, shaking at 120 rpm.  Where noted, spherulation was induced under the same conditions with different media: DMEM (UCSF Media Core) containing 20 % FBS (Corning) or RPMI (UCSF Media Core) containing 10 % FBS. For hyphal growth, polypropylene flasks containing Converse media were inoculated with 1 x 10^6 arthroconidia/mL and grown at 25˚C (Figures 2, S2) or room temperature (RT) (Figure 4, S4) shaking at 120 rpm. All growth experiments were performed in 125 mL polypropylene flasks with 50 mL of media except for experiments in Figures 2, S2, which were performed in 1 L flasks with 350 mL of media (except for replicate 3 of ryp1∆ mutant in spherulation conditions, which was placed in 300 mL of media given limited arthroconidia stock, to maintain the same concentration across all samples) and Figures 4, S4, which were performed in 1 L flasks with 330 mL Converse for wildtype and 500 mL flasks with 100 mL Converse for ryp1∆ mutant.Arthroconidia were generated on 2x GYE agar (2% Dextrose (Fisher), 1% Yeast extract (Gibco), 1.5% Bacto-Agar (BD)) + Penicillin/Streptomycin (100 U/ml penicillin and 100 g/ml streptomycin, UCSF Media Core) in T225 tissue culture flasks for 4-6 weeks at 30˚C, 25˚C, or 37˚C. Arthroconidia were then collected through scraping and washing as previously described (Mead et al 2020, PMID 32894648) and stocks were stored in PBS until use.

extract_protocol:
For RNA-Seq: RNA from arthroconidia were collected from the same arthroconidia stock in triplicate by placing 5x10^7 arthroconidia into Trizol LS (Ambion) and bead beating for 2 minutes. For all other samples, at indicated timepoints, RNA was extracted by pelleting cells by centrifugation at 1200 x g for 5 minutes at RT, removing supernatants, and flash freezing cell pellets in liquid nitrogen. Cell pellets were resuspended in Trizol, thawed, and bead beat for 2 minutes. Samples were stored at -80˚C until all samples at all timepoints in an individual experiment had been collected. RNA was extracted using the Direct-zol RNA Miniprep Plus isolation kit (Zymo) with on-column DNAse digestion step extended for 15-30 minutes.
For RNA-Seq: Sequencing libraries were prepared using the Ultra II Directional RNA Library Prep kit with dual-indexed multiplexing barcodes with polyA selection. Library quality and adaptor dimer contamination were analyzed using Agilent High Sensitivity DNA Chip. An additional round of library size selection was performed using homemade Serapure size selection beads (Rohland et al 2012, PMID 22267522) for libraries containing significant adaptor dimers.


title: RNA-seq WT spherules D3 RPMI Replicate 3 FigureS5

value: RPMI


title: RNA-seq Ryp1 arthroconidia arthroconidia Replicate 1 Figure2


title: RNA-seq WT spherules D3 RPMI Replicate 2 FigureS5


title: RNA-seq Ryp1 arthroconidia arthroconidia Replicate 2 Figure2


title: RNA-seq WT arthroconidia arthroconidia Replicate 3 Figure2


title: RNA-seq Ryp1 spherules 8Hour Replicate 3 Figure2


title: RNA-seq WT spherules D3 RPMI Replicate 1 FigureS5


title: RNA-seq Ryp1 arthroconidia arthroconidia Replicate 3 Figure2


title: RNA-seq Ryp1 spherules 8Hour Replicate 2 Figure2


title: RNA-seq Ryp1 spherules 8Hour Replicate 1 Figure2


title: RNA-seq WT spherules 8Hour Replicate 1 Figure2


title: RNA-seq WT spherules 8Hour Replicate 2 Figure2


title: RNA-seq WT spherules 8Hour Replicate 3 Figure2


title: RNA-seq WT hyphae 8Hour Replicate 3 Figure2


title: ChIP-Seq WT spherules D1 Replicate 3 Figure4


title: RNA-seq WT hyphae 8Hour Replicate 1 Figure2


title: ChIP-Seq WT spherules D1 Replicate 2 Figure4


title: RNA-seq Ryp1 hyphae 8Hour Replicate 2 Figure2


title: RNA-seq Ryp1 hyphae 8Hour Replicate 3 Figure2


title: RNA-seq Ryp1 hyphae 8Hour Replicate 1 Figure2


title: RNA-seq WT spherules D3 DMEM Replicate 3 FigureS5

value: DMEM


title: RNA-seq WT hyphae 8Hour Replicate 2 Figure2


title: RNA-seq WT spherules D6 Replicate 1 Figure2


title: RNA-seq WT arthroconidia arthroconidia Replicate 2 Figure2


title: RNA-seq WT spherules D6 Replicate 2 Figure2


title: RNA-seq WT hyphae D6 Replicate 2 Figure2


title: RNA-seq Ryp1 spherules D6 Replicate 1 Figure2


title: RNA-seq Ryp1 spherules D6 Replicate 2 Figure2


title: RNA-seq Ryp1 hyphae D6 Replicate 1 Figure2


title: RNA-seq Ryp1 hyphae D6 Replicate 3 Figure2


title: RNA-seq WT spherules D5 Replicate 3 Figure2


title: RNA-seq Ryp1 spherules D5 Replicate 3 Figure2


title: RNA-seq Ryp1 spherules D5 Replicate 2 Figure2


title: RNA-seq Ryp1 spherules D6 Replicate 3 Figure2


title: RNA-seq Ryp1 spherules D5 Replicate 1 Figure2


title: RNA-seq WT spherules D5 Replicate 2 Figure2


title: RNA-seq WT spherules D5 Replicate 1 Figure2


title: RNA-seq WT spherules D3 DMEM Replicate 2 FigureS5


title: RNA-seq WT hyphae D6 Replicate 1 Figure2


title: RNA-seq WT spherules D4 Replicate 3 Figure2


title: RNA-seq WT spherules D4 Replicate 2 Figure2


title: RNA-seq WT spherules D3 DMEM Replicate 1 FigureS5


title: RNA-seq Ryp1 spherules D4 Replicate 3 Figure2


title: RNA-seq WT spherules D4 Replicate 1 Figure2


title: RNA-seq WT spherules D6 Replicate 3 Figure2


title: RNA-seq WT spherules D3 Replicate 3 Figure2


title: RNA-seq WT spherules D3 Replicate 1 Figure2


title: RNA-seq WT hyphae D6 Replicate 3 Figure2


title: RNA-seq Ryp1 spherules D4 Replicate 1 Figure2


title: RNA-seq Ryp1 spherules D3 Replicate 3 Figure2


title: RNA-seq Ryp1 spherules D4 Replicate 2 Figure2


title: RNA-seq Ryp1 spherules D3 Replicate 1 Figure2


title: RNA-seq Ryp1 spherules D3 Replicate 2 Figure2


title: RNA-seq Ryp1 hyphae D6 Replicate 2 Figure2


title: RNA-seq WT spherules D3 Replicate 2 Figure2


title: RNA-seq WT hyphae D3 Replicate 3 Figure2


title: RNA-seq WT hyphae D3 Replicate 1 Figure2


title: RNA-seq Ryp1 hyphae D3 Replicate 2 Figure2


title: RNA-seq Ryp1 hyphae D3 Replicate 3 Figure2


title: RNA-seq WT hyphae D3 Replicate 2 Figure2


title: RNA-seq Ryp1 hyphae D3 Replicate 1 Figure2


title: RNA-seq WT spherules D2 Replicate 3 Figure2


title: RNA-seq WT spherules D2 Replicate 2 Figure2


title: RNA-seq Ryp1 spherules D2 Replicate 2 Figure2


title: RNA-seq Ryp1 spherules D2 Replicate 3 Figure2


title: RNA-seq Ryp1 spherules D2 Replicate 1 Figure2


title: RNA-seq WT hyphae D2 Replicate 3 Figure2


title: w1206,cerebellum,dup

first: Rachita

last: Yadav

address: 185 Cambridge street

department: Neurology

institute: MGH

data_processing:
Each bulk RNAseq library of mouse sample was aligned to mouse reference genome GRCm38 version 83 using STAR aligner. Expression counts for each sample was also generated by STAR aligner.
Differential expression analysis was performed by DESeq2 + SVA pipeline, whereas co-expression analysis was performed by WGCNA.
Supplementary files format and content: "all.cnts.tsv" - tab delimited text file for raw counts of mouse bulk RNAseq data.

source_name: HPC

extract_protocol:
All RNA samples were extracted with Trizol reagent according to the manufacturer’s instruction (Invitrogen).
Mouse RNASeq libraries were prepared with customized version of strand specific dUTP method and TruSeq Stranded mRNA Library Kit (Illumina)

tag: tissue

value: HPC

value: dup

tag: Sex

value: female


title: w1205,striatum,dup

value: male


title: RNA-seq WT hyphae D2 Replicate 1 Figure2


title: RNA-seq WT hyphae D2 Replicate 2 Figure2


title: RNA-seq Ryp1 hyphae D2 Replicate 3 Figure2


title: w1205,cerebellum,dup


title: w1204,striatum,dup

source_name: mPFC

value: mPFC


title: w1204,cortex,dup

value: wt


title: RNA-seq WT spherules D2 Replicate 1 Figure2


title: w1204,cerebellum,dup


title: w1203,striatum,dup

value: trip


title: RNA-seq Ryp1 hyphae D2 Replicate 1 Figure2


title: human GBM 2513, 2513

type: RNA

city: Lausanne

first: Pierre

last: Bady

address: Quartier UNIL-Sorge

department: Swiss Institute of Bioinformatics

institute: CHUV / BCF / SIB

description: Resected glioblastoma tissues untreated by gefitinib

hyb_protocol: Affymetrix hybridisation protocol

scan_protocol: GeneChip Operating Software instructions using GeneChip Scanner 3000 High-Resolution Scanning Patch

data_processing: RMA: background substruction, quantile normalization and median polish summarization

label: biotin

source_name: Surgical resection GBM_TuBa2513

label_protocol: Affymetrix Small sample target labelling assay (double amplification) with ENZO kit, start with 100ng

extract_protocol: Qiagen Rneasy Lipid Tissue mini kit protocol

tag: type

value: human

tag: disease

value: GBM


title: human GBM NCH1152, 1152

description: GBM derived xenograft tissues untreated by gefitinib

source_name: mouse xenograft of human glioblastoma_TuBa1152

value: xenograft


title: human GBM NCH1157, 1157

description: GBM derived xenograft tissues treated by gefitinib

source_name: mouse xenograft of human glioblastoma_TuBa1157


title: human GBM NCH1155, 1155

source_name: mouse xenograft of human glioblastoma_TuBa1155


title: human GBM NCH1161, 1161

source_name: mouse xenograft of human glioblastoma_TuBa1161


title: w1203,cerebellum,dup


title: human GBM NCH1159, 1159

source_name: mouse xenograft of human glioblastoma_TuBa1159


title: RNA-seq WT spherules D1 Replicate 3 Figure2

value: fungal cell

value: WT

value: spherules


title: human GBM NCH1154, 1154

source_name: mouse xenograft of human glioblastoma_TuBa1154


title: human GBM ZH-18, 2511

description: Resected glioblastoma tissues treated by gefitinib

source_name: Surgical resection GBM_TuBa2511


title: w1205,cortex,dup


title: w1202,cerebellum,dup


title: w1202,striatum,dup


title: RNA-seq WT spherules D1 Replicate 2 Figure2

value: Converse


title: human GBM 2509, 2509

source_name: Surgical resection GBM_TuBa2509


title: w1202,cortex,dup


title: RNA-seq WT spherules D1 Replicate 1 Figure2


title: RNA-seq Ryp1 hyphae D2 Replicate 2 Figure2

value: hyphae


title: w1201,cerebellum,dup


title: w1201,striatum,dup


title: human GBM 2507, 2507

source_name: Surgical resection GBM_TuBa2507


title: human GBM 2508, 2508

source_name: Surgical resection GBM_TuBa2508


title: human GBM 2506, 2506

source_name: Surgical resection GBM_TuBa2506


title: w1203,cortex,dup


title: w1201,cortex,dup


title: human GBM 2504, 2504

source_name: Surgical resection GBM_TuBa2504


title: T1993,cortex,del

value: del


title: T1994,cortex,del


title: RNA-seq Ryp1 spherules D1 Replicate 2 Figure2


title: RNA-seq Ryp1 spherules D1 Replicate 3 Figure2


title: t1994,cerebellum,del


title: t1992,cerebellum,del


title: t1994,striatum,del


title: t1993,striatum,del


title: T1992,cortex,del


title: t1993,cerebellum,del


title: t1992,striatum,del


title: RNA-seq WT hyphae D1 Replicate 1 Figure2


title: human GBM 2502, 2502

source_name: Surgical resection GBM_TuBa2502


title: RNA-seq WT hyphae D1 Replicate 2 Figure2

source_name: liquid culture


title: T1991,cortex,del

source_name: HPC


title: t1991,striatum,del

source_name: mPFC


title: RNA-seq Ryp1 hyphae D1 Replicate 3 Figure2


title: RNA-seq WT hyphae D1 Replicate 3 Figure2


title: RNA-seq Ryp1 spherules D1 Replicate 1 Figure2


title: t1990,striatum,del-wt


title: human GBM 2501, 2501

source_name: Surgical resection GBM_TuBa2501


title: t1991,cerebellum,del


title: human GBM 2500, 2500

source_name: Surgical resection GBM_TuBa2500


title: human GBM 2499, 2499

source_name: Surgical resection GBM_TuBa2499


title: human GBM 2497, 2497

source_name: Surgical resection GBM_TuBa2497


title: RNA-seq Ryp1 hyphae D1 Replicate 2 Figure2


title: human GBM ZH-17, 2496

source_name: Surgical resection GBM_TuBa2496


title: human GBM ZH-14, 2493

source_name: Surgical resection GBM_TuBa2493


title: t1989,striatum,del-wt


title: human GBM ZH-13, 2492

source_name: Surgical resection GBM_TuBa2492


title: RNA-seq Ryp1 hyphae D1 Replicate 1 Figure2


title: T1989,cortex,del-wt


title: RNA-seq WT arthroconidia arthroconidia Replicate 2 Figure1

value: arthroconidia

value: PBS


title: t1990,cerebellum,del-wt

value: HPC


title: T1988,cortex,del-wt

value: female


title: t1988,striatum,del-wt


title: t1987,striatum,del-wt


title: t1988,cerebellum,del-wt


title: RNA-seq WT spherules D6 Replicate 2 Figure1


title: RNA-seq WT arthroconidia arthroconidia Replicate 3 Figure1


title: RNA-seq WT arthroconidia arthroconidia Replicate 1 Figure1


title: T1990,cortex,del-wt

value: male


title: T1987,cortex,del-wt

value: mPFC


title: t1987,cerebellum,del-wt

value: wt


title: t1986,striatum,dup


title: t1989,cerebellum,del-wt


title: human GBM ZH-12, 2491

source_name: Surgical resection GBM_TuBa2491


title: RNA-seq WT spherules D6 Replicate 3 Figure1


title: human GBM ZH-11, 2490

source_name: Surgical resection GBM_TuBa2490


title: human GBM ZH-09, 2489

source_name: Surgical resection GBM_TuBa2489


title: human GBM ZH-07, 2487

source_name: Surgical resection GBM_TuBa2487


title: RNA-seq WT spherules D6 Replicate 1 Figure1


title: RNA-seq WT spherules D5 Replicate 3 Figure1


title: T1984,cortex,dup

value: dup


title: t1984,striatum,dup


title: human GBM ZH-08, 2488

source_name: Surgical resection GBM_TuBa2488

value: human


title: human GBM ZH-05, 2485

source_name: Surgical resection GBM_TuBa2485

value: GBM


title: T1985,cortex,dup


title: RNA-seq WT spherules D5 Replicate 1 Figure1


title: t1983,striatum,dup


title: t1984,cerebellum,dup


title: t1986,cerebellum,dup


title: RNA-seq WT spherules D4 Replicate 1 Figure1


title: T1986,cortex,dup


title: t1985,striatum,dup


title: t1983,cerebellum,dup


title: t1985,cerebellum,dup


title: T1983,cortex,dup


title: t1982,striatum,dup-wt


title: RNA-seq WT spherules D4 Replicate 3 Figure1


title: t1982,cerebellum,dup-wt


title: T1982,cortex,dup-wt


title: RNA-seq WT spherules D5 Replicate 2 Figure1


title: human GBM BE-05, 2468

source_name: Surgical resection GBM_TuBa2468


title: RNA-seq WT spherules D4 Replicate 2 Figure1

source_name: liquid culture


title: WT mirVAna Purified Control Rep 2

city: Worcester

first: Oliver

last: Rando

state: Massachusetts

address: 364 Plantation St

department: BMP

institute: University of Massachusetts

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt v2.9, when UMI was present reads were deduplicated with seqkit v0.14.0 and UMI sequence was trimmed with cutadapt.
Trimmed reads where then mapped to sacCer3 or mm10 with tRAX using default settings.
Assembly: mm10, sacCer3
Supplementary files format and content: Each processed data file contains information about read-start/stop site, coveage, and  misinicorporation rate.

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: For full length tRNA experiments, yTG66 and yTG109 were grown overnight in selective synthetic media containing 2% dextrose, saturated cultures were diluted to OD600=0.1 and grown in selective synthetic media containing 2% dextrose until they reached OD600=0.5-07. For tRF experiments, yTG72 were grown overnight in selective synthetic media containing 2% raffinose. Saturated cultures were diluted to OD600=0.1 in selective synthetic media containing 2% raffinose and grown until early-midlog (OD600= 0.3-0.4). Cells were then centrifuged and diluted in selective synthetic media containing 2% galactose to an OD600 so that they reach OD600=0.5-0.7 in 360 minutes (“WT” samples were resuspended in selective synthetic media containing 2% galactose, centrifuged, and snap frozen immediately).

extract_protocol:
Mouse RNA was extracted using standard TRIZol protocol. Yeast RNA was extracted by beadbeating in TNE buffer (50 mM Tris-Cl pH7.4, 100 mM NaCl, 10 mM EDTA), followed by an acid Phenol extraction.
Libraries were constructed following published protocols.

tag: growth media

value: SC-Ura Dextrose


title: human GBM BE-04, 2467

source_name: Surgical resection GBM_TuBa2467


title: t1981,striatum,dup-wt

source_name: mPFC


title: human GBM ZH-06, 2486

source_name: Surgical resection GBM_TuBa2486


title: human GBM ZH-04, 2484

source_name: Surgical resection GBM_TuBa2484


title: WT mirVAna Purified Control Rep 1


title: T1981,cortex,dup-wt

value: trip


title: t1981,cerebellum,dup-wt

source_name: HPC


title: RNA-seq WT spherules D3 Replicate 1 Figure1

value: fungal cell

value: WT


title: t1980,striatum,dup-wt


title: WT mirVAna Purified AlkB Rep 2


title: T1980,cortex,dup-wt


title: WT mirVAna Purified AlkB Rep 1


title: RNA-seq WT spherules D3 Replicate 3 Figure1

value: spherules

value: Converse


title: t1979,striatum,dup-wt


title: TRM1Δ pGAL-RNY1 tRF OTTR Control Rep 4

value: SC-Ura Galactose


title: RNA-seq WT spherules D3 Replicate 2 Figure1


title: t1979,cerebellum,dup-wt


title: t1980,cerebellum,dup-wt


title: TRM1Δ pGAL-RNY1 tRF OTTR Control Rep 3


title: RNA-seq WT spherules D2 Replicate 2 Figure1


title: RNA-seq WT spherules D2 Replicate 3 Figure1


title: Displaced matS_1, Xer recombinase

city: Gif sur Yvette

first: Elena

last: ESPINOSA

address: 1, Avenue de la Terrasse

country: France

institute: CNRS

data_processing:
Cutadapt was used to trim adapter and transposon sequences. Also, Cutadapt was used to create the files with total reads and the files with the reads in which the reporter cassette was excised.
BWA software was used for the alignment of reads on genomes
MatLab was used to create the files with the transposon hits in the genome
Assembly: N16961.fa
Assembly: MCH1.fa
Assembly: EPV496.fa
Assembly: EPV487.fa
Supplementary files format and content: Two tables per sample containing the total transposon instertion positions  and the recombined positions at a besa pair resolution, respectively
Library strategy: HiSC2 (Adapted from Tn-seq)

organism: Vibrio cholerae

source_name: O1 biovar El Tor str. N16961

growth_protocol: V. cholerae transposon libraries were grown in M9 minimal medium supplemented with 0.2% fructose, 1 μg/ml thiamine and 0.1 mM of IPTG at 37°C until exponential phase

extract_protocol:
gDNA was extracted with GenElute bacterial genomics DNA kit (Sigma-Aldrich)
Briefly, gDNA was digested with MmeI, then, fragments containing Mariner transposon were size selected using Pippinprep and custom-made adpaters were ligated. Finally, libraries were amplified and size selected using Pippinprep.

treatment_protocol: V. cholerae transposon libraries were supplemented with arabinose up to a final concentration of 0.02% to induce recombinase expression

value: O1 biovar El Tor str. N16961

value: ChapR {delta}lacZ::PBAD-xerC-invPlac-aadA1 {delta}vc1488 vca0560::vc1488

tag: recombination cassette

value: short dif-dif


title: Inverted ter ΔmatP_1, Xer recombinase

tag: strain

value: ChapR {delta}lacZ::PBAD-xerC-invPlac-aadA1 INV(attP-dif) matP::bla


title: Displaced matS_2, Xer recombinase

value: ChapR {delta}lacZ::PBAD-xerC-invPlac-aadA1 {delta}vc1488 vca0560::vc1489


title: T1979,cortex,dup-wt

value: mPFC

value: male


title: MCH1_1, Xer recombinase


title: WT, Xer recombinase long reporter cassette

value: long dif-dif


title: TRM1Δ pGAL-RNY1 tRF OTTR AlkB Rep 4


title: RNA-seq WT spherules D1 Replicate 2 Figure1


title: TRM1Δ pGAL-RNY1 tRF OTTR AlkB Rep 3


title: Inverted ter_1, Xer recombinase


title: TRM1Δ pGAL-RNY1 tRF OTTR Control Rep 2


title: human GBM BE-03, 2248

source_name: Surgical resection GBM_TuBa2248

value: human


title: RNA-seq WT spherules D2 Replicate 1 Figure1


title: TRM1Δ pGAL-RNY1 tRF OTTR Control Rep 1


title: RNA-seq WT spherules D1 Replicate 1 Figure1


title: MCH1ΔmatP_1,  Cre recombinase

value: MCH1 ChapR {delta}lacZ::PBAD-cre-invPlac-ble matP::bla

value: short loxP-loxP


title: ΔmatP_2, Xer recombinase


title: ΔmatP_1, Xer recombinase


title: TRM1Δ pGAL-RNY1 tRF OTTR AlkB Rep 2


title: RNA-seq WT spherules 8Hour Replicate 3 Figure1


title: ΔmatP_1, Cre recombinase


title: TRM1Δ pGAL-RNY1 tRF OTTR AlkB Rep 1


title: WT_2, Cre recombinase

value: ChapR {delta}lacZ::PBAD-cre-invPlac-ble


title: MCH1_1, Cre recombinase


title: pGAL-RNY1 tRF OTTR Control Rep 4


title: WT_1, Cre recombinase


title: WT_1, Xer recombinase


title: pGAL-RNY1 tRF OTTR Control Rep 3


title: RNA-seq WT spherules 8Hour Replicate 2 Figure1

value: fungal cell


title: RNA-seq WT spherules 8Hour Replicate 1 Figure1

value: WT


title: pGAL-RNY1 tRF OTTR AlkB Rep 4


title: MCH1ΔmatP_1,  Xer recombinase

value: MCH1 ChapR {delta}lacZ::PBAD-xerC-invPlac-aadA1 matP::bla


title: salivary DNA from control post 72

type: genomic

city: Girona

first: Anna

last: Prats-Puig

state: Girona

address: Carrer del President Francesc Macià, 65, 17190 Salt, Girona

country: Spain

institute: University School of Health and Sport

description: salivary DNA from control post 72

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to human Illumina 900K (EPIC) microarray using standar Illumina protocol.

scan_protocol: Arrays were imaged using the BeadArray redader (HiScan) and the strandard recommended Illumina scanner setting.

data_processing: Rn Beads package in R environment.

source_name: saliva

label_protocol: Protocol outlined in manufacturer's instructions.

extract_protocol: Genomic DNA was extracted from saliva using the prepIT®•L2P reagent (PT-L2P-5; DNA Genotek, USA) and 500 μL of Oragene samples, according to the manufacturer’s instructions.

value: saliva

value: M

tag: control/intervention

value: control


title: salivary DNA from control post 71

description: salivary DNA from control post 71

value: F


title: salivary DNA from control pre 71

description: salivary DNA from control pre 71


title: pGAL-RNY1 tRF OTTR AlkB Rep 3

value: SC-Ura Galactose


title: Treatment of MCF-7 cells with 2% O2 for 24 hours rep2

city: Shenyang

first: Huanyu

last: Wu

state: Liaoning

address: No. 77 Puhe Road

department: Pathology Teaching and Research Office of Basic Medical College

institute: China Medical University

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

tag: cell line

tag: group

value: Hypoxia

tag: treatment


title: Treatment of MCF-7 cells with 2% O2 for 24 hours rep1


title: salivary DNA from control pre 70

description: salivary DNA from control pre 70


title: salivary DNA from control post 69

description: salivary DNA from control post 69


title: pGAL-RNY1 tRF OTTR Control Rep 2


title: RNA-seq WT spherules D1 Replicate 3 Figure1

tag: morphology

value: spherules

tag: timepoint

value: Converse


title: salivary DNA from control pre 69

description: salivary DNA from control pre 69


title: human GBM ZH-01, 2482

source_name: Surgical resection GBM_TuBa2482

value: GBM


title: salivary DNA from intervention post 66

description: salivary DNA from intervention post 66

value: intervention


title: Aerobic treatment of MCF-7 cells rep3

value: Normoxia

value: Aerobic treatment of MCF-7 cells


title: pGAL-RNY1 tRF OTTR Control Rep 1


title: salivary DNA from intervention pre 66

description: salivary DNA from intervention pre 66


title: salivary DNA from control pre 72

description: salivary DNA from control pre 72


title: salivary DNA from intervention post 65

description: salivary DNA from intervention post 65


title: Aerobic treatment of MCF-7 cells rep2


title: Aerobic treatment of MCF-7 cells rep1


title: salivary DNA from control post 70

description: salivary DNA from control post 70


title: salivary DNA from intervention post 63

description: salivary DNA from intervention post 63


title: salivary DNA from intervention pre 63

description: salivary DNA from intervention pre 63


title: pGAL-RNY1 tRF OTTR AlkB Rep 1


title: salivary DNA from intervention post 62

description: salivary DNA from intervention post 62


title: salivary DNA from intervention pre 62

description: salivary DNA from intervention pre 62


title: WT tRF OTTR Control Rep 2


title: salivary DNA from intervention post 54

description: salivary DNA from intervention post 54


title: salivary DNA from intervention pre 54

description: salivary DNA from intervention pre 54


title: salivary DNA from intervention pre 53

description: salivary DNA from intervention pre 53


title: WT tRF OTTR AlkB Rep 2


title: salivary DNA from intervention post 52

description: salivary DNA from intervention post 52


title: salivary DNA from intervention post 53

description: salivary DNA from intervention post 53


title: pGAL-RNY1 tRF OTTR AlkB Rep 2


title: WT tRF OTTR AlkB Rep 1


title: salivary DNA from intervention pre 65

description: salivary DNA from intervention pre 65


title: salivary DNA from intervention pre 52

description: salivary DNA from intervention pre 52


title: salivary DNA from intervention post 50

description: salivary DNA from intervention post 50


title: salivary DNA from intervention post 51

description: salivary DNA from intervention post 51


title: salivary DNA from intervention pre 51

description: salivary DNA from intervention pre 51