title: Cocult_10Gy_1

first: Manuel

last: Valiente

state: MADRID

address: Calle de Melchor Fernández Almagro, 3

institute: Centro Nacional de Investigaciones Oncológicas

description: H2030-BrM lung adenocarcinoma co-cultured with glial cells 24 hours post-irradiation (10Gy)

data_processing:
RNA-seq processing:
Read files were quality-checked with FastQC.
Reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.10 (using Bowtie 1.0.0 and Samtools 0.1.19), allowing 2 mismatches and 5 multihits.
Transcripts quantification and differential expression calculated with Cufflinks 2.2.1
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tables were generated with Cufflinks 2.2.1 and contain transcripts abundance measured in FPKM values

source_name: H2030-BrM lung adenocarcinoma

growth_protocol: Adherent cultures: H2030-BrM were cultured in RPMI1640 media supplemented with 10% FBS, 2 mM L-glutamine, 100 IU/ml penicillin/streptomycin, and 1 mg/ml amphotericin B; Oncospheres: 1 x 103 BrM cells were plated in low-attachment plates in in Humec medium (12753018, Gibco) supplemented with 10 ng/ml basic human fibroblast growth factor (bFGF; 13256-029, Gibco), 20 ng/ml Epidermal growth factor (EGF; E9644, Sigma-Aldrich), 5 µg/ml insulin solution from bovine pancreas (IGF1; I0516, Sigma-Aldrich), and B27 supplement (17500-044, Gibco). H2030-BrM cells were grown for 7 days and E0771-BrM cells for 4 days, so formed oncospheres are approximately the same size and number. After this period, oncospheres were irradiated with a single dose of 10Gy. Glial cell co-culture: 1.5 x 104 BrM cells were plated in the lower chamber of 24-well-plates on poly-lysine-treated glass coverslips. Co-culture media consisted of RPMI1640 media supplemented with 0.25% FBS, 2 mM L-glutamine, 100 IU/ml penicillin/streptomycin and 1 mg/ml amphotericin B. For indirect co-culture, 4.5 x 104 primary glia cells were plated in a cell culture insert (0,4 µm pore size; 353495, Falcon). For direct co-culture, 4.5 x 104 primary glia cells were plated in the lower chamber together with BrM cells. Co-cultures were irradiated with a single dose 10Gy 18h later.

extract_protocol:
For RNA-seq Total RNA was extracted using the RNeasy kit (Qiagen)
1 µg of total RNA samples was used as provided by the user. Sample RNA Integrity Numbers were in the range 7.6 to 9.4 (average 8.7) when assayed on an Agilent 2100 Bioanalyzer. PolyA+ fraction was purified and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D" kit (this kit incorporates dUTP during 2nd strand cDNA synthesis, which implies that only the cDNA strand generated during 1st strand synthesis is eventually sequenced). Adapter-ligated library was completed by PCR with Illumina PE primers (9 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina instrument (see below) by following manufacturer's protocols.

treatment_protocol: RNA was obtained 14 hours of a single dose of radiation (10Gy)

tag: cell line

tag: protocol


title: BasL_008

status: Public on Feb 14 2022

type: RNA

city: Copenhagen Ø

first: Maria

last: Rossing

address: Blegdamsvej 9

department: Center for Genomic Medicine

country: Denmark

institute: Rigshospitalet

description: Gene expression data from human breast cancer

hyb_protocol: Following fragmentation, approx. 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. The arrays were washed and stained with phycoerytrin-conjugated streptavidin using the Affymetrix Fluidics Station 450.

scan_protocol: The Affymetrix GeneArray 3000 7G scanner was used to generate fluorescent images. Probe intensity files (.CEL files) were generated in the GeneChip Command Console Software (AGCC; Affymetrix, Santa Clara, CA, USA). These were anonymized using R v. 4.0.0 and modified functions from the affxparser package.

data_processing: CEL files were loaded into R 3.6.1 using justRMA from affy. For processing, the BrainArray Entrez Gene Custom CDF v. 24 was used, and otherwise default parameter settings were used. Entrez Gene IDs were subsequently translated to HGNC symbols using the BrainArray annotation from hgu133plus2hsentrezg.db. After filtering out data with missing HGNC annotation and control probes, expression data for 20,418 genes remained.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Breast cancer tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for 12 ug total RNA.

extract_protocol: RNA was isolated using the AllPrep DNA/RNA purification kit (Qiagen, Hilden, Germany). The integrity of the RNA was measured using the Agilent RNA 6000 Nano Kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA).

treatment_protocol: Fresh tumor specimens, extracted during surgery, were inspected by pathologists, and tumor biopsies of around 100 mg were stored in RNALater (Thermo Fisher Scientific, Waltham, MA, USA).

tag: tissue

value: Breast cancer

tag: citbcmst subtype

value: BasL

tag: sn status

value: Negative

tag: ihc er status


title: Cocult_10Gy_2

type: SRA

city: Madrid

country: Spain

library_source: transcriptomic

value: co-cultured with glial cells 24 hours post-irradiation (10Gy)


title: BasL_007


title: Embryonic day E18.5 Hypothalamus, Control, F4530_E2S2

city: Brisbane

first: Brad

last: Balderson

state: QLD

address: Chemistry Bld, 68 Cooper Rd

department: The School of Chemistry and Molecular Bioscience

country: Australia

institute: The University of Queensland

description: ScRNA-seq run from E18.5 Mus musculus hypothalamus

data_processing:
Base calling was performed using the Illumina BaseSpace application FASTQ Generation v1.0.0
Bam files and count matrices per sample were generated using the Illumina BaseSpace application SureCell RNA Single-Cell v1.2.0, using STAR (v2.5.2b) to align the cDNA reads to the mm10 genome (the second read mate, R2) and Samtools (v1.3) to append cell barcodes to aligned reads (derived from the first read mate, R1). Cell barcodes and UMIs in R1 are corrected and counted via the aforementioned Illumina Application.
Counts per cell in each sample were downloaded from Illumina Base Space and concatenated into a single count matrix to generate counts.txt.gz.
Genome_build: mm10
Supplementary_files_format_and_content: counts.txt contains the read counts for each gene in each cell (rows are genes, columns are cells). The cell names are in the format: {sample_prefix}_{treatment}_{sex}_{day}_{}_{cell_barcode}.
Supplementary_files_format_and_content: sample_meta.txt contains meta-data related to each sample. Each row corresponds to a particular read pair, matches to the prefix of the fq files. Contains information about the sex (M for male, or F for female), the treatment (WT for wild-type, or KO for Eed-cKO), and the corresponding fastq file read mates; as well as checksums to make sure data is downloaded properly.

organism: Mus musculus

source_name: Embryonic day E18.5 Hypothalamus

growth_protocol: Mice were reared at normal 12:12h day:night cycle, on water and chow.

extract_protocol:
The hypothalamus of control and Eed-cKO embryos was dissected out in ice-cold RPMI-1640 medium (cat.no. 11530586, Thermo Fisher Scientific, Waltham, MA, USA). The dissected hypothalamis were further divided into 2-4 pieces before cell dissociation for single cell isolation using Papain Dissociation System (cat no. LK003150, Worthington Biochemical Corporation, Lakewood, NJ, USA). The tissues were incubated with papain solution at +37°C for 60 min. Isolated single cells were re-suspended in ice-cold 1xPBS, 0.1% BSA, to a final concentration of 2,500 cells/μl (+/- 10%). Cells were checked for viability using a Bio-Rad TC10 automated cell counter (Bio-Rad, Hercules, CA, USA).
Single cells and barcode beads were encapsulated into droplets using Bio-Rad ddSEQ Single-Cell Isolator for cell lysis and barcoding (cat.no. 12004336, Bio-Rad, Hercules, CA, USA). Subsequently, RNA-seq libraries were generated using Illumina SureCell WTA 3' Library Prep Kit for the ddSEQ System (6 cartridge version, cat.no. 20014280, Illumina, San Diego, CA, USA). Libraries were assessed for quality, using 1µl of undiluted cDNA, on an Agilent Technology 2100 Bioanalyzer using an Agilent High Sensitivity DNA chip (cat.no. 5067-4626, Agilent, Santa Clara, CA, USA) to determine fragment size and yield. Samples were stored at -20℃ until sequencing.
Libraries were pooled according to their molar concentration (yield), fragment size, and the unique Nextera i7 indices (8bp). Each sequencing run consisted of four samples with different Nextera i7 indices. The libraries were sequenced on an Illumina NextSeq500 system, using NextSeq 500/550 High Output Kit v2.5 (150 Cycles, cat.no. 20024907, Illumina, San Diego, CA, USA), paired-end read type and Single-Index.

treatment_protocol: Control (Eed fl/fl) and Eed-cKO (Eed fl/fl; Sox1-Cre)

tag: Sex

value: M

tag: genotype

value: Control (Eed fl/fl)

tag: timepoint

value: hypothalamus


title: Insert_10Gy_2

description: H2030-BrM lung adenocarcinoma co-cultured with glial cells separated by an insert 24 hours post-irradiation (10Gy)


title: Insert_10Gy_1

value: co-cultured with glial cells separated by an insert 24 hours post-irradiation (10Gy)


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F502_E6S2

value: Eed-cKO (Eed fl/fl; Sox1-Cre/+)


title: LR7-24

city: Tartu

first: Vijayachitra

last: Modhukur

address: L. Puusepa 8

country: Estonia

institute: University of Tartu

data_processing:
Adapted from Hagemann-Jensen et al. Small-seq for single-cell small-RNA sequencing. Nature Protocols.2018;13(10):2407-24.
Genome_build: hg38

source_name: Uterine fluid

extract_protocol:
RNA extraction using Guanidium based RLT plus Buffer
Hagemann-Jensen et al. Small-seq for single-cell small-RNA sequencing. Nature Protocols.2018;13(10):2407-24.

value: Uterine fluid

tag: study group

value: Recurrent implantation failure

tag: age

tag: bmi


title: BasL_006

value: Positive


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F502_E9S4

value: F


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0652_E5S2


title: LR7-23


title: BasL_012


title: Onco_10Gy_2

description: H2030-BrM lung adenocarcinoma oncospheres 24 hours post-irradiation (10Gy)


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0652_E8S4


title: BasL_003


title: LR7-22


title: BasL_004


title: Adh_10Gy_2

description: H2030-BrM lung adenocarcinoma cultured in adherent standard conditions 24 hours post-irradiation (10Gy)


title: LR7-25


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0588_E7S6


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0652_E5S5


title: Onco_10Gy_1

value: oncospheres 24 hours post-irradiation (10Gy)


title: Adh_10Gy_1

value: cultured in adherent standard conditions 24 hours post-irradiation (10Gy)


title: BasL_005


title: Cocult_0Gy_3

description: H2030-BrM lung adenocarcinoma co-cultured with glial cells without irradiation


title: LR7-20


title: LR7-21


title: BasL_001


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0589_E1S8


title: BasL_002


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0571_E3S1


title: Cocult_0Gy_2

value: co-cultured with glial cells without irradiation


title: LR7-18


title: REF (rep3) reanalyisis

city: Istanbul

first: Halil

middle: ibrahim

last: KISAKESEN

state: Istanbul

address: ITU MOBGAM, SARIYER

department: Molecular Biology, Genetics and Biotechnology

country: Turkey

institute: Istanbul Technical University

description: Gene expression at log-phase in Yeast Minimal Medium

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µL containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Yeast V2 Oligo Microarrays (G4813A-016322) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 016322_D_F_20070321). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Saccharomyces cerevisiae

source_name: Log-phase rep3

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 0.2 µg RNA using the One-color Low Input Quick Amp Kit (Agilent) according to the manufacturer's instructions, followed by Agilent Nano-prep RNA purification (Agilent, Santa Clara, CA). Dye incorporation and cRNA yield were checked with the NanoDrop-2000 spectrophotometer.

growth_protocol: Precultures of oxidative stress resistant Saccharomyces cerevisiae (H7) mutant strain and reference strain were prepared in yeast minimal medium (2% glucose and 0.67% yeast nitrogen base without amino acid (Difco)) by incubating at 30°C and 150 rpm for about ~ 16 hour. Precultures were inoculated into fresh yeast minimal medium to an initial OD600 of 0.1. Then, cultures were incubated at 30°C and 150 rpm. When cultures OD600 value reach the of about 1.0 (correspoinding to mid-exponential phase). Cells were harvested and total RNA extraction was done.

extract_protocol: Total RNA of yeast cells were extracted by using RNeasy Mini Kit supplied from QIAGEN according to the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: There is no treatment protocol in this study.

tag: tag

value: Reference strain


title: LR7-17


title: Embryonic day E18.5 Hypothalamus, Control, F4650_E1S5


title: REF (rep2) reanalyisis

source_name: Log-phase rep2


title: Cocult_0Gy_1


title: Embryonic day E18.5 Hypothalamus, Eed-cKO, F0652_E8S8


title: Insert_0Gy_2

description: H2030-BrM lung adenocarcinoma co-cultured with glial cells separated by an insert without irradiation


title: H7-Log phase-Rep 3

description: Gene expression in the log phase of cell growth

source_name: Oxidative stress resistant Saccharomyces cerevisiae, log. Phase, replicate 3

value: CEN.PK 113.7D (MATa)


title: LR7-16


title: REF (rep1) reanalyisis

source_name: Log-phase rep1


title: LR7-15


title: CD34+CD45+ hematopoietic progenitor cell, ROH HPC #2

city: New York

first: Stephanie

last: Luff

state: NY

address: 1425 Madison Ave

department: Cell, Developmental, & Regenerative Biology

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
ROH HPC #2
counts.txt
FPKM.txt

data_processing:
Basecalling with Illumina RTA 1.9.
Demultiplexing with custom demultipler written in python.
Fastq files were aligned to using STAR (version 2.7.1a).
Gene counts were obtained using Subread (version 1.6.5).
Expression values were filtered to only include protein coding genes using Ensembl BioMart.
FPKM calculation was performed using DESeq2 (version 1.24.0).
Genome_build: GENCODE GRCh38 version 23
Supplementary_files_format_and_content: Gene counts in tab-delimited text format

source_name: Hematopoietic progenitor cell

growth_protocol: The H1 hESC lines were maintained on irradiated mouse embryonic fibroblasts in hESC media. For differentiation, hPSC were cultured on Matrigel-coated plasticware for 24 hours, followed by embryoid body generation. hPSCs were dissociated with brief trypsin-EDTA (0.05%) treatment, followed by scraping. Aggregates were resuspended in serum-free media (SFD) supplemented with L-glutamine (2 mM), ascorbic acid (1 mM), monothioglycerol (MTG, 4x10-4 M), transferrin (150 ug/mL), and BMP-4 (10 ng/mL). On day one, bFGF (5 ng/mL) was added. On day two, Activin A, SB-431542 (6 uM), CHIR99021 (3 uM), and/or IWP2 (3 uM) were added. On the third day of differentiation, embryoid bodies were changed to StemPro-34 media supplemented as above, with VEGF (15 ng/mL) and bFGF (5 ng/mL). On day six, IL-6 (10 ng/mL), IGF-1 (25 ng/mL), IL-11 (5 ng/mL), SCF (50 ng/mL), EPO (2 U/mL final) were added.

extract_protocol:
CD34+CD43-CD73-CD184- cells were sorted using an BD Aria II. RNA was isolated with the miRNeasy Mini kit (Qiagen).
Libraries were prepared using the Clontech SMARTer kit.

treatment_protocol: DEAB or retinol was applied from days 3 (mesoderm) to day 8 (hemogenic endothelium)

tag: cell type

value: ES-derived arterial endothelium

tag: treatment

value: Retinol


title: Insert_0Gy_1

value: co-cultured with glial cells separated by an insert without irradiation


title: CD34+CD45+ hematopoietic progenitor cell, ROH HPC #3

description:
ROH HPC #3
counts.txt
FPKM.txt


title: Onco_0Gy_2

description: H2030-BrM lung adenocarcinoma oncospheres without irradiation

value: oncospheres without irradiation


title: CD34+CD45+ hematopoietic progenitor cell, ROH HPC #1

description:
ROH HPC #1
counts.txt
FPKM.txt


title: LR7-13


title: Onco_0Gy_1


title: Blank cells-rep1

city: Guangzhou

first: Xiaobao

last: Huang

state: Guangdong

address: No. 58 Zhongshan Second Road, Guangzhou, Guangdong, China

department: Department of dermatology

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University

description: gene expression in HeLa cells without infeciton

hyb_protocol: 0.6 ug of Cy3-labelled cRNA （specific activity >10.0 pmol Cy 3/ug cRNA）was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22. 5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression（8*60k） for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1（Agilent）and 1 minute with 37°C GE Wash buffer 2（Agilent）, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1（Agilent） using default parameters to obtain background subtracted and spatiall detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13. 0（Agilent） Probe that at least 1 out of 2 samples flagged as "Detected" were maintained.

source_name: HeLa cells, penicillin, replicate 1

label_protocol: Cyanine-3（Cy3）labeled cRNA was prepared from 0. 2 ug RNA using the One-color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific)and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Chlamydia trachomatis serovar D at an MOI of 2 was added and incubated with the HeLa cells by centrifugation at 3000 rpm/min at 37 ℃ for 1 hour. Samples were then incubated for another hour at 37℃ in 5% CO2. Extracellular bacteria were removed by aspirating the supernatant followed by the addition of fresh RPMI 1640 medium supplemented with 10% fetal bovine serum, 0.5% glucose, and 100 U/ml penicillin G. HeLa cells without chlamydial infection treated with the same medium containing 100U/ml penicillin G were used as control mock cells. The cells were maintained at 37℃ in 5% CO2.

tag: stain

tag: cell

value: HeLa cell


title: Blank cells-rep2

source_name: HeLa cells, penicillin, replicate 2


title: H7-Log phase-Rep 2

source_name: Oxidative stress resistant Saccharomyces cerevisiae, log. Phase, replicate 2


title: H7-Log phase-Rep 1

source_name: Oxidative stress resistant Saccharomyces cerevisiae, log. Phase, replicate 1


title: CD34+CD45+ hematopoietic progenitor cell, DEAB HPC #3

description:
DEAB HPC #3
counts.txt
FPKM.txt

value: DEAB


title: Blank cells-rep3

source_name: HeLa cells, penicillin, replicate 3


title: Adh_0Gy_2

description: H2030-BrM lung adenocarcinoma cultured in adherent standard conditions without irradiation

tag: cell line


title: CD34+CD45+ hematopoietic progenitor cell, DEAB HPC #2

description:
DEAB HPC #2
counts.txt
FPKM.txt


title: LR7-19


title: Adh_0Gy_1

tag: protocol

value: cultured in adherent standard conditions without irradiation


title: LR7-11

tag: tissue


title: CD34+CD45+ hematopoietic progenitor cell, DEAB HPC #1

description:
DEAB HPC #1
counts.txt
FPKM.txt


title: CD34+CXCR4+CD73- arterial endothelium, replicate 3

description:
AEC #3
counts.txt
FPKM.txt

source_name: Arterial endothelium


title: Persistent chlamydial infected-rep1

description: gene expression in HeLa cells persistently infected with Chlamydia trachomatis

source_name: HeLa cells, Ct.D, penicillin, replicate 1

value: Chlamydia trachomatis serovar D


title: RNA-seq_jmj26_Rep2

city: Fukuoka

first: Eriko

last: Sasaki

state: Fukuoka

address: 744 Nishi-ku, Motooka

country: Japan

institute: Kyushu University

library_source: genomic

data_processing:
QC and Adapter trimming by FASTP.
Reads were aligned on the reference genome (Araport11; Cheng CY et al. (2017)) using STAR v2.7 (Dobin et al., 2013) with default settings
Mapped read counts were conducted using featureCounts v2.0.1 in Subread package (Liao et al., 2013) with accepting reads that were mapped on multiple genes (option -M)
Genome_build: Araport11
Supplementary_files_format_and_content: Tab separate file of Gene and TE transcripts. Column 1: Gene and TE ID, Column 2: read counts

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: rosette

growth_protocol: After 2 days stratification in the dark at 4ºC, plants were grown on soil under 16 h long day condition at 21ºC.

extract_protocol:
Total RNA was extracted using ZR Plant MiniPrep Kit (Zymo Research) including a DNase I treatment and was quantified by fluorometer Qubit 4 (Invitrogen). Total RNA was treated with the poly(A) RNA Selection Kit (Lexogen).
Libraries were prepared according to the manufacturer’s protocol in NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs) and individually indexed with NEBNext Multiplex Oligos for Illumina (New England BioLabs). The quantity and quality of each amplified library were analyzed by using Fragment Analyzer (Agilent) and HS NGS Fragment Kit (Agilent).

value: rosette

tag: Stage

value: nine-leaf stage

tag: strain

tag: type

value: t-DNA insertion line


title: LR7-9

value: Uterine fluid

value: Recurrent implantation failure


title: LR7-10


title: CD34+CXCR4+CD73- arterial endothelium, replicate 2

description:
AEC #2
counts.txt
FPKM.txt


title: Melanoma cells cultured in cyclic stretch 3

city: Oviedo

first: Guillermo

middle: M

last: Albaiceta

address: Avenida de Roma s/n

institute: Instituto de Investigación Sanitaria del Principado de Asturias

description:
RNA-9
counts_matrix_B16.csv

data_processing:
Basecalling and trimming were performed according to BGI standards.
Counts were calculated using the pseudoalignment tool salmon v1.4.0 with the default parameters for mapping-based quantification.
Reads were loaded in R using the tximport library.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: counts_matrix_B16.csv: Comma-separated text file includes raw counts and was generated based on the txi matrix imported in R.

source_name: Melanoma cells

growth_protocol: Mouse melanoma B16F10luc2 cells were cultured in elastic plates (Bioflex culture plates, Flexcell int., USA) in DMEM + 10% FBS and standard culture conditions (37°C, 21% O2, 5% CO2).

extract_protocol:
After treatment, cells were collected with Trizol and RNA was extracted using the RNeasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard BGI protocols.

treatment_protocol: Cells were exposed to cyclic stretch (15% equibiaxial elongation, 15 cycles/min, 1:1 stretch:relaxation ratio) for 24 h. Non-stretched cells, cultured in the same plates were used as control.

tag: condition

value: Cyclic stretch


title: LR7-8


title: CD34+CXCR4+CD73- arterial endothelium, replicate 1

description:
AEC #1
counts.txt
FPKM.txt


title: LR7-7


title: Melanoma cells cultured in cyclic stretch 2

description:
RNA-8
counts_matrix_B16.csv


title: 9771_mir823a_CRISPR line3

data_processing:
Methylated cytosine calls were made using the pipeline described in Lister et al. Human DNA methylomes at base resolution show widespread epigenomic differences. 2009. Nature
Genome_build: Araport11
Supplementary_files_format_and_content: Tab separated file of methylated cytosine positions. Column 1: chromosome, Column 2: position, Column 3: strand, Column 4: class, Column 5: # of C basecalls, Column 6: # of C+T basecalls.

extract_protocol:
Genomic DNA was extracted using GeneJET Plant Genomic DNA Purification Kit (Thermo Scientific) and sheared by E220 Focused-ultrasonicator (Covaris) to target average fragments around 350 bp.
Sequencing libraries were prepared using NebNext Ultra II DNA Library Prep Kit (New England BioLabs) with Methylated Adaptor (New England BioLabs). Adapter-ligated DNA was carried through the bisulfite conversion using EZ-96 DNA Methylation-Gold™ MagPrep Kit (Zymo Research). Bisulfite-treated samples were amplified by EpiMark Hot Start Taq DNA Polymerase and indexed with NEBNext Multiplex Oligos for Illumina (New England BioLabs).

value: CRISPR mutant


title: 9771 mir823a CRISPR line2


title: WT_9771_sample13

value: WT


title: Melanoma cells cultured in cyclic stretch 1

description:
RNA-7
counts_matrix_B16.csv


title: Persistent chlamydial infected-rep3

source_name: HeLa cells, Ct.D, penicillin, replicate 3


title: LR7-6


title: CD34+CXCR4-CD73- hemogenic endothelium treated from retinol-treated mesoderm, replicate 3

description:
counts.txt
FPKM.txt

source_name: Hemogenic endothelium

value: ES-derived hemogenic endothelium


title: CD34+CXCR4-CD73- hemogenic endothelium treated from retinol-treated mesoderm, replicate 2

description:
counts.txt
FPKM.txt


title: Persistent chlamydial infected-rep2

source_name: HeLa cells, Ct.D, penicillin, replicate 2


title: Col-0 mir823a_CRISPR


title: Melanoma cells cultured in static conditions 3

description:
RNA-3
counts_matrix_B16.csv

value: Static


title: LR7-14

source_name: Uterine fluid


title: LR7-12


title: Melanoma cells cultured in static conditions 2

description:
RNA-2
counts_matrix_B16.csv


title: LR7-5


title: CD34+CXCR4-CD73- hemogenic endothelium treated from retinol-treated mesoderm, replicate 1

description:
counts.txt
FPKM.txt

value: Retinol


title: LR7-4


title: CD34+CXCR4-CD73- hemogenic endothelium treated from DEAB-treated mesoderm, replicate 3

description:
counts.txt
FPKM.txt


title: RNA-seq_Col-0_Rep2


title: RNA-seq_Col-0_Rep1


title: LR7-3


title: CD34+CXCR4-CD73- hemogenic endothelium treated from DEAB-treated mesoderm, replicate 2

description:
counts.txt
FPKM.txt


title: Melanoma cells cultured in static conditions 1

description:
RNA-1
counts_matrix_B16.csv


title: CT26 Usp8 KO-3

city: Wuhan

first: Wenjun

last: Xiong

state: Hubei

address: Room 1106, Medical Research Institute, Wuhan University, Donghu Road, No. 115, Wuchang District, Wuhan, Hubei Province, P.R. China.

department: Medical Research Institute

institute: Wuhan University

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute using BGISEQ platform.
Sequenced reads were trimmed for adaptor sequence and low quality sequances, then pseudoaligned to GRCm38 whole transcriptome using hisat2(version 2.2.1) with default parameters
FeatureCounts were used to summary raw counts from bam files
rlog normalize  and  differential genes' expression  were performed by  DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: csv files include normalized reads each Sample

source_name: Colon

growth_protocol: Usp8 WT or KO CT26 cells were routinely cultured in DMEM (Hyclone) medium supplemented with 10% FBS (Gibco), 100 units of penicillin and 100 mg/ml streptomycin.

extract_protocol:
Total RNA was extracted from Usp8 WT or KO CT26 cells using TRIzol reagent (Invitrogen) according to manufacturer protocol.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using BGISEQ platform.

treatment_protocol: Generating the Usp8 knock out (KO) CT26 cells: sgRNAs targeting Usp8 were constructed into pSpCas9(BB)-2A-GFP. CT26 cells with 60-80% confluence were transfected with the pSpCas9(BB)-2A-GFP-sgUsp8. After 48 h, cells were sorted based on the GFP signal to seed single cell in each well of 96 well plate by BD Aria. Incubating for 3 weeks, cells were tested to confirm the Usp8 KO efficiency by western blot.

value: Colon cancer cells

value: Colon

value: BALB/c

tag: genotype

value: Usp8 KO


title: LR7-2


title: LR7-1


title: msi1-2 1.1 Rep2 heterozygous

value: EMS mutatn


title: msi1-2 1.1 Rep3 heterozygous


title: RNA-seq_jmj26_Rep1


title: CT26 Usp8 WT-3

value: Usp8 WT


title: msi1-2 1.1 Rep1 heterozygous

value: rosette


title: LH7-19

value: Healthy fertile women


title: CT26 Usp8 KO-1


title: WT C24 Rep3

value: nine-leaf stage


title: LH7-18

value: Uterine fluid


title: LH7-16


title: CD34+CXCR4-CD73- hemogenic endothelium treated from DEAB-treated mesoderm, replicate 1

description:
counts.txt
FPKM.txt

value: DEAB


title: KDR+CXCR4+ replicate #3

description:
counts.txt
FPKM.txt

data_processing:
Basecalling with Illumina RTA 1.9.
Demultiplexing with custom demultipler written in python.
Fastq files were aligned to using STAR (version 2.7.1a).
Gene counts were obtained using Subread (version 1.6.5).
Expression values were filtered to only include protein coding genes using Ensembl BioMart.
FPKM calculation was performed using DESeq2 (version 1.24.0).
Genome_build: GENCODE GRCh38 version 23
Supplementary_files_format_and_content: Gene counts in tab-delimited text format.

source_name: mesoderm

growth_protocol: The H1 hESC lines were maintained on irradiated mouse embryonic fibroblasts in hESC media. For differentiation, hPSC were cultured on matrigel-coated plasticware for 24 hours, followed by embryoid body generation. hPSCs were dissociated with brief trypsin-EDTA (0.05%) treatment, followed by scraping. Aggregates were resuspended in serum-free media (SFD) supplemented with L-glutamine (2 mM), ascorbic acid (1 mM), monothioglycerol (MTG, 4x10-4 M), transferrin (150 ug/mL), and BMP-4 (10 ng/mL). On day one, bFGF (5 ng/mL) was added. On day two, Activin A, SB-431542 (6 uM), CHIR99021 (3 uM), and/or IWP2 (3 uM) were added.

extract_protocol:
KDR+CXCR4+ and KDR+CXCR4- cells were sorted using an BD Aria II. RNA was isolated with the miRNeasy Mini kit (Qiagen).
Libraries were prepared using the Clontech SMARTer kit.

value: ES-derived mesoderm


title: WT C24 Rep2


title: CT26 Usp8 WT-1


title: CT26 Usp8 WT-2


title: KDR+CXCR4+ replicate #2

description:
counts.txt
FPKM.txt


title: LH7-15


title: KDR+CXCR4+ replicate #1

description:
counts.txt
FPKM.txt


title: Col-0 mir823a tDNA

value: t-DNA insertion line


title: KDR+CXCR4- replicate #2

description:
counts.txt
FPKM.txt


title: CT26 Usp8 KO-2


title: CHIR

description:
allcells_matrix.txt
metadata.txt

data_processing:
Sequencing reads were processed using the Cell Ranger software pipeline (version 3.1.0) using default arguments.
Using Seurat (version 3.2.2) implemented in R (version 3.6.2), the dataset was filtered by removing genes expressed in fewer than 3 cells and cells where greater than 10% of the UMIs are mitochondrial genes.
Dataset was filtered to retain cells with unique gene counts between 200 and 6000.
Remaining UMI counts were log-normalized with a scale factor of 10,000 and variable features were calculated using the vst selection method.
Data were then scaled by regressing out mitochondrial gene percentage and UMI count.
Genome_build: Ensembl GRCh38
Supplementary_files_format_and_content: Gene counts in tab-delimited text
Supplementary_files_format_and_content: Metadata in tab-delimited text

extract_protocol:
Unsorted cells from CHIR+SB or IWP2 day 3 differentiation cultures were methanol-fixed as described in doi: 10.1186/s12915-017-0383-5.
Libraries were prepared following the manufacturer's instruction using the 10X Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v2 (PN-120237), Chromium Single Cell 3′ Chip kit v2 (PN-120236), and Chromium i7 Multiplex Kit (PN-120262).


title: WT C24 Rep1

value: WT


title: KDR+CXCR4- replicate #1

description:
counts.txt
FPKM.txt


title: IWP2

description:
allcells_matrix.txt
metadata.txt

value: IWP2 + ACTIVIN A


title: Pediatric acute lymphoblastic leukemia [16-141]

city: Montreal

first: Daniel

last: Sinnett

state: QC

address: 2900 Edouard Montpetit Blvd

country: Canada

institute: University of Montreal

description:
16-141
Strand-specific RNA-seq

data_processing:
Raw reads were aligned to the GRCh37 genome reference using STAR v2.5.3a.
Expression counts were obtained using htseq-count v0.9.0 on the Ensembl Homo_sapiens.GRCh37.75.gtf.
Genome_build: GRCh37
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include raw expression counts.

source_name: Pediatric acute lymphoblastic leukemia

extract_protocol:
Mini AllPrep DNA/RNA kits from Qiagen.
Ribo-Zero Gold Kit according to Illumina's protocol.

tag: diagnosis

value: bone marrow

tag: gender

value: Male


title: KDR+CXCR4- replicate #3

description:
counts.txt
FPKM.txt


title: WT_6909


title: LH7-12

tag: study group

tag: age


title: LH7-14

tag: bmi


title: Acral melanoma, MOF-AM8-Node-RNA

city: Tampa

first: Keiran

last: Smalley

state: FL

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

data_processing:
Sequence reads for each sample were aligned and processed using cellranger/3.0.2
Genome_build: GRCh38
Supplementary_files_format_and_content: h5. filtered gene expression counts for called cells, along with cell annotations

source_name: single cell suspension of tumor

extract_protocol:
Upon collection, samples were immediately placed on ice and transferred for processing. Samples were digested using Miltenyi Tissue Dissociation Kit (Bergisch Gladbach, Germany) and enriched for live cells using FACS sorting prior to quantification and loading
Sample were quantified and viability was analyzed using the Nexcelom Cellometer K2. The samples were then loaded onto 10X Genomics Chromium Single Cell Controller (10X Genomics, CA) to prepare single-cell RNA-sequencing libraries. Around 25,000 to 50,000 mean sequencing reads per cell were generated on Illumina NextSeq 500 instrument using v2.5 flow cells
scRNA-seq

tag: disease state

value: acral melanoma

tag: site

value: metastatic from node

tag: kit


title: LH7-11


title: Acral melanoma, MOF-AM8-Toe-RNA

value: primary from toe


title: Acral melanoma, MOF-AM7-RNA

value: metastatic node dissection


title: H3

city: Tianjin

first: Xiaoli

last: Zhao

address: Changling Road 88, Xiqing District

institute: First Teaching Hospital of Tianjin University of Traditional Chinese Medicine

data_processing:
Base calling was performed using Illumina bcl2fastq v2.20 software.
Raw read data were first processed with Trim Galore software (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove low-quality base calls and adapter sequences and then filtered to get clean high-quality reads.
The clean paired-end reads were mapped to mouse reference genome 10 (GRCm38/mm10) using HISAT2.
Transcript abundance values were obtained from gene-level count matrices generated by StringTie.
Differential gene expression was analyzed using DESeq2.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

growth_protocol: Mice were fed standard rodent chow and housed under standard laboratory conditions: 12h/12h light/dark cycle, room temperature 22±2℃, humidity 65±5%.

extract_protocol:
Fifteen isolated oocytes from each mouse were transferred to a 0.2 ml PCR tube containing Triton X-100 lysis buffer and RNase inhibitor. SMART-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories, CA, USA) based on SMART-Seq2 method was used to synthesize and amplify cDNA directly from oocytes. Amplified cDNA was purified using AMPure XP kit (Beckman Coulter, IN, USA).
TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Nanjing, China) was used for library preparation. Briefly, cDNA was fragmented and added at both ends with adaptors by incubating with Tn5 transposase at 55℃ for 10min. The primed fragments were subjected to limited-cycle PCR amplification and the products were purified with SPRIselect (Beckman Coulter). The quantity and size distribution of the library were measured by Qubit 3.0 fluorometer (Thermo Fisher Scientific, Shanghai, China) and Agilent 2100 Bioanalyzer, respectively. RNA sequencing (RNAseq) was performed on a Novaseq 6000 system (Illumina, USA) using a NavaSeq 6000 S4 Reagent kit (Illumina).

treatment_protocol: Mice in the stressed group were treated with one of the stressors each day including tail pinch (10min), swim in cold (13±1℃), water or food deprivation (24h), wet bedding (24h), continuous lighting (24h) and restraint for 60min. Mice in the KYZY groups were first treated with the stressors for 6 weeks as in the stressed group. Subsequently they were subjected to intragastric administration of 0.1 ml of the KYZY decoction once per day for 4 weeks. No stress was applied for the control group. Then the mice were super-ovulated by intraperitoneal injection with 7.5 IU PMSG and 7.5 IU HCG. Cumulus oocyte complexes (COC) were collected 16 hours after HCG injection by dissecting the enlarged portion of oviducts. The COC were incubated with 100IU/ml hyaluronidase for 10min at 37℃ to release the oocytes halted at the second metaphase stage (MII) for RNAseq.

value: ICR

tag: Sex

value: female

value: 4-5 week-old

tag: treatment

value: stress plus herbal medicine


title: H2


title: Col-0_Rep2

value: rosette

value: nine-leaf stage


title: H1


title: LH7-8

value: Uterine fluid

value: Healthy fertile women


title: 9771 mir823a CRISPR line1

value: CRISPR mutant


title: WT_9771_sample6

value: WT


title: LH7-7


title: Acral melanoma, MOF-AM5

value: metastatic right foot thigh or lateral knee


title: Acral melanoma, MOF-AM6-RNA


title: jmj26 + Alt JMJ26 Rep2

value: rescued line


title: LH7-6


title: Acral melanoma, MOF-AM4

value: primary from foot


title: LH7-4


title: jmj26 + Alt JMJ26 Rep1


title: LH7-10


title: LH7-3


title: Col-0_Rep1


title: jmj26 + Col-0 JMJ26


title: Acral melanoma, MOF-AM3

value: acral melanoma


title: Acral melanoma, MOF-AM2

value: primary from heel


title: Acral melanoma, Acral-01


title: LH7-2


title: C1

extract_protocol:
Fifteen isolated oocytes from each mouse were transferred to a 0.2 ml PCR tube containing Triton X-100 lysis buffer and RNase inhibitor. SMART-Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories, CA, USA) based on SMART-Seq2 method was used to synthesize and amplify cDNA directly from oocytes. Amplified cDNA was purified using AMPure XP kit (Beckman Coulter, IN, USA).
TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Nanjing, China) was used for library preparation. Briefly, cDNA was fragmented and added at both ends with adaptors by incubating with Tn5 transposase at 55℃ for 10min. The primed fragments were subjected to limited-cycle PCR amplification and the products were purified with SPRIselect (Beckman Coulter). The quantity and size distribution of the library were measured by Qubit 3.0 fluorometer (Thermo Fisher Scientific, Shanghai, China) and Agilent 2100 Bioanalyzer, respectively. Clustering of index-coded samples was performed on Illumina cBot Cluster station using TruSeq PE Cluster Kit v3-cBot-HS (Illumina, Shanghai, China) according to the manufacture’s instruction.

value: control

tag: cell type

value: Oocytes


title: LH7-1

tag: tissue


title: jmj26_Rep2

tag: Stage

value: t-DNA insertion line


title: C3

tag: strain

value: ICR

value: female


title: M3

value: 4-5 week-old

value: stress in chronic unpredictable mild stress (CUMS) model


title: M2


title: jmj26_Rep1

value: rosette

value: nine-leaf stage

tag: type


title: M1


title: C2


title: BasL_015

source_name: Breast cancer tissue

value: Breast cancer

tag: citbcmst subtype

value: BasL

tag: sn status

value: Negative

tag: ihc er status


title: Heart Mettl5-cKO TAC rep3

status: Public on Feb 13 2022

first: Tailai

last: Du

address: No.58, Zhongshan 2nd road

department: The First Affiliated Hospital

institute: Sun Yat-sen University

description: TAC Ctrl and Mettl5-cKO mice

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%.
The clean reads were mapped to the mouse genome (Mus_musculus.GRCm38) or rat genome (Rattus_norvegicus.Rnor_6.0)  or using HISAT2(v2.0.4). Expression level of gene was calculated by StringTie (v2.1.4).
Differential expression analysis was performed using the DESeq2(v1.4.5) with adjusted p value≤ 0.05.
Genome_build: Mus_musculus.GRCm38; Rattus_norvegicus.Rnor_6.0

source_name: Heart

growth_protocol: All isolated NRVMs were pre-plated for 1 h to remove fibroblasts. Nonadherent cells were then plated on 0.5% gelatin-coated plates and cultured in DMEM high-glucose medium (Gibco) containing 10% fetal bovine serum, sodium pyruvate (1×), GlutaMAX (1×) and antibiotics.

extract_protocol:
Total RNAs were isolated using Trizol Reagent from NRVMs and tissue samples.
RNA libraries were prepared for sequencing using standard BGIseq protocols

treatment_protocol: NRVMs treated with PE (20uM) for 24h

value: 3-month old

tag: genotype/variation


title: Heart Ctrl3 rep1

description: TAC Ctrl and Mettl5-cKO mice

value: Ctrl


title: Heart Ctrl3 rep2

description: TAC Ctrl and Mettl5-cKO mice


title: Heart Mettl5-cKO TAC rep1

description: TAC Ctrl and Mettl5-cKO mice


title: Heart Mettl5-cKO TAC rep2

description: TAC Ctrl and Mettl5-cKO mice


title: Heart Ctrl3 rep4

description: TAC Ctrl and Mettl5-cKO mice


title: Heart Ctrl3 rep3

description: TAC Ctrl and Mettl5-cKO mice


title: Heart Mettl5-cKO TAC rep4

description: TAC Ctrl and Mettl5-cKO mice


title: Heart Mettl5-cKO rep4

description: 3-month old Ctrl and Mettl5-cKO mice


title: 27B_S37

city: University Park

first: Etya

last: Amsalem

state: PA

address: 202 Huck Life Sciences Building

institute: The Pennsylvania State University

data_processing:
Cleaning: the removal of TruSeq3-SE adapters, reads with phred score < 25 and smaller than 36 bp were performed by using Trimmomatic-v0.39
Alignment: cleaned reads were mapped to the Bombus impatiens genome BIMP_2.2 version (release 102) using STAR-v2.7 aligner implemented in RSEM-v1.3.3.
Data nomalization and identification of differentially expressed genes were performes using DESeq2-v1.28
Supplementary_files_format_and_content: comma separated values file with raw gene counts for all genes and samples

organism: Bombus impatiens

source_name: brain

extract_protocol:
RNeasy Mini kit (Qiagen)
Illumina TruSeq Stranded mRNA kit

value: Brain

value: alone (C)

value: 3 days


title: 26B_S36

value: young brood (CB)


title: 48B_S47

value: queen and young brood (young brood (CB)Q)


title: 37B_S40

value: queen (CQ)


title: 43B_S45


title: 38B_S41


title: 19B_S33


title: 24B_S35


title: 42B_S44


title: 33B_S39


title: 22B_S34


title: 39B_S42


title: 30B_S38


title: 49B_S48


title: 9B_S28


title: 15B_S30


title: 45B_S46


title: 41B_S43


title: 16B_S31


title: 10B_S29


title: 18B_S32


title: Heart Mettl5-cKO rep3

description: 3-month old Ctrl and Mettl5-cKO mice


title: Heart Mettl5-cKO rep2

description: 3-month old Ctrl and Mettl5-cKO mice


title: Heart Mettl5-cKO rep1

description: 3-month old Ctrl and Mettl5-cKO mice


title: 5B_S25


title: ATAC_RPMI8226_CO2

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

data_processing:
Pair-end Omni-ATAC sequence reads were aligned to hg38 using Bowtie2 (PMID: 19261174). Reads mapped to multiple positions of the genome were excluded and only one read was kept if multiple reads mapped to the same position.
Read enriched regions (peaks) were predicted by MACS3 (PMID: 18798982).
We compiled a list of reference peaks for each MM cell line with in-house script: a peak is in the reference if it presents in at least three samples.
Genome_build: hg38
Supplementary_files_format_and_content: Txt file, from left to right represent chr, start, end, number of libs supporting the peak

source_name: Cell line derived from human plasma cell myelom

extract_protocol:
Cells were washed with cold PBS and pelleted by centrifugation (500g, 5min, 4°C). Nuclei were isolated by subjecting cells to 100uL of RSB-lysis buffer (10mM Tris-HCl ph 7.4, 10mM NaCl, 3mM MgCl2, 1uL/mL of Digitonin, 1uL/mL of Tween20, and 1uL/mL of NP40) for 3-5 min on ice.  1mL RSB buffer (10mM Tris-HCl ph 7.4, 10mM NaCl, 3mM MgCl2, and 1uL/mL of Tween20) was added to neutralize RSB-lysis buffer. Cells were pelleted by centrifugation (500g, 10min, 4°C) and supernatant was removed. Cells were resuspended in 50uL Transposase mix (25 uL of 2x TD buffer, 2.5 ul of transposase, 16.5 ul of PBS, 0.5 ul of digitonin, 0.5 ul Tween 20, and 5 uL of nuclease free water). The samples were incubated on a thermomixer at 37°C, 1000rpm for 30min. Samples were cleaned up using Zymo DNA Clean & Concentrator-5 kit (D4014) according to manufacturer’s instruction in 21uL water.
Libraries were prepared with approximately 5x10^4 sorted cells using a Tagment DNA Enzyme and Buffer Large Kit (Illumina, 20034198) and following the Omni-ATAC protocol (PMID: 28846090).

tag: cell line

value: RPMI8226 (ATCC, CCL-155)

value: Human myeloma cell line

tag: culture condition

value: in the lower chamber from a transwell coculture with HS5

tag: repeat


title: ATAC_RPMI8226_CO1


title: Heart Ctrl2 rep4

description: 3-month old Ctrl and Mettl5-cKO mice

tag: age


title: ATAC_RPMI8226_MONO1

value: in monoculture


title: Heart Ctrl2 rep3

description: 3-month old Ctrl and Mettl5-cKO mice


title: ATAC_RPMI8226_TSW1

value: in the upper transwell from a transwell coculture with HS5


title: ATAC_MM1S_CO2

value: MM.1S (ATCC, CRL-2974)


title: ATAC_MM1S_MONO3


title: ATAC_MM1S_TSW1


title: ATAC_MM1S_TSW3


title: ATAC_MM1S_TSW2


title: Heart Ctrl1 rep4

description: 1-month old Ctrl and Mettl5-KO mice

value: 1-month old


title: Heart Ctrl1 rep1

description: 1-month old Ctrl and Mettl5-KO mice


title: Heart Mettl5-KO rep2

description: 1-month old Ctrl and Mettl5-KO mice


title: Heart Mettl5-KO rep3

description: 1-month old Ctrl and Mettl5-KO mice


title: ATAC_RPMI8226_TSW2


title: Heart Ctrl2 rep2

description: 3-month old Ctrl and Mettl5-cKO mice


title: Heart Ctrl2 rep1

description: 3-month old Ctrl and Mettl5-cKO mice


title: ATAC_MM1S_CO3


title: Heart Mettl5-KO rep4

description: 1-month old Ctrl and Mettl5-KO mice


title: Heart Ctrl1 rep3

description: 1-month old Ctrl and Mettl5-KO mice


title: 7B_S26


title: 8B_S27


title: ATAC_MM1S_MONO2


title: RNA_RPMI8226_CO2

data_processing:
Reads were aligned to mouse genome (hg38) with subread-align version 2.0.1 (PMID: 23558742)
Read counts were calculated with the featureCounts function from Rsubread version 2.0.1 (PMID: 24227677) against RefSeq gene annotation
Gene expression level from RNA-Seq is measured by RPKM (PMID: 18516045) with an in-house script.
Genome_build: hg38
Supplementary_files_format_and_content: Txt file, from left to right represent entrz ID, gene symbol, and gene expression values in log2(RPKM+1) for each samples.

extract_protocol:
RNA was isolated from approximately 10^5 sorted cells for each sample using Qi-agen kit (RNeasy Plus Mini Kit, 74134) according to manufacturer’s instructions.
250-500ng of total RNA was used for each sample as a starting material for RNA-Seq library prep using KAPA mRNA HyperPrep Kit (Roche Diagnostics, 08098123702) according to manufacturer’s instruction.


title: mannitol_15g/L_1

first: Yuchen

last: Yang

address: Xingangxi Road 135

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
The alignment was performed using hisat2 against the reference Punica granatum isolate: Tunisia-2019 RefSeq Genome (Assembly: GCA_007655135.2)
Gene counts were obtained using featureCounts.
Genome_build: Punica granatum isolate: Tunisia-2019 RefSeq Genome (Assembly: GCA_007655135.2)
Supplementary_files_format_and_content: One csv file containing raw count values for each sample

organism: Punica granatum

source_name: leaf

growth_protocol: All the plant materials used in this study were collected from the ‘Hongmanao’ pomegranates planting base of Anhui Science and Technology University. Tips of 2 - 3 cm were retrieved from the tender stems of the pomegranates well-grown and free of diseases and insect pests, and cultivated in water for 2 -3 days. Then, the growth point of each stem tip was collected and rinsed with clean water in a beaker for 15 min, 75% alcohol for 30 sec and sterile water for 2 - 3 times, to remove surface dust and other impurities. Rinsed materials were then disinfected with 0.1% HgCl2 for 8 min and rinsed with sterile water for 3 - 5 times. The growth point of the leaf primordium (approximately 0.3 - 0.5 mm) was collected from the disinfected materials and inoculated to a prepared culture medium. The explants were grown in the WPM medium (containing 0.8 mg/L IBA 3%, sucrose and 0.55% agar under a pH of 6.5) at the culture chamber under a controlled culture conditions: a 12/12 h light/dark photoperiod of 3000 LX illumination, 25±1 °C temperature and 50% relative humidity. After three cycles of subculture (35 - 40 days for each cycle), 0.8 mg/L IBA was added to in WPM culture media to induce the proliferation of stem tips.

extract_protocol:
Total RNAs was extracted from the leaves of each plant using TRIzol.
Illumina libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: The seedlings of the same growth condition were selected and assigned into four experimental groups, where the first three groups were treated with paclobutrazol, daminozide and mannitol, and the rest one group was treated with the same amount of distilled water as control (CK). For each PGR, plants were treated at two desired concentrations (6 and 8 mg/L for paclobutrazol, 6 and 8 mg/L for B9, and 2.5 and 15 g/L for mannitol) for 90 days and RNA-seq were performed using leaf tissue.

tag: cultivar

value: Hongmanao

value: leaf

value: 90 days

tag: genotype

value: wt


title: ATAC_MM1S_MONO1


title: Heart Mettl5-KO rep1

description: 1-month old Ctrl and Mettl5-KO mice


title: Heart Ctrl1 rep2

description: 1-month old Ctrl and Mettl5-KO mice

value: Ctrl


title: ATAC_MM1S_CO1


title: RNA_RPMI8226_CO1


title: RNA_RPMI8226_TSW1


title: mannitol_2.5g/L_2


title: B9_8mg/L_2


title: mannitol_2.5g/L_1


title: RNA_MM1S_CO3


title: RNA_RPMI8226_TSW2


title: B9_6mg/L_2


title: B9_6mg/L_1


title: B9_8mg/L_1


title: paclobutrazol_6mg/L_2


title: RNA_RPMI8226_MONO2


title: CK_2

value: CK


title: RNA_MM1S_TSW1


title: paclobutrazol_8mg/L_1


title: RNA_MM1S_TSW3


title: paclobutrazol_6mg/L_1


title: CK_1


title: RNA_MM1S_TSW2


title: RNA_RPMI8226_MONO1


title: RNA_MM1S_CO1


title: RNA_MM1S_MONO3


title: paclobutrazol_8mg/L_2


title: mannitol_15g/L_2


title: RNA_MM1S_MONO2


title: RNA_MM1S_MONO1


title: RNA_MM1S_CO2


title: EpCAM_Positive_2

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

data_processing:
Basecalls and mapping performed using Cell Ranger ver 6.0
Genome_build: mm10
Supplementary_files_format_and_content: barcodes, features and matrix tsv files

source_name: Lung

extract_protocol:
Cells of CD45+ or Epcam+ fractions and xxx that were freshly prepared from mice conjunctival tissue and sorted using a BD FACS Aria II (10,000 cells each, cell viability >98%) were encapsulated into droplets.
Libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3 according to manufacturer’s protocol (10X Genomics).

treatment_protocol: C57BL/6 mice were sensitized intraperitoneally with a mixture of 20g OVA (Sigma-Aldrich) in 4 mg alum (Thermo) (days 0 and 14) with 50 g of smES or 1 l of 1 mM synthesized ascarosides or solvent vehicle as a control.  On day 24, the mice were anesthetized with isoflurane and challenged intranasally with 30 l phosphate-buffered saline (PBS) containing 100 g OVA.

value: Wild-type

value: Lung

value: Epithelial cells

tag: group

value: positive control


title: EpCAM_Negative_1

value: negative control


title: EpCAM_Negative_2


title: EpCAM_Positive_1


title: RNA_Bplus_rep2

city: Tokyo

first: Naoyuki

last: Sotta

address: 1-1-1 Yayoi, Bunkyo-ku

department: Department of Applied Biological Chemistry

institute: Graduate School of Agricultural and Life Sciences, The University of Tokyo

data_processing:
Quality filtering: fastq_quality_filter -q 20 -p 85
Adapter trimming: (Ribo-seq) fastx_clipper  -a AGATCGGAAGAGCACACGTCT
rRNA removal: bowtie2  -L 20 -p 8 --un
Mapping: bowtie2  -L 20 -p 8
Extract uniquely mapped reads: samtools view -q 10 -F 0xFF -h
Genome_build: Araport11
Supplementary_files_format_and_content: CSV files for read counts within CDS. Ribo-seq reads were counted on the basis of the estimated P-site position. RNA-seq reads were sum of read depth over all nucleotide positions within CDS.

source_name: whole shoot

growth_protocol: Arabidopsis thaliana ecotype Col-0 was grown under sterile conditions. After surface sterilization by sodium hypochlorite and detergent, seeds were incubated in water for 4 days at 4°C for stratification. For quick sampling, seeds were sown on nylon mesh (308 μm) placed on MGRL medium (20) that had different boric acid concentrations (–B, 0.3 µM; Ctrl, 30 µM; ++B, 500 µM). The medium was supplemented with 1.0% sucrose and was solidified by 0.15% gellan gum. Medium plates with seeds were placed horizontally in a growth chamber at 22°C under 16 h light (4000 to 4500 lux) – 8 h dark conditions.

extract_protocol:
Whole shoot tissues of 14-day-old seedlings (approximately 300 individuals per replicate) were harvested and frozen immediately with liquid nitrogen. For Ribo-seq, Tissue was frozen in liquid nitrogen, powdered by using a chilled mortar and pestle, and homogenized in ice-cold polysome extraction buffer [100 mM Tris-HCl (pH 8.0), 40 mM KCl, 20 mM MgCl2, 1 mM dithiothreitol, 100 μg/mL cycloheximide, 2% polyoxyethylene (10) tridecyl ether, 1% deoxycholic acid, 10 U/mL DNase I (Qiagen, Hilden, Germany)]. After incubation on ice for 10 min, tissues were homogenized on ice by using a tight-fitting Dounce homogenizer. The homogenates were centrifuged for 30 min at 16,000g and 4 °C in a JA25.50 rotor (Beckman Coulter, California, United States) to pellet the insoluble cell debris. The supernatant was layered on top of a 1.75-M sucrose cushion [100 mM Tris-HCl (pH 8.0), 40 mM KCl, 20 mM MgCl2, 1 mM dithiothreitol, 100 μg/mL cycloheximide, 1.75 M sucrose] and centrifuged for 18 h at 170,000g and 4 °C in a TY70 Ti rotor (Beckman) to obtain a polysome pellet. The pellet was resuspended in RNase I digestion buffer [100 mM Tris-HCl (pH 8.0), 40 mM KCl, 20 mM MgCl2, 1 mM dithiothreitol, 100 μg/mL cycloheximide]. The OD260 was determined by using a Nanodrop1000 spectrophotometer (Thermo Fisher Scientific, Massachusetts, United States). Then, 2000 OD units of polysome was digested with 2000 units of RNase I (Thermo Fisher Scientific) in a 185-L reaction mixture for 2 h at 25 °C with gentle rotation. Digestion was stopped by adding 15 L of SUPERase-In RNase inhibitor (Thermo Fisher Scientific). Monosome isolation in illustra MicroSpin S-400 HR columns (GE Healthcare, Illinois, United States), RNA extraction and concentration by using an RNA Clean & Concentrator kit (Zymo Research, California, United States), and rRNA depletion with a Ribo-Zero Plant Leaf kit (Illumina, California, United States) were performed as described by Hsu PY, et al. (Proceedings of the National Academy of Sciences, 2016, 113.45, E7126-E7135.). For RNA-seq, total RNA was extracted by using an RNeasy Plant Mini Kit with DNase I treatment on a column in accordance with the manufacturer’s protocol (Qiagen).
For Ribo-seq, purified RNA was separated by 12% 7M urea PAGE in TBE buffer, and gel slices from 28 to 30 nt long were excised. Ribosome footprint extraction from the gel slice and subsequent Ribo-seq library construction and amplification by PCR were performed as described in the manufacturer’s protocol [TruSeqRibo Profile (Mammalian) kit, Illumina]. Libraries #1 and #2 were amplified by 11 and 13 cycles, respectively, of PCR.  For RNA-seq, ibrary preparation and sequencing were performed by a commercial service (BGI, Shenzhen, China).

value: wild type

tag: ecotype

value: 14 days old


title: CD45_Positive_2

tag: cell type

value: WBC


title: CD45_Positive_1

tag: tissue


title: Ribo_Bplus_rep2

data_processing:
Library strategy: Ribo-seq
Quality filtering: fastq_quality_filter -q 20 -p 85
Adapter trimming: (Ribo-seq) fastx_clipper  -a AGATCGGAAGAGCACACGTCT
rRNA removal: bowtie2  -L 20 -p 8 --un
Mapping: bowtie2  -L 20 -p 8
Extract uniquely mapped reads: samtools view -q 10 -F 0xFF -h
Genome_build: Araport11
Supplementary_files_format_and_content: CSV files for read counts within CDS. Ribo-seq reads were counted on the basis of the estimated P-site position. RNA-seq reads were sum of read depth over all nucleotide positions within CDS.


title: EpCAM_Ascr_1


title: EpCAM_Ascr_2


title: RNA_Bminus_rep2


title: RNA_Bminus_rep1


title: CD45_Negative_2


title: RNA_Ctrl_rep1


title: Ribo_Ctrl_rep1

growth_protocol: Arabidopsis thaliana ecotype Col-0 was grown under sterile conditions. After surface sterilization by sodium hypochlorite and detergent, seeds were incubated in water for 4 days at 4°C for stratification. For quick sampling, seeds were sown on nylon mesh (308 μm) placed on MGRL medium (Fujiwara et al., Plant Physiology, 1992, 99.1: 263-268.) that had different boric acid concentrations (–B, 0.3 µM; Ctrl, 30 µM; ++B, 500 µM). The medium was supplemented with 1.0% sucrose and was solidified by 0.15% gellan gum. Medium plates with seeds were placed horizontally in a growth chamber at 22°C under 16 h light (4000 to 4500 lux) – 8 h dark conditions.

extract_protocol:
Whole shoot tissues of 14-day-old seedlings (approximately 300 individuals per replicate) were harvested and frozen immediately with liquid nitrogen. For Ribo-seq, Tissue was frozen in liquid nitrogen, powdered by using a chilled mortar and pestle, and homogenized in ice-cold polysome extraction buffer [100 mM Tris-HCl (pH 8.0), 40 mM KCl, 20 mM MgCl2, 1 mM dithiothreitol, 100 μg/mL cycloheximide, 2% polyoxyethylene (10) tridecyl ether, 1% deoxycholic acid, 10 U/mL DNase I (Qiagen, Hilden, Germany)]. After incubation on ice for 10 min, tissues were homogenized on ice by using a tight-fitting Dounce homogenizer. The homogenates were centrifuged for 30 min at 16,000g and 4 °C in a JA25.50 rotor (Beckman Coulter, California, United States) to pellet the insoluble cell debris. The supernatant was layered on top of a 1.75-M sucrose cushion [100 mM Tris-HCl (pH 8.0), 40 mM KCl, 20 mM MgCl2, 1 mM dithiothreitol, 100 μg/mL cycloheximide, 1.75 M sucrose] and centrifuged for 18 h at 170,000g and 4 °C in a TY70 Ti rotor (Beckman) to obtain a polysome pellet. The pellet was resuspended in RNase I digestion buffer [100 mM Tris-HCl (pH 8.0), 40 mM KCl, 20 mM MgCl2, 1 mM dithiothreitol, 100 μg/mL cycloheximide]. The OD260 was determined by using a Nanodrop1000 spectrophotometer (Thermo Fisher Scientific, Massachusetts, United States). Then, 2000 OD units of polysome was digested with 2000 units of RNase I (Thermo Fisher Scientific) in a 185-μL reaction mixture for 2 h at 25 °C with gentle rotation. Digestion was stopped by adding 15 μL of SUPERase-In RNase inhibitor (Thermo Fisher Scientific). Monosome isolation in illustra MicroSpin S-400 HR columns (GE Healthcare, Illinois, United States), RNA extraction and concentration by using an RNA Clean & Concentrator kit (Zymo Research, California, United States), and rRNA depletion with a Ribo-Zero Plant Leaf kit (Illumina, California, United States) were performed as described by Hsu PY, et al. (Proceedings of the National Academy of Sciences, 2016, 113.45, E7126-E7135.). For RNA-seq, total RNA was extracted by using an RNeasy Plant Mini Kit with DNase I treatment on a column in accordance with the manufacturer’s protocol (Qiagen).
For Ribo-seq, purified RNA was separated by 12% 7M urea PAGE in TBE buffer, and gel slices from 28 to 30 nt long were excised. Ribosome footprint extraction from the gel slice and subsequent Ribo-seq library construction and amplification by PCR were performed as described in the manufacturer’s protocol [TruSeqRibo Profile (Mammalian) kit, Illumina]. Libraries #1 and #2 were amplified by 11 and 13 cycles, respectively, of PCR.  For RNA-seq, ibrary preparation and sequencing were performed by a commercial service (BGI, Shenzhen, China).


title: CD45_Negative_1


title: Th17 KO replicate 2, input

city: Freiburg im Breisgau

first: Josip

middle: Stefan

last: Herman

address: Stuebeweg 51

department: Quantitative Single Cell Biology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
For image acquisition, intensity extraction and base calling NovaSeq Control Software v1.7.5 was used. Conversion of bcl2 files was performed using bcl2fastq 2.20.0.422
The raw fastq data files were processed using the snakePipes pipeline (version 2.5.0) for DNA Mapping and ChIP-Seq (https://snakepipes.readthedocs.io). Mapping was performed using the following commands: DNA-mapping --DAG --trim --UMIDedup --mapq 3 -j 20 -i input_files -o output_files mm10. Fastq files were pre-processed using cutadapt 2.8 and then mapped to the GRCm38 genome assembly (mm10) using Bowtie2 (version 2.3.5.1) with default parameters.
The bam files were de-duplicated using sambamba markdup and umitools dedup. The resulting bam files were then processed using the ChIP-seq command from the snakePipes pipeline by providing sample information (WT or Slc2a3fl/flCd4Cre) under the --sampleSheet flag and by specifying the corresponding input sample and information about the expected peak signal (broad: False) in the config file. Briefly, we used the deeptools package (3.3.2) (http://deeptools.ie-freiburg.mpg.de) for comparing bam files and plotting mapped regions. In addition, peaks were called using MACS2 (version 2.2.6) with macs2 callpeak and the flags: -f BAM --mfold 0 50 -g 2652783500 --nomodel --extsize228 --keep-dup all --qvalue 0.001. Differential binding on the MACS2 peak files was performed using the CSAW R package (version 1.20.0) as part of the snakePipes pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: .bam: mapped fastq files using Bowtie2
Supplementary_files_format_and_content: .bw: bigWig Track Format of bam files for Genome Browser
Supplementary_files_format_and_content: .narrowPeak: Peaks that were called using MACS2
Supplementary_files_format_and_content: .bed, .txt: Differential binding analysis using CSAW. Bed file contains regions and .txt file the scores for the differential analysis.

source_name: CD4+ T cells

growth_protocol: Naive T cells were differentiated for 3 days in vitro under Th17 polarizing conditions.

extract_protocol:
3x10^6 Th17 cells were fixed with formaldehyde for 15 min at RT to perform the RELACS protocol as previously described (Arrigoni et al., 2018). Briefly, cells were resuspended in lysis buffer and nuclei were extracted by sonication using the E220 sonicator (Covaris, 75 W peak incident power, 2% duty factor, 200 cycles/burst, 90 seconds of treatment). ~ 106 nuclei per sample were digested overnight at 20°C using 50 units of CviKi-1 (NEB). Nuclei were washed once, quantified again and normalized using buffer EB (Qiagen) to concentration of 500,000 nuclei per 25 µl.
Samples were barcoded using the RELACS procedure, which includes intra-nuclei A-tailing and ligation of barcoded hairpin sequencing adaptors to the digested chromatin. Six samples were barcoded and pooled together, resuspended in 300 µl of shearing buffer and lysed. A third of the volume of chromatin has been used for ChIP, corresponding to about 2x106 nuclei per ChIP total (~ 330,000 per each pooled sample). Chromatin was mixed 1:1 with the ChIP buffer H from the Auto Histone ChIP-seq Kit (Diagenode), supplemented with protease inhibitor cocktail and 5 µg of anti-H3K9/14ac (Diagenode). A fraction of original chromatin (~ 0.1%) was set aside as input. The immunoprecipitation, washing and elution of immunocomplexes from the beads was performed using solutions and protocols from the Auto Histone ChIP-seq Kit and the automatic liquid handler SX-8G Compact IP-Star (Diagenode) following these parameters: indirect method, 200 µl sample volume of ChIP reactions, 10 h antibody incubation, 3 h beads incubation, 5 min washes (all steps at 4°C). Eluates were de-crosslinked for 2 h at 65 °C and DNA was purified using MinElute columns (Qiagen). Samples were USER-treated and amplified with 10 PCR cycles. For these steps components of NEBNext Ultra II DNA Library Prep kit for Illumina (NEB) kit were used as described before (Arrigoni et al., 2018). Libraries were quality controlled and sequenced on a NovaSeq Illumina sequencer, using 50 bp paired-end read length.

treatment_protocol: 3 h re-stimulation with PMA and ionomycin in the presence of Bref A and Monensin

value: Slc2a3-fl/fl Cd4-cre

tag: chip antibody

tag: treatment

value: 3 h stimulation with PMA and ionomycin


title: CD45_Ascr_2

tag: strain


title: Th17 KO replicate 3, input


title: Th17 KO replicate 1, input


title: CD45_Ascr_1


title: RNA_Bplus_rep1


title: Th17 WT replicate 3, input


title: RNA_Ctrl_rep2


title: Ribo_Ctrl_rep2


title: Ribo_Bminus_rep2


title: Ribo_Bplus_rep1


title: Ribo_Bminus_rep1


title: Th17 WT replicate 1, input


title: S3T3 SHH rep3

city: DALLAS

first: James

last: Kim

state: TX

address: 5323 HARRY HINES BLVD

department: Internal Medicine

institute: UNIVERSITY OF TEXAS SOUTHWESTERN

description:
adherent
s3T3_SHHN_3

data_processing:
Basecalls were performed using bcl2fastq
Reads were aligned to mm10 geneome assembly and transcript assembly was performed using tophat (v.2.0.12)
FPKM calculation and differential expression analysis was performed using cufflinks (v.2.2.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: MLg and NIH-3T3 cell lines were grown in DMEM (Life Technologies) with 10% FBS for MLg and 10% bovine calf serum (BSC) for NIH-3T3. Both cell lines were maintained at 37°C, with 5% CO2, and under humidified conditions.

extract_protocol:
RNA was extracted with TriZol (Invitrogen) and purified using PureLink RNA Mini Kit (Invitrogen) following manufacturer protocol.
Library construction and RNA sequencing were performed by Admera Health, LLC (South Plainfield, NJ).

treatment_protocol: NIH3T3 or MLg were grown to 85% confluence in 6 well tissue culture plates, then treated with control vehicle or 1 g/ml recombinant SHHN in DMEM containing 0.5% FBS for 48 hours.  RNA was extracted with TriZol (Invitrogen) and purified using PureLink RNA Mini Kit (Invitrogen) following manufacturer protocol.

value: SHHN

value: NIH/Swiss

value: embryo

value: fibroblast


title: S3T3 SHH rep2

description:
adherent
s3T3_SHHN_2


title: Gibbin_hESC_rep2

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drvie

department: Dermatology

institute: Stanford University

data_processing:
bowtie2.3.4.1 used for alignment.
duplicate fragments were removed using samtools1.8
macs2 used for peak calling
deeptools used for heatmaps
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: hESC

growth_protocol: Human embryonic stem cells (H9, female) were maintained in E8 medium (Life Technologies) on Matrigel (Stem Cell Technologies) coated plates, dissociated using 0.5mM EDTA, and passaged at 1:10 ratio.

extract_protocol:
Briefly, cells were detached with Accutase and crosslinked in solution for 10 minutes in freshly prepared 1% formaldehyde (Thermo Scientific) in PBS. Cell were quenched in 0.125M glycine, followed by two washes with cold PBS. 25x106 cross-linked cells were used per ChIP replicate. Cells were lysed in lysis buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 0.5% SDS, 1X protease inhibitors) for 30 minutes on ice and sonicated twice for 10 minutes on a Diagenode Bioruptor to achieve a chromatin between 200 and 400bp in size. Chromatin was centrifuged, quantified and diluted in dilution buffer up to 2mL (50mM Tris-HCl pH 8.0, 10mM EDTA, 1X protease inhibitors). Sheared chromatin was incubated overnight at 4°C with a TFAP2A antibody. The next day lysates were incubated with 30μL of Dynabead protein G beads (Invitrogen) for 4 hours at 4°C. Beads were washed twice each with low salt buffer (50mM Tris-HCl pH 8.0, 0.15M NaCl, 1mM EDTA pH 8.0, 0.1% SDS, 1% triton X-100, 0.1% sodium deoxycholate), high salt buffer (50mM Tris-HCl pH 8.0, 0.5M NaCl, 1mM EDTA pH 8.0, 0.1% SDS, 1% triton X-100, 0.1% sodium deoxycholate), and LiCl buffer (50mM Tris-HCl pH 8.0, 0.15M LiCl, 1mM EDTA pH 8.0, 1% Nonidet P-40, 0.1% sodium deoxycholate). DNA was eluted in 100μL of elution buffer (50mM NaHCO3, 1% SDS) and crosslinks were reversed with 4μL of 5M NaCl incubated shaking for 16 hours at 67°C. RNA was removed by adding 1μL of 10mg/mL RNase A for 30 minutes at 37°C. DNA was cleaned using the Qiaquick PCR purification kit (Qiagen) and quantified using Qubit (Invitrogen).
10ng of DNA was used to make libraries with the NEBNext kit (New England Biolabs) and AMPure XP beads (Beckman Coulter) according to the manufacturer instructions.

value: hESC


title: Th17 KO replicate 3

value: 5 microg of anti-H3K9/14ac (Diagenode, C15410005)


title: Th17 KO replicate 2


title: S3T3 SHH rep1

description:
adherent
s3T3_SHHN_1


title: Gibbin_hESC_rep1


title: S3T3 Ctrl rep3

description:
adherent
s3T3_Ctrl_3

value: Ctrl


title: S3T3 Ctrl rep2

description:
adherent
s3T3_Ctrl_2


title: ACLY-KO_Th17 #3

city: Wuerzburg

first: Sophia

middle: Martina

last: Hochrein

address: Versbacher Str 9

institute: University of Wuerzburg

data_processing:
Demultiplexed FASTQ files were generated with bcl2fastq2 v2.20.0.422 (Illumina) To assure high sequence quality, Illumina reads were quality- and adapter-trimmed via Cutadapt [1] version 2.5 using a cutoff Phred score of 20 in NextSeq mode, and reads without any remaining bases were discarded (command line parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC). Processed reads were subsequently mapped to the mouse genome (GRCm38.p6 primary assembly and mitochondrion) using STAR v2.7.2b with default parameters based on RefSeq annotation version 108.20200622 for GRCm38.p6 [2].
Read counts on exon level summarized for each gene were generated using featureCounts v1.6.4 from the Subread package. Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (command line parameters: -s 2 -t exon -M -O --fraction). The count output was utilized to identify differentially expressed genes using DESeq2 [4] version 1.24.0. Read counts were normalized by DESeq2 and fold-change shrinkage was applied by setting the parameter “betaPrior=TRUE”. Differential expression of genes was assumed at an adjusted p-value (padj) after Benjamini-Hochberg correction < 0.05 and |log2FoldChange| ≥ 1.

growth_protocol: Naive T cells were differentiated  in vitro under Th17 polarizing conditions. After 48h, cells were incubated with or without 20 mM acetate for another 24h.

extract_protocol:
1x10^6 T cells were harvested in RNAprotect Cell Reagent and stored at -80°C o/n before total RNA was extracted using the RNeasy Plus Micro Kit (both Quiagen)
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was >7.8. cDNA libraries were prepared from 500 ng of total RNA with TruSeq mRNA Stranded Library Prep Kit from Illumina according to manufacturer’s instructions (1/2 volume). Libraries were quantified by QubitTM Flex Fluorometer (ThermoFisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA and DNA 1000 Kit (Agilent)
Sequencing of pooled libraries, spiked with 1% PhiX control library, was performed at ~20 million reads/sample in single-end mode with 75 nt read length on the NextSeq 500 platform (Illumina) with 1 High Output Kit v2.5. Demultiplexed FASTQ files were generated with bcl2fastq2 v2.20.0.422 (Illumina).

treatment_protocol: Stimulation with anti-.CD3/CD28 with cytokines for Th17 cell differentiation. 20mM acetate for 24h. Re-stimulation with PMA/Iono + Bref A and Monensin for 5h

tag: genetic background

value: Acly-fl/fl Cd4-cre


title: Th17 KO replicate 1


title: ACLY-KO_Th17 + acetate #3


title: ACLY-KO_Th17 + acetate  #2


title: Th17 WT replicate 3


title: S3T3 Ctrl rep1

description:
adherent
s3T3_Ctrl_1


title: Th17 WT replicate 2, input


title: ACLY-KO_Th17 #1


title: ACLY-KO_Th17 + acetate  #1


title: ACLY-KO_Th17 #2


title: WT_Fam111a_1

city: Nijmegen

first: Jeroen

last: de Baaij

address: Geert Grooteplein 26-28

department: Physiology

country: Netherlands

institute: Radboudumc

data_processing:
Low quality filtering and adapter trimming was performed using Trim Galore!, V0.4.4_dev 9 (Babraham Bioinformatics), a wrapper tool around the tools Cutadapt v1.18 and FastQC tool v0.11.5 (Babraham Bioinformatics).
On average between 8-11 million total reads per individual library were retrieved. Filtered and trimmed reads were mapped to a human reference genome (GRCm38, Ensemble) with Star v2.6.0a (19) resulting in BAM. BAM files were counted (number of reads mapped to a feature, e.g. a gene) with HTSeq (HTSeq-count tool v0.11.0 (39)) using a complementary .gtf file, containing annotation for GRCm38 (Ensemble).
MultiQC was used to combine results and quality checks of all the samples. Less than 1% of all reads were comprised of overrepresented sequences, and 6-8.5 million reads were uniquely mapped with a mean alignment of 80%.
Given the absence of sample replicates, individuals of the same disease group were considered biological replicates. Hence, differential gene expression analysis was carried out with DESeq2 v1.22.0 in R v3.5 (21), with internal statistical and normalization method (i.e. correction for multiple testing with Benjamini–Hochberg). The average mRNA expression between two groups was analyzed. Genes with a P-adjusted value <0.05and with log2 fold change of >±2 were considered differentially expressed genes (DEG).
Genome_build: Version 81 of mouse reference genome GRCm38
Supplementary_files_format_and_content: Text files (.counts.txt) containing expression values in counts for each gene. Files are generated by HTSeq-count.

source_name: kidneys

growth_protocol: Mice (8-10 weeks old) were placed in metabolic cages and left to acclimatise for 24 hours. During the next 24 hours, the mice were weighed and urine and faeces were collected. In addition, water and food consumption were measured. The following day, the mice were anaesthetised by 4% (v/v) isoflurane inhalation, serum/blood was collected and the mice were sacrificed. Kidney, thyroid glands, duodenum and colon were collected and snap frozen in liquid nitrogen and stored at -80ºC until further analysis.

extract_protocol:
Total RNA was extracted from kidney tissue using TRIzol reagent (Invitrogen) according to the manufacturer’s protocol.
24x lllumina TruSeq strand-specific mRNA library

tag: background strain

value: 8-10 weeks old


title: KO_Fam111a_3

description: The non-conditional allele Fam111atm1(KOMP)Vlcg was generated by insertion of ZEN-UB1 cassette targeting chromosome 19 in ES cells.


title: WT_Fam111a_4


title: KO_Fam111a_1


title: WT_Fam111a_3


title: KO_Fam111a_2


title: WT_Fam111a_2


title: CCL206 SHH rep3

description:
adherent
CCL_206_SHHN_3

source_name: MLg

value: ddY

value: lung

value: MLg

value: newborn


title: GLUT3-KO Th17 + acetate #3


title: CCL206 SHH rep2

description:
adherent
CCL_206_SHHN_2


title: WT single fiber 4

first: Vahab

last: Soleimani

address: 3640 rue University

department: Human Genetics

institute: McGill University

data_processing:
Illumina BaseSpace software was used for basecalling.
Data was analysed using the GenPipes pipeline v.3.1.5 (https://academic.oup.com/gigascience/article/8/6/giz037/5513895)
Peaks were called using MACS2(v2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: The bigWig files are normalized genome-wide signal coverage tracks used for visual inspection of the peaks and comparison between conditions

source_name: The Jackson Laboratory

extract_protocol:
EDL muscle was dissected and myofibers were isolated as previously described (Blackburn, D.M. et al. Journal of Biological Chemistry, 2019). After isolation and selection of a single myofiber, myofibers were lysed with water and then permeabilized with 0.5% Triton X-100  for 15 minutes at room temperature (RT). The permeabilization step was followed by two washes with PBS1X. 5000 MuSCS were freshly isolated by Fluorescence Activated Cell Sorting (FACS) as previously described from Pax7/GFP+ mice  (Tichy, E et al. Skeletal Muscle, 2018).
Myofiber ATAC-Seq samples were lysed as described above and the ATAC-Seq library preparation was performed with modified version of OMNI ATAC-Seq protocol (Corces, M.R. et al. Nature Methods, 2017). Isolated MuSCs were freshly sorted into ATAC-Seq lysis buffer and samples were processed with modified version of the OMNI ATAC-Seq protcol (Corces, M.R. et al. Nature Methods, 2017).

treatment_protocol: For the smfATAC-Seq of injured myofibers, extensor Digitorum Longus (EDL) muscle of WT C57Bl mice was injured by intramuscular injection of cardiotoxin (CTX) . 7 days post-injury, mice were sacrificed and the EDL was collected from each mouse with the contra lateral EDL being used for the uninjured myofibers.

value: 4 weeks

value: skeletal muscle


title: WT single fiber 3


title: R8

city: Prahran

first: Sonika

last: Tyagi

state: VIC

address: 99 commercial road

department: Infectious Diseases

institute: Monash University

data_processing:
Clean RNA sequencing reads were aligned to human genome build hg38 using the HISAT236 aligner. The aligned (.bam) files were then used to summarise counts for known protein coding and noncoding gene annotations (GENCODE version 33) using the featureCounts
EdgeR and GSEA were used to perform differential expression and coexpression analysis
ncRNA were analysed using corresponfing miRBASE and lncRNACOmpare database as described in the manuscript
Ehancer and promoter analysis was performed using Enhncer Atlas and JASPAR
Known TADs were extract from Rao et al to map genes to chromatin domains
Genome_build: hg38, GENCODE
Supplementary_files_format_and_content: Gene counts

source_name: Myometrium (Uterus)

extract_protocol:
Illumina Ribo-zero Gold associated protocol
Illumina Ribo-zero Gold
Illumina HiSeq 2500

tag: condition

value: Late Labour


title: CCL206 Ctrl rep3

description:
adherent
CCL_206_ctrl_3


title: R6


title: GLUT3-KO_Th17#2

value: Slc2a3-fl/fl Cd4-cre


title: R7


title: GLUT3-KO Th17 + acetate #2


title: GLUT3-KO_Th17 #3


title: CCL206 Ctrl rep2

description:
adherent
CCL_206_ctrl_2


title: Th17 WT replicate 2

value: wild type

value: 3 h stimulation with PMA and ionomycin


title: WT single fiber 2


title: R5


title: GLUT3-KO Th17 + acetate #1


title: GLUT3-KO Th17 #1


title: WT single fiber 1


title: Th17 WT replicate 1


title: 20_Sc20

value: Early labour


title: MDX single fiber 3


title: R1


title: WT_Th17 + acetate  #3


title: MDX single fiber 1


title: CCL206 Ctrl rep1

description:
adherent
CCL_206_ctrl_1

value: fibroblast


title: MDX single fiber 2


title: WT_Th17 #3


title: WT_Th17 + acetate  #2


title: R4


title: 10_Sc10


title: WT_Th17 + acetate  #1


title: mt

city: Cincinnati

first: Guolun

last: Wang

state: OH

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The standard celllranger mkfastq software version 3.0 used for basecalling.
The standard celllranger count software version 3.0 used to produced raw expression matrix.
The matrix were normalized and scaled by Seurat v3.0 in R3.5.3 environment.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix

source_name: lung

extract_protocol:
The lung samples were harvested from E18.5 heterozygous mouse embryo. The samples were dissociated into small pieces and digested into single cell suspension. The CD45+ cells were depleted by MACS column and CD45- cells used to prepare library.
The libraries were prepared for sequencing using standard 10X 3'v3 protocols

tag: cell subset

value: Foxf1 S52F heterozygous


title: Injured single fiber 3

source_name: Injured single fiber

value: single fiber

tag: injury status

value: Injured


title: WT_Th17 #2


title: CCL206 SHH rep1

description:
adherent
CCL_206_SHHN_1

value: SHHN

tag: cell line


title: CEC1_Am48


title: WT_Th17 #1


title: 7_Sc7_1


title: wt

value: WT


title: Injured single fiber 2


title: 14_Sc14


title: WT_hESC_rep2

data_processing:
Tophat used for alignment.
Homer for raw counts and RPKM values
DESEQ2 used for differential expression
Genome_build: hg38
Supplementary_files_format_and_content: text file, raw counts

extract_protocol:
Cells were removed from the plate with Accutase. For RNA extraction, cells were lysed in Trizol (Invitrogen), the aqueous layer was isolated as indicated by the manufacturer, and RNA was purified with RNeasy columns (Qiagen). DNase (Qiagen) treatment was added to the column prior to elution as per manufacturer instructions.
Libraries for RNA-seq were prepared using the KAPA kit for PolyA enriched mRNA-seq (Illumina) according to the manufacturer’s protocol.

value: hESC


title: Uninjured single fiber 2

source_name: Uninjured single fiber

value: Uninjured


title: Uninjured single fiber 1


title: EC5

value: Not in labour


title: Th17 KO replicate 2

data_processing:
Demultiplexed FASTQ files were generated with bcl2fastq2 v2.20.0.422 (Illumina). To assure high sequence quality, Illumina reads were quality- and adapter-trimmed via Cutadapt [1] version 2.5 using a cutoff Phred score of 20 in NextSeq mode, and reads without any remaining bases were discarded (command line parameters: --nextseq-trim=20 -m 1 -a CTGTCTCTTATACACATCT). Processed reads were subsequently mapped to the mouse genome (GRCm38.p6 primary assembly and mitochondrion) using STAR v2.7.2b with default parameters based on RefSeq annotation version 108.20200622 for GRCm38.p6
Read counts on exon level summarized for each gene were generated using featureCounts v1.6.4 from the Subread package. Multi-mapping and multi-overlapping reads were counted non-strand-specific with a fractional count for each alignment and overlapping feature (command line parameters: -s 0 -t exon -M -O --fraction). The count output was utilized to identify differentially expressed genes using DESeq2 version 1.24.0. Read counts were normalized by DESeq2 and fold-change shrinkage was applied by setting the parameter “betaPrior=TRUE”. Differences in gene expression were considered significant if padj < 0.05.

growth_protocol: Naive T cells were differentiated for 3 days in vitro under Th1 and Th17 polarizing conditions.

extract_protocol:
1x10^6 T cells were harvested in RNAprotect Cell Reagent and stored at -80°C o/n before total RNA was extracted using the RNeasy Plus Micro Kit (both Quiagen)
RNA quality and quantity were checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies) and RNA Pico kit depending on the sample concentration. The RIN for all samples was >7. cDNA libraries suitable for sequencing were prepared from 5 ng of total RNA with SMART-Seq v4 Ultra Low Input RNA Kit (Takara) according to manufacturer’s instructions (1/4 volume). Libraries were quantified by QubitTM 3.0 Fluometer (ThermoFisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent). 0.5 ng of each library was subjected to a tagmentation-based protocol (Nextera XT, Illumina) using a quarter of the recommended reagent volumes. Libraries were quantified again by QubitTM 3.0 Fluometer (Thermo Fisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent) before pooling. Sequencing of pooled libraries, spiked with 1% PhiX control library, was performed at 19-36 million reads/sample in single-end mode with 75 nt read length on the NextSeq 500 platform (Illumina) with 1 High Output Kit v2.5.
Sequencing of pooled libraries, spiked with 1% PhiX control library, was performed at ~20 million reads/sample in single-end mode with 75 nt read length on the NextSeq 500 platform (Illumina) with 1 High Output Kit v2.5. Demultiplexed FASTQ files were generated with bcl2fastq2 v2.20.0.422 (Illumina).

treatment_protocol: Stimulation with anti-.CD3/CD28 with cytokines for Th1 and Th17 cell differentiation


title: Th17 KO replicate 1


title: Th17 WT replicate 3


title: Injured single fiber 1


title: Th17 KO replicate 3


title: EC3


title: EC6


title: EC4


title: WT_hESC_rep1


title: EC1


title: GKO_hESC_rep2

value: GKO


title: Th17 WT replicate 1


title: Th17 WT replicate 2


title: NRVM AdMettl5-PE rep4

city: Guangzhou

description: PE AdGFP and AdMettl5 NRVM

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%.
The clean reads were mapped to the mouse genome (Mus_musculus.GRCm38) or rat genome (Rattus_norvegicus.Rnor_6.0)  or using HISAT2(v2.0.4). Expression level of gene was calculated by StringTie (v2.1.4).
Differential expression analysis was performed using the DESeq2(v1.4.5) with adjusted p value≤ 0.05.
Genome_build: Mus_musculus.GRCm38; Rattus_norvegicus.Rnor_6.0

organism: Rattus norvegicus

source_name: cardiac ventricle

extract_protocol:
Total RNAs were isolated using Trizol Reagent from NRVMs and tissue samples.
RNA libraries were prepared for sequencing using standard BGIseq protocols

value: Sprague Dawley

value: post natal day 2

value: Neonatal rat ventricular cardiomyocytes


title: EC2


title: Young MuSC 3

source_name: Muscle stem cells

value: 4 weeks

value: skeletal muscle

value: Muscle stem cells


title: ADSC3

last: Zhou

state: Hubei Province

address: 1277 Jiefang Avenue

institute: Wuhan Union Hospital

description: miRNA

data_processing:
The basic reads were converted into sequence data (also called raw data/reads) by base calling. Low quality reads were filtered, and the reads with 5’ primer contaminants and poly (A) were removed. The reads without 3’adapter and insert tag, the reads shorter than 15 nt or longer than 41 nt from the raw data were filtered, and the clean reads were obtained.
For primary analysis, the length distribution of the clean sequences in the reference genome was determined. Non-coding RNAs were annotated as rRNAs, tRNAs, small nuclear RNAs (snRNAs), and so on. These RNAs were aligned and then subjected to the Bowtie search against Rfam v.10.1 (http://www.sanger.ac.uk/software/Rfam). The known miRNAs were identified by aligning against miRBase v22 database (http://www.mirbase.org/), and the known miRNA expression patterns in different samples were analyzed. After that, unannotated reads were analyzed by mirdeep2 to predict novel miRNAs. Based on the hairpin structure of a pre-miRNA and the miRBase database, the corresponding miRNA star sequence and miRNA mature sequence were also identified.
In order to investigate the expression profiles of miRNAs, the frequency of miRNA counts was normalized to TPM (tags per million) using the following formula: normalized expression = actual miRNA read count /total clean read count x 106. Differentially expressed miRNAs between the paired groups were analyzed by using DEGseq.
Genome_build: NCBI_GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: adipose-derived stem cells

growth_protocol: Adipose-derived stem cells (ADSCs) were isolated from the subcutaneous fat from healthy donors. Cells from the third passages were used in this study. Then, ADSCs were cultured in α-MEM growth media (Gibco; Thermo Fisher Scientific, Inc.) supplemented with 10% FBS (Gibco; Thermo Fisher Scientific, Inc.).

extract_protocol:
Total RNA was extracted using mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol. Quantitation of total RNA was carried out using the Nanodrop 2000 (Thermo Fisher Scientific Inc., USA). RNA integrity was assessed by Agilent 2100 Bioanalyzer (Agilent Technology, USA). 1 μg total RNA of each sample was used for the small RNA library construction.
Libraries were prepared according to Illumina's instructions accompanying TruSeq Small RNA Sample Prep Kits (Cat. No. RS-200-0012, Illumina, USA.). Briefly, total RNA were ligated to adapters at each end. Then the adapter-ligated RNA were reverse transcribed to cDNA and performed PCR amplification. The PCR products ranging from 140–160 bp were isolated and purified as small RNA libraries. Library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips. The libraries were finally sequenced using the Illumina NovaSeq6000 platform. 150 bp paired-end reads were generated. The small RNA sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

treatment_protocol: Exosomes were isolated from the supernatant of a rat Schwann cell line (RSC96) using ultracentrifugation method. ADSCs induced by RSC96-Exosomes (Exo-ADSCs) were cultured a-MEM supplemented with 10% FBS and RSC96-Exosomes (20 µg/ml) for 8 days, and the media was changed every 2 days with the exosomes replenished each time. In the control group, ADSCs were cultured in α-MEM supplemented with 10% FBS.

value: adipose-derived stem cells

value: untreated


title: GKO_hESC_rep1


title: NRVM AdMettl5-PE rep1

description: PE AdGFP and AdMettl5 NRVM


title: NRVM AdMettl5-PE rep2

description: PE AdGFP and AdMettl5 NRVM


title: ADSC2

description: miRNA


title: NRVM AdMettl5-PE rep3

description: PE AdGFP and AdMettl5 NRVM


title: Th1 KO replicate 3

value: Slc2a3-fl/fl Cd4-cre


title: CON rep2

city: Hangzhou

first: Zhipan

last: Wu

address: College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, Zhejiang

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Pancreatic cancer cell

growth_protocol: PANC-1 cells were maintained in a DMEM medium supplemented with 10% fetal bovine serum. Cells were cultured in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were plated in 10-cm dishes overnight and treated with 8 μM CMR for 48 h. Subsequently, total RNA was extracted using TriZol reagent according to the manufacturer's procedure.

value: Pancreatic cancer cell

value: control


title: CON rep3


title: Th1 KO replicate 2


title: CON rep1


title: Th1 KO replicate 1


title: ADSC1

city: Wuhan

description: miRNA


title: Th1 WT replicate 3

value: wild type


title: EXO-ADSC2

description: miRNA

source_name: Exosome induced adipose-derived stem cells

value: treated with Schwann cell-derived exosomes for 8 days


title: NRVM AdGFP-PE rep4

description: PE AdGFP and AdMettl5 NRVM


title: NRVM AdGFP-PE rep3

description: PE AdGFP and AdMettl5 NRVM


title: Th1 WT replicate 2


title: CMR rep3

value: 8 μM CMR for 48 h


title: EXO-ADSC3

description: miRNA

value: Exosome induced adipose-derived stem cells


title: CMR rep2


title: NRVM AdGFP-PE rep1

description: PE AdGFP and AdMettl5 NRVM


title: NRVM AdGFP-PE rep2

description: PE AdGFP and AdMettl5 NRVM


title: EXO-ADSC1

description: miRNA


title: Th1 WT replicate 1


title: CMR rep1


title: HepG2-input-2

status: Public on Feb 12 2022

first: Xuefen

last: Li

state: China

address: 79 Qingchun Road

institute: the First Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
FastQC
BWA or bowtie software
SAMtools
MACS2
IGV

growth_protocol: HepG2 was incubated at 37 °C in 5% CO2.The medium was supplemented with 10% FBS (GIBCO), 100 mg/mL penicillin, and 100 mg/mL streptomycin. After 24 h of culture, the cells were transfected with plasmids.

extract_protocol:
Lysates were incubated with protein A, Dynabeads, and 5 μg antibody overnight at 4 °C. After immunoprecipitation, the magnetic beads were recovered with a magnet and washed. DNA was eluted, de-crosslinked at 65 °C for 4 h, and then purified with the QIAGEN Kit.
Sequencing libraries were constructed with 5 ng of purified ChIP DNA and they were sequenced using Illumina HiSeq X Ten.

treatment_protocol: c-Jun was crosslinked with 1% formaldehyde for 10 min at 25 °C, ligating c-Jun with IL-35 subunit p35 or EBI3 chromatin. Wash and dissolve crosslinked cells (20 million cells/sample), prepare nucleic acid extract, and stain by ultrasonic shearing quality.

value: human hepatoma cells


title: HepG2-input-1


title: HepG2-C-jun

description: HepG2 cells were transfected with plasmids expressing HBV protein or pCMV-Tag2 and pGL3-IL-35 for 48h