title: 2735

city: Amsterdam

first: Esther

last: Lips

address: Plesmanlaan 121

department: Molecular Pathology

country: Netherlands

institute: NKI-AVL

data_processing:
Reads were aligned to the human transcriptome (Homo_sapiens.GRCh37.75.gtf) using Tophat v2.1[54]. Readcounts per gene were calculated using lcount[55], and normalized using DESeq2[56]. The SVA R package[57] was used to combine and batch correct gene expression datasets. Gene expression levels were associated with chemotherapy response using samr[58]; differential gene expression between pre- and post-treatment samples was analyzed using DESeq2[56]. Subsequent pathway / GO-term enrichment was performed using the Reactome Cytoscape plugin[59, 60] and geneset enrichment was performed using GSEA[61]. The most significant genes from the samr analysis (FDR < 5%) were selected for a ‘core enrichment’ set, based on unsupervised clustering and pathway and GO-term enrichment (Supplementary Table S1). Metagene scores for all three processes were created by calculating the median expression of genes assigned to each cluster. Expression above or below the metagene median was used to stratify patients into a HHL (Proliferation High, Immune High, ECM Low) or LLH (Proliferation Low, Immune Low, ECM High) profile. RNA-seq reads of the pre-post dataset were also aligned to the human reference genome version 37.75 (hg19) using bwa[45] to be able to confirm somatic mutations and indels in the expression data.
Genome_build: 37.75 (hg19)
Supplementary_files_format_and_content: The processed data file is in txt format, and contains readcounts.

source_name: human breast

extract_protocol:
RNA was isolated from samples with a tumor percentage > 50%, from thirty 30-μm cryosections. A 5-μm section halfway through the biopsy was stained for hematoxylin and eosin and analyzed by a pathologist for tumor percentage. Total RNA was isolated with RNA-Bee (Bio-Connect, Huissen, The Netherlands, Cat No. CS-100B), DNase-treated by using the Qiagen RNase-free DNase Set (Qiagen, Venlo, The Netherlands, Cat No. 79254) and RNeasy spin columns (Qiagen, Cat No. 74104) and dissolved in RNase-free H2O. Quality and quantity of the total RNA was assessed by the 2100 Bioanalyzer using a Nano chip (Agilent, Santa Clara, CA); samples having RIN>6.4 were subjected to library generation. mRNA libraries were generated using the TruSeq RNA Library Preparation Kit v2 (Illumina Inc., San Diego, Cat.No RS-122-2001/2) according to the manufacturer's instruction (Part # 15026495 Rev. B). The libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent, Santa Clara, CA), diluted and pooled equimolar into a 10nM sequencing pool containing 9 libraries each, and sequenced with 50 basepair single reads (pre-treatment samples only) or 65 basepair single reads (pre-post treatment set) on a HiSeq2000 using V3 chemistry (Illumina Inc., San Diego).
mRNA libraries were generated using the TruSeq RNA Library Preparation Kit v2 (Illumina Inc., San Diego, Cat.No RS-122-2001/2) according to the manufacturer's instruction (Part # 15026495 Rev. B). The libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent, Santa Clara, CA), diluted and pooled equimolar into a 10nM sequencing pool containing 9 libraries each, and sequenced with 50 basepair single reads (pre-treatment samples only) or 65 basepair single reads (pre-post treatment set) on a HiSeq2000 using V3 chemistry (Illumina Inc., San Diego).

tag: tissue type

value: biopsy

tag: pathological complete response (pcr)

value: pCR

tag: neoadjuvant response index (nri)

tag: t-stage

tag: n-stage (0, neg; 1, pos)

tag: subtype

value: TN

tag: recurrence

value: No

tag: rfs (years)


title: 2688

status: Public on Dec 28 2021

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: age

value: No pCR


title: 2701


title: 2694


title: Col-0_replicate2

city: Seoul

first: Souvik

last: Dhar

state: Gwanak gu

address: 1, Gwanak ro

country: South Korea

institute: Seoul National University

data_processing:
Base-calling was performed using CASAVA (Version 1.8.2)
Reads were mapped using Tophat v2.0.13 based on the reference sequences
gtf file (annotation file) for each sample was produced using cufflink v2.2.0. Each file was merged by cuffmerge and quantification for each sample was performed using cuffquant.
Abundant calculation (FPKM) were perfomed using cuffdiff v2.2.0.
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM values for each sample and each sample group

organism: Arabidopsis thaliana

source_name: Wild type

growth_protocol: Seedlings were plated on half MS medium and allowed for germination for 24 hours.Then they were grown in dark for 5 days on half MS medium at 22 ℃. The hypocotyl part were excised from the seedlings and were used for RNA isolation.

extract_protocol:
Total RNA samples were extracted from 5-day-old dark-grown hypocotyls using TRI REAGENT (Molecular Research Center, USA) according to the manufacturer’s instructions. The samples were cleaned up with RNeasy Plant Mini Kit (Qiagen, Germany) according to the manufacturer’s instructions.
Libraries were prepared using Truseq Stranded mRNA Prep Kit

tag: ecotype

value: 5 d-old

tag: tissue

value: root tip

tag: genotype/variation

value: Wild type


title: Patient3 ovarian cancer tissue

city: Nanjing

first: Shanliang

last: Zhong

address: Baiziting 42

country: China

institute: The Affiliated Cancer Hospital of Nanjing Medical University

data_processing:
nonr provided by the submitter
Genome_build: hg38

source_name: ovary

extract_protocol: none provided by the submitter

value: ovarian tumors

tag: age (years)

tag: Stage

value: FIGO III


title: Patient2 normal ovarian tissues

value: normal ovarian tissues


title: Shr-2_replicate1

source_name: shr mutant


title: Shr-2_replicate2


title: 2673


title: 2675


title: 2711


title: Col-0_replicate1


title: Patient1 normal ovarian tissues


title: 2699

value: LUM


title: 2666


title: 2665


title: 2644


title: 2623


title: 2605


title: 2731


title: 2571


title: 2565

value: Yes


title: 2563


title: 2556


title: 2555


title: 2549


title: 2519


title: 2537


title: 2538


title: 2514


title: 2541


title: 2546


title: 2512


title: 2532


title: 2500


title: 2491


title: 2490


title: 2502


title: 2499


title: 2492


title: 2489


title: 2608


title: 2486


title: 2483


title: 2589


title: 2479


title: SG_40D1 (rrbs)

city: Udine

first: Emanuele

last: De Paoli

state: UDINE

address: via delle Scienze 206

department: Agricultural, Food, Environmental and Animal Sciences

country: Italy

institute: University of Udine

library_source: genomic

data_processing:
Quality of raw sequencing data was evaluated with the FastQC software (Babraham Institute, Cambridge, UK).
Adaptor sequences were removed using the TRIM GALORE program (Babraham Institute, Cambridge, UK) with default settings for RRBS-seq data.
Cleaned reads were aligned to the grapevine reference genome (Jaillon et al., 2007) and converted into DNA methylation data using the bisulfite sequencing alignment tool ERNE-BS5 from the ERNE 2 software package (Prezza et al., 2012); http://erne.sourceforge.net/).
Genome_build: V1 version of the PN40024 12X reference genome  (Jaillon et al., 2007)
Supplementary_files_format_and_content: DNA methylation data in the ERNE-BS5 tab-delimited text format from the ERNE 2 software package (Prezza et al., 2012) (chromosome, cytosine position, strand, sequence context, sequencing depth, methylation level, unused field).

molecule: genomic DNA

organism: Vitis vinifera

source_name: Undifferentiated callus tissues at 40d of culture

growth_protocol: Anthers (A) were cultured on a previously described callus induction medium supplemented with 4.5 µM 2,4-dichlorophenoxyacetic acid (2,4-D) and 8.9 μM 6-benzylaminopurine (BAP) (Gribaudo et al., 2004; Gambino et al., 2007). The cultures were maintained at 26 °C in the dark. Three months after the initiation of the culture, calli were transferred for 1 months to embryo proliferation medium (Gribaudo et al., 2004; Gambino et al., 2007) containing 10 µM 2-Napthoxyacetic acid (NOA), 1 μM BAP, 20 µM Indole-3-acetic acid (IAA) and 2.5% activated charcoal. The frequency of callogenesis and embryogenesis for both cultivars was calculated in two consecutive years at 4 months after the initiation of the culture, and calli were classified as embryogenic (EC) or non-embryogenic (NEC) under a stereomicroscope.

extract_protocol:
Genomic DNA was extracted from 50 mg of 40d calli, EC and NEC following methods of Doyle and Doyle (1990) with minor modifications.
Reduced Representation Bisulfite Sequencing (RRBS) libraries were constructed acccording to Gu et al. 2011 with modifications. DNA was digested with TaqI enzyme (recognition site T^CGA, NEB, Ipswich, MA, USA) at 65°C for 2 h. After purification using the QIAquick PCR Purification kit (QIAGEN, Germany), fragment ends were repaired and ligated using adapters and the protocol provided by the Ovation Ultralow Methyl-Seq DR Multiplex Kit (NuGEN, CA, USA). Ligated products corresponding to 100–1500 bp DNA fragments were purified by 2% Low-Range agarose gel electrophoresis. A final end-repair step of the purified fragments was performed using the same NuGEN kit. Bisulfite conversion was conducted using a EpiTect Fast DNA Bisulfite Kit (QIAGEN, Germany). The final RRBS libraries were generated by PCR amplification and validated by an Agilent 2100 Bioanalyzer (Agilent Technologies).
Reduced Representation Bisulfite Sequencing (RRBS) libraries sequenced using the Illumina HiSeq2500 platform (Illumina, San Diego, CA, USA) in paired-ended (PE), 125 bp runs

tag: cultivar

value: Sangiovese

tag: biological replicate


title: SG_40D2 (rrbs)

value: Undifferentiated callus tissues at 40d of culture


title: 2473


title: SG_NEC2 (rrbs)

source_name: Not Embryogenic callus tissue

value: Not Embryogenic callus tissue


title: SG_NEC1 (rrbs)


title: 2463


title: 2509


title: SG_EC2 (rrbs)

source_name: Embryogenic callus tissue

value: Embryogenic callus tissue


title: 2498

value: biopsy


title: 2455


title: 2449


title: 2448

value: pCR


title: CS_40D2 (rrbs)

value: Cabernet Sauvignon


title: 2453

value: TN

value: No


title: SG_EC1 (rrbs)


title: CS_40D1 (rrbs)


title: 2445

value: No pCR


title: CS_NEC2 (rrbs)


title: 2444


title: CS_NEC1 (rrbs)


title: CS_EC2 (rrbs)


title: 2442


title: 2472


title: 2435


title: CS_EC1 (rrbs)


title: 2432


title: SG_40D2 (small RNA-seq)

data_processing:
base-calling (Illumina Casava v. 1.8.2)
Illumina quality filtering (custom script)
Adapter trimming by Cutadapt v.1.9 (Martin 2011 )
Quality trimming by FASTX toolkit v.14 (http://hannonlab.cshl.edu/fastx_toolkit/)
Genome_build: 12X
Supplementary_files_format_and_content: counts

extract_protocol:
Total RNA was extracted from approximately 100 mg of anthers, 40d calli, EC and NEC. For each biological replicate, the plant material ground in liquid nitrogen using the tissue lyser system (TissueLyser II, Qiagen), was extracted using the Spectrum Plant Total RNA extraction kit (Sigma Aldrich). The integrity and quantity of RNA were checked with a 2100 Bioanalyzer Chip RNA 7500 series II (Agilent, Santa Clara, CA, USA)) and a Nanodrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA).
40d calli, NEC and EC triplicate samples yielded from the two varieties yielded 18 small RNA libraries using the Illumina TruSeq® Small RNA Library Prep  Protocol (Illumina Inc., San Diego CA, USA) according to the manufacturer’s instructions.


title: SG_40D3 (small RNA-seq)


title: 2420


title: SG_40D1 (small RNA-seq)


title: SG_NEC3 (small RNA-seq)


title: 2419


title: 2416


title: SG_NEC2 (small RNA-seq)


title: 2412


title: SG_NEC1 (small RNA-seq)


title: 2407


title: SG_EC3 (small RNA-seq)


title: SG_EC2 (small RNA-seq)


title: 2402


title: 2443


title: 2400


title: SG_EC1 (small RNA-seq)


title: CS_40D2 (small RNA-seq)


title: CS_40D3 (small RNA-seq)


title: 2393


title: 2396


title: 2390


title: CS_NEC2 (small RNA-seq)


title: CS_NEC1 (small RNA-seq)


title: 2383


title: CS_EC3 (small RNA-seq)


title: 2381


title: CS_EC2 (small RNA-seq)


title: 2398


title: MII young oocyte untreated batch 2-1

city: Hong Kong

first: Tin Lap

last: Lee

address: The Chinese University of Hong Kong, Shatin, NT, Hong Kong

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Raw reads from both RNA-seq and scBS-seq were checked by FastQC (v0.11.8, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and trimmed by Trim Galore (v0.4.5, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
For RNA-seq data, trimmed reads were mapped to the mouse reference genome (mm10) by TopHat (v2.1.1) with default parameters and Cufflinks was employed to quantify gene expression level with gene annotation obtained from Ensembl GRCm38.
Gene expression level was calculated in the form of fragments per kilobase million (FPKM). Genes with undetected expression level in all the samples were excluded in the following analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files that include TPM and FPKM values for each sample

organism: Mus musculus

source_name: Oocyte

extract_protocol:
7 µl of soft lysis buffer containing 500 mM KCl (Sigma), 100mM pH 8.0 Tris-HCl (Sigma), 1.35 mM MgCl2 (Sigma), 4.5 mM DTT (Thermo Fisher Scientific), 0.45% Nonidet P-40 (Sigma), 0.18U SUPERase-In (Thermo Fisher) and 0.36U recombination RNase-inhibitor (Thermo Fisher) were added into each PCR tube containing a single oocyte and were incubated at 4˚C for 30 min. Then, the lysate was vortexed at room temperature for 1 min and centrifuged at 1000g for 5 min to allow the nucleus to sink to the bottom of the tube. 6.5 µl of supernatant containing RNA was carefully transferred to a new PCR tube for generating scRNA-seq library.
RNA libraries were prepared for sequencing the TruePrep DNA Library Prep Kit V2

treatment_protocol: Aged (12 month old) mice and were fed with Nicotinamide Mononucleotide (NMN) in drinking water (2g/L) for 4 weeks, aged and young (4 weeks old) control mice were fed with drinking water without NMN. GV and MII oocytes were extracted from mouse ovaries.

tag: cell type

value: Oocyte (Metaphase II)

tag: strain

tag: treatment

value: control


title: GV young oocyte untreated batch 2-1

value: Oocyte (Germinal Vesicle)


title: GV young oocyte untreated batch 2-2


title: CS_40D1 (small RNA-seq)


title: 2401

tag: tissue type

tag: pathological complete response (pcr)

tag: neoadjuvant response index (nri)


title: 2376

tag: subtype


title: MII aged oocyte NMN batch 2-1

value: 2g/L NMN in drinking water for 4 weeks


title: CS_EC1 (small RNA-seq)


title: 2354

tag: t-stage

tag: n-stage (0, neg; 1, pos)

tag: recurrence


title: CS_NEC3 (small RNA-seq)


title: 2352

tag: age

tag: rfs (years)


title: Human right ventricle - 16_144608 - snRNA-seq

city: Utica

first: Nathan

last: Tucker

state: NY

address: 2150 Bleecker St

country: USA

institute: Masonic Medical Research Institute

description: nuclear RNA

data_processing:
Library strategy: single nuclei RNA-seq
Cellranger 4.0.0 in Cumulus workflow to generate FASTQ
CutAdapt v2.8 to trim template switch oligo sequence and its complement, and homopolymers (A30, T30, G30, C30)
CellRanger Count v12 to generate count matrices
CellBender v2.0 to filter ambient RNA byproducts
Scrinvex v13 to filter likely cytoplasmic transcripts
Scrublet to remove doublets
Genome_build: hg38
Supplementary_files_format_and_content: Normalized and log scale count matrix

source_name: Human right ventricle

extract_protocol:
Nuclei were isolated from flash frozen post-mortem cardiac tissue for microfluidic encapsulation using 10X Genomics' 10X Genomics Chromium Controller v3.1 Next GEM Single Cell 3'. Approximately 100mg of tissue was sectioned to a thickness of 100um then subjected to differential centrifugation and filtering.
10X Genomics Chromium Controller v3.1 Next GEM Single Cell 3'

tag: tissue

value: Heart (right ventricle)

tag: disease state

tag: microthrombi presence

value: Positive


title: MII aged oocyte untreated batch 2-1


title: Human right ventricle - 15_144548 - snRNA-seq

description: nuclear RNA

value: Negative


title: 2351

value: Yes


title: Human right ventricle - 17_144579 - snRNA-seq

description: nuclear RNA


title: GV aged oocyte untreated batch 2-2


title: Human right ventricle - 13_144471 - snRNA-seq

description: nuclear RNA


title: 2347


title: GV aged oocyte untreated batch 2-1


title: Human right ventricle - 11_144422 - snRNA-seq

description: nuclear RNA


title: MII old oocyte NMN batch 2


title: 2377


title: GV aged oocyte NMN batch 2-1


title: 2340

value: LUM


title: MII old oocyte NMN batch 1


title: Human right ventricle - 10_144421 - snRNA-seq

description: nuclear RNA


title: 2337


title: MII old oocyte untreated 2


title: Human right ventricle - 10_144396 - snRNA-seq

description: nuclear RNA


title: 2334


title: MII young oocyte untreated 2


title: Human right ventricle - 8_144391 - snRNA-seq

description: nuclear RNA


title: 2313


title: 2328


title: CRTC2TY1_input

city: Tianjin

first: Zeyun

last: Mi

address: Qi Xiang Tai Road

institute: Tianjin Medical University

data_processing:
Bowtie2 (version 2.3.4.1) was used to align paired-end 150 bp sequence reads to human (hg38)
HOMER (version 4.10) findPeaks command was used to call peak
BamCoverage within deeptools (version 3.3.0) were used to generate bigwig files from bam files.
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig

source_name: WT9-12 cells

growth_protocol: WT9-12 cells were cultured in DMEM-F12 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
WT9-12 cells were cross-linked with 1% formaldehyde for 10 min at RT. The crosslink was stopped by adding 1/20 volume of 2.5 M glycine. Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (100-500 bp) with Bioruptor Sonicator. Immunoprecipitation was performed with H3K27ac antibody (Abcam cat# ab4729). After elution and reversal cross-linking, DNA was purified.
Library construction were performed using VAHTS Universal DNA Library Prep Kit (Vazyme, ND607-02) and VATHS DNA Adapters set2 for Illumina (Vazyme Biotech, Cat.N802-01)

treatment_protocol: WT9-12 cells were infected with sgCRTC2 and CRTC2-TY1 viruses.

value: cell line


title: CRTC2TY1_ChIP

tag: chip antibody

value: Invitrogen Cat.no.MA523513


title: 2312

value: biopsy


title: GV aged oocyte NMN 2


title: MII young oocyte untreated 1


title: sgCRTC2_1

data_processing:
HISAT2 (version 2.1.0) was used to align paired-end reads to human (hg38) genome. Only unique mapped reads were used in further analysis.
FeatureCounts (version 1.6.0) was used to count reads number for each sample.
R package DESeq2 was used to identify differentially expressed genes, cut-offs were set at foldchange = 1.5 and P value at 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

molecule: polyA RNA

extract_protocol:
Total RNA isolation was performed using TRIzol (Invitrogen). Total RNAs from cultured cells were subjected to Oligo dT selection and adaptor ligation.
Construction of RNA-seq library was finished by Novogene company (Beijing, China).

treatment_protocol: WT9-12 cells were infected with sgControl or sgCRTC2 viruses.

tag: cell line

value: WT9-12 cells


title: 2303

value: pCR


title: GV aged oocyte untreated 1

tag: cell type


title: 2300


title: GV young oocyte untreated 1

tag: strain


title: sgControl_2


title: sgControl_1


title: ST-CHACE-2_Total-Cherry-Rep3

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

description: red fluorescent protein (mCherry)

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 2.9. Only sequences at least 25 nucleotides (nt) in length were considered for further analysis.
Bowtie version 2.1.0, with default parameters, was used for alignment on the reference genome
Sars-cov-2 genome coverages were computed with bedtools 2.17.0 genomecov for each strand.
Genome_build: hCoV-19/France/GES-1973/2020, GISAID accession Id: EPI_ISL_414631
Supplementary_files_format_and_content: Coverage files from bedtools genomeCov

organism: Severe acute respiratory syndrome coronavirus 2

source_name: HEK293 (human embryonic kidney cells) cell lines expressing One-STrEP-tagged Cherry overexpressing ACE-2

growth_protocol: ST-CHACE-2 cells were seeded into polylysine-coated (SIGMA) T150 flasks 1 day before infection (20x106 cells/flask).

extract_protocol:
Total RNA was extracted using TriLS (TriLS, Sigma) reagent protocol
Libraries were built using a TruSeq mRNA-Seq library preparation kit (Illumina), according to the manufacturer’s recommendations. Quality control was performed on an Agilent Bioanalyzer. Sequencing was performed on the Illumina NextSeq 500 platform to generate single-end 75 bp reads bearing strand specificity.

treatment_protocol: Virus infections were carried out at an MOI of 1. Viruses were diluted with DMEM 0%FCS to obtain a final inoculum volume of 5 ml. Cells were incubated with virus for 1 h at 37 C with gentle shaking. Twenty-five milliliters of DMEM containing 0%FCS was added to each T150 flask, and cells were incubated at 37°C until infections were stopped by cell lysis 24 h later.

tag: condition

value: One-STrEP-tagged

tag: infected with

value: SARS-CoV-2 at MOI of 1

tag: host cells


title: KO

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

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 Ensembl_GRCm38.90 whole genome using tophat2 with parameters -p 8 -N 2 --read-edit-dist 2.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. Then, FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: Ensembl_GRCm38.90
Supplementary_files_format_and_content: *_fpkm.txt: Tab-delimited text files include FPKM values.

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on liquid nitrogen, and total RNA was harvested using TriPure reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: GBP5 knockout and WT control mice (9 weeks old) were treated with GalN (800 μg/g body weight) and LPS (100 ng/g body weight) for 6 h.

tag: strain/background

tag: genotype/variation

value: Liver

value: 9 weeks

tag: treatment

value: GalN/LPS


title: 2288

tag: tissue type

tag: pathological complete response (pcr)

value: No pCR

tag: neoadjuvant response index (nri)

tag: t-stage

tag: n-stage (0, neg; 1, pos)

tag: subtype

value: No


title: 2292

tag: age

tag: recurrence

tag: rfs (years)


title: ST-CHACE-2_Total-Cherry-Rep2

description: red fluorescent protein (mCherry)

value: EK293 (human embryonic kidney cells) cell lines expressing One-STrEP-tagged Cherry overexpressing ACE-2


title: MII old oocyte untreated 1

tag: cell type

value: Oocyte (Metaphase II)

value: control


title: sgCRTC2_2

tag: cell line


title: 2311

value: TN


title: GV aged oocyte NMN 1

value: Oocyte (Germinal Vesicle)

tag: strain

value: 2g/L NMN in drinking water for 4 weeks


title: WT

value: wild type

tag: tissue


title: p10_3

status: Public on Dec 27 2021

city: Shanghai

first: Chuandong

last: Wang

address: NO.1665 Kongjiang Road

institute: Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

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.
The known miRNA sequences of species were obtained from miRBase database, and the known miRNA was identified by mirdeep2 software.
The counts of mature miRNA were quantified and normalized to CPM (reads count per million) by mirdeep2 software.
Genome_build: hg18
Supplementary_files_format_and_content: Table with CPM values for every miRNA

source_name: Bone Marrow Mesenchymal Stem Cells

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone Marrow

value: Bone Marrow Mesenchymal Stem Cells

value: subcultured P10

tag: disease state

value: Developmental dysplasia of the hip


title: p1_2

value: subcultured P1


title: p10_2


title: p1_3


title: p1_1


title: p10_1


title: MNB_1

city: Urbana

first: Xin

last: Li

state: IL

address: 601 S. Goodwin Avenue, B107 CLSL

department: CDB

institute: University of Illinois Urbana-Champaign

data_processing:
Basecalling and demultiplexing of raw data was done with the mkfastq command of the software Cell Ranger 3.1.0 (10x Genomics)
The sequencing reads were aligned to Ensembl’s BDGP6.22 using Cell Ranger (version3.0.1 for1st experiment, and version 3.1.0 for 2nd experiment) from 10x Genomics.
Gene expression levels were counted using Cellranger “Count”,“EmptyDrops” method was used to call cells.
Quality control on the count data, integration of two datasets and further analysis were performed using the package Seurat (version 3.2.3)
Genome_build: Ensembl’s BDGP6.22
Supplementary_files_format_and_content: matrix of counts for every gene and every cell
Supplementary_files_format_and_content: reference file for gene features
Supplementary_files_format_and_content: reference file for cell identities

organism: Drosophila melanogaster

source_name: medulla neuroblasts from larval brain

growth_protocol: Drosophila larvae were grown at 25oC until wondering 3rd instar stage.

extract_protocol:
For each scRNA-seq experiment, 120 third instar larvae of the genotype E(spl)mγGFP ;  SoxNGal4 UAS-RedStinger /TM6B were washed with PBS twice, and with 70% ethanal for 1 min, and with PBS once again. Each of the brains was dissected on ice in complete Schneider’s culture medium (Schneider’s Insect medium, supplemented with 10% fetal bovine serum, 2% Pen/Strep and 0.02 mg/mL insulin), and was directly transferred into a glass dish on ice containing DPBS. The dissection was completed within one hour, and then the supernatant (mainly DPBS) was replaced by 1 mL TrypLE with 1mg/mL collagenase I and 1mg/mL papain. The brains were incubated for 10 min at 30°C, with gentle shaking at 55 rpm. After removal of the dissociation solution, the brains were carefully washed with complete Schneider’s culture medium once and with DPBS twice. The brains were disrupted in 1.4 ml of DPBS with 0.04% BSA by manual pipetting using a P1000, and then 0.4 ml of DPBS with 0.04% BSA was added to make a total volume of 1.8 mL. The cell suspension was filtered through the cell strainer cap into a 5mL BDFalcon FACS tube. FACS sorting was done immediately after on BD FACS ARIA II with gentle settings (85 μm nozzle and low pressure of 20 psi). Trypan blue was added before sorting. Among the singlet live cells, GFP and RFP double positive cells were selected, and sorted into DPBS with 0.04% BSA.
FACS sorted cells were immediately concentrated by centrifugation at 500g for 5 minutes, then an additional 800g for 5 minutes to a 40ul volume. This entire volume was used as input for the 10x library. The single cell suspension was converted into an individually barcoded cDNA library with the Chromium Next GEM Single-Cell 3’ single-index kit version 3 from 10X Genomics (Pleasanton, CA) following the manufacturer’s protocols. Following ds-cDNA synthesis, sequencing library compatible with the Illumina chemistry was constructed. The final library was quantitated on Qubit and the average size determined on the AATI Fragment Analyzer (Advanced Analytics, Ames, IA).  The final library was diluted to 5nM concentration and further quantitated by qPCR on a Bio-Rad CFX Connect Real-Time System (Bio-Rad Laboratories, Inc. CA). The final library was sequenced on one lane of an Illumina NovaSeq 6000 S1 flowcell (exp1) or a half lane of an Illumina NovaSeq 6000 S4 flowcell, as paired-reads with 28 cycles for read 1, 8 cycles for the index read, and 150 cycles for read 2.

treatment_protocol: No treatment

value: Drosophila medulla neuroblasts

tag: developmental stage

value: 3rd instar larva

value: No treatment

tag: genotype

value: E(spl)mgammaGFP; SoxNGal4 UAS-RedStinger /TM6B


title: MNB_2

tag: treatment


title: Human Sertoli cells-derived extracellular vesicles

type: RNA

city: Beijing

first: Xiao-Hui

last: Tan

address: 8, Xishiku Street, Xicheng District

institute: Peking University First Hospital

description: HSerCs-EVs Sample1

hyb_protocol: Biotin-labeled miRNAs were hybridized to Affymetrix GeneChip miRNA 4.0 array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner 3000

data_processing:
Microarray data were assessed for quality using the Transcriptome Analysis Console software (version 4.0, ThermoFisher Scientific)
Data were normalized by the intensity by the robust multi-array average
As we only evaluated the expression of miRNAs in the species Homo sapiens, a total of 6631 values are valid.

label: biotin

source_name: extracellular vesicles

label_protocol: Total RNAs were labeled using the FlashTag™ Biotin HSR RNA Labeling Kit (Affymetrix), following the manufacturer’s instructions (User manual of the FlashTag™ Biotin HSR RNA Labeling Kit, Affymetrix)

growth_protocol: HSerCs were incubated in a conventional humidified atmosphere of 5% CO2/95% air at 37℃, the cells were maintained in Sertoli Cell Medium (Cat. No. 4521, ScienCell) supplemented with fetal bovine serum (5%), antibiotic solution (1%, penicillin/streptomycin), and Sertoli cell growth supplement (1%).

extract_protocol: HSerCs-EVs were separated using differential centrifugation. miRNAs were isolated from HSerCs-EVs using Qiagen miRNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

value: primary Sertoli cells

tag: sample type

value: EVs derived from Sertoli cells

value: normal

value: untreated


title: 2123

tag: tissue type

value: biopsy

tag: pathological complete response (pcr)

value: No pCR

value: TN


title: ST-CHACE-2_Total-Cherry-Rep1

description: red fluorescent protein (mCherry)

tag: condition

value: One-STrEP-tagged

tag: infected with

value: SARS-CoV-2 at MOI of 1

tag: host cells

value: EK293 (human embryonic kidney cells) cell lines expressing One-STrEP-tagged Cherry overexpressing ACE-2


title: unstimulated control

city: Vienna

first: Rainer

last: de Martin

address: Schwarzspanierstr. 17

department: Vascular Biology

country: Austria

institute: Medical University of Vienna

description: control RdM_4

hyb_protocol: Human Clariom® S Arrays were washed, stained and scanned according to the protocol described in  GeneChip™ WT PLUS Reagent Kit USER GUIDE

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

source_name: HUVEC

label_protocol: 100ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Applied Biosystems, Waltham, Massachusetts, USA)

growth_protocol: Human umbilical vein endothelial cells (HUVEC) were isolated from the umbilical cords and cultured in M199 medium (Lonza, Basel, Switzerland, #12-119F) with 20% FBS (Sigma, St. Louis, MO, USA, #F6765), penicillin (100 units/mL), streptomycin (100 μg/mL), (Pen-Strep, Lonza, Basel, Switzerland, #DE17-602E), 2 mM L-glutamine (Sigma; #G7513), 5 units/mL heparin, and 25 microgram/mL ECGS (Promocell, Heidelberg, Germany, ECGS/Heparin #C-30140).

extract_protocol: RNeasy Plus Micro Kit (Qiagen, Hilden, Germany) including DNAse digestion

treatment_protocol: HUVEC were pre-treated with 50micrograms/mL of P. santalinus extract, then stimulated with 5 ng/mL IL-1 for 2 hours

tag: cell line/type

value: Human umbilical vein endothelial cells (HUVECs)

value: unstimulated control


title: P. santalinus control

description: SH only RdM_3

value: P. santalinus control


title: IL-1 control

description: IL-1 only RdM_2

value: IL-1 control


title: BY4743 in YPG medium in 30˚C - replicate 2

city: Krakow

first: Hanna

last: Tutaj

address: Gronostajowa 7

country: Poland

institute: Jagiellonian University

data_processing:
Illumina software used for basecalling.
Reads aligned to the Saccharomyces cerevisiae genome using histat2 v. 2.1.0 with the following parameters: -t --dta-cufflinks -p 4 --new-summary
Alignment BAM files sorted and indexed with samtools (1.9)
Gene counts created with cuffquant with the following parameters: -v -p 4 --no-effective-length-correction and then normalized with cuffnorm with -p 4 -v -library-norm-method.classic-fpkm
Genome_build: R64-1-1
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Saccharomyces cerevisiae

source_name: Cultures in advanced growth phase

growth_protocol: Strains were cultured either in SC (in 30˚C (standard conditions),  37 ˚C or 40 g/l of NaCl added) or in rich YPD medium (with temperature shifted to 24 ˚C or 32 ˚C or kept at 30 ˚C but with glucose replaced with 3% glycerol)

extract_protocol:
Total RNA was extracted using RiboPure™ RNA Purification Kit
Non-paired RNA libraries were prepared for sequencing by Novagene Co., Ltd

tag: medium

value: YPD

value: grown at 30C


title: BY4743 in SC medium in 37˚C - replicate 2

value: SC

value: grown at 37C


title: BY4743 in YPG medium in 30˚C - replicate 1


title: BY4743 in SC medium in 37˚C - replicate 1


title: Mouse 6h Sham replicate 2

city: Toronto

first: Michael

last: Tymianski

state: ON

address: 60 Leonard Ave.

department: Fundamental Neurobiology

country: Canada

institute: Krembil Research Institute

description: Gene expression data in the ipsilateral brain region of mouse at 6hrs after sham surgery

hyb_protocol: The hybridization procedure was performed at the Center for Applied Genomics (TCAG, Research Institute of Hospital for Sick Children, Canada). The hybridization protocol follows the Affymetrix GeneChip WT PLUS Reagent Kit manufacturer's user guide. The labeled cRNA were hybridized with GeneChip arrays (Affymetrix GeneChip Probe Array: Mouse Gene 2.0 ST and Rat Gene 2.0 ST, ThermoFisher Scientific) in hybridization chamber at 45°C for 16hrs.

scan_protocol: The scanning of the gene chips was performed at the Center for Applied Genomics (TCAG, Research Institute of Hospital for Sick Children, Canada). After hybridization, gene chips were washed and scanned in the Affymetrix station at TCAG and raw data was retrieved in .CEL files.

data_processing: Raw microarray data were analyzed at Network Biology Collaborative Centre (NBCC, Lunenfeld-Tanenbaum Research Institute, Ontario, Canada). The whole analysis was performed with the oligo and limma  R and bioconductor packages. The raw microarray data was normalized using the Oligo R package. Gene expression levels were compared between MCAO and sham animals at 2hrs or 6hrs using the Limma R package.

source_name: Mouse control tissue at 6hrs after sham surgery

label_protocol: The labeling procedure was performed at the Center for Applied Genomics (TCAG, Research Institute of Hospital for Sick Children, Canada). For In Vitro transcription (IVT), >200ng/5µl total RNA with good quality (RIN>7.5; checked by Agilent Bioanalyzer) was used to label with dUTP. The labeling protocol follows the Affymetrix GeneChip WT PLUS Reagent Kit manufacturer's user guide.

growth_protocol: Adult male Sprague-Dawley rats (270-300g; age 8-12 weeks) and adult male C57 Black 6 mice (21.9-29.7g; age 8-10 weeks) were kept at 21 °C, 65% humidity, and a regulated 12-hour light/dark cycle with free access to food and water.

extract_protocol: In all animals 3x3mm tissue samples were obtained from the penumbras of rat and mouse brains at 2 hrs or 6 hrs after pMCAO. Control samples were obtained from similar ipsilateral regions of sham-operated brains of each species. Total RNA was isolated from tissue samples using a commercial kit (RNeasy Mini Kit, QIAGEN) following the manufacturer’s instructions.

treatment_protocol: Animals were randomly assigned to permanent MCAO (pMCAO) or sham group (n=3/group). In the pMCAO  groups, the left MCA of rats was occluded by the intraluminal suture method of Longa et al. (Longa et al. 1989).In brief, rats were anaesthetized with isoflurane (5% for induction and 2% for surgery) mixed with oxygen. Rectal body temperature was maintained at 36.8 ± 0.18°C with a heating pad. MCAO was achieved by introducing a 0.39 ± 0.02mm width silicone coated filament into the ECA and advancing through the ICA to occlude the left MCA origin. The filament was then ligated in-situ. The right MCA of mice was occluded using the intraluminal suture method of Koizumi et al. (Koizumi J 1986) and adapted by Clark(Clark et al. 1997) to the mouse. The mice were anaesthetized with isoflurane (3% for induction and 2% for surgery) mixed with oxygen. Rectal body temperature was maintained at 36.9 ± 0.17°C with a heating pad. MCAO was achieved by inserting a standard 0.21± 0.02mm width filament in the ECA and advancing through the ICA to occlude the right MCA origin. The filament was left ligated in-situ. Sham animals underwent identical procedures without MCAO.

value: sham surgery

tag: time point

value: 2hrs after the indicated surgery

value: control brain tissue


title: BY4743 in YPD medium in 32˚C - replicate 2

value: grown at 32C


title: Mouse 6h Sham replicate 3


title: BY4743 in YPD medium in 32˚C - replicate 1


title: Mouse 6h Sham replicate 1


title: BY4743 in SC medium in 30˚C - replicate 2


title: Mouse 6h MCAO replicate 2

description: Gene expression data in the ischemic penumbra of mouse at 6hrs after pMCAO

source_name: Mouse penumbra tissue at 6hrs after pMCAO surgery

value: permanent middle cerebral artery occlusion (pMCAO) surgery

value: penumbras tissue of brains


title: BY4743 in SC medium in 30˚C - replicate 1


title: Mouse 2h Sham replicate 3

description: Gene expression data in the ipsilateral brain region of mouse at 2hrs after sham surgery

source_name: Mouse control tissue at 2hrs after sham surgery


title: BY4743 in SC medium with 40g/l NaCl in 30˚C - replicate 2

value: addition of NaCl and grown at 30C


title: drdd B Rosette leaf RNA-seq

city: Cambridge

first: Mary

last: Gehring

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
FastQC was used to examine read quality. Low quality reads were removed with trim_galore with parameters --clip_R1 8, --clip_R2 8, --stringency 3, -q 25, -r1 32, -r2 32 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/, version from 16 July 2014).
RNA-seq libraries were mapped with STAR, permitting 0.05 mismatches as a fraction of total read length.
Differentially expressed genes were identified using ht-seq count and DEseq2
Genome_build: Araport11
Supplementary_files_format_and_content: HTseq output files contain a list of all Araport11 loci (column 1) and read counts calculated by htseq-count (column 2).
Supplementary_files_format_and_content: DE-seq 2 output files contain tab-delimited tables of all statistical analysis of differential gene expression calculated using DE-seq 2. The first row of each file specifies the content of each column. Subsequent rows list differential expression statistics for each gene in the genome.

source_name: Rosette leaf

growth_protocol: Plants were grown in a growth chamber (Conviron ATC26) in long-day conditions (16 hours light) at 22C and 50% relative humidity.

extract_protocol:
Qiagen RNeasy plant mini kit
Qiagen QIAseq mRNA select kit

treatment_protocol: WT compared with DNA demethylation mutants

value: pAGL61:DME; dme-2; ros1-3; dml2-1; dml3-1

value: 5th Rosette leaf, day 21


title: rdd C Rosette leaf RNA-seq

value: pAGL61:DME; ros1-3; dml2-1; dml3-1


title: drdd C Rosette leaf RNA-seq


title: rdd D Rosette leaf RNA-seq


title: drdd D Rosette leaf RNA-seq


title: Mouse 2h Sham replicate 2


title: IL-1 plus P. santalinus

description: IL-1 SH RdM_1

value: Human umbilical vein endothelial cells (HUVECs)

value: IL-1 plus P. santalinus


title: Mouse 6h MCAO replicate 1


title: BY4743 in YPD medium in 24˚C - replicate 1

value: grown at 24C


title: BY4743 in SC medium with 40g/l NaCl in 30˚C - replicate 1


title: BY4743 in YPD medium in 24˚C - replicate 2

value: YPD


title: Mouse 2h MCAO replicate 2

description: Gene expression data in the ischemic penumbra of mouse at 2hrs after pMCAO

source_name: Mouse penumbra tissue at 2hrs after pMCAO surgery


title: Mouse 2h MCAO replicate 3


title: Mouse 2h MCAO replicate 1


title: rdd A Rosette leaf RNA-seq


title: Mouse 2h Sham replicate 1


title: Mouse 6h MCAO replicate 3


title: dme D Rosette leaf RNA-seq

value: pAGL61::DME; dme-2


title: dme A Rosette leaf RNA-seq


title: dme B Rosette leaf RNA-seq


title: WT D Rosette leaf RNA-seq

value: pAGL61::DME WT segregant (DRDD)


title: rdd B Rosette leaf RNA-seq


title: WT C Rosette leaf RNA-seq


title: WT A Rosette leaf RNA-seq


title: dme C Rosette leaf RNA-seq


title: FVB_rep1

city: Zurich

first: Ursula

last: Quitterer

address: Winterthurerstrasse 190

department: Molecular Pharmacology

country: Switzerland

institute: ETH Zurich

description: FVB/N heart 1

data_processing:
Trimmed RNA-Seq reads in FASTQ format were generated by GATC Biotech AG. RNA-Seq reads in FASTQ format were imported into the program CLC Genomics workbench 20 version 20.0.4 (QIAGEN Bioinformatics, QIAGEN Aarhus A/S) and aligned to the reference genome (Mouse GRCm39) in frame of the RNA Sequencing Workflow of CLC Genomics workbench 20.
The trimmed RNA-Seq reads in FASTQ format were mapped to the reference genome (Mouse GRCm39) in frame of the RNA Sequencing Workflow of CLC Genomics workbench 20. The following mapping settings were used: Mismatch count: 2; Insertion cost: 3; Deletion cost: 3; Length fraction: 0.8; Similarity fraction: 0.8; Maximum number of hits for a read: 10; Expression value: TPM. Gene and transcript annotations of the reference genome were added to the mapped reads. With these settings, read tracks and reports were generated. The processed data files show transcripts per million (TPM) for every transcript and every sample.
Genome_build: Mouse GRCm39
Supplementary_files_format_and_content: Tab-separated text (txt) files include TPM values for each sample and transcript. The following tab-separated columns are presented in the processed data files: Name; Chromosome; Region; TPM; Gene name; Transcript length; Exons; Gene ID; Transcript ID; ENSEMBL; Biotype.
Supplementary_files_format_and_content: The supplementary file is a matrix table with total transcript reads for every transcript and every sample. The following tab-separated columns are included in the supplementary matrix table (Total_transcript_reads_matrix.txt): Name; Chromosome; Region; Gene name; Transcript length; Exons; Gene ID; Transcript ID; ENSEMBL; Biotype; Total transcript reads of 9 samples.

source_name: Heart

growth_protocol: After weaning at an age of 3-4 weeks, Tg-RKIP mice, Tg-GRK2 mice and non-transgenic FVB/N control mice were housed until the end of the observation period at an age of 8 months in groups of 2-5 mice under SPF conditions with a 12 h dark cycle in individually ventilated cages. All mice had free access to food and water and were fed a standard rodent diet.

extract_protocol:
Hearts were rapidly isolated from euthanized, male, eight-month-old Tg-RKIP, Tg-GRK2 and non-transgenic FVB/N mice, and rapidly frozen in liquid nitrogen. Hearts were pulverized under liquid nitrogen, and total RNA was isolated with the RNeasy midi kit (Qiagen).
RNA libraries were prepared for transcriptome sequencing by GATC Biotech AG, an Eurofins Genomics Company, using standard Illumina protocols in frame of the INVIEW Transcriptome Explore protocol. For library preparation, mRNA was fragmented, and random hexamer-primed cDNA synthesis was performed. Illumina single read (SR) sequencing (1 x 50 bp) with guaranteed 30 million reads per sample was performed by the Genome Sequencer Illumina HiSeq, in the sequence mode HiSeq 4000.

value: FVB/N

value: heart

tag: Sex

value: male

tag: age

value: 8 months

tag: transgene

value: non-transgenic


title: Tg_RKIP_rep3

description: Tg_RKIP heart 3

tag: strain

tag: tissue

value: RKIP


title: Tg_RKIP_rep2

description: Tg_RKIP heart 2


title: Tg_GRK2_rep3

description: Tg_GRK2 heart 3


title: FVB_rep3

description: FVB/N heart 3


title: Tg_GRK2_rep1

description: Tg_GRK2 heart 1


title: Control rep1

city: Montreal

first: Jean-Jacques

last: Lebrun

state: QC

address: 1001 Boulevard Decarie

institute: McGill University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data was analyzed by GenomeStudio at McGill University and Genome Quebec Innovation Center. The data was further normalized by performing background correction followed by quantile normalization using limma package.

source_name: Triple negative breast cancer cell line

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: SCP2 cells were cultured in DMEM (Sigma-Aldrich) containing 10% FBS

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: SCP2 cells were serum-starved for overnight and treated or not with 100 pM TGFβ for 24 hours in serum-free medium

tag: cell line

value: control


title: FVB_rep2

description: FVB/N heart 2


title: WT_4

city: 深圳

first: keqiang

last: yan

state: Not US or Canada

address: 深圳市盐田区北山工业区华大基因二办

institute: BGI

data_processing:
BGISEQ 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 bowtie2 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200
Fragments 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.
Genome_build: mm8
Supplementary_files_format_and_content: Excel, gene expression

source_name: heart

extract_protocol:
RNA extraction, mRNA isolation by polyA enrichment were performed at the Beijing Genomics Institute
cDNA library preparation was performed at the Beijing Genomics Institute

value: Wild Type


title: Tg_GRK2_rep2

description: Tg_GRK2 heart 2


title: WT_3

address: 深圳市盐田区北山工业区华大基因二办


title: TGFβ treated rep1

value: TGFBeta-treated


title: drdd Rosette leaf EM-seq

description: 5th Rosette leaf, day 21

data_processing:
FastQC was used to examine read quality. Low quality reads were removed with trim_galore with parameters --clip_R1 8, --clip_R2 8, --stringency 3, -q 25, -r1 32, -r2 32 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/, version from 16 July 2014).
Libraries were mapped using Bismark 0.20.1 permitting one mismatch (all other parameters default).
PCR duplicate reads were removed using Bismark.
Bismark methylation extractor and custom scripts previously described were used to obtain per base methylation and to identify DMRs.
Genome_build: Araport11
Supplementary_files_format_and_content: Methylation level at single base resolution in CHH, CHG, and CG context for WT and demethylation or methylation mutants

growth_protocol: Plants were grown in a growth chamber (Conviron ATC26) in long-day conditions (16 hours light, 8 hours dark) at 22C and 50% relative humidity.

extract_protocol:
DNA was extracted using a CTAB protocol.
BS-seq: Bisulfite conversion was performed on 200ng of DNA using an Invitrogen MethylCode bisulfite conversion kit. Libraries were prepared with a QIAGEN QiaSeq Methyl Library Kit following manufacturer’s instructions. 6-11 cycles were used for amplification.  EM-seq: 100ng of DNA in TE buffer was sheared to an average 200bp fragment size using a Covaris S220. Following fragmentation, a 2.5x bead cleanup was performed with a final elution in water. Conversion and library preparation was performed using an NEBNext Enzymatic Methyl-Seq Kit (including spike-in controls) according to manufacturer’s instructions with 6 cycles of amplification.

treatment_protocol: WT compared with DNA demethylation or methylation mutants

tag: genotype

value: pAGL61:DME; dme-2; ros1-3; dml2-1; dml3-1

tag: library construction

value: Enzymatic-methyl (EM)-sequencing

value: 5th Rosette leaf, day 21


title: rdr2 Flower buds BS-seq

description: Closed Flower buds, day 35

source_name: Closed flower buds

value: Whole-genome bisulfite sequencing (Qiagen MethylSeq)

value: Closed Flower buds, day 35


title: WT Rosette leaf EM-seq

description: 5th Rosette leaf, day 21


title: rdr2 Embryos BS-seq

description: Embryos, day 50

source_name: Embryos

value: Embryos, day 50


title: WT Col-0 5E Embryos BS-seq

description: Embryos, day 50

value: WT Col-0


title: rdr2 Cauline leaf BS-seq

description: 2nd Cauline leaf, day 35

source_name: Cauline leaf

value: 2nd Cauline leaf, day 35


title: rdr2 Rosette leaf BS-seq

description: 5th Rosette leaf, day 21


title: Control rep2

tag: treatment


title: TGFβ treated rep2


title: WT_2

address: 深圳市盐田区北山工业区华大基因二办


title: WT Col-0 3F Embryos BS-seq

description: Embryos, day 50


title: TG_4

address: 深圳市盐田区北山工业区华大基因二办

value: Carns transgenic


title: TG_3

address: 深圳市盐田区北山工业区华大基因二办

value: heart


title: WT_1

address: 深圳市盐田区北山工业区华大基因二办


title: TG_2

address: 深圳市盐田区北山工业区华大基因二办


title: 3 dpa (pilot)

city: Seattle

first: Weishene

middle: Joyce

last: Tang

address: 850 Republican Street

department: Orthopedics & Sports Medicine/Institute for Stem Cell and Regenerative Medicine

institute: University of Washington

description: pilot experiment from 25 fins at 3 dpa

data_processing:
Base calls were converted to fastq format using Illumina's bcl2fastq v2.20, tolerating one mismatched base in barcodes. The reads were further demultiplexed using a custom demultiplexing script.:
https://github.com/bbi-lab/bbi-dmux
Demultiplexed reads were then adaptor clipped using trim_galore with default settings (cutadapt/1.18:trim_galore/0.6.5).
Reads were originally paired-end. R1 contained cell barcodes and sample information, while the R2 reads contain the transcriptome sequence. In the demultiplexing process, the cell barcode and cell id was appended to the read name. Only R2 with modified read name was submitted.
Trimmed reads were mapped to the 3'UTR extended reference STAR index generated above with default settings (STAR v.2.5.2b).
Uniquely mapping reads were extracted, and duplicates were removed using the UMI sequence, reverse transcription (RT) index, and read 2 end-coordinate, tolerating 1bp mismatches in UMIs (samtools v1.9).
To generate expression matrices, the number of UMIs for each cell mapping to the exonic and intronic regions of each gene are calculated. This step outputs a sparse counts matrix in matrix market format.
Genome_build: GRCz11.96
Supplementary_files_format_and_content: tab-delimited text files containing cell barcodes, gene annotations, and a gene count sparse matrix for each Sample

organism: Danio rerio

source_name: adult caudal fin

extract_protocol:
Fin tissues were collected and immediately frozen at -80C. Nuclei were extracted, fixed in 4% paraformaldehyde, and prepared for sci-RNA-seq3 (please see details at http://atlas.gs.washington.edu/mouse-rna).
The library preparation scheme for sci-RNA-seq3 on paraformaldehyde-fixed nuclei was followed, with the following modifications: 2 uL of oligo-dT primers were added to each well with 80,000 nuclei for reverse transcription, the Quick Ligation kit (New England Biolabs) was used in place of T4 ligase, and tagmentation was performed using 1/40th uL per well of i7-loaded TDE1 enzyme (prepared at the University of Washington following published protocols).

value: AB

value: caudal fin

tag: timepoint

value: 3 days post amputation

tag: molecule subtype

value: nuclear RNA


title: 5 dpa

description: tissue from 100 fins at 5 dpa

value: 5 days post amputation


title: 3 dpa

description: tissue from 100 fins at 3 dpa


title: GPE_3

city: Taipei

first: MingYing

last: Lan

address: No.201, Sec. 2, Shipai Rd., Beitou District

department: Department of Otolaryngology-Head and Neck Surgery

country: Taiwan

institute: Taipei Veterans General Hospital, Taipei, Taiwan

description: gene expression after 72 hours 2.15 ug/ml GO-PEG_erlotinib treatment in NPC cell line

data_processing:
Basecalls performed using the software Zebra call
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence usingSOAPnuke v1.5.2 with parameters -l 15 -q 0.5 -n 0.1
Genome mapping used HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) v2.0.4 with parameters -p 8 --phred64 --sensitive -I 1 -X 1000
Map clean reads to reference transcripts using Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200, then calculate gene expression level for each sample with RSEM
Remove batch effect using limma (R package; v3.36.5)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: cell line derived from biopsy specimens of nasopharyngeal carcinoma patient

growth_protocol: The NPC cell line was maintained in DMEM with 10% FBS at 37°C under 5% CO2.

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: NPC cells treated with or without 2.15 ug/ml GO-PEG_erltinib (GPE) for 72 hours at 37°C

tag: cell type

value: nasopharyngeal carcinoma (NPC)

tag: passage

value: passage at p3-p10


title: Tg_RKIP_rep1

description: Tg_RKIP heart 1

value: FVB/N

value: male

value: 8 months

value: RKIP


title: WT Col-0 5E Flower buds BS-seq

description: Closed Flower buds, day 35

value: Whole-genome bisulfite sequencing (Qiagen MethylSeq)

value: Closed Flower buds, day 35


title: TG_1

address: 深圳市盐田区北山工业区华大基因二办


title: WT Col-0 5E Cauline leaf BS-seq

description: 2nd Cauline leaf, day 35

value: WT Col-0


title: GPE_4


title: HCT15-ARID3B-Cas9

first: Tsai-Tsen

last: Liao

state: State...

address: No.201, Sec.2, Shih-Pai Rd. Peitou, Taipei, Taiwan, 11221, R.O.C

institute: Institute of Clinical Medicine

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

scan_protocol: Arrays were scanned with the Affymetrix GeneChip® Scanner 3000 7G and the data was extracted using Microarray Analysis Suite 5.0 (Affymetrix).

data_processing: RMA

label: Biotin

source_name: HCT15 cells receving ARID3B-Cas9

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

growth_protocol: cultivated in RPMI + 10% fetal bovine serum

extract_protocol: Cells were lysed by adding 2 ml of trizol reagent (Invitrogen) and homogenized by passing through a syringe with a needle (26G). RNA was picked up in the aqueous phase following phase separation by chloroform. The RNA was then precipitate with isopropanol, washed with ethanol (75%), dissolved in DEPC-treated RNAse/DNAse free water and quantified by spectrophotometry.

treatment_protocol: HCT15 cells were receving ARID3B-Cas9 or control.

value: ARID3B knockout


title: WT Col-0 3F Flower buds BS-seq

description: Closed Flower buds, day 35


title: HCT15-Ctrl

source_name: HCT15 cells receving Ctrl

value: control


title: WT Col-0 5E Rosette leaf BS-seq

description: 5th Rosette leaf, day 21

value: 5th Rosette leaf, day 21


title: SH-SY5Y_Ft_2

city: Newark

first: Aysegul

last: Guvenek

state: New Jersey

address: 205 South Orange Ave.

institute: Rutgers University

data_processing:
Adpter trimming performed using Cutadapt
3'READs reads were aligned to hg19  using bowtie2
Reads with a mapping quality score (MAPQ) ≥10 were kept for further analysis. Reads with ≥2 non-genomic 5’Ts after alignment were called polyA site supporting (PASS) reads. pAs within 24 nt of each other were clustered. pAs with less than 5 PASS reads in all the samples were first trimmed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each pAs

source_name: human neuroblast

extract_protocol: 3'READS: The 3’READS procedure has been described in (Hoque et al, 2013; Zheng et al., 2016). Briefly, Poly(A)+ RNA in 0.1-15 µg of total RNA was captured using 10 µl of oligo(dT)25 magnetic beads in 100 µl 1x binding buffer (10 mM Tris-Cl, pH7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III in 30 µl RNase III buffer (10 mM Tris-Cl pH8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) at 37 °C for 15 min. After washing away unbound RNA fragments with binding buffer, poly(A)+ fragments were eluted from the beads with TE buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated with ethanol, followed by ligation to 3 pmol of heat-denatured 5’ adapter (5’-CCUUGGCACCCGAGAAUUCCANNNN) in the presence of 1 mM ATP, 0.1 µl of SuperaseIn, and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 h. The ligation products were captured by 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1. After washing with washing buffer (10 mM Tris-Cl pH7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H at 37 °C for 30 min in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H buffer, RNA fragments were eluted from the beads in elution buffer (1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) at 50 °C, precipitated with ethanol, and then ligated to 3 pmol of heat-denatured 5’ adenylated 3’ adapter (5’-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC) with 0.25 µl T4 RNA ligase 2 (truncated KQ version) at 22 °C for 1 h in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. The ligation products were then precipitated and reverse transcribed using M-MLV reverse transcriptase, followed by PCR amplification using Phusion high-fidelity DNA polymerase and bar-coded PCR primers for 13-18 cycles (13 cycles for 5 µg input, 15 cycles for 1 µg input, and 18 cycles for inputs below 1 µg).   PCR products were size-selected twice with AMPure XP beads, using 0.6 volumes of beads (relative to the PCR reaction volume) to remove large DNA molecules and an additional 0.4 volumes of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The size and quantity of the libraries eluted from the AMPure beads were examined using a high sensitivity DNA kit on an Agilent Bioanalyzer.

value: Flow-through


title: WT Col-0 3F Cauline leaf BS-seq

description: 2nd Cauline leaf, day 35

value: 2nd Cauline leaf, day 35


title: Control_4

description: gene expression after 72 hours  no treatment in NPC cell line


title: GPE_2


title: SH-SY5Y_Ft_1


title: Control_3


title: SH-SY5Y_4sU_2


title: Control_2

description: gene expression after 72 hours no treatment in NPC cell line


title: KO

first: Zhenyu

last: Zuo

address: 5 Dongdan Santiao

department: Biochemistry and Molecular Biology

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description:
single cell RNA
AllNormalizedCounts.txt

data_processing:
RNA: Reads filtering under criteria removing reads with 20% of the base quality lower than 13
RNA: HISAT2.1.0 mapping to reference genome
RNA: count counting
scRNA: Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
scRNA: 1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria: MT% < 20%;  Cell Gene Number < Median Gene Number * 2;  Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. Graphcluster and K-mean was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: mouse embryonic stem cells

growth_protocol: The medium of ES cells was prepared from Knockout DMEM (Gibco), with 15% fetal bovine serum (FBS, Gibco), 0.1 mM β-mercaptoethanol (Millipore), 2 mM GlutaMax (Gibco), 0.1 mM MEM nonessential amino acids (Gibco) and 1000 U/ml LIF (Millipore).

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: E14 cells

value: Prmt1 knockout


title: KO2-2

description: all.counts.exp.txt


title: WT

description:
single cell RNA
AllNormalizedCounts.txt

value: wild type


title: KO2-1

description: all.counts.exp.txt


title: KO2-3

description: all.counts.exp.txt


title: SH-SY5Y_4sU_1


title: WT Col-0 3F Rosette leaf BS-seq

description: 5th Rosette leaf, day 21


title: drdd C Rosette leaf BS-seq

description: 5th Rosette leaf, day 21

value: pAGL61:DME; dme-2; ros1-3; dml2-1; dml3-1


title: drdd D Rosette leaf BS-seq

description: 5th Rosette leaf, day 21


title: SH-SY5Y_T

value: Untreated/total


title: HepG2_T

source_name: human hepatoma


title: KO1-2

description: all.counts.exp.txt


title: KO1-3

description: all.counts.exp.txt


title: WT-2

description: all.counts.exp.txt

value: wide type


title: KO1-1

description: all.counts.exp.txt


title: HepG2_Ft_2


title: WT-3

description: all.counts.exp.txt


title: WT-1

description: all.counts.exp.txt


title: drdd A Rosette leaf BS-seq

description: 5th Rosette leaf, day 21


title: drdd B Rosette leaf BS-seq

description: 5th Rosette leaf, day 21


title: rdd D Rosette leaf BS-seq

description: 5th Rosette leaf, day 21

value: pAGL61:DME; ros1-3; dml2-1; dml3-1


title: rdd C Rosette leaf BS-seq

description: 5th Rosette leaf, day 21


title: HepG2_Ft_1


title: Early Grastic Cancer 09 Non-tumor

first: Wu

last: Zhenhua

address: Fenglin Road

institute: Department of Medical Oncology

data_processing:
Alignment using HISAT
Generate count files using FeatureCount
Genome_build: hg38
Supplementary_files_format_and_content: Fragments Per Kilobase of exon model per Million mapped fragments in Excel format

source_name: adjacent non-tumor tissues

extract_protocol:
Total RNA of these samples was extracted using TRIzol total RNA extraction protocol
RNA-seq libraries constructed using TruSeq RNA Sample Prep Kit (Illumina)

value: adjacent non-tumor tissues


title: Early Grastic Cancer 09

source_name: gastric cancer tissues

value: gastric cancer tissues


title: Early Grastic Cancer 11


title: Early Grastic Cancer 11 Non-tumor


title: rdd B Rosette leaf BS-seq

description: 5th Rosette leaf, day 21

source_name: Rosette leaf

value: Whole-genome bisulfite sequencing (Qiagen MethylSeq)


title: Early Grastic Cancer 05 Non-tumor


title: Early Grastic Cancer 07


title: rdd A Rosette leaf BS-seq

description: 5th Rosette leaf, day 21


title: Early Grastic Cancer 07 Non-tumor


title: dme D Rosette leaf BS-seq

description: 5th Rosette leaf, day 21

value: pAGL61::DME; dme-2


title: Early Grastic Cancer 03 Non-tumor


title: HEK293T_T

source_name: human kidney


title: HepG2_4sU_1


title: HepG2_4sU_2


title: Early Grastic Cancer 03


title: HEK293T_Ft_2


title: dme C Rosette leaf BS-seq

description: 5th Rosette leaf, day 21


title: HEK293T_Ft_1


title: HEK293T_4sU_2


title: Early Grastic Cancer 01


title: Early Grastic Cancer 01 Non-tumor


title: dme B Rosette leaf BS-seq

description: 5th Rosette leaf, day 21


title: siSIRT7 with radiation treament

city: Guangzhou

first: Bingyao

last: Meng

address: No. 1023-1063, Shatai South Road, Baiyun District, Guangzhou,

institute: southern medical universitity

data_processing:
After obtaining the raw sequencing data (Raw Data), you first need to filter the data, remove the adapter sequence, and process low-quality reads, and then evaluate the sequencing quality to obtain high-quality data (Clean Data). And compare the Clean Data with the reference genome to get the BAM file.
Use the HISAT2 software to compare the sequencing data with the reference genome, and make a comprehensive evaluation of the coverage area and coverage depth of the sequencing data. HISAT2 is the successor of TopHat2/Bowtie2. It uses an improved BWT algorithm (FM index). HISAT uses a large number of FM indexes to cover the entire genome, and combines several comparison strategies to achieve an efficient and faster comparison of RNA-seq data.
In RNA sequencing, RPKM (expected number of Reads Per Kilobase of transcript sequence per Millions basepairs sequenced) is the number of reads from a gene per kilobase length per million reads, which also considers the sequence depth and gene length pair The influence of read count is currently the most commonly used method for estimating gene expression levels. Map the bam file obtained by sequencing to the gtf file of the reference species to obtain the gene expression level, and perform regional statistics on the gene expression level of the genome according to the statistical method to reflect the overall expression level of the sample.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: A375 cells

extract_protocol:
Total RNAs from cells were extracted using TRIzol reagent (Life Technologies) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treament

value: radiation

tag: transfection


title: siSIRT7 with non-radiation treament

value: non-radiation


title: siNC with radiation treament

value: siNC


title: dme A Rosette leaf BS-seq

description: 5th Rosette leaf, day 21

value: 5th Rosette leaf, day 21


title: C1 spheroids STINGsh DAMPs (J8)

city: Columbia

first: Ramji

last: Bhandari

state: MO

address: 1200 University Ave

department: Division of Biological Sciences

institute: University of Missouri

data_processing:
The sequencing reads were checked for quality using FastQC and were found to be of good quality. The reads were mapped to human genome hg38 using STAR aligner (STAR_2.5.2b) with gencode gtf annotation (gencode.v25.GRCh38.gtf) provided as guide.
All the Samples were analyzed and normalized together using DESeq2 (v1.20.0). Normalized counts were obtained by dividing the actual counts with the size factor using the function estimateSizeFactors() of DESeq2. Differential analysis was done by dividing the normalized counts of respective samples. Since there were no replicates, it was not possible to calculate the p-values.
Supplementary_files_format_and_content: esarcoma_normExpr_log2_JSDA.tsv: Normalized log2 expression values for all samples

source_name: Spherogenic culture from Ewing sarcoma, C1  A673, STINGsh treated with DAMPs - 24hrs

growth_protocol: Spheroids were cultured in IMDM (Gibco, USA), supplemented with 20% KO serum (Gibco, USA), 10 ng/mL human recombinant EGF and bFGF (Invitrogen, USA), and 1% Pen/Strep (Gibco, USA) in ultra-low attachment flasks (Corning, USA).    Adherents were cultured in IMDM/RPMI (Gibco, USA), supplemented with 10% FBS (Gibco, USA) and 1% Pen/Strep (Gibco, USA) in normal adherent plates (Corning, USA).

extract_protocol:
Total RNA was extracted using the RNeasy mini Kit (Qiagen), following the standard manufacturer protocol using the Illumina Tru-seq library preparation kit following the manufacturer instructions.
Illumina TruSeq protocol

treatment_protocol: EwS spheroids and adherent were treated with DAMPs or solvent (water), and RNA and were harvested at 4 hours post DAMPs treatment. (Sample 1 – 4)    EwS spheroids and adherent were treated with cGAMP or solvent (water), and RNA and were harvested at 4 hours post cGAMP treatment. (Sample 5 – 18)    EwS spheroids were infected with CONTROL shRNA or STING shRNA lentiviral vectors, and RNA was harvested 72 hours after post-infection. (Sample 19 – 22)    EwS spheroids were infected with CONTROL shRNA or STING shRNA lentiviral vectors, DAMPs, or water was added, and RNA was harvested at 4 and 24 hours post DAMPs treatment. (Sample 23 – 30)

tag: damps treatment

value: DAMPs treatment

tag: cgamp treatment

tag: shRNA

value: STING shRNA


title: Early Grastic Cancer 05


title: C1 spheroids  CONTROLsh DAMPs (J7)

source_name: Spherogenic culture from Ewing sarcoma, C1 A673, CONTROLsh treated with DAMPs - 24hrs

value: Control shRNA


title: siNC with non-radiation treament


title: WT D Rosette leaf BS-seq

description: 5th Rosette leaf, day 21

value: pAGL61::DME WT segregant (DRDD)


title: WT C Rosette leaf BS-seq

description: 5th Rosette leaf, day 21


title: WT B Rosette leaf BS-seq

description: 5th Rosette leaf, day 21


title: C1 spheroids STINGsh  (J6)

source_name: Spherogenic culture from Ewing sarcoma, C1 A673, STINGsh treated with water - 24hrs


title: WT A Rosette leaf BS-seq

description: 5th Rosette leaf, day 21


title: HEK293T_4sU_1


title: C1 spheroids STINGsh DAMPs (J4)

source_name: Spherogenic culture from Ewing sarcoma, C1  A673, STINGsh treated with DAMPs - 4hrs


title: Neuron_div35

source_name: human differentiated neurons

value: Neuron

value: Untreated


title: P28_dr_3_b

city: Berkeley

first: Salwan

last: Butrus

state: California

address: Stanley Hall Rm

department: Chemical and Biomolecular Engineering

institute: UC Berkeley

description: 15 mice bio rep 2, lib rep 2

data_processing:
Sample demultiplexing using Cell Ranger v3.1.0 10X Genomics
Sample alignment to the mouse reference transcriptome (Ensembl 92, GRCm38.92), which was converted to a pre-mRNA reference package by following Cell Ranger guidelines.
Genome_build: GRCm38.92
Supplementary_files_format_and_content: CSV files containing counts gene expression matrix and metadata from all 35 samples

source_name: Visual cortex

growth_protocol: Mouse breeding and husbandry procedures were carried out in accordance with UCLA's animal care and use committee protocol number 2009-031-31A, at University of California, Los Angeles. Mice were given food and water ad libitum, and lived in a 12-hr day/night cycle with up to four adult animals per cage. Only virgin male C57BL/6J wild-type mice were used in this study.

extract_protocol:
Extracted brains were placed on a metal mold and the slice containing V1 was isolated by inserting blade 0.5 mm posterior to lambda suture. A second blade was inserted 1.5 mm anterior (2 spaces on the mold). This slice was removed and lowered to Hibernate A in a 60cc petri dish which was placed on top of a ruler under a dissecting scope. Midline was lined up with a ruler and the first cut was bilaterally 3.2 mm out from the midline. The second cut was 1 mm medial to the first cut. The cortex was peeled off the underlying white matter. The V1 piece with a total of 1 mm cortex depth by 1.5 mm thickness was transferred to a dish containing 600 ul of RNAlater (Thermo Fisher Cat# AM7020) and kept on ice until dissections were complete. Dissected tissues were  then kept in RNAlater at 4C overnight, and transferred to -20C the next day, where they were kept up to 1 month prior to being processed for snRNA-seq.
Droplet RNA sequencing experiments using the 10X chromium platform were performed according to the manufacturer's instructions with no modifications. The cDNA libraries were sequenced on the Illumina NovaSeq™ 6000 Sequencing System (S2) to a depth of ~30,000 reads per cell.

treatment_protocol: Mice were anesthetized in an isoflurane chamber, decapitated, and the brain was immediately removed and submerged in Hibernate A

value: Visual cortex


title: P38_dr_2_b

description: 15 mice bio rep 2, lib rep 2


title: P28_dl_1_b

description: 15 mice bio rep 1, lib rep 2


title: P38_dr_1_b

description: 15 mice bio rep 1, lib rep 2


title: P28_dl_2_a

description: 15 mice bio rep 2, lib rep 1


title: P28_dr_3_a

description: 15 mice bio rep 2, lib rep 1


title: P38_dr_2_a

description: 15 mice bio rep 2, lib rep 1


title: P28_dl_1_a

description: 15 mice bio rep 1, lib rep 1


title: P28_dl_2_b

description: 15 mice bio rep 2, lib rep 2


title: P28_dr_1_b

description: 15 mice bio rep 1, lib rep 2


title: C1 spheroids  CONTROLsh DAMPs (J3)

source_name: Spherogenic culture from Ewing sarcoma, C1  A673, CONTROLsh treated with DAMPs - 4hrs


title: C1 spheroids  CONTROLsh  (J5)

source_name: Spherogenic culture from Ewing sarcoma, C1  A673, CONTROLsh treated with water (control) - 24hrs


title: P28_dr_1_a

description: 15 mice bio rep 1, lib rep 1


title: C1 spheroids STINGsh  (J2)

source_name: Spherogenic culture from Ewing sarcoma, C1 A673, STINGsh treated with water - 4hrs


title: hNSC

source_name: human neural stem cell

value: hNSC


title: CCI-016_Sx

city: Edmonton

first: Judith

last: Hugh

state: Alberta

address: 87 ave and 114 st

department: Laboratory Medicine and Pathology

institute: University of Alberta

description: featureCounts.txt

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing
Paired-end reads were trimmed by 5 bp at the 3' end using fastx_trimmer v 0.0.13
Trimmed reads were aligned to hg38 using RNA STAR v2.6.0b-1 on the usegalaxy.org platform.
Mapped reads were counted using featureCounts v1.6.3
Differential gene analysis was done using DeSeq2 v1.18.1
Genome_build: hg38
Supplementary_files_format_and_content: normalized read counts
Supplementary_files_format_and_content: counted reads

source_name: tissue from breast surgical biopsy

extract_protocol:
Total RNA was extracted from formalin-fixed paraffin embedded breast tissues using the Roche High Pure RNA Tissue kit.
Libraries were prepared on 100 ng RNA using the NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: Surgical specimens were obtained from patients after 8-14 days of 6 mg daily estradiol.

tag: patient id

value: breast cancer

tag: nodal status (0=negative, 1= positive)

tag: core or surgical specimen

value: surgical


title: P38_dr_1_a

description: 15 mice bio rep 1, lib rep 1

tag: strain

tag: tissue


title: P38_nr_2_b

description: 15 mice bio rep 2, lib rep 1


title: P38_nr_2_a

description: 15 mice bio rep 1, lib rep 2


title: C1 spheroids CONTROLsh  (J1)

source_name: Spherogenic culture from Ewing sarcoma, C1 A673,  CONTROLsh treated with water (control) - 4hrs


title: P28_nr_2_b

description: 15 mice bio rep 2, lib rep 2


title: CCI-005_Sx

description: featureCounts.txt


title: CCI-011_Sx

description: featureCounts.txt


title: P38_nr_1_a

description: 15 mice bio rep 1, lib rep 1


title: CCI-018_Sx


title: P28_nr_2_a

description: 15 mice bio rep 2, lib rep 1


title: P28_nr_1_b

description: 15 mice bio rep 1, lib rep 2


title: P1 spheroids  STINGsh  (S12)

source_name: Spherogenic culture from Ewing sarcoma, P1, STINGsh


title: P28_nr_1_a

description: 15 mice bio rep 1, lib rep 1


title: P1 spheroids   CONTROLsh (S11)

source_name: Spherogenic culture from Ewing sarcoma P1, CONTROLsh


title: C1 adherent CONTROLsh (S13)

source_name: Adherent culture from Ewing sarcoma C1 A673, CONTROLsh


title: P21_nr_2_b

description: 15 mice bio rep 2, lib rep 2


title: P1 spheroids + cGAMP - in vivo (A2)

source_name: Spherogenic culture from Ewing sarcoma, P1- in vivo, treated with cGAMP

value: cGAMP treatment


title: CCI-021_Bx

source_name: tissue from breast needle-core biopsy

value: core


title: P21_nr_1_a

description: 15 mice bio rep 1, lib rep 1


title: CCI-021_Sx


title: P17_nr_2_b

description: 15 mice bio rep 2, lib rep 2


title: P21_nr_2_a

description: 15 mice bio rep 2, lib rep 1


title: CCI-018_Bx


title: P1 spheroids control - in vivo (A1)

source_name: Spherogenic culture from Ewing sarcoma P1 - in vivo, treated with water (control)


title: P21_nr_1_b

description: 15 mice bio rep 1, lib rep 2


title: P17_nr_1_b

description: 15 mice bio rep 1, lib rep 2


title: CCI-022_Sx


title: P17_nr_1_a

description: 15 mice bio rep 1, lib rep 1


title: C1 adherent STINGsh (S14)

source_name: Adherent culture from Ewing sarcoma C1 A673, STINGsh


title: C1 adherent + cGAMP- in vivo  (D6)

source_name: Adherent culture from Ewing sarcoma C1, A673 cell line - in vivo, treated with cGAMP


title: CCI-022_Bx


title: P14_nr_2_a

description: 15 mice bio rep 2, lib rep 1


title: CCI-014_Sx


title: P14_nr_1_b

description: 15 mice bio rep 1, lib rep 2


title: C1 adherent control - in vivo  (D5)

source_name: Adherent culture from Ewing sarcoma C1, A673 cell line - in vivo, treated with water (control)


title: P17_nr_2_a

description: 15 mice bio rep 2, lib rep 1


title: P14_nr_1_a

description: 15 mice bio rep 1, lib rep 1


title: C1 adherent + cGAMP  (S10)

source_name: Adherent culture from Ewing sarcoma C1, A673 cell line, treated with cGAMP


title: P8_nr_2_b

description: 15 mice bio rep 2, lib rep 2

source_name: Visual cortex


title: P8_nr_2_a

description: 15 mice bio rep 2, lib rep 1


title: C1 adherent control  (S9)

source_name: Adherent culture from Ewing sarcoma C1, A673 cell line, treated with water (control)


title: P8_nr_1_b

description: 15 mice bio rep 1, lib rep 2


title: CCI-014_Bx


title: P8_nr_1_a

description: 15 mice bio rep 1, lib rep 1


title: CCI-023_Sx


title: CCI-012_Sx


title: CCI-012_Bx


title: P14_nr_2_b

description: 15 mice bio rep 2, lib rep 2


title: CCI-023_Bx


title: P2 adherent control  (S7)

source_name: Adherent culture from Ewing sarcoma P2, treated with water (control)


title: P2 spheroids control  (S5)

source_name: Spherogenic culture from Ewing sarcoma P2, treated with water (control)


title: P2 spheroids + cGAMP  (S6)

source_name: Spherogenic culture from Ewing sarcoma P2, treated with cGAMP


title: D7-IRI-mice4-right kidney tissue

first: Xu-Tao

last: Chen

state: Guangdong

address: 58# Zhongshan Road 2

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

source_name: kidney tissue

growth_protocol: All mice were individually housed in a biosafety level 2 room until Week 9.

extract_protocol:
Total RNAs were extracted from samples using the RNeasyMini Kit (Qiagen, Hilden, Germany). RNA quality was assessed by using NanoDrop (Thermo Fisher Scientific, Waltham, MA) and Qubit Fluorometer (Invitrogen).
High-quality RNA samples (28 S/18 S = 2.0−2.2, RIN > 9.0) were used to construct sequencing libraries following a standardized procedure on the Illumina HiSeq 2000 Sequencing System.

treatment_protocol: In IRI group, IRI was established by clamping the left renal pedicle for 30 minutes. In IS group, tacrolimus (2.5 mg/kg) and mycophenolic acid (50 mg/kg) were administered by gastric gavage once daily.

tag: Sex

value: male

value: All renal cells

value: renal ischemia-reperfusion injury

tag: infection

value: non-infection

tag: time

value: 7 days

value: right kidney


title: D7-IRI-mice4-left kidney tissue

data_processing:
RNA quality was assessed by using NanoDrop (Thermo Fisher Scientific, Waltham, MA) and Qubit Fluorometer (Invitrogen).
High-quality RNA samples (28 S/18 S = 2.0−2.2, RIN > 9.0) were used to construct sequencing libraries following a standardized procedure on the Illumina HiSeq 2000 Sequencing System.

tag: treatment

value: mouse polyomavirus (MPyV)

value: left kidney


title: D7-IRI-mice1-right kidney tissue


title: D7-IRI-mice3-right kidney tissue


title: WT B Rosette leaf RNA-seq

source_name: Rosette leaf

tag: genotype

value: pAGL61::DME WT segregant (DRDD)

value: 5th Rosette leaf, day 21


title: D7-IRI-mice2-right kidney tissue

tag: cell type


title: P1 adherent + cGAMP  (S4)

source_name: Adherent culture from Ewing sarcoma P1, treated with cGAMP


title: D7-IRI-mice3-left kidney tissue


title: CCI-020_Bx


title: D7-IRI-mice2-left kidney tissue


title: Rat 6h Sham replicate 2

description: Gene expression data in the ipsilateral brain region of rat at 6hrs after sham surgery

data_processing: Raw microarray data were analyzed at Network Biology Collaborative Centre (NBCC, Lunenfeld-Tanenbaum Research Institute, Ontario, Canada). The whole analysis was performed with the oligo and limma  R and bioconductor packages. The raw microarray data was normalized using the Oligo R package. Gene expression levels were compared between MCAO and sham animals at 2hrs or 6hrs using the Limma R package.

organism: Rattus norvegicus

source_name: Rat control tissue at 6hrs after sham surgery

extract_protocol: In all animals 3x3mm tissue samples were obtained from the penumbras of rat and mouse brains at 2 hrs or 6 hrs after pMCAO. Control samples were obtained from similar ipsilateral regions of sham-operated brains of each species. Total RNA was isolated from tissue samples using a commercial kit (RNeasy Mini Kit, QIAGEN) following the manufacturer’s instructions.

value: Sprague-Dawley

value: sham surgery

tag: time point

value: 2hrs after the indicated surgery

value: control brain tissue


title: P1 adherent control  (S3)

source_name: Adherent culture from Ewing sarcoma P1, treated with water (control)


title: D7-IRI-mice1-left kidney tissue


title: CCI-017_Sx

source_name: tissue from breast surgical biopsy

value: breast cancer

value: surgical


title: P2 adherent + cGAMP  (S8)

source_name: Adherent culture from Ewing sarcoma P2, treated with cGAMP

value: cGAMP treatment


title: Rat 6h Sham replicate 1


title: P1 spheroids + cGAMP  (S2)

source_name: Spherogenic culture from Ewing sarcoma P1, treated with cGAMP


title: CCI-017_Bx

source_name: tissue from breast needle-core biopsy

value: core


title: Rat 6h Sham replicate 3


title: P1 spheroids control  (S1)

source_name: Spherogenic culture from Ewing sarcoma P1, treated with water (control)


title: CCI-002_Sx


title: Rat 6h MCAO replicate 3

description: Gene expression data in the ischemic penumbra of rat at 6hrs after pMCAO

source_name: Rat penumbra tissue at 6hrs after pMCAO surgery

value: permanent middle cerebral artery occlusion (pMCAO) surgery

value: penumbras tissue of brains


title: D3-IRI-mice4-right kidney tissue

value: male

value: All renal cells

value: renal ischemia-reperfusion injury

value: non-infection

value: 3 days


title: P1 adherent + DAMPs  (D4)

source_name: Adherent culture from Ewing sarcoma P1, treated with DAMPs

value: DAMPs treatment


title: Rat 6h MCAO replicate 2


title: CCI-002_Bx


title: D3-IRI-mice3-right kidney tissue

value: right kidney


title: D3-IRI-mice2-right kidney tissue


title: P1 adherent control (D3)


title: CCI-020_Sx


title: CCI-010_Sx


title: D3-IRI-mice1-right kidney tissue


title: P1 spheroids + DAMPs (D2)

source_name: Spherogenic culture from Ewing sarcoma P1, treated with DAMPs


title: CCI-010_Bx


title: D3-IRI-mice4-left kidney tissue

value: mouse polyomavirus (MPyV)

value: left kidney


title: Rat 2h Sham replicate 3

description: Gene expression data in the ipsilateral brain region of rat at 2hrs after sham surgery

source_name: Rat control tissue at 2hrs after sham surgery

value: Sprague-Dawley

value: sham surgery

value: 2hrs after the indicated surgery


title: P1 spheroids control  (D1)


title: CCI-004_Sx

description: featureCounts.txt

value: breast cancer

value: surgical


title: D3-IRI-mice3-left kidney tissue


title: Rat 2h Sham replicate 1

value: control brain tissue


title: CCI-019_Sx

description: featureCounts.txt


title: D3-IRI-mice2-left kidney tissue


title: Rat 2h MCAO replicate 3

description: Gene expression data in the ischemic penumbra of rat at 2hrs after pMCAO

source_name: Rat penumbra tissue at 2hrs after pMCAO surgery

value: permanent middle cerebral artery occlusion (pMCAO) surgery


title: CCI-015_Sx

description: featureCounts.txt


title: Rat 2h MCAO replicate 2

value: penumbras tissue of brains


title: D3-IRI-mice1-left kidney tissue

value: male


title: D3-IS-mice3-left kidney tissue

value: All renal cells

value: immunosuppressants


title: Rat 2h MCAO replicate 1


title: ΔfadBA ΔFadZ + pBAD-FadZ - Rep2

city: Shanghai

first: Chuan

last: Wang

address: 131 # Dong An Road

institute: Fudan University

data_processing:
RNA-seq was performed by BGI Group, Shenzhen, Guangdong, China. Briefly, a strand-specific cDNA library was constructed for each sample to keep the direction of RNA transcription. The obtained cDNA libraries were sequenced on an Illumina HiSeq 4000 machine.
SOAP (v2.21, -m 0 -x 1000 -s 28 -l 32 -v 5 -r 1 -p 3).The rest reads with adaptor， or with unknown bases more than 5%  ,or with more than 20% low-quality bases were cleared by a software developed by BGI group. After, clear reads were mapped to reference genome (Salmonella enterica subsp. enterica serovar Typhimurium SL1344 (https://www.ncbi.nlm.nih.gov/nuccore/NC_016810.1?report=fasta)(https://www.ncbi.nlm.nih.gov/nuccore/NC_016810.1?report=genbank) with Bowtie2： v2.2.5 -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --), and expression value was caculated with RSEM (http://deweylab.biostat.wisc.edu/RSEM）
Genome_build: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2, complete genome(https://www.ncbi.nlm.nih.gov/nuccore/NC_003197.2) and plasmid (https://www.ncbi.nlm.nih.gov/nuccore/NC_003277.2)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: ΔfadBA ΔFadZ + pBAD-FadZ

growth_protocol: Overnight cultures were grown from a single colony, diluted 1:100 in fresh LB medium, and grown to the OD600 ~ 1.0 at 37°C  with shaking at 220 rpm

extract_protocol:
Bacterial cultures were mixed with 0.2 (v/v) of stop solution (95% ethanol and 5% phenol) and immediately frozen within liquid nitrogen. Total RNA was isolated using the hot phenol method. Briefly, 2.0 OD600 cell pellet was resuspended with 300 μL lysozyme (#L3790, Sigma-Aldrich) at 0.5 mg/mL, 30 μL 10% SDS and 33 μL 3M sodium acetate (pH5.2). Cleared lysate was mixed with 375 μL saturated phenol (pH4.5) and incubated at 64°C for 6 min with shaking. The aqueous phase was collected after centrifuge and mixed with 375 μL chloroform in Phase Lock Gel tube (#WM5-2302820, TIANGEN Biotech). RNA was precipitated at -80 °C overnight by mixing the aqueous phase (~350 μL) with 700 μL 30:1 ethanol: sodium acetate (pH 6.5) mix. RNA pellets were washed with 80% ethanol and dissolved in ultra-pure water (#10977, Thermo Fisher Scientific), and was quantified using NanoDrop 2000.
Ribosomal RNAs was removed by Biotin-labeled rRNA probe. RNA was fragmented with BGI fragmentation buffer and was reverse transcribed with random hexamer. Double chain cDNA was then blunted and phosphorylated for the 5’ end, and overhang A base in the 3’ end and ligated with T-overhang adapter. After PCR application, samples were sequenced in BGISeq-500 platform

treatment_protocol: Bacterial cultures were added with 0.2% L-arabinose for 10-min in LB broth

value: fadBA-FadZ deletion

value: FadZ-induced overexpressed plasmid pBAD-FadZ

value: Bacterial cells


title: Clostridioides difficile 630∆erm∆gdpP∆busR_rep4

city: Gif-sur-Yvette

first: Johann

last: Peltier

address: 1, avenue de la terasse

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using AlienTrimmer_0.4.0. Only sequence with a minimum length of 30 were considered.
Sequenced were mapped to Clostridiaceae difficile 630 whole genome sequence complemented by the known ncRNA using bowtie v2
HtSeqCount was used for counting genes with default parameters
Statistical analyses were performed using R version 3 and Bioconductor packages.
The whole dataset was first normalized using the normalization function of DESeq2 and with default parameters.
The statistical test function of DESeq2 was then applied with the  630∆erm∆gdpP as a reference for reporting the expression data of 630∆erm∆gdpP∆busR.
Genome_build: Peptoclostridium difficile 630 (NC_009089.1) complemented by the known ncRNA (PMID: 23675309)
Supplementary_files_format_and_content: Raw Counts and Normalized Counts

organism: Clostridioides difficile 630

extract_protocol:
Total RNA was extracted using phenol, Trizol reagent and chloroform/isoamylalcohol.
RNA libraries were prepared for sequencing using standard Illumina protocols; Truseq stranded RNA seq kit

tag: strain/genotype

value: vegetative cells


title: ΔfadBA ΔFadZ + pBAD-Control - Rep2

source_name: ΔfadBA ΔFadZ + pBAD-Control

value: empty plasmid pBAD-Control


title: ΔfadBA ΔFadZ + pBAD-FadZ - Rep1


title: Rat 2h Sham replicate 2

first: Michael

last: Tymianski

address: 60 Leonard Ave.

institute: Krembil Research Institute


title: D3-IS-mice2-left kidney tissue

source_name: kidney tissue

value: mouse polyomavirus (MPyV)

value: 3 days

value: left kidney


title: Rat 6h MCAO replicate 1

value: Sprague-Dawley

value: 2hrs after the indicated surgery


title: Clostridioides difficile 630∆erm∆gdpP∆busR_rep3


title: ΔfadBA ΔFadZ + pBAD-Control - Rep1


title: CCI-006_Sx

value: breast cancer

value: surgical


title: CCI-003_Bx

value: core


title: P62_drug,gpr

city: Shenyang

first: Xinyi

last: Long

address: Shenyang

institute: China Medical university

description: miRNA expression profiles in p62-knockdown AML exosomes after GDC-0152 treatment.

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual.      a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first            denatured for 2 min at 95°C, incubated on ice for 2 min      b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization            System - Nimblegen Systems, Inc., Madison, WI, USA)        c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: GDC-0152+p62-knockdown U937 cells

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:  a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling  reaction was incubated for 1 h at 16°C      c, Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) . RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis. section stained by May-Giemsa. Careful attention was paid to the mi

treatment_protocol: The human acute monocytic leukemia cell line, U937, was purchased from Bena Culture Collection (Beijing, China) and stored in our laboratory. U937 cells were cultured in RPMI-1640 (HyClone; GE Healthcare Life Sciences, Logan, UT, USA) with 10% fetal bovine serum (Biological Industries, Beit, HaEmek, Israel), 100 U/mL penicillin, and 0.1 mg/mL streptomycin (Gibco/Thermo Fisher Scientific, Waltham, MA, USA). The cells were grown in a 37°C incubator with 5% CO2. A recombinant lentivirus vector–mediated SQSTM1 gene (LV-SQSTM1-RNAi) and an empty recombinant adenovirus vector (Hu6-MCS-CMV-EGFP) were constructed. U937 cells were placed in a six-well plate. Polybrene (Gene, Shanghai, China) was used for the transfection. The transfection system included 1.8 mL of RPMI-1640 with 10% fetal bovine serum, 10 μL of LV-SQSTM1-RNAi or Hu6-MCS-CMV-EGFP and 0.9 μL of polybrene. After transfection for 24 h, the cell suspension was collected and centrifuged at 800 rpm for 5 min, the supernatant with lentivirus discarded, and 2 mL of RPMI-1640 with 10% fetal bovine serum then added.

tag: rna fraction

value: exosome

tag: cell line

tag: gender


title: CCI-006_Bx


title: p62.gpr

description: miRNA expression profiles in p62-knockdown AML exosomes.

source_name: p62-knockdown U937 cells

value: male


title: Clostridioides difficile 630∆erm∆gdpP∆busR_rep2


title: CCI-013_Sx


title: Cont_drug.gpr

description: miRNA expression profiles in AML exosomes after GDC-0152 treatment.

source_name: GDC-0152+U937 cells


title: CCI-013_Bx


title: D3-IS-mice4-left kidney tissue

value: All renal cells


title: CCI-003_Sx


title: PB2

city: Beijing

first: Hongbin

last: Jin

state: Beijing

address: Haidian District

institute: Tsinghua University

data_processing:
Illumina Casava software was used for basecalling.
RNA-Seq reads were aligned to the reference genome OryCun2.0 using HISAT2 (v2.0.4; Kim, Langmead, & Salzberg, 2015) with default parameters.
Gene-level read counts were calculated using HTSeq (v0.6.1p1; Anders, Pyl, & Huber, 2015) based on the Ensembl gene annotation v85. DEseq2 (v1.18.1) was used for data normalization (Love, Huber, & Anders, 2014).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: Mouse embryo

growth_protocol: Mouse 1-cell embryos were colloected from oviduct, and cultured in KSOM media in 37C incubator filled with 5% CO2.

extract_protocol:
At late 1-cell stage, zona pellucida was removed by treating in acid Tyrode's solution. Then embryos were transfered to 0.25% Trypsin and PB2 was split from the embryo by continuous pipetting. Samples were collected into lysis buffer from Vazyme Single Cell Full Length mRNA-Amplication Kit (N712) for mRNA amplification.
RNA libraries are prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme, TD503) protocols.

value: Embryo

tag: developmental stage

value: untreated


title: Oleic Acid Growth - Rep1

source_name: Oleic Acid Growth

growth_protocol: Overnight cultures were grown from a single colony, diluted 1:100 in fresh M9CA minimal medium supplemented with 0.4% Brij-58 and 0.1 % glucose (Group GLU) or 0.1 % oleic acid (Group OAG) , and grown to the OD600 ~ 1.0 at 37°C  with shaking at 220 rpm

treatment_protocol: Cells from GLU groups were washed twice with PBS at room temperature and resuspend in M9CA minimal medium supplemented with 0.4% Brij-58 and 0.1 % oleic acid and cultivated for 10 min (OAS).

value: wild-type

value: Oleic Acid Growth (OAG)


title: Zygote


title: Clostridioides difficile 630∆erm∆gdpP∆busR_rep1

value: vegetative cells


title: Cont.gpr

description: miRNA expression profiles in AML exosomes

source_name: U937 cells


title: Clostridioides difficile 630∆erm∆gdpP_rep4


title: Oleic Acid Shock - Rep1

source_name: Oleic Acid Shock

value: Oleic Acid Shock (OAS)

value: Bacterial cells


title: Clostridioides difficile 630∆erm∆gdpP_rep3


title: Glucose Growth - Rep2

source_name: Glucose Growth

value: Glucose Growth (GLU)


title: Oleic Acid Shock - Rep2