title: Bulk-RNA-seq_KO-RPE-P30-4

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

data_processing:
Sc RNAseq:  The preprocessing steps such as generation and demultiplexing of FASTQ files from the sequencing reads, aligning to UCSC mm10 transcriptome, and generating raw count matrices were conducted using Cell Ranger v2.1 (10x Genomics) with default parameters. We performed downstream analysis using the R software package Seurat v3.2.2 (Butler et al., 2018). We removed low-quality cells with less than 500 genes detected and all genes expressed in less than 10 cells, leaving 26,764 cells and 19,324 genes for further analysis. Principal Component Analysis (PCA) was performed on a submatrix of the top 1,000 most variable genes computed, using the function FindVariableGenes from the Seurat package. Then, we removed the batch effect between samples using the package Harmony (Korsunsky et al., 2019). In particular, we removed variables associated with two separate sequencing runs (B1 and B2) and WT and AdipoR1-/- conditions to remove the non-cell-type-specific factors that impact cell clustering. We evaluated the number of top principal components by the elbow method keeping 17 PCs for clustering and data visualization. The cells were clustered using a shared nearest neighbor (SNN) modularity optimization-based clustering algorithm (FindClusters in the Seurat package). To visualize cells in two dimensions, we used Uniform Manifold Approximation and Projection (UMAP) (Becht et al., 2019). The cluster-specific genes were computed using FindAllMarkers from the Seurat package, using the MAST test with the number of UMIs detected as a latent variable (Finak et al., 2015). The same test was used to compute differentially expressed genes between WT and AdipoR1-/- within cell clusters. Cell clusters were annotated by assessing known cell-type-specific markers.
Bulk RNAseq:  Sequence data were demultiplexed using bcl2fastq software (Illumina), and their quality was assessed using FastQC (Babraham Bioinformatics). Reads were aligned to the reference mouse genome assembly (mm10) and quantified using the Rsubread software package with standard parameters (Liao et al., 2019), yielding on average 29 million counts per sample. Differential expression analysis was performed with EdgeR (v3.20.9) (Robinson et al., 2010).
Sc and bulk RNAseq:  Functional enrichment analysis was conducted on the identified differentially expressed genes, using the findGO.pl function from the HOMER suite (Hypergeometric Optimization of Motif Enrichment, v4.9.1) (Heinz et al., 2010). To correct for multiple hypotheses testing, the Benjamini and Hochberg FDR correction was used, and we retained terms at FDR < 0.05.
Genome_build: mm10

source_name: retinal pigmented epithelium cells

growth_protocol: Animals were housed under 12 hr light/12 hr dark cycles and bred using standard procedures.

extract_protocol:
Sc RNAseq:  Eyes were enucleated for retina tissue isolation. After removing the anterior chamber and lens, retinal cells were dissociated using the Papain Dissociation System (#LK003153, Worthington Biochemical) following the manufacturer's instructions. In each of the six experimental groups (WT and AdipoR1-/- at P19, P25, and P30), four retinae were used to prepare single-cell suspensions at a final concentration of 1,000 cells/µl.    Bulk RNAseq:   Eyes from AdipoR1-/- and WT mice at P30 were enucleated and placed in 60 mm dishes with PBS immediately following cervical dislocation. The anterior segment of the eye, including cornea, iris, and lens, was removed using dissecting scissors. The retinas from both eyes were carefully removed and transferred to 400 µl of RNAlater stabilization solution (#AM7920, Thermo Fisher). The posterior eyecups, consisting of RPE, choroid, and sclera, were transferred to 400 µl of RNAprotect tissue reagent (#76104, Qiagen). Eyecups were incubated at room temperature for 10 min and briefly agitated to detach RPE cells from the choroid/sclera. After removing the choroid-sclera, the remaining RPE cells were pelleted by centrifugation for 5 min at 685 x g. The isolated retinas and RPE cells in stabilization solution were subjected to extraction of total RNA using RNeasy Micro Kit (#74004, Qiagen) following the manufacturer's protocol.
Sc RNA-Seq:   For each group, freshly dissociated cells (~10,000) were loaded into a 10x Genomics Chromium Single Cell system using v2 chemistry following the manufacturer's instructions. In the first batch (B1: WT and AdipoR1-/- at P30), two libraries were pooled and sequenced on Illumina NextSeq500 with ~76 million reads per library. In the second batch (B2: WT and AdipoR1-/- at P19 and P25), four libraries were pooled and sequenced on Illumina NovaSeq6000 with ~143 million reads per library.  Bulk RNAseq:   Total RNA (~100 ng per sample) was used for library preparation by following the Illumina TruSeq Stranded Total RNA Library Prep Kit protocol. Libraries were then sequenced (paired-end 100 cycles) with the Illumina NextSeq 500 platform, yielding approximately 40 million raw reads per library.

value: retinal pigmented epithelium cells

tag: age (days)


title: 8505 CRABP2

status: Public on Mar 02 2022

type: SRA

city: Taipei

first: Shih-Ping

last: Cheng

address: 92, Chung-Shan North Road, Section 2

department: Department of Surgery

country: Taiwan

institute: MacKay Memorial Hospital

description: 8505C cells transfected with CRABP2-overexpressing vector

library_source: transcriptomic

data_processing:
FastQC
Trimmomatic v0.38 (parameter: LEADING:3, TRAILING:3, SLIDINGWINDOW:4:20, MINLEN:36)
HISHAT2 v2.1.0
featureCounts v2.0.0
Genome_build: GRCh38
Supplementary_files_format_and_content: a tab-delimited text file contains FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Thyroid cancer cells

extract_protocol:
Cells were harvested, and RNA was extracted using Trizol reagent. RNA QC: total >= 2 ug, concentration >= 50 ng/ul, RIN >= 6.8, RQN >= 7.6, OD260/OD230 >= 2.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: treatment

value: CRABP2 overexpression


title: FTC133 siCRABP2

description: FTC-133 cells transfected with CRABP2 siRNA


title: 264_TA_20

type: RNA

city: Canyon

first: Matthew

middle: Adam

last: Scott

state: TX

address: 3201 Russell Long Blvd

department: Large Animal Clinical Sciences

country: USA

institute: Texas A&M University

description:
mRNA count data
AWO22587-0148-264-TA-20

hyb_protocol: NanoString nCounter PrepStation

scan_protocol: NanoString SPRINT Profiler set to high resolution (550)

data_processing: NanoString nSolver Analysis Software v4.0 was utilized for quality assessment and raw gene count accession. Four housekeeping, six positive spike-in, and eight negative control genes were used for intersample count normalization.

label: Biotin

organism: Bos taurus

source_name: Whole blood

label_protocol: NanoString nCounter mRNA Bovine Custom Panel

extract_protocol: Total RNA was isolated from Tempus Blood Tubes with Tempus Spin RNA Isolation Kit

tag: treatment group

value: Healthy

tag: study

tag: location

value: MS

tag: animal info

value: Heifer

tag: vaccinated

tag: dewormed


title: BHT101 siCRABP2

description: BHT-101 cells transfected with CRABP2 siRNA


title: FTC133 siControl

description: FTC-133 cells transfected with control siRNA

value: siControl


title: BHT101 siControl

description: BHT-101 cells transfected with control siRNA


title: C12_012Chip8_FPKM

city: New Haven

first: Naftali

last: Kaminski

state: CT

address: 300 Cedar St

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale School of Medicine

description: FFPE tissues

data_processing:
Basecalls using Torrent Suite Software Version 5.0.5
mRNA-seq reads were aligned to hg19 using a two stage mapping strategy. In the first stage, tophat version 2.0.12 was used with annotation and the --b2-very-sensitive option. In the second stage, bowtie 2.0.5 was used with local alignment and the --very-sensitive option.
Cufflinks was used to calculate Fragments per Kilobase of exon per Million (FPKM) values.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with FPKM gene counts for every gene and every sample

source_name: lung

extract_protocol:
Laser capture microdissection was performed upon formalin fixed paraffin embedded (FFPE) control non-fibrotic lung tissue (alveolar septae (n=10)) and UIP/IPF FFPE lung tissue (myofibroblast foci, (n=10) and adjacent non-affected alveolar septae (n=10)).
Regions of interest (non-fibrotic control lung tissue alveolar septae, IPF lung tissue fibroblast foci or adjacent non-affected alveolar septae) were selected using a drawing tool on the Leica Laser Microdissection software, and then cut with a laser beam into separate RNase-free tubes containing RecoverAll Total Nucleic Acid digestion buffer (Ambion). RNA isolation was performed using Micro Filter Cartridges from RNAqueous-Micro Total RNA Isolation Kit (Invitrogen) according to the manufacturer’s instructions.
15ng of total RNA was used to make cDNA libraries using Ion Ampli‐Seq‐transcriptome human gene expression kit (Ion Torrent, Life Technologies).
An Ion Torrent Proton Sequencer (RNA-Seq) was used to produce ~20 million single-end ~100bp reads/sample.

tag: disease

value: control alveolar septae

tag: tissue

value: control lung


title: 238_PS_19

description:
mRNA count data
AWO22587-0146-238-PS-19


title: 159_MH_19

description:
mRNA count data
AWO22587-0147-159-MH-19


title: Bulk-RNA-seq_KO-RPE-P30-2

organism: Mus musculus

tag: strain

tag: genotype


title: S3_1

city: Shanghai

first: Ruizhe

last: He

address: No. 639, Zhizaoju Road

country: China

institute: Shanghai Jiao Tong University

description: SULF2 knockdown using sgRNA3 rep1

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

extract_protocol:
SULF2 knockdown group and control cells were treated with TRIzol to extract RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: pancreatic cancer

value: SULF2 knockdown using sgRNA3


title: S3_2

description: SULF2 knockdown using sgRNA3 rep2


title: S1_2

description: SULF2 knockdown using sgRNA1 rep2

value: SULF2 knockdown using sgRNA1


title: 8505 Empty

description: 8505C cells transfected with empty vector

value: Empty


title: HCT116 cells - transfected with empty vector_rep2

city: Kunming

first: Li

middle: ru

last: hong

address: 245 Huancheng East Road

institute: Yan 'an Hospital affiliated to Kunming Medical University

data_processing:
removing reads containing adapters
removing reads containing polyA and polyG
removing reads containing more than 5% of unknown nucleotides (N)
removing low quality reads containing more than 20% of low quality (Q-value≤20) bases
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data. After that, a total of G bp of cleaned, paired-end reads were produced
Genome_build: We aligned reads of all samples to the < research species > reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome
Supplementary_files_format_and_content: clean Data and Gene FPKM value

source_name: Human colon cancer cell

growth_protocol: Human colon cancer cell HCT116 was purchased from the Culture bank of Chinese Academy of Sciences (Shanghai).  Briefly, the HCT116 cell line was maintained in McCoy's 5A medium (iCell, China) supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin and streptomycin (Gibco).  Cell lines were placed in a humidified incubator containing 5% CO2 and cultured at 37℃.

extract_protocol:
The total RNA of NC group and overEXP group was extracted with TRIzol reagent (Invitrogen, CA, USA) following the manufacturer’s instructions.
RNA sequencing was performed on an Illumina NovaSeq 6000 system of LC Sciences (USA).

treatment_protocol: In simple terms, NC group consisted of normal cultured HCT116 cells, and overEXP group consisted of constructed HCT116 cells stably transfected with EPHX2

value: untreated


title: Bulk-RNA-seq_WT-RPE-P30-4

value: WT


title: Bulk-RNA-seq_KO-RPE-P30-1


title: LACZ_1

description: LACZ knockdown rep1

value: LACZ knockdown


title: LACZ_2

description: LACZ knockdown rep2


title: S1_1

description: SULF2 knockdown using sgRNA1 rep1


title: 124_MH_19

description:
mRNA count data
AWO22587-0143-124-MH-19


title: Bulk-RNA-seq_WT-RPE-P30-3


title: 267_PS_19

description:
mRNA count data
AWO22587-0144-267-PS-19


title: hESC-EC_siRNA_control_2

city: Edinburgh

first: Ian

middle: R

last: McCracken

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: University of Edinburgh

description: Illumina, strand-specific RNAseq

data_processing:
Data processed using the 10X Cell Ranger pipeline v3.1.0 ( 10X Genomics) using default parameters.
Genome_build: GRCh38-3.0.0

molecule: polyA RNA

source_name: human embryonic stem cell derived endotehlial cells

growth_protocol: Human embryonic stem cells differentiated to endothelial cells (hESC-EC) using differentiation protocol from MacAskill et al (Molecular Therapy, 2018). Cells transfected with siRNA 7 days after initiating differentiation and CD144+ hESC-EC isolated by MACS 72 hours later.

extract_protocol:
NA
strand-specific RNAseq  with PolyA selection

treatment_protocol: control siRNA

tag: post-conceptional age


title: hESC-EC_siRNA_control_3

description: Illumina, strand-specific RNAseq


title: Bulk-RNA-seq_WT-RPE-P30-2


title: Bulk-RNA-seq_WT-RPE-P30-1


title: hESC-EC_siRNA_control_1

description: Illumina, strand-specific RNAseq


title: hESC-EC_siRNA_MECOM_3

description: Illumina, strand-specific RNAseq

treatment_protocol: MECOM siRNA


title: Bulk-RNA-seq_KO-RPE-P30-3


title: hESC-EC_siRNA_MECOM_1

description: Illumina, strand-specific RNAseq


title: 14_week_cardiac_EC

description: 10X Genomics Single cell 3' gene expression V3.1

source_name: CD31+/CD45- endothelial cells isolated from 14 week human fetal heart tissue

extract_protocol:
Enzymatic digestion and FACS isolation of CD31+/CD45- endothelial cells.
Library construction was conducted using the Single Cell 3’  Reagent Kit (V3.1) (10X Genomics)

value: fetal heart

value: 15 weeks


title: hESC-EC_siRNA_MECOM_2

description: Illumina, strand-specific RNAseq


title: Bulk-RNA-seq_KO-retina-P30-4

source_name: retina

value: retina


title: 133_MH_19

description:
mRNA count data
AWO22587-0138-133-MH-19

value: Steer


title: 189_VD_17

description:
mRNA count data
AWO22587-0140-189-VD-17


title: 227_TA_20

description:
mRNA count data
AWO22587-0139-227-TA-20

value: Healthy


title: Bulk-RNA-seq_KO-retina-P30-1


title: 136_PS_19

description:
mRNA count data
AWO22587-0145-136-PS-19

value: MS


title: hESC-EC_siRNA_control_4

description: Illumina, strand-specific RNAseq


title: Bulk-RNA-seq_WT-retina-P30-4


title: DIP_8oxodG_MCF10A_NAC_treated_IP_rep1

city: Naples

first: Stefano

last: Amente

address: via pansini, 5

department: Department of  Molecular Medicine and Medical Biotechnologies

country: Italy

institute: University of Naples "FEDERICO II"

description:
NAC-treated MCF10A cells
OxiDIP-Seq_NAC_IP_R1_rep1

library_source: genomic

data_processing:
Alignments were performed with BWA  to hg18 using default parameters.
Genome_build: hg18
SAMtools and BEDtools were used for filtering steps and file formats conversion.
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

source_name: MCF10A cells

growth_protocol: MCF10A cells were cultured in 1:1 mixture DMEM-F12 supplemented with 5% horse serum  for 48hrs and incubated at 37°C in humidified atmosphere with 5% CO2.

extract_protocol:
Genomic DNA from MCF10A cells was extracted by using Dneasy Blood&Tissue kit. Genomic DNA were sonicated and immunoprecipitated with antibodies anti 8-oxodG O/N. Eluted DNA was processed for library preparation.
Libraries were prepared according to Illumina's instructions

treatment_protocol: For UV treatment, exponentially growing MCF10A cells were exposed to 40J/m2 UV light (254 nm). Medium was refreshed after irradiation and cells were incubated for 30 minutes at 37°C. Then, cells were washed twice with ice-cold phosphate buffered saline (PBS) and collected (14, 15). For NAC treatment, 1 mM N-acetyl cysteine (A7250, Sigma) was added to the medium for 1 hours and then MCF10A cells were washed twice with ice-cold phosphate buffered saline (PBS) and collected.

value: NAC-treated

tag: chip antibody


title: Bulk-RNA-seq_KO-retina-P30-2


title: DIP_8oxodG_MCF10A_NAC_treated_IP_rep2

description:
NAC-treated MCF10A cells
OxiDIP-Seq_NAC_IP_R1_rep2


title: Bulk-RNA-seq_WT-retina-P30-3


title: hESC-EC_siRNA_MECOM_4

description: Illumina, strand-specific RNAseq


title: Human umbilical vein endothelial cells Ctrl 3

city: Sigapore

first: Jong Huat

last: Tee

state: Singapore

address: Blk S3 level 6, Science Dr 4

department: Biological Sciences

country: Singapore

institute: National University Singapore

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
(1)Remove reads with adaptor contamination.
(2)Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%).
(3)Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
STAR software is used to accomplish the mapping. Reads Per Kilobase of exon per Megabase of library size (RPKM) 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: grch38
Supplementary_files_format_and_content: Files include FPKM values and readcount for each sample

source_name: Human neonatal umbilical cords

growth_protocol: Early passages of primary ECs were seeded on 0.2% gelatin-coated culture flasks in EndoGRO-LS complete culture media (Merck, SCME001) and cultured at 37°C incubators with 5% CO2. Cells would be harvested from T75 flasks and seeded into 6-well plates for treatment after O/N incubation at 37C (0.25x10^6 /well in 6-well plate)

extract_protocol:
RNA was harvested from treated ECs using TRIzol reagent (InvitrogenTM, Cat. No. 15596018) and its established protocol. Harvested RNA samples were quantified by NanoDrop and 1ug/sample was sent to Novogene Singapore for RNA-seq
RNA libraries were prepared using directional mRNA library preparation (poly A enrichment) for Illumina NovaSeq 6000 Sequencing System

treatment_protocol: 70-80% confluent ECs in 6-well plate were treated with 250nM TS5-p45 for 12h in 20ng/ml VEGF-containing media along with Control condition with 20ng/ml VEGF for 12h. Cells were incubated at 37C for the entire duration of treatments

value: Human neonatal umbilical cords

tag: cell type

value: Primary endothelial cell (EC)

tag: passage number

value: Control


title: Human umbilical vein endothelial cells Ctrl 2


title: DIP_8oxodG_MCF10A_NAC_treated_Input

description:
NAC-treated MCF10A cells
OxiDIP-Seq_NAC_R1_Input


title: Human umbilical vein endothelial cells TS5-p45 3


title: 135_VD_17

description:
mRNA count data
AWO22587-0137-135-VD-17

value: Heifer


title: 163_MH_19

description:
mRNA count data
AWO22587-0136-163-MH-19


title: Human umbilical vein endothelial cells TS5-p45 1


title: Human umbilical vein endothelial cells Ctrl 1


title: Bulk-RNA-seq_WT-retina-P30-2

tag: age (days)


title: 201_PS_19

description:
mRNA count data
AWO22587-0141-201-PS-19


title: Bulk-RNA-seq_KO-retina-P30-3


title: 183_PS_19

description:
mRNA count data
AWO22587-0133-183-PS-19


title: W1_DG_18

description:
mRNA count data
AWO22587-0134-W1-DG-18

value: MO


title: 129_MH_19

description:
mRNA count data
AWO22587-0142-129-MH-19


title: F1-RNA-5-P6-TBT

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

data_processing:
FASTQ files were filtered through trimGalore! to remove low-quality (Q < 30) reads and adaptor sequences.
FASTQ files were mapped using the STAR aligner to obtain BAM files.
R/Bioconductor package Rsubreads was used to count reads on exons of mRNA transcripts.
The mRNA raw counts were normalized by the negative binominal trimmed mean of M-values (TMM) method using R/Bioconductgor package edgeR.
Differentially expressed mRNA transcripts were identified using the generalized linear model likelihood ratio test implemented by edgeR.
mERV counting, normalization, and identification of differentially expressed mERVs from the BAM files were performed using the ERVmap pipeline with modification for the use of the mm10 mouse genome reference sequence.
MBDseq data analysis from the BAM files was performed using the R/Bioconductor package QSEA.
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq (mRNA): an EXCEL spreadsheet of normalized mRNA counts.
Supplementary_files_format_and_content: RNAseq (mouse endogenous retroviruses: mERVs): text files of normalized mERV counts.
Supplementary_files_format_and_content: MBDseq: text files of normalized counts of genomic DNA fragments enriched by the MBD precipiation (simialr to ChIP-seq procedure).

source_name: E18.5 fetus

extract_protocol:
Genomic DNA and total RNA were isolated from FACS-enriched germ cells and somatic cells of E18.5 fetal testes using the QIAGEN AllPrep Micro kit.
RNA-seq Illumina libraries were contructed using Takara Bio's SMART-seq mRNA-seq kit, which involve cDNA synthesis using an oligo-dT primer. MBD-seq libraries were constructed using ThermoFisuer MethylMiner kit.
RNA-seq [targeting mRNA and endogenous retrovirus RNA containing poly(A) tail]; MBD-seq [using a Methyl Binding Domain protein to enrich DNA fragments containing methylated CpG dinucleotides]

treatment_protocol: Pregnant F0 dams of the OG2 mouse strain were gestationally exposed to 50 nM tributyltin or DMSO.

tag: cells

value: P6 somatic cells

tag: f0 exposure

value: TBT


title: 620-jian

city: guiyang

first: guanghui

last: wang

address: zhongshan road

institute: hospital

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 hg18 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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: GR38p7
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: colorectal cancer cell line

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: treatment

value: control


title: 620-jia

value: SHMT2 knockdown


title: scRNA-seq_KO-P30


title: Y58_DG_18

description:
mRNA count data
AWO22587-0135-Y58-DG-18

tag: treatment group

tag: study

tag: location


title: Neurons - PTHS patient #3 - replicate C

city: Campinas

first: Fabio

last: Papes

state: SP

address: Rua Carl Von Linaeus

country: Brazil

institute: University of Campinas

data_processing:
Transcript-level quantification using Salmon (version 0.14.1)
Genome_build: GENCODE 32 basic annotation (GRCh38)
Supplementary_files_format_and_content: Salmon quantification outputs

source_name: Neurons

growth_protocol: Neurons were cultured in Neurobasal medium containing GEM21 suplement.

extract_protocol:
Total RNA was extracted using Rneasy Mini Plus kit (Qiagen).
Libraries were made using the TruSeq Stranded mRNA kit (Illumina) and sequenced on a NovaSeq6000 S4 instrument to produce 150 PE read at ~40M reads per library (6Gb production)

treatment_protocol: Cells were not treated.

value: iPSC-derived neurons

value: PTHS patient


title: R7_DG_18

description:
mRNA count data
AWO22587-0132-R7-DG-18

tag: animal info

tag: vaccinated

tag: dewormed


title: Neurons - PTHS patient #3 - replicate B


title: Neurons - PTHS patient #3 - replicate A


title: 198_VD_17

description:
mRNA count data
AWO22587-0131-198-VD-17


title: Neurons - PTHS patient #2 - replicate C


title: Neurons - PTHS patient #2 - replicate B


title: Bulk-RNA-seq_WT-retina-P30-1

tag: tissue

tag: strain

value: WT


title: M2-exosome

city: Baltimore

first: Gijung

last: Kwak

state: Maryland

address: 400 N. Broadway

department: School of Medicine

institute: Johns Hopkins University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: Exosomes from M2-BMDMs

growth_protocol: Bone marrow cells were plated Ф150 petri dishes at a density of 9 × 10^6 cells and cultured for 7 days with cell growth media containing 10 ng/mL of M-CSF. For differentiation to M1- or M2-phenotype, cultured cells were maintained for 1 days with 20 ng/mL of IFN-γ or 20 ng/mL of IL-4, respectively. Exosomes of M1- or M2-polarized BMDMs were isolated by the ultracentrifugation method. M1- or M2-polarized BMDMs were incubated with serum free media for 2 days. Each supernatant was collected and serially centrifuged at 300 × g at 4 ℃ for 10 min, 2,000 × g at 4 ℃ for 10 min, and 10,000 × g at 4 ℃ for 30 min. After filtration through 0.22 μm pore filter, exosomes-containing supernatants were ultracentrifuged at 150,000 × g at 4 ℃ for 3 h in a 45 Ti rotor (Beckman Coulter, Brea, CA, USA). The pellet of exosomes was resuspended in PBS.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small  RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.

tag: agent

value: differenciated with IL-4 (20 ng/mL) for 1 day

tag: age

value: 5-6 weeks


title: Neurons - PTHS patient #2 - replicate A

tag: cell type

tag: genotype


title: scRNA-seq_WT-P30

value: retina

tag: age (days)


title: 204_TA_20

description:
mRNA count data
AWO22587-0130-204-TA-20

value: Healthy

value: MS


title: 221_TA_20

description:
mRNA count data
AWO22587-0129-221-TA-20

value: Steer


title: M1-exosome

source_name: Exosomes from M1-BMDMs

value: differenciated with IFNg (20 ng/mL) for 1 day


title: 480-jian


title: Neurons - parent #2 - replicate B

value: parental control


title: 126693

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
Illumina standard primers were trimmed
Paired reads were mapped to the mouse reference genome mm10 using STAR
Number of reads for each gene was counted using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: raw read count matrix (genes x samples)

source_name: skin

growth_protocol: Murine Merkel cell carcinoma-like tumors were obtained from a 20 week old K5-CreERT2;R26-LSL-rtTA;tetO-sT/tLT;tetO-Atoh1;Trp53 fl/wt mouse, after 17 weeks of transgene induction. Dorsal skin biopsies were harvested from age matched control mice. Basal cell carcinomas arising in K5-Gli2 mice were harvested at 7-9 months of age.

extract_protocol:
Frozen mouse tissue was disrupted and homogenized in QIAzol Lysis Reagent with a 5-mm stainless steel bead with the TissueLyser II. RNA purification was carried out with the miRNAeasy Kit as per manufacturer’s instructions.
RNA libraries were prepared for sequencing from stranded mRNA following poly-A enrichment and sequenced on the NextSeq platform according to Illumina standard protocols.

value: dorsal skin

value: wildtype


title: 13_week_cardiac_EC

source_name: CD31+/CD45- endothelial cells isolated from 13 week human fetal heart tissue

value: fetal heart

tag: post-conceptional age

value: 13 weeks


title: Neurons - PTHS patient #1 - replicate C


title: Neurons - parent #2 - replicate A


title: 126692

value: Basal cell carcinoma


title: 211_TA_20

description:
mRNA count data
AWO22587-0127-211-TA-20

value: Heifer


title: Neurons - parent #1 - replicate B

value: iPSC-derived neurons


title: Neurons - parent #1 - replicate C


title: Neurons - PTHS patient #1 - replicate A

value: PTHS patient


title: Neurons - parent #1 - replicate A


title: 480-jia

value: SHMT2 knockdown


title: Human umbilical vein endothelial cells TS5-p45 2

value: Human neonatal umbilical cords

value: Primary endothelial cell (EC)

tag: passage number


title: 126204


title: 126207


title: 175_VD_17

description:
mRNA count data
AWO22587-0126-175-VD-17


title: 126203


title: 193_PS_19

description:
mRNA count data
AWO22587-0125-193-PS-19

value: Bull


title: 126202


title: Neurons - parent #2 - replicate C


title: 126201

value: Merkel cell carcinoma


title: 217_TA_20

description:
mRNA count data
AWO22587-0122-217-TA-20

value: Healthy

value: MS


title: 282_TA_20

description:
mRNA count data
AWO22587-0124-282-TA-20

value: Steer


title: 126200


title: 109_DG_17

description:
mRNA count data
AWO22587-0123-109-DG-17

value: MO


title: 193_VD_17

description:
mRNA count data
AWO22587-0120-193-VD-17


title: 103_VD_17

description:
mRNA count data
AWO22587-0128-103-VD-17


title: 126199


title: 118_MH_19

description:
mRNA count data
AWO22587-0119-118-MH-19


title: 126208

value: dorsal skin


title: R10_DG_18

description:
mRNA count data
AWO22587-0118-R10-DG-18


title: Neurons - PTHS patient #1 - replicate B


title: 188_VD_17

description:
mRNA count data
AWO22587-0116-188-VD-17


title: 36_DG_17

description:
mRNA count data
AWO22587-0117-36-DG-17


title: 1G11-SOD3-Rep3

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: 1G11 cell line (mouse endotelial) overexpressing SOD3

hyb_protocol: Preparation of probes and hybridization were performed as described in the One-Color Microarray-Based Gene Expression Analysis Manual Ver. 6.5, Agilent Technologies

scan_protocol: Images were captured with an Agilent Microarray Scanner and spots were quantified using Feature Extraction Software (Agilent Technologies)

data_processing: Local background was corrected by normexp method of limma package with an offset of 50 (Smyth, 2004). Background corrected intensities were transformed to log scale (base 2). To have similar intensity distribution across all arrays, background-corrected-intensity values were normalized by adjusting their quantiles (Bolstad et al., 2003).

source_name: endothelial cell line

label_protocol: cRNA was synthesized and 200 ng were amplified with the One Color Low Input Quick Amp Labeling kit (Agilent Technologies) and further purified with the RNeasy Mini kit (Qiagen)

growth_protocol: Cells were incubated with N202.1A conditioned medium for 6 hours

extract_protocol: Total RNA was isolated with Tri-Reagent and further cleaned with the RNeasy kit (Qiagen). RNA quality was confirmed by electropherogram (Agilent 2100 Bioanalyzer)

tag: cell line

tag: sod3 overexpression

value: YES


title: 161_MH_19

description:
mRNA count data
AWO22587-0115-161-MH-19

tag: treatment group


title: CAFs stimulated with shHNR-1 supernatant [2-2]

city: Zhengzhou

first: zhuoyu

last: gu

state: China

address: No. 50, Jianshe East Road, Erqi District

institute: First Affiliated Hospital of Zhengzhou University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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: NOT PROVIDED
Supplementary_files_format_and_content: abundance measurements

source_name: lung adenocarcinoma

value: CAFs

value: lung adenocarcinoma

value: Fifth generation

tag: treatment

value: stimulated with H1299 shHNR-1 supernatant


title: CAFs stimulated with sh-NC supernatant [1-2]

value: stimulated with H1299 sh-NC supernatant


title: 1G11-SOD3-Rep1


title: 1G11-mock-Rep2

description: 1G11 cell line (mouse endotelial)

value: NO


title: Severe_AD H3K27me3 rep4

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

institute: UNIVERSITA' DI PADOVA

data_processing:
Reads were aligned to hg19 using ‘bwa’
Unmapped reads, reads with a MAPQ smaller then 1, duplicate reads and those that mapped outside of chr 1-19 and Chr X were removed using ‘samtools
Peak calling was performed using MACS2 or Epic2 for H3K4me3 and H3K27me3 respectively
Genome_build: hg19
Supplementary_files_format_and_content: Text file containing enriched regions coordinates

source_name: Enthorinal Cortex

extract_protocol:
Chromatin extraction was performed starting  from 10 mg of tissue. amples were homogenized with a dounce homogenizer in 0.5 ml of fixation solution and fixed for 10 minutes at 37°C. After centrifugation, samples were resuspend-ed in 0.5 ml of lysis buffer and incubated 30 min at room temperature on a rotating platform. After re-suspension in 0.3 ml of extraction buffer, samples were sonicated with three pulses of 30 s each, interrupted by 60 s pauses, in a thermoblock refrigerated at − 20 °C, with an amplitude of 40% using the EpiShear sonicator (Active Motif, Carlsbad, CA, USA). After being cleared by centrifugation, supernatants containing chromatin were saved and an aliquot of 30 μl was purified using the PCR Purification Kit (Qiagen, Hilden, Germany) and used for the DNA amount estimation by Qubit (Invitrogen, Eugene, OR, USA) using the dsDNA HS Assay Kit (Invitrogen, Eu-gene, OR, USA) and to control the chromatin size by agarose gel electrophoresis. The chromatin immunoselection was conducted using anti-H3K4me3 (#39159, Lot. 25817005; Active Motif, Carlsbad, CA, USA) or anti-H3K27me3 (#07-449, Lot. 3091919; Millipore, Temecula, CA, USA) antibodies. Immunoselected DNA once purified and quantified.
Libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: severe Alzheimer’s disease

value: Enthorinal Cortex

tag: antibody


title: Severe_AD H3K27me3 rep6


title: 169_MH_19

description:
mRNA count data
AWO22587-0121-169-MH-19

source_name: Whole blood

tag: study

tag: location

tag: animal info

tag: vaccinated


title: 118_VD_17

description:
mRNA count data
AWO22587-0110-118-VD-17

tag: dewormed


title: 145_MH_19

description:
mRNA count data
AWO22587-0109-145-MH-19


title: Severe_AD H3K27me3 rep5

tag: tissue


title: 1G11-SOD3-Rep2

tag: strain


title: 1G11-mock-Rep1

description: 1G11 cell line (mouse endotelial)


title: 272_TA_20

description:
mRNA count data
AWO22587-0111-272-TA-20

value: Heifer


title: 102_MH_19

description:
mRNA count data
AWO22587-0108-102-MH-19


title: 77_DG_17

description:
mRNA count data
AWO22587-0107-77-DG-17


title: 160_DG_17

description:
mRNA count data
AWO22587-0113-160-DG-17


title: 206_TA_20

description:
mRNA count data
AWO22587-0105-206-TA-20


title: 278_TA_20

description:
mRNA count data
AWO22587-0112-278-TA-20


title: Severe_AD H3K27me3 rep1


title: Severe_AD H3K27me3 rep3


title: Severe_AD H3K27me3 rep2


title: Control H3K27me3 rep9

value: control


title: 274_TA_20

description:
mRNA count data
AWO22587-0104-274-TA-20


title: R5_DG_18

description:
mRNA count data
AWO22587-0102-R5-DG-18


title: 143_MH_19

description:
mRNA count data
AWO22587-0103-143-MH-19


title: Control H3K27me3 rep7


title: 1G11-mock-Rep3

description: 1G11 cell line (mouse endotelial)


title: 215_TA_20

description:
mRNA count data
AWO22587-0101-215-TA-20


title: Control H3K27me3 rep3


title: Control H3K27me3 rep1


title: 197_VD_17

description:
mRNA count data
AWO22587-0099-197-VD-17


title: Control H3K27me3 rep6


title: W8_DG_18

description:
mRNA count data
AWO22587-0100-W8-DG-18


title: Severe_AD H3K4me3 rep5


title: 180_MH_19

description:
mRNA count data
AWO22587-0114-180-MH-19

value: Bull


title: Severe_AD H3K4me3 rep6


title: Control H3K27me3 rep5


title: Control H3K27me3 rep4


title: Severe_AD H3K4me3 rep3


title: 52_DG_17

description:
mRNA count data
AWO22587-0097-52-DG-17


title: Severe_AD H3K4me3 rep4


title: 168_MH_19

description:
mRNA count data
AWO22587-0093-168-MH-19

value: Healthy


title: 144_MH_19

description:
mRNA count data
AWO22587-0089-144-MH-19

value: MS


title: 171_VD_17

description:
mRNA count data
AWO22587-0098-171-VD-17


title: 153_MH_19

description:
mRNA count data
AWO22587-0094-153-MH-19


title: Control H3K27me3 rep8


title: 120_VD_17

description:
mRNA count data
AWO22587-0096-120-VD-17


title: 137_MH_19

description:
mRNA count data
AWO22587-0088-137-MH-19

value: Steer


title: 105_DG_18

description:
mRNA count data
AWO22587-0092-105-DG-18

value: MO


title: 245_TA_20

description:
mRNA count data
AWO22587-0090-245-TA-20


title: 134_DG_17

description:
mRNA count data
AWO22587-0091-134-DG-17


title: 249_TA_20

description:
mRNA count data
AWO22587-0095-249-TA-20


title: Control H3K4me3 rep9


title: 171_PS_19

description:
mRNA count data
AWO22587-0086-171-PS-19


title: Control H3K27me3 rep2


title: 255_TA_20

description:
mRNA count data
AWO22587-0087-255-TA-20


title: Control H3K4me3 rep3


title: Control H3K4me3 rep7


title: 88_DG_17

description:
mRNA count data
AWO22587-0085-88-DG-17


title: 101_PS_19

description:
mRNA count data
AWO22587-0084-101-PS-19


title: Control H3K4me3 rep5


title: 223_TA_20

description:
mRNA count data
AWO22587-0081-223-TA-20


title: Control H3K4me3 rep4


title: W4_DG_18

description:
mRNA count data
AWO22587-0083-W4-DG-18


title: 112_VD_17

description:
mRNA count data
AWO22587-0082-112-VD-17


title: Control H3K4me3 rep1


title: Control H3K4me3 rep2


title: DIP_8oxodG_MCF10A_UV_treated_IP

description:
UV-treated MCF10A cells
OxiDIP-Seq_UV_IP

value: UV-treated

tag: chip antibody


title: Severe_AD H3K4me3 rep1


title: DIP_8oxodG_MCF10A_UV_treated_Input

description:
UV-treated MCF10A cells
OxiDIP-Seq_UV_Input


title: 140_VD_17

description:
mRNA count data
AWO22587-0079-140-VD-17


title: Control H3K4me3 rep6


title: Severe_AD H3K4me3 rep2


title: Y59_DG_18

description:
mRNA count data
AWO22587-0080-Y59-DG-18


title: 164_VD_17

description:
mRNA count data
AWO22587-0077-164-VD-17


title: 126_VD_17

description:
mRNA count data
AWO22587-0076-126-VD-17


title: TGS_2

city: Wilmington

first: Anilkumar

last: Gopalakrishnapillai

state: DE

address: 200 Powder Mill road

institute: Nemours Children's Health

data_processing:
HiSeq Control Software for base calling
RNA-Seq reads were aligned to human reference genome hg38 with STAR
Number of read counts per gene locus was summarized using 'featureCounts' using hg38 annotation
Read counts normalized using TMM normalization (edgeR)
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text file with TMM normalized read counts

source_name: iPSC derived cells

growth_protocol: HSPCs were collected at day 12 following hematopoeitic differentiation by using STEMdiff hematopoeitic kit, StemCell Technologies. For generating megakaryocytes, differenitation was stopped at day 10 and floating cells were collected and resuspended in megakaryocytic lineage expansion media (StemCell Technologies).

extract_protocol:
Total RNA was isolated from indicated cells using Qiagen Rneasy Plus Micro kit
RNA library preparations, sequencing reactions, and initial bioinformatics analysis were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA).

treatment_protocol: CRISPR-Cas9 mediated mutagenesis to introduce disease-specific mutations

tag: cell type

value: HSPCs

tag: mutation

value: GATA1, STAG2

tag: experimental batch

value: Experimental Batch 1


title: TG_2


title: TG_1


title: Y52_DG_18

description:
mRNA count data
AWO22587-0078-Y52-DG-18


title: 116_MH_19

description:
mRNA count data
AWO22587-0075-116-MH-19


title: TGS_1


title: T_2


title: TG_ME_2

value: Megakaryocytes


title: 246_TA_20

description:
mRNA count data
AWO22587-0070-246-TA-20


title: TG_ME_1


title: 107_VD_17

description:
mRNA count data
AWO22587-0071-107-VD-17


title: 146_DG_17

description:
mRNA count data
AWO22587-0073-146-DG-17


title: 121_MH_19

description:
mRNA count data
AWO22587-0069-121-MH-19


title: TS_ME_2


title: T_ME_2


title: TGS_ME_1

value: Experimental Batch 2


title: 260_PS_19

description:
mRNA count data
AWO22587-0064-260-PS-19


title: 110_PS_19

description:
mRNA count data
AWO22587-0066-110-PS-19


title: 119_MH_19

description:
mRNA count data
AWO22587-0067-119-MH-19


title: TG_ME_4


title: 182_VD_17

description:
mRNA count data
AWO22587-0065-182-VD-17


title: 110_VD_17

description:
mRNA count data
AWO22587-0068-110-VD-17


title: TS_ME_1


title: 190_VD_17

description:
mRNA count data
AWO22587-0074-190-VD-17


title: TGS_ME_2


title: TG_ME_3


title: T_ME_3


title: 68_DG_17

description:
mRNA count data
AWO22587-0061-68-DG-17


title: T_1


title: 162_PS_19

description:
mRNA count data
AWO22587-0060-162-PS-19


title: D3_DC

city: Jena

first: Bastian

last: Seelbinder

address: Adolf-Reichwein-Straße 23

department: Systems Biology and Bioinformatics

country: Germany

institute: Hans-Knoell-Institute Jena

description: Unstimatulated DC

data_processing:
trimmomatic v0.36; single-end mode; Illumina adapter trimming; LEADING:3; TRAILING:3; SLIDINGWINDOW:15:25; MINLEN:30
hisat2 exon-indexing of human GRCH38-109 from 2018-03-26
featureCounts as implemented in Rsubread 1.34.0
Genome_build: GRCH38-109
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with median-by-ratio normalized gene counts for every gene and every sample; MRN normalization as implemented in EBSeq and GEO2RNAseq

source_name: dendritic cells

extract_protocol:
Human dendritic cell cultures were frozen and stored at -80°C before shipping. Library preparation was performed with the Illumina TruSeq Stranded mRNA (incl. poly-T oligo pulldown) technology, according to the manufacturer ́s protocol. Then, samples were quality controlled using the RNA 6000 Pico LabChip kit was used on the 2100 Bioanalyzer (Agilent Technologies). All libraries were quantified using the highly sensitive fluorescent dye-based Qubit® ds DNA HS Assay Kit (Thermo Fisher Scientific). All single libraries were pooled into several sequencing library pools with an equal DNA amount per sample. Subsequently, the sequencing library pools were pooled separately with libraries of other projects for sequencing in several NextSeq HighOutput runs. Clustering of the library pools was performed on the NextSeq® 500 sequencing system (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ia

value: mock

tag: subject


title: R8_DG_18

city: Canyon

first: Matthew

last: Scott

address: 3201 Russell Long Blvd

institute: Texas A&M University

description:
mRNA count data
AWO22587-0062-R8-DG-18

data_processing: NanoString nSolver Analysis Software v4.0 was utilized for quality assessment and raw gene count accession. Four housekeeping, six positive spike-in, and eight negative control genes were used for intersample count normalization.

extract_protocol: Total RNA was isolated from Tempus Blood Tubes with Tempus Spin RNA Isolation Kit

tag: treatment group


title: MaelKD_totalRNA_rep2

city: Tokyo

first: Yurika

last: Namba

state: --- Select a state ---

address: 2-11-16 Yayoi, Bunkyo-ku

department: Department of Biological Sciences, Graduate School of Science

country: Japan

institute: The University of Tokyo

data_processing:
smRNA-seq: Analysis of PIWI-associated small RNA sequences were performed essentially as described previously (Iwasaki et al., 2017) with some modifications. After removal of adaptor sequences by cutadapt (version 3.1) (Martin et al., 2011), 22-35 nt reads were mapped to the genome using bowtie (version 1.3.0) (Langmead et al., 2009) in random and multiple counting methods not allowing mismatch. Genome mapped reads were processed using SAMtools (H. Li et al., 2009) and BEDTools (Quinlan and Hall, 2010) and used for further analysis with normalized by the number of the genome mapped reads. The genome mapped reads were aligned to the transposon library using bowtie in random and multiple counting methods allowing up to two mismatches.
RNA-seq: Analysis of RNA sequences were performed essentially as described previously (Iwasaki et al., 2017) with some modifications. After cleaning and removal of adaptor sequences by using Rcorrector, TranscriptomeAssemblyTools, and TrimGalore, 36- nt reads were mapped to the genome and to the transposon library using STAR (version 2.7.9a) (Dobin et al., 2012) in random and multiple counting methods allowing up to 4% of mismatches relative to read length. Mapped reads were processed using SAMtools (Li et al., 2009) and BEDTools (Quinlan and Hall, 2010).
Genome_build: silkworm reference genome obtained from Silkbase (Genome assembly; Nov. 2016) (Kawamoto et al., 2019)
Supplementary_files_format_and_content: smRNA-seq: Tab-separated text files include normalized count of reads mapped to each transposon sequences in antisense direction.
Supplementary_files_format_and_content: RNA-seq: Tab-separated text files include normalized count of reads mapped to each transposon sequences in sense direction.

organism: Bombyx mori

source_name: BmN4 cells

growth_protocol: BmN4 cells were cultured at 26°C in EX-CELL 420 Serum-Free Medium for Insect cells (Sigma) supplemented 10% fetal bovine serum (FBS) (Equitech-Bio) and penicillin-streptomycin-glutamine (Gibco).

extract_protocol:
Total RNAs were isolated using ISOGEN II and DNase (Life technologies)  and used to generate RNA libraries.
RNA libraries were prepared from Luc, Mael, and Siwi KD BmN4 cells with VAHTS Stranded mRNA-seq Library Prep Kit for Illumina (Vazyme) and sequenced using Illumina NovaSeq to obtain paired-end reads.

treatment_protocol: To knockdown (KD) endogenous proteins, BmN4 cells (1 × 106 cells) were transfected with 500 pmol of siRNA duplex in 100 μL of EP buffer [137 mM NaCl, 5 mM KCl, 0.5 mM Na2HPO4 and 2.1 mM HEPES-KOH (pH 7.1)] using program T-001 of Nucleofector 2b device (Lonza). siRNA transfection was performed again to raise the RNAi effect. After KD, the cells were cultured for total 10 days and harvested. Luciferase (Luc) siRNA was used as a control. The sequences of siRNAs are summarized in Table S1. To exogenously express proteins, BmN4 cells (6 × 105 cells) were transfected with 2-8 μg of plasmids and 5-20 μL of FuGENE HD transfection reagent (Promega) in 100 μL of complete medium without FBS and added 10% FBS into cell medium 3 h later. After transfection, the cells were cultured for 2 days and harvested.

value: Cultured cell derived from ovary

tag: cell line

tag: knockdown

value: siMael

tag: molecule subtype

value: total RNA

tag: rip antibody


title: T_ME_1


title: D2_DC

description: Unstimatulated DC


title: MaelKD_totalRNA_rep1


title: 109_MH_19

description:
mRNA count data
AWO22587-0059-109-MH-19

tag: study

tag: location


title: SiwiKD_totalRNA_rep2

value: siSiwi


title: D1_DC

description: Unstimatulated DC


title: 273_PS_19

description:
mRNA count data
AWO22587-0058-273-PS-19

tag: animal info

tag: vaccinated


title: 263_PS_19

description:
mRNA count data
AWO22587-0057-263-PS-19

value: Heifer

tag: dewormed


title: LucKD_totalRNA_rep2

value: siLuc


title: SiwiKD_totalRNA_rep1


title: 190_PS_19

description:
mRNA count data
AWO22587-0056-190-PS-19

value: Healthy


title: LucKD_totalRNA_rep1


title: T_ME_4


title: D2_AF

description: DC cells challenged with Aspergillus fumigatus

value: stimluated


title: 281_PS_19

description:
mRNA count data
AWO22587-0063-281-PS-19

value: MS

value: Steer


title: D1_AF

description: DC challenged with Aspergillus fumigatus


title: Keratinocytes OLFM4-treated rep2

city: Tartu

first: Mariliis

last: Klaas

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

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 using CutAdapt 1.16 with Python 3.6.4.
RNA STAR (Galaxy version 2.7.7a) was used for sequence alignment to reference genome GRCh38/h38.87 and featureCounts (Galaxy version 2.0.1) was used to count the number of reads.
Differential gene expression was analysed using DESeq2 package
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 result values for each sample

source_name: Cultured skin keratinocytes

growth_protocol: Primary human fibroblasts were cultured in a growth medium containing 89% DMEM, 10% FBS and 1% Penicillin/Streptomycin solution (all Gibco, Invitrogen). Primary human keratinocytes were cultured in Keratinocyte-SFM medium containing 50 µg/ml bovine pituitary extract, 0.5 ng/ml recombinant epidermal growth factor and 10 ng/ml recombinant keratinocyte growth factor (all Thermo Fisher Scientific, Grand Island, NY, USA) and antibiotic-antimycotic solution (Gibco, Thermo Fisher Scientific, Grand Island, USA) with a final concentration of 100 U/ml penicillin, 100 µg/ml streptomycin and 0.25 µg/ml amphotericin B.  Before start of the experiment, the cells were cultured on 60mm-diameter cell culture dishes (Falcon, Corning) until 70-80% confluency.

extract_protocol:
Total RNA was separated using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Adherent cells were treated for 4 h with 1 ug/ml recombinant OLFM4 protein (R&D Systems, Minneapolis, MN, USA, product code 10261-OL-050) or vehicle control (PBS) in regular growth medium.

tag: tissue

value: skin

tag: treatment

value: recombinant OLFM4 protein 1 ug/ml 4 h

value: keratinocytes


title: Keratinocytes OLFM4-treated rep3

tag: cell type


title: 209_TA_20

description:
mRNA count data
AWO22587-0054-209-TA-20


title: 178_MH_19

description:
mRNA count data
AWO22587-0055-178-MH-19

value: Bull


title: 275_TA_20

description:
mRNA count data
AWO22587-0106-275-TA-20


title: 107_PS_19

description:
mRNA count data
AWO22587-0052-107-PS-19


title: Keratinocytes OLFM4-treated rep1


title: D3_AF


title: bladder tissue (28 days after spinal cord injury) rep3 [S12-1]

city: Beijing

first: Jimeng

last: Ruan

address: No. 45 Changchun Street, Xuanwu District

institute: Xuanwu Hospital Capital Medical University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The remaining reads were filtered against the rRNA database to remove possible ribosomal RNA contamination,  and then mapped to the rn6 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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: rn6
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: bladder

growth_protocol: All the animals were housed in cages at a room temperature of 25 ℃ with 30-70% humidity. All rats had free access to appropriate food and fresh water.

extract_protocol:
Total RNA was extracted from bladder tissues using TRIzol  and quantified using a spectrophotometer . Ribosomal RNA was depleted from total RNA using a RiboMinus kit. RNA-Seq was conducted using a HiSeq 2500 Sequencing System with a single-end 50 bp.RNA-seq libraries were constructed using the Illumina TruSeq protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Spinal cord was completely transected using a sharp scalpel at the T10 segmental level without disrupting the dura.

tag: strain

value: Wistar

value: bladder

tag: age

value: post natal 10-12 weeks

value: spinal cord was completely transected at the T10 segmental level

tag: timepoint

value: 28 days after spinal cord injury


title: bladder tissue (28 days after spinal cord injury) rep2 [S11-1]


title: Y60_DG_18

description:
mRNA count data
AWO22587-0053-Y60-DG-18

value: MO


title: bladder tissue (28 days after spinal cord injury) rep1 [S10-1]


title: Keratinocytes control rep3

value: control (PBS)


title: 265_PS_19

description:
mRNA count data
AWO22587-0051-265-PS-19

value: Heifer


title: bladder tissue (normal control) rep3 [S9-1]

value: normal control


title: Keratinocytes control rep2


title: bladder tissue (normal control) rep2 [S8-1]


title: Keratinocytes control rep1


title: Fibroblasts OLFM4-treated rep2

source_name: Cultured skin fibroblasts

value: fibroblasts


title: bladder tissue (normal control) rep1 [S7-1]


title: bladder tissue (14 days after spinal cord injury) rep3 [S6-1]

value: 14 days after spinal cord injury


title: 270_TA_20

description:
mRNA count data
AWO22587-0049-270-TA-20

value: MS


title: 172_MH_19

description:
mRNA count data
AWO22587-0048-172-MH-19

value: Steer


title: Fibroblasts control rep2

value: skin


title: Y51_DG_18

description:
mRNA count data
AWO22587-0072-Y51-DG-18

value: Healthy


title: 230_PS_19

description:
mRNA count data
AWO22587-0046-230-PS-19


title: bladder tissue (14 days after spinal cord injury) rep2 [S5-1]


title: bladder tissue (14 days after spinal cord injury) rep1 [S4-1]


title: Fibroblasts OLFM4-treated rep1

value: recombinant OLFM4 protein 1 ug/ml 4 h


title: bladder tissue (7 days after spinal cord injury) rep3 [S3-1]

value: 7 days after spinal cord injury


title: PZ72_p_ESOSOMI_MDA24h2

first: Gerolama

last: Condorelli

address: Via Pansini,5

department: Department od Molecular Medicine and Medical Biotechnology

institute: University of Naples "Federico II"

data_processing:
bcl2fastq Conversion Software v1.8.4
Adapter cleavage, quality filter analysis with Cutadapt
map input reads against known miRNAs from miRBase v.20 (miRAnalyzer)
Differential expression analysis with DESeq2 v1.16
Genome_build: hg19
Supplementary_files_format_and_content: raw counts, normalized counts and differential expression analysis

source_name: PZ72 (primary  fibroblasts)

growth_protocol: Primary fibroblasts were obtained from human patients' biopsies of breast fibroadenomas

extract_protocol:
After 24h of exosome treatment, cells were collected and RNA was extracted using TRIZOL reagent
small RNA libraries were prepared from 1 ug of RNA using Truseq small RNA seq library prep (Illumina) and sequencing performed on NextSeq 500 in single end reads

treatment_protocol: Exosomes ( 40ug) from MDA-MB-231 cells were incubated with primary fibroblasts (5x10^5)  plated in 100mm culture dishes. Treatment with the same volume of PBS was performed as negative control ( untreated, NT)

value: primary fibroblasts from breast fibroadenoma

value: treated with MDA-MB-231 exosomes for 24h

value: small RNA


title: bladder tissue (7 days after spinal cord injury) rep2 [S2-1]

value: Wistar

value: bladder

value: post natal 10-12 weeks

value: spinal cord was completely transected at the T10 segmental level


title: PZ72_p_ESOSOMI_MDA24h_3


title: Fibroblasts control rep1

value: control (PBS)


title: 127_MH_19

description:
mRNA count data
AWO22587-0047-127-MH-19

value: Heifer


title: 106_MH_19

description:
mRNA count data
AWO22587-0044-106-MH-19


title: PZ72_NT1_3

value: untreated


title: 189_PS_19

description:
mRNA count data
AWO22587-0045-189-PS-19

value: Bull


title: 147_VD_17

description:
mRNA count data
AWO22587-0050-147-VD-17

value: MS


title: PZ72_NT1_2


title: 9-3_HL3FVCCXY_L4

city: GUANGZHOU

first: kayleigh

last: huang

state: Not Applicable

address: 6F BLDG D 188 KAIYUAN AVE HUANGPU DISTRICT

institute: GUANGZHOU MENDEL GENES

data_processing:
filtering and QC
alignment
Quantitative analysis of gene expression
analysis of genes differential expression
GO and KEGG
Genome_build: mm10
Supplementary_files_format_and_content: txt,reads count

source_name: brain

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

tag: strain background

value: case (transgene)

value: brain


title: 150_MH_19

description:
mRNA count data
AWO22587-0041-150-MH-19

tag: treatment group


title: 8-7N_HL3FVCCXY_L4


title: 8-5N_HL3FVCCXY_L4

value: control


title: 174_PS_19

description:
mRNA count data
AWO22587-0039-174-PS-19

value: Healthy


title: P063 control male 50

source_name: blood

extract_protocol:
Human blood samples were preserved in Tempus Blood RNA tubes for shipping. Library preparation was performed with the Illumina TruSeq Stranded mRNA (incl. Ribo-Zero Globin) technology, according to the manufacturer ́s protocol. After depletion of cytoplasmic and mitochondrial rRNA as well as globin mRNA using the Ribo-Zero Globin technology, included in the TruSeq® Stranded Total RNA library prep kit, the samples were quality controlled. Therefore, the RNA 6000 Pico LabChip kit was used on the 2100 Bioanalyzer (Agilent Technologies). All libraries were quantified using the highly sensitive fluorescent dye-based Qubit® ds DNA HS Assay Kit (Thermo Fisher Scientific). All single libraries were pooled into several sequencing library pools with an equal DNA amount per sample. Subsequently, the sequencing library pools were pooled separately with libraries of other projects for sequencing in several NextSeq HighOutput runs. Clustering of the library pools was performed on the NextSeq® 500 sequencing system (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ia

tag: subject

tag: Sex

value: male


title: P063 control male 40


title: 7-5N_HL3FVCCXY_L8


title: W6_DG_18

description:
mRNA count data
AWO22587-0042-W6-DG-18

value: MO


title: P063 control male 28


title: 7-1_HL3FVCCXY_L4


title: P063 control male 24


title: bladder tissue (7 days after spinal cord injury) rep1 [S1-1]

value: 7 days after spinal cord injury


title: 276_TA_20

description:
mRNA count data
AWO22587-0038-276-TA-20


title: 6-10_HL3FVCCXY_L4


title: 202_TA_20

description:
mRNA count data
AWO22587-0035-202-TA-20


title: 6-4_HL3FVCCXY_L4


title: Control H3K4me3 rep8

tag: disease state

value: Enthorinal Cortex

tag: antibody


title: 5-5_HL3FVCCXY_L4


title: 165_VD_17

description:
mRNA count data
AWO22587-0036-165-VD-17

tag: study

tag: location


title: 5-4N_HL3FVCCXY_L4


title: P063 control male 12


title: 7-6N_HL3FVCCXY_L8


title: 19_DG_17

description:
mRNA count data
AWO22587-0034-19-DG-17

tag: animal info

value: Steer

tag: vaccinated


title: 138_VD_17

description:
mRNA count data
AWO22587-0037-138-VD-17

tag: dewormed


title: P063 control male 21


title: 152_PS_19

description:
mRNA count data
AWO22587-0040-152-PS-19


title: P055 IA male 28

value: InvasiveAspergillosis


title: 128_VD_17

description:
mRNA count data
AWO22587-0043-128-VD-17


title: 134_MH_19

description:
mRNA count data
AWO22587-0033-134-MH-19


title: 4-6_HL3FVCCXY_L4

tag: treatment

tag: tissue


title: P055 IA male 54


title: P055 IA male 48


title: 146_MH_19

description:
mRNA count data
AWO22587-0030-146-MH-19


title: 4-4_HL3FVCCXY_L2


title: P055 IA male 41


title: P055 IA male 22


title: 5-1_HL57YCCXY_L6


title: 261_TA_20

description:
mRNA count data
AWO22587-0029-261-TA-20


title: 107_MH_19

description:
mRNA count data
AWO22587-0028-107-MH-19


title: P055 IA male 25


title: 273_TA_20

description:
mRNA count data
AWO22587-0031-273-TA-20


title: P055 IA male 15


title: 232_PS_19

description:
mRNA count data
AWO22587-0027-232-PS-19


title: 180_VD_17

description:
mRNA count data
AWO22587-0032-180-VD-17


title: P055 IA male 12


title: 3-9N_HL3FVCCXY_L8


title: 3-1N_HL3FVCCXY_L8


title: 4-3N_HL3FVCCXY_L8


title: 121_VD_17

description:
mRNA count data
AWO22587-0026-121-VD-17


title: 114_MH_19

description:
mRNA count data
AWO22587-0025-114-MH-19


title: P50_3

city: Jeju

first: Mi Gyeong

last: Jang

address: 102 Jejudaehakno

country: South Korea

institute: Jeju National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Tophat
FPKM calculation using Cufflink
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: liver

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

tag: strain

value: liver

tag: group

value: PRF group

value: post natal day 100


title: 4-9N_HL3FVCCXY_L8


title: P50_10

tag: age


title: P053 control male 127

tag: timepoint


title: ND_9

value: Normal diet group


title: P50_9


title: 205_TA_20

description:
mRNA count data
AWO22587-0024-205-TA-20

tag: treatment group

value: Heifer


title: ND_7


title: 152_VD_17

description:
mRNA count data
AWO22587-0021-152-VD-17


title: P053 control male 100

tag: ia


title: P053 control male 82

tag: subject


title: 178_VD_17

description:
mRNA count data
AWO22587-0023-178-VD-17


title: 129_VD_17

description:
mRNA count data
AWO22587-0020-129-VD-17


title: P053 control male 113

tag: Sex


title: 292_PS_19

description:
mRNA count data
AWO22587-0019-292-PS-19


title: P055 IA male 8


title: 278_PS_19

description:
mRNA count data
AWO22587-0022-278-PS-19


title: HFD_1

value: high-fat diet group


title: P053 control male 75


title: 143_VD_17

description:
mRNA count data
AWO22587-0017-143-VD-17

value: MS

value: Bull


title: ND_6


title: 154_VD_17

description:
mRNA count data
AWO22587-0018-154-VD-17


title: HFD_3


title: Angptl4-knockout Day-5 post wounding

city: Singapore

first: Hong Sheng

last: Cheng

address: 11 Mandalay Road

department: Lee Kong Chian School of Medicine,

institute: Nanyang Technological University

data_processing:
Libraries were sequenced on Illumina NovaSeq6000.
Cell Ranger (v.3.1.0) was used to convert raw Illumina BCL files to FASTQ, perform alignment to mouse mm10 reference genome and UMI filtering to produce gene barcode matrices.
Gene expression matrices were processed using Seurat (v3.0) to perform normalization, transformation, cell clustering, and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Gene count matrices in mtx format as well as cell barcodes and features in tsv format.

source_name: CD45+ immune cells from wound tissues

extract_protocol:
Skin tissues were dissociated using 1mg/ml Type 3 collagenase and 10U/ml DNAseI for 1 hour in a 37°C water bath. The cells were strained through a 30 μm strainer and washed with PBS. Cells were blocked with 3% BSA containing Fc Blocker for 30 minutes, and then stained with CD45-APC (pan-hematopoietic cell marker) and propidium iodide (Live/Dead stain) for 1 hour on ice. After staining, cells were washed twice with PBS before sorting on the FACSAria Fusion cell sorter. Live immune cells (CD45+ PI-) cells were collected, washed twice with PBS, and counted on a hemocytometer before proceeding to single cell library preparation.
Single cell droplets and cDNA libraries were prepared using the 10X Genomics Chromium Single Cell 3’ V3 kit together with the Chromium Controller as per manufacturer’s instructions.

treatment_protocol: 3 mm excisional wounds were performed on shaved and depilated wild-type C57BL6/J and Angptl4-/- mice using a biopsy punch. Mice were euthanized 1- and 5-days post wounding, and wound tissue was harvested.

tag: genotype

tag: cell type

value: CD45+ immune cells from skin wound

value: Day-5 post wounding


title: HFD_2


title: P043 IA female 88

value: female


title: P053 control male 55

value: control

value: male


title: P043 IA female 91


title: P043 IA female 84


title: Wild type Day-5 post wounding


title: 207_TA_20

description:
mRNA count data
AWO22587-0013-207-TA-20

tag: study


title: Angptl4-knockout Day-1 post wounding

value: Day-1 post wounding


title: P053 control male 91


title: P043 IA female 77


title: 111_PS_19

description:
mRNA count data
AWO22587-0015-111-PS-19

value: Healthy

tag: location


title: P043 IA female 74


title: P053 control male 69


title: 101_MH_19

description:
mRNA count data
AWO22587-0016-101-MH-19

tag: animal info


title: 70_DG_17

description:
mRNA count data
AWO22587-0010-70-DG-17

value: MO

tag: vaccinated


title: 244_TA_20

description:
mRNA count data
AWO22587-0012-244-TA-20

tag: dewormed


title: 136_VD_17

description:
mRNA count data
AWO22587-0011-136-VD-17


title: scRNA-seq_KO-P25

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

institute: International Centre for Translational Eye Research

data_processing:
Sc RNAseq:  The preprocessing steps such as generation and demultiplexing of FASTQ files from the sequencing reads, aligning to UCSC mm10 transcriptome, and generating raw count matrices were conducted using Cell Ranger v2.1 (10x Genomics) with default parameters. We performed downstream analysis using the R software package Seurat v3.2.2 (Butler et al., 2018). We removed low-quality cells with less than 500 genes detected and all genes expressed in less than 10 cells, leaving 26,764 cells and 19,324 genes for further analysis. Principal Component Analysis (PCA) was performed on a submatrix of the top 1,000 most variable genes computed, using the function FindVariableGenes from the Seurat package. Then, we removed the batch effect between samples using the package Harmony (Korsunsky et al., 2019). In particular, we removed variables associated with two separate sequencing runs (B1 and B2) and WT and AdipoR1-/- conditions to remove the non-cell-type-specific factors that impact cell clustering. We evaluated the number of top principal components by the elbow method keeping 17 PCs for clustering and data visualization. The cells were clustered using a shared nearest neighbor (SNN) modularity optimization-based clustering algorithm (FindClusters in the Seurat package). To visualize cells in two dimensions, we used Uniform Manifold Approximation and Projection (UMAP) (Becht et al., 2019). The cluster-specific genes were computed using FindAllMarkers from the Seurat package, using the MAST test with the number of UMIs detected as a latent variable (Finak et al., 2015). The same test was used to compute differentially expressed genes between WT and AdipoR1-/- within cell clusters. Cell clusters were annotated by assessing known cell-type-specific markers.
Bulk RNAseq:  Sequence data were demultiplexed using bcl2fastq software (Illumina), and their quality was assessed using FastQC (Babraham Bioinformatics). Reads were aligned to the reference mouse genome assembly (mm10) and quantified using the Rsubread software package with standard parameters (Liao et al., 2019), yielding on average 29 million counts per sample. Differential expression analysis was performed with EdgeR (v3.20.9) (Robinson et al., 2010).
Sc and bulk RNAseq:  Functional enrichment analysis was conducted on the identified differentially expressed genes, using the findGO.pl function from the HOMER suite (Hypergeometric Optimization of Motif Enrichment, v4.9.1) (Heinz et al., 2010). To correct for multiple hypotheses testing, the Benjamini and Hochberg FDR correction was used, and we retained terms at FDR < 0.05.
Genome_build: mm10

source_name: retina

extract_protocol:
Sc RNAseq:  Eyes were enucleated for retina tissue isolation. After removing the anterior chamber and lens, retinal cells were dissociated using the Papain Dissociation System (#LK003153, Worthington Biochemical) following the manufacturer's instructions. In each of the six experimental groups (WT and AdipoR1-/- at P19, P25, and P30), four retinae were used to prepare single-cell suspensions at a final concentration of 1,000 cells/µl.    Bulk RNAseq:   Eyes from AdipoR1-/- and WT mice at P30 were enucleated and placed in 60 mm dishes with PBS immediately following cervical dislocation. The anterior segment of the eye, including cornea, iris, and lens, was removed using dissecting scissors. The retinas from both eyes were carefully removed and transferred to 400 µl of RNAlater stabilization solution (#AM7920, Thermo Fisher). The posterior eyecups, consisting of RPE, choroid, and sclera, were transferred to 400 µl of RNAprotect tissue reagent (#76104, Qiagen). Eyecups were incubated at room temperature for 10 min and briefly agitated to detach RPE cells from the choroid/sclera. After removing the choroid-sclera, the remaining RPE cells were pelleted by centrifugation for 5 min at 685 x g. The isolated retinas and RPE cells in stabilization solution were subjected to extraction of total RNA using RNeasy Micro Kit (#74004, Qiagen) following the manufacturer's protocol.
Sc RNA-Seq:   For each group, freshly dissociated cells (~10,000) were loaded into a 10x Genomics Chromium Single Cell system using v2 chemistry following the manufacturer's instructions. In the first batch (B1: WT and AdipoR1-/- at P30), two libraries were pooled and sequenced on Illumina NextSeq500 with ~76 million reads per library. In the second batch (B2: WT and AdipoR1-/- at P19 and P25), four libraries were pooled and sequenced on Illumina NovaSeq6000 with ~143 million reads per library.  Bulk RNAseq:   Total RNA (~100 ng per sample) was used for library preparation by following the Illumina TruSeq Stranded Total RNA Library Prep Kit protocol. Libraries were then sequenced (paired-end 100 cycles) with the Illumina NextSeq 500 platform, yielding approximately 40 million raw reads per library.

value: retina

tag: age (days)


title: 266_TA_20

description:
mRNA count data
AWO22587-0009-266-TA-20

value: Steer


title: P043 IA female 70

value: InvasiveAspergillosis


title: scRNA-seq_WT-P25

tag: tissue

value: WT


title: scRNA-seq_KO-P19

tag: strain


title: SiO2-56d spatial transcriptomics

city: Nanjing

first: Chao

last: Jie

state: Jiangsu

address: 87 Dingjiaqiao Rd

department: Department of Physiology

institute: Southeast University

data_processing:
Library strategy: Spatial Transcriptomics
bcl2fastq tools for base calling
Spaceranger software for single spot identifying
PCA and UMAP/TSNE for dimensionality reduction
Spaceranger and Seurat for finding clusters
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression text files with tab-delimited

source_name: lung section

growth_protocol: Male C57BL/6 were raised in a cage at a stable temperature (22 °C ± 2 °C) and humidity (40% ± 10%) with a 12-h light–dark cycle.

extract_protocol:
The total cDNA was extracted  for libraries construction by Visium Spatial Gene Expression kit according the standard protocol
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Male C57BL/6J mice (6 weeks of age, 22±1 g weight) were anaesthetized with pentobarbital sodium (1%, 50 mg/kg in ddH2O) administered by intraperitoneal injection. After the fur on the neck was shaved, the skin was disinfected with 75% alcohol, and an incision (1 cm) was made on the skin along the midline. We bluntly separated the soft tissue in front of the neck to expose the trachea. For the mice in the SiO2-7d and SiO2-56d groups, we administered 100 µl of silica suspension (50 mg/ml) to the lungs via intratracheal instillation. For the mice in the NS-7d and NS-56d groups, we administered NS via the same method. For the model group (mice instilled with SiO2 suspension), mouse with obviously high density shadow  on CT were included. Lung samples  for spatial transcriptomics sequencing were collected from four mice, namely the NS-7d, SiO2-7d, NS-56d, and SiO2-56d samples. Whole lung of each mouse was removed as fast as fossible after euthanasia. Lung tissues were trimmed near the hilum in the horizontal direction and then immediately frozen in OCT on dry ice.

value: lung section

tag: treatment

value: instilllation of SiO2 suspension for 56d


title: 72_VD_15

description:
mRNA count data
AWO22587-0007-72-VD-15


title: scRNA-seq_WT-P19


title: 195_PS_19

description:
mRNA count data
AWO22587-0014-195-PS-19


title: P063 control male 15

tag: age


title: P043 IA female 67

tag: timepoint


title: P043 IA female 60


title: 101_VD_17

description:
mRNA count data
AWO22587-0008-101-VD-17

tag: treatment group


title: 68_VD_15

description:
mRNA count data
AWO22587-0006-68-VD-15


title: P043 IA female 53

tag: ia


title: P043 IA female 49

tag: subject


title: P043 IA female 42

tag: Sex


title: NS-56d spatial transcriptomics

value: instilllation of NS for 56d


title: Wild type Day-1 post wounding

tag: genotype


title: SiO2-7d spatial transcriptomics

value: instilllation of SiO2 suspension for 7d


title: vas deferens rep_4 from the 21 months old mice

city: Guangzhou

first: Yun

last: Xie

address: No. 58 Zhongshan 2nd Road, Yuexiu District, 0080, China.

institute: sun yat-sen university

data_processing:
Cutadapt was used to trim adapters and filter for sequences.
The 150 bp paired-end reads were mapped to the reference genome by using hisat2.
The reads mapped the genome were calculated using HTseq.
Genome_build: mm10
Supplementary_files_format_and_content: read counts table

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
The library was prepared using Illumina TruSeq Stranded Total RNA Library Prep Kit (Illumina Inc., San Diego, CA, USA)

value: vas deferens

value: 21 months


title: P043 IA female 81


title: P043 IA female 56


title: 6_VD_15

description:
mRNA count data
AWO22587-0005-6-VD-15

value: MS

value: Bull


title: NS-7d spatial transcriptomics

value: instilllation of NS for 7d


title: P043 IA female 15

value: female


title: 55_VD_15

description:
mRNA count data
AWO22587-0004-55-VD-15


title: cauda epididymis rep_2 from the 21 months old mice

value: cauda epididymis


title: W3_DG_18

description:
mRNA count data
AWO22587-0239-W3-DG-18

value: Healthy


title: vas deferens rep_3 from the 21 months old mice


title: 40_VD_15

description:
mRNA count data
AWO22587-0003-40-VD-15


title: P018 control female 90

value: control


title: vas deferens rep_2 from the 21 months old mice


title: vas deferens rep_1 from the 21 months old mice


title: P043 IA female 63


title: P043 IA female 46


title: 20_VD_15

description:
mRNA count data
AWO22587-0002-20-VD-15

value: Heifer


title: corpus epididymis rep_4 from the 21 months old mice

value: corpus epididymis


title: P043 IA female 22

value: InvasiveAspergillosis


title: 140_DG_17

description:
mRNA count data
AWO22587-0235-140-DG-17

value: MO

value: Steer


title: 58_DG_17

description:
mRNA count data
AWO22587-0236-58-DG-17


title: P018 control female 67


title: corpus epididymis rep_2 from the 21 months old mice


title: 162_MH_19

description:
mRNA count data
AWO22587-0240-162-MH-19


title: cauda epididymis rep_3 from the 21 months old mice


title: cauda epididymis rep_4 from the 21 months old mice


title: P018 control female 63


title: corpus epididymis rep_1 from the 21 months old mice


title: P018 control female 56


title: caput epididymis rep_3 from the 21 months old mice

value: caput epididymis


title: 140_MH_19

description:
mRNA count data
AWO22587-0233-140-MH-19


title: 179_MH_19

description:
mRNA count data
AWO22587-0238-179-MH-19


title: P018 control female 70


title: P018 control female 83


title: P043 IA female 1


title: corpus epididymis rep_3 from the 21 months old mice


title: caput epididymis rep_1 from the 21 months old mice


title: 148_DG_17

description:
mRNA count data
AWO22587-0229-148-DG-17


title: 243_PS_19

description:
mRNA count data
AWO22587-0234-243-PS-19


title: initial segment rep_3 from the 21 months old mice

value: initial segment


title: cauda epididymis rep_1 from the 21 months old mice


title: 15_VD_15

description:
mRNA count data
AWO22587-0001-15-VD-15


title: 109_DG_18

description:
mRNA count data
AWO22587-0232-O109-DG-18


title: caput epididymis rep_4 from the 21 months old mice


title: P018 control female 1


title: 131_MH_19

description:
mRNA count data
AWO22587-0231-131-MH-19


title: 281_TA_20

description:
mRNA count data
AWO22587-0225-281-TA-20


title: P015 IA male 151

value: male


title: 130_PS_19

description:
mRNA count data
AWO22587-0237-130-PS-19


title: P018 control female 46


title: caput epididymis rep_2 from the 21 months old mice


title: 132_MH_19

description:
mRNA count data
AWO22587-0230-132-MH-19


title: P018 control female 39


title: efferent ductules rep_3 from the 21 months old mice

value: efferent ductules


title: efferent ductules rep_2 from the 21 months old mice

value: 21 months


title: Y53_DG_18

description:
mRNA count data
AWO22587-0226-Y53-DG-18


title: KYSE-30-shTFAM rep3

city: Kaifeng

first: Dengke

last: Bao

state: Henan

address: Jinming Road

department: School of Pharmacy

institute: Henan University

data_processing:
Sequencing was carried out using a 2x150 paired-end (PE) configuration; image analysis and base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq instrument，image analysis and base calling were conducted by the NovaSeq Control Software (NCS) + OLB + GAPipeline-1.6 (Illumina) on the NovaSeq instrument，image analysis and base calling were conducted by the Zebeacall on the MGI2000 instrument.
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: Human ESCC cell lines KYSE-30 with Drp1 overexpression or TFAM knockdown were routinely cultured in RPMI-1640 (10040-CVR, Corning) medium supplemented with 10% fetal bovine serum (04-001-1Acs, BI).

extract_protocol:
Total RNA of ESCC cells as indicated were extraction using TRIzol Reagent (Qiagen).
The integrity of RNA from ESCC cells were examined with Bioanalyzer 2100 (Agilent, Santa Clara, CA), and RNA samples with RIN > 7 were subjected to library construction using standard Illumina protocols and sequenced on Illumina novaseq by Genewiz Suzhou, In.

treatment_protocol: For transfection, KYSE-30 cells were seeded in 6-well plates to 60% to 80% confluence. Then the vectors pcDNA3.1(+)-Drp1 or pSilencer3.1-H1 neo-shTFAM were respectively transfected into ESCC cells using the Lipofectamine 2000 reagent (11668019, Invitrogen) according to the manufacturer’s instructions. Stable transfectants were generated by limiting dilution after selection with G418 (10131027, Invitrogen) for 3 weeks.

tag: cell line

tag: cell type

value: Human esophageal squamous cell carcinoma (ESCC) cell lines

value: Stable transfection with pSilencer3.1-H1 neo-shTFAM


title: 174_MH_19

description:
mRNA count data
AWO22587-0223-174-MH-19

tag: study

tag: location

value: MS

value: Bull


title: efferent ductules rep_1 from the 21 months old mice


title: initial segment rep_4 from the 21 months old mice


title: P018 control female 22

value: female


title: P015 IA male 106


title: initial segment rep_1 from the 21 months old mice


title: 184_VD_17

description:
mRNA count data
AWO22587-0224-184-VD-17

tag: animal info

tag: vaccinated


title: KYSE-30-shTFAM rep1


title: 127_VD_17

description:
mRNA count data
AWO22587-0219-127-VD-17

tag: dewormed


title: R1_DG_18

description:
mRNA count data
AWO22587-0228-R1-DG-18


title: P018 control female 15


title: KYSE-30-Drp1 rep3

value: Stable transfection with pcDNA3.1(+)-Drp1


title: P018 control female 19

value: control


title: P015 IA male 144


title: 154_PS_19

description:
mRNA count data
AWO22587-0218-154-PS-19

value: Healthy


title: efferent ductules rep_4 from the 21 months old mice

tag: tissue


title: initial segment rep_2 from the 21 months old mice

tag: strain


title: 147_MH_19

description:
mRNA count data
AWO22587-0227-147-MH-19

value: Heifer


title: P015 IA male 141

value: InvasiveAspergillosis


title: 154_MH_19

description:
mRNA count data
AWO22587-0217-154-MH-19


title: P015 IA male 137


title: KYSE-30-Drp1 rep2

tag: treatment


title: P015 IA male 113

tag: age


title: 108_PS_19

description:
mRNA count data
AWO22587-0221-108-PS-19


title: vas deferens rep_4 from the 3 months old mice

value: vas deferens

value: 3 months


title: 151_MH_19

description:
mRNA count data
AWO22587-0216-151-MH-19

value: Steer


title: W2_DG_18

description:
mRNA count data
AWO22587-0222-W2-DG-18

value: MO


title: testis rep_4 from the 21 months old mice

value: testis


title: KYSE-30-shTFAM rep2


title: 192_VD_17

description:
mRNA count data
AWO22587-0220-192-VD-17


title: P015 IA male 92

tag: timepoint

value: male


title: 158_MH_19

description:
mRNA count data
AWO22587-0215-158-MH-19

tag: treatment group


title: vas deferens rep_3 from the 3 months old mice


title: testis rep_3 from the 21 months old mice

value: 21 months


title: P015 IA male 75

tag: ia


title: P015 IA male 82

tag: subject


title: testis rep_2 from the 21 months old mice


title: testis rep_1 from the 21 months old mice


title: vas deferens rep_1 from the 3 months old mice


title: KYSE-30-Drp1 rep1

value: Human esophageal squamous cell carcinoma (ESCC) cell lines


title: P015 IA male 66

tag: Sex


title: Non-inflammatory bowel disease, sample 216

city: Ithica

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

institute: Cornell University

description:
nIBD_17_0236_216
10XDISCEL_004_S4
Separated colonic epithelial cells from non-inflammatory bowel disease - sample 216

data_processing:
Sequencing was demultiplexed, aligned to the genome, and quality checked using 10X Genomics Cell Ranger software.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data contains barcodes, gene list, and counts matrix.

source_name: Non-inflammatory bowel disease_colon

extract_protocol:
Extracted non-inflamed portions of colon
Libraries were prepped according to 10X Genomics Chromium Single Cell 3' kits (v3 chemistry)

tag: subject status

value: non-inflammatory bowel disease

value: colon

value: separated colonic epithelial cells


title: Human MDM mock-infected, rep2

city: Provo

first: Brett

middle: E

last: Pickett

state: UT

department: Microbiology and Molecular Biology

institute: Brigham Young University

data_processing:
Trimming: TrimGalore v0.6.4, default parameters
Mapping: Salmon v1.2.0, default parameters
Quality Control: FastQCv0.11.8, default parameters
Differential Expression: edgeRv3.32.0, default parameters
Genome_build: Homo_sapiens GRCh38.98
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: Monocyte-derived macrophage

growth_protocol: Monocyte cells were then induced to become adherent macrophages by exposing them to phorbol 12-mystrate 13-acetate (PMA) and incubating in 3 mL of RPMI 1640 complete media at 37⁰C for 24 hours.

extract_protocol:
Total RNA was extracted from cells using Trizol reagent according to manufacturer’s protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Infected with Chikungunya virus (CHIKV-LR strain) at 0.1 multiplicity of infection (MOI)

tag: cell line

value: uninfected


title: KYSE-30 Control rep3

tag: cell type

value: untreated


title: KYSE-30 Control rep2


title: Non-inflammatory bowel disease, sample 217

description:
nIBD_17_0236_217
10XDISCEL_005_S5
Separated colonic epithelial cells from non-inflammatory bowel disease - sample 217


title: P015 IA male 54


title: cauda epididymis rep_4 from the 3 months old mice

value: cauda epididymis


title: cauda epididymis rep_3 from the 3 months old mice


title: Non-inflammatory bowel disease, sample 206

description:
nIBD_17_0236_206
10XDISCEL_002_S2
Separated colonic epithelial cells from non-inflammatory bowel disease - sample 206

value: Crohn's Disease


title: vas deferens rep_2 from the 3 months old mice


title: Crohn's disease, sample 364

description:
CD_uninflamed_17_0236_364
10XDISCEL_008_S8
Separated colonic epithelial cells from Crohn's Disease - sample 364

source_name: Crohn's disease_colon


title: 124_VD_17

state: TX

description:
mRNA count data
AWO22587-0214-124-VD-17

source_name: Whole blood

tag: study

value: MS

value: Bull


title: Human MDM infected (24hpi), rep1

value: infected


title: 220_PS_19

description:
mRNA count data
AWO22587-0212-220-PS-19

tag: location

value: Heifer


title: Crohn's disease, sample 299

description:
CD_uninflamed_17_0236_299
10XDISCEL_006_S6
Separated colonic epithelial cells from Crohn's Disease - sample 299


title: Human MDM mock-infected, rep1


title: cauda epididymis rep_1 from the 3 months old mice

value: 3 months


title: Human MDM infected (24hpi), rep2


title: cauda epididymis rep_2 from the 3 months old mice


title: 165_MH_19

description:
mRNA count data
AWO22587-0209-165-MH-19

value: Healthy

tag: animal info


title: KYSE-30 Control rep1


title: Non-inflammatory bowel disease, sample 214

description:
nIBD_17_0236_214
10XDISCEL_003_S3
Separated colonic epithelial cells from non-inflammatory bowel disease - sample 214


title: Crohn's disease, sample 189

description:
CD_uninflamed_17_0236_189
10XDISCEL_001_S1
Separated colonic epithelial cells from Crohn's Disease - sample 189


title: GABAergic-enriched brain organoids from parent #4

city: Campinas

first: Fabio

last: Papes

address: Rua Carl Von Linaeus

institute: University of Campinas

data_processing:
Individual feature count matrices were generated with the ‘cellranger count’ command from CellRanger 4.0.0
The aggregated matrix was generated with the ‘cellranger aggr’ command from CellRanger 4.0.0
Genome_build: GRCh38 2020-A (by 10x Genomics)
Supplementary_files_format_and_content: CellRanger outputs containing feature count matrices

source_name: sub-pallial brain organoid

growth_protocol: Brain organoids were produced from iPSCs, using mTeSR medium for 3 days, Neurobasal medium containing N2 and GEM21 suplements for 7 days, Neurobasal medium containing GEM21 and FGF-2 (20ng/mL) for 14 days, followed by maturation in Neurobasal medium

extract_protocol:
Single cell RNA-Seq libraries were produced using the 10x genomics protocol and the Chromium Single Cell 3ʹ Reagent Kit v3
Illumina libraries were generated using the Chromium Single Cell 3ʹ Reagent Kit v3 and sequenced at a depth of 20,000 per single cell, totaling  ~400M reads per library.
single cell RNA-Seq

treatment_protocol: Organoids in samples 5 and 7 were treated with CHIR99021 (3uM) for 2 days starting at 10 days in vitro

value: iPSC-derived brain organoids

tag: genotype

value: parental control


title: 103_DG_18

description:
mRNA count data
AWO22587-0213-O103-DG-18

value: MO

value: Steer

tag: vaccinated

tag: dewormed


title: Human MDM infected (8hpi), rep1


title: 111_VD_17

description:
mRNA count data
AWO22587-0211-111-VD-17


title: 126_MH_19

description:
mRNA count data
AWO22587-0208-126-MH-19


title: corpus epididymis rep_1 from the 3 months old mice

tag: tissue

value: corpus epididymis

tag: strain


title: 108_MH_19

description:
mRNA count data
AWO22587-0205-108-MH-19


title: corpus epididymis rep_4 from the 3 months old mice

tag: age


title: 110_DG_18

description:
mRNA count data
AWO22587-0207-O110-DG-18


title: GABAergic-enriched brain organoids from PTHS patient #4

tag: treatment

value: with Wnt agonist CHIR99021

value: PTHS patient


title: corpus epididymis rep_2 from the 3 months old mice


title: 296_PS_19

description:
mRNA count data
AWO22587-0204-296-PS-19

tag: treatment group


title: caput epididymis rep_4 from the 3 months old mice

value: caput epididymis


title: treated pallial brain organoids from PTHS patient #4

source_name: pallial (cortical) brain organoid


title: caput epididymis rep_3 from the 3 months old mice


title: 64_DG_17

description:
mRNA count data
AWO22587-0206-64-DG-17


title: Human MDM infected (8hpi), rep2

tag: timepoint


title: 108_VD_17

description:
mRNA count data
AWO22587-0210-108-VD-17


title: V-rep2

city: Shanghai

first: Xi

last: Chen

address: 8th Panshan Road

institute: Second Military Medical University

description: Gene expression in Hela cells transfected with vector

hyb_protocol: Sample hybridization was performed for 16 hours at 45°C according to standard protocol. Washing and staining was performed on Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip scanner 3000.

data_processing: The data were processed with Expression Console Software. Normalization was performed by the Signal Space Transformation-Robust multi-array average method (sst-RMA).

label: biotin

label_protocol: Labeling was performed according to manufacturer's standard protocol.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: HeLa cell lines expressing wild-type and mutant HBx stably was constructed.

value: HeLa

tag: genotype/variation

value: transfected with vector


title: pallial brain organoids from PTHS patient #4


title: 294_PS_19

description:
mRNA count data
AWO22587-0202-294-PS-19

extract_protocol: Total RNA was isolated from Tempus Blood Tubes with Tempus Spin RNA Isolation Kit


title: WT-rep1

description: Gene expression in Hela cells transfected with wild-type HBx

source_name: Hela_wild-type HBx

value: transfected with wild-type HBx


title: 39_DG_17

description:
mRNA count data
AWO22587-0203-39-DG-17


title: corpus epididymis rep_3 from the 3 months old mice


title: caput epididymis rep_2 from the 3 months old mice


title: caput epididymis rep_1 from the 3 months old mice


title: pallial brain organoids from parent #4 (replicate 2)


title: M2-rep1

description: Gene expression in Hela cells transfected with  mutat-2 HBx

source_name: Hela_mutat-2 HBx

value: transfected with  mutat-2 HBx


title: WT-rep2


title: V-rep1


title: 170_MH_19

description:
mRNA count data
AWO22587-0201-170-MH-19

value: MS

value: Bull


title: 284_TA_20

description:
mRNA count data
AWO22587-0200-284-TA-20


title: pallial brain organoids from parent #4 (replicate 1)


title: M1-rep2

description: Gene expression in Hela cells transfected with  mutat-1 HBx

source_name: Hela_mutat-1 HBx

value: transfected with  mutat-1 HBx


title: M2-rep2


title: pallial brain organoids from parent #4 (replicate 3)


title: initial segment rep_3 from the 3 months old mice

value: initial segment

value: 3 months


title: Neural progenitor cells (low passage) - PTHS patient #4 - replicate 3

data_processing:
Transcript-level quantification using Salmon (version 0.14.1)
Genome_build: GENCODE 32 basic annotation (GRCh38)
Supplementary_files_format_and_content: Salmon quantification outputs

source_name: Neural progenitor cells

growth_protocol: Neural progenitor cells (passage 5) were cultured in DMEM/F12 medium containing N2 and SM1 suplements, along with FGF-2 (20 ng/mL).

extract_protocol:
Total RNA was extracted using Rneasy Mini Plus kit (Qiagen).
Libraries were made using the TruSeq Stranded mRNA kit (Illumina) and sequenced on a NovaSeq6000 S4 instrument to produce 150 PE read at ~40M reads per library (6Gb production)

value: iPSC-derived neural progenitor cells


title: M1-rep1


title: 196_VD_17

description:
mRNA count data
AWO22587-0199-196-VD-17

data_processing: NanoString nSolver Analysis Software v4.0 was utilized for quality assessment and raw gene count accession. Four housekeeping, six positive spike-in, and eight negative control genes were used for intersample count normalization.

value: Healthy

value: Heifer


title: 173_DG_17

description:
mRNA count data
AWO22587-0198-173-DG-17

value: MO


title: initial segment rep_2 from the 3 months old mice


title: 106_VD_17

description:
mRNA count data
AWO22587-0197-106-VD-17

value: Steer


title: M3-rep1

description: Gene expression in Hela cells transfected with  mutat-3 HBx

source_name: Hela_mutat-3 HBx

value: transfected with  mutat-3 HBx


title: 125_MH_19

description:
mRNA count data
AWO22587-0196-125-MH-19


title: 172_VD_17

description:
mRNA count data
AWO22587-0195-172-VD-17


title: efferent ductules rep_4 from the 3 months old mice

value: efferent ductules


title: Neural progenitor cells (low passage) - PTHS patient #4 - replicate 1

value: PTHS patient


title: M3-rep2

value: HeLa


title: Neural progenitor cells (low passage) - parent #4 - replicate 2

value: parental control


title: initial segment rep_4 from the 3 months old mice


title: efferent ductules rep_2 from the 3 months old mice


title: 155_MH_19

description:
mRNA count data
AWO22587-0193-155-MH-19


title: M4-rep1

description: Gene expression in Hela cells transfected with  mutat-4 HBx

source_name: Hela_mutat-4 HBx

value: transfected with  mutat-4 HBx


title: Neural progenitor cells (low passage) - PTHS patient #1 - replicate 3


title: Ct-rep1

description: Gene expression in Hela cells transfected with C-terminal truncated mutation HBx

source_name: Hela_C-terminal truncated mutation HBx


title: efferent ductules rep_1 from the 3 months old mice


title: efferent ductules rep_3 from the 3 months old mice


title: Neural progenitor cells (low passage) - parent #4 - replicate 3


title: Neural progenitor cells (low passage) - PTHS patient #4 - replicate 2


title: 160_MH_19

description:
mRNA count data
AWO22587-0194-160-MH-19


title: testis rep_3 from the 3 months old mice

source_name: testis rep_3 from the 3 months old mice

value: testis


title: 18

first: Jinfei

last: Zhang

state: Guangdong

address: 483 Wushan Road

institute: SCAU

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) 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.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Salmonella enterica subsp. enterica serovar Typhimurium

growth_protocol: RNA was extracted from clones cultured in LB broth after 4 h mating

extract_protocol:
Bacterial cells were collected by 8000×g centrifugation for 10 min
The library was constructed using an Illumina TruSeq RNA sample Prep Kit v2

treatment_protocol: In the absence of antibiotics

tag: evolved lins

value: Evolved clone

tag: antibiotics treatment

value: no

tag: plasmid-bearing

value: yes


title: M4-rep2

tag: cell line


title: Neural progenitor cells (low passage) - parent #4 - replicate 1

tag: cell type


title: Neural progenitor cells (low passage) - PTHS patient #1 - replicate 1