title: Rpd3-KD

city: Tokyo

first: Kaoru

last: Sato

address: 35-2 Sakae-cho, Itabashi-ku

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

description:
4 days knockdown
siRpd3-4days

data_processing:
adaptors were trimmed in BGI
depletion of dm6 ribosomal RNAs by bowtie2 v2.2.4
mapped to dm6 transcriptome by bowtie2 v2.2.4
culculating FPKM
Genome_build: Drosophila melanogaster dm6
Supplementary_files_format_and_content: siMi2-genes-FPKM.csv
Supplementary_files_format_and_content: siMi2-TE-FPKM.csv

source_name: OSC

growth_protocol: OSCs were grown at 26°C in culture medium prepared from Shields and Sang M3 Insect Medium (Sigma) supplemented with 0.6 mg/mL glutathione, 10% FBS, 10 mU/mL insulin, and 10% fly extract (Saito et al. 2009).

extract_protocol: RNA libraries were raised using TruSeq RNA Library Prep Kit (illunima) according to the manufacturer’s instructions in BGI.

treatment_protocol: Total RNAs were isolated using ISOGEN (Nippon Gene) according to the manufacturer’s instructions.

value: Drosophila ovarian somatic cell

tag: knockdown

value: rpd3 4days


title: A. viteae F

status: Public on Apr 10 2020

type: SRA

city: Sainte-Anne-de-Bellevue

first: Lucienne

last: Tritten

state: QC

address: 21111 Lakeshore Road

department: Institute of Parasitology

country: Canada

institute: McGill University

library_source: transcriptomic

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Genome_build: https://parasite.wormbase.org/Acanthocheilonema_viteae_prjeb1697/Info/Index
Supplementary_files_format_and_content: excel, expression profiles: summary of miRNA candidates identified in secretions of A. viteae adult females and males

molecule: total RNA

organism: Acanthocheilonema viteae

source_name: in vitro culture media, secretions

growth_protocol: Females and males were separated and cultured for up to 3 weeks at 1-2 worms per ml RPMI-1640 containing 200 U/ml penicillin and 200 µg streptomycin, and 4 mM L-glutamine, at 37 °C, 5 % CO2.

extract_protocol:
Total RNA purification kit (Norgen Biotek #17200, blood protocol
Illumina Truseq Small RNA Preparation

treatment_protocol: Collected culture media were spun at 1000 x g for 30 min at 4 °C, filtered through 0.22 µm pores, and frozen at -20 °C for several weeks. Upon thawing, media were concentrated over a 3 kDA membrane. Concentrated media were further spun 45 min at 12,000 x g and ultracentrifuged as follws:  2 h at 100,000 x g, 4°C; the pellet was washed once with PBS, and centrifuged again for 2h at 100,000 x g, 4 °C.

tag: Sex

value: Female

tag: Stage

value: adult


title: JJN3_clone_F21

type: RNA

city: Salamanca

first: Ana Belén

last: Herrero Hernández

state: Salamanca

address: Campus Universitario Miguel de Unamuno

department: Hematology

country: Spain

institute: Cancer Research Institute of Salamanca

hyb_protocol: Total RNA was hybridized to Affymetrix PrimeView Human Gene Expression Arrays following the manufacturer’s instructions

scan_protocol: Fluorescence signals were detected using the GeneChip Scanner 3000 7G (Affymetrix) and data stored as .CEL files

data_processing: Raw data was normalized with the Robust Multi-array Average (RMA) algorithm, which included sequential background correction, intra- and inter-microarray well normalization, probe set summarization and calculation of expression signals

label: biotin

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA

growth_protocol: Cell were grown in RPMI 1640 supplemented with 10% fetal bovine serum and antibiotics at 37ºC with 5% of CO2

extract_protocol: Total RNA was extracted from three independent FAM46C WT or KO clones using an RNeasy mini kit (Qiagen, Valencia, CA, USA)

treatment_protocol: Not applicable

tag: cell line

value: JJN3 plasma cell leukemia cell line

tag: genotype

value: FAM46C KO


title: BL_LOV_4M_SL_3

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

country: Italy

institute: University of Trento

data_processing:
RNASeq data were aligned on the P. communis genome using the new Tuxedo protocol. Alignment was carried out with HiSAT2, while read counting analysis was performed with StringTie. For the analysis fo the genes differentially expressed was used DEseq2.
Genome_build: Pyrus communis Genome v1.0 Draft Assembly & Annotation (see GDR database, www.rosaceae.org)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Pyrus communis

source_name: pear skin

extract_protocol:
RNA extraction was performed, for each of the three biological replicates with the Spectrum Plant total RNA kit (Sigma-Aldrich Co., St. Luis, MO, USA). RNA was quantified using a NanoDrop ND-8000 spectrophotometer (Thermo Scientific, Waltham, MA, USA), while its purity and integrity was assessed with a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
For each replicate/sample, 3 mg of RNA was used for the construction of a non-directional Illumina RNA-seq library, using TrySeq RNA sample preparation kits, v2 (Illumina, San Diego, CA, USA). Libraries were quantified using quantitative PCR and quality control was performed with the DNA 1000 series II chip bioanalyzer (Agilent, Santa Clara, CA, USA). Sequencing of libraries was performed with an Illumina HiSeq 1000 Sequencer using TruSeq SBS v3-HS kit (100 cycles) and TruSeq SR Cluster v3-cBot-HS kits (Illumina, San Diego, CA, USA) generating 100-bp reads.

value: postharvest

tag: cultivar

value: cv. Blanquilla


title: JJN3_clone_F3


title: 1_9_pat_GROseq: GRO-seq from ovaries of 1.9 pat transgenic strain

city: Moscow

first: Pavel

last: Komarov

address: Kurchatov sq. 2

country: Russia

institute: Institute of Molecular Genetics of the Russian Academy of Sciences

data_processing:
Library strategy: GRO-seq
smallRNA-seq: Reads with clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG) were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie2 to dm3 genome assembly and transgene sequences.
GRO-seq: Reads were clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG), reads smaller than 19 nt were discarded. Reads were mapped to the dm3/R5 genomic assembly of transgene sequence by bowtie2 and deduplexed. Only single-mapped reads were used for the construction the genomic profiles.
Genome_build: dm3
Supplementary_files_format_and_content: smallRNA-seq: Tab-delimited file include the raw counts of clipped read occurrences.  GRO-seq: Genomic profiles of RPM-normalized single-mapped reads.

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were grown according to standard protocols.

extract_protocol:
smallRNA-seq: Total RNA was isolated by Trizol (Invitrogene) and size-fractioned by PAGE (19-29 nt).
smallRNA-seq: Libraries of small RNAs 19-29 nt were constructed as previously described in (Muerdter et al. 2012)
GRO-seq: Nuclei were purified from homogenized ovaries, and were used for run-on reacton with Br-UTP in vitro (Rozkov et al. 2013).
GRO-seq: De novo synthesized RNA was subjected to library preparation for RNA-seq.

tag: tissue

value: ovaries

tag: strain

value: 1.9 pat

tag: molecule subtype

value: nascent RNAs


title: BL_LOV_4M_SL_2


title: BL_LOV_4M_SL_1


title: SS BAL DC2_3 1

city: Newcastle

first: Laura

last: Jardine

address: Framlington Place

department: Faculty of Medical Sciences

country: United Kingdom

institute: Newcastle University

hyb_protocol: Transcripts were detected using a NanoString Immunology v2 panel according to the manufacturer's instructions. Experiments using blood and BAL DC2/3 included an additional 30-gene add-on to the Immunology v2 panel, designed to detect DC and monocyte/macrophage genes. Hybridisation occurred under 'High Sensitivity' settings.

scan_protocol: FOV 555

data_processing: Data normalization was performed in nSolver version 3.

source_name: Saline BAL, DC2/3

extract_protocol: Lysates from 1-2x10e4 cells per sorted population were prepared using 5μl buffer RLT (Qiagen) with 1% beta-mercaptoethanol (Sigma).

tag: sample type

value: Saline Control BAL

tag: treatment

value: Saline

tag: cell type

value: BAL, DC2/3


title: JJN3_clone_F2


title: JJN3_control_5

value: Control


title: Amplodipine 1

city: Stanford

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

country: USA

institute: Stanford's Postdoctoral Scholar programs

data_processing:
TrimGalore
STAR
RSEM
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression values (TPM) generated by RSEM

source_name: iPSC-CM

growth_protocol: Cardiogenic differentiation of human iPSC was performed using a chemically defined protocol using activator and inhibitors of the Wnt signaling pathway.

extract_protocol: Total RNA was isolated using Direct-zol RNA MiniPrep Plus (Zymo Research) in accordance to manufacturer’s instructions, followed by DNAse treatment.

treatment_protocol: iPSC-CMs were treated with calcium channel blockers or DMSO as a vehicle for a period of 14 days. Each calcium channel blocker was applied at its serum peak concentration.

tag: agent

value: Amplodipine

value: iPSC-CM

tag: cell origin

value: Human


title: Breast_Atypia_S-10-10

city: Amherst

first: D.

middle: Joseph

last: Jerry

state: MA

address: 661 North Pleasant St

department: Veterinary and Animal Sciences

institute: University of Massachusetts

description: Gene expression from laser capture microdissection of breast epithelium

hyb_protocol: The biotin labeled cDNA was hybridized to GeneChip® Human Gene 1.0 ST Arrays (Affymetrix) for 16 hrs. Chips were washed and stained with phycoerythrein-conjugated streptavidin (Life Technologies, Carlsbad, CA) in a Fluidics Station 450 (Affymetrix) according to the manufacturer’s recommended procedures.

scan_protocol: Arrays were scanned and fluorescence intensities determined using the GeneChip Scanner 3000 7G with autoloader instrument system and Affymetrix GeneChip Command Console (AGCC) Scan Control Software (v 4.0.0.1567), producing CEL files.

data_processing: Analysis of microarray data: The data were normalized using the Single-Channel Array Normalization (SCAN) and Universal exPression Codes (UPC) methods from the BioConductor R package “SCAN.UPC” (Gentleman et al., 2004). This package produces standardized expression measures that are used to estimate whether a given gene or probe is active in a specific sample (Piccolo et al., 2012; Piccolo et al., 2013). “ComBat”, an empirical Bayesian framework for adjusting data for batch effects (Johnson et al., 2007), was applied. Limma (Smyth, 2004) was used to identify differentially expressed genes in a paired-sample model, with HNB and AH samples paired by patient. A total of 1039 probesets were selected with adjusted p<0.05. Two methods were employed to identify gene signatures distinguishing AH and normal benign tissue. Agglomerative clustering was performed using AGNES (Kaufman, 2005a) to visualize gene expression patterns. Prediction Analysis of Microarrays (PAM) was used as an alternative approach to define a minimal gene expression signature (Kaufman, 2005b).

label: Biotin

source_name: Laser capture microdissection of breast epithelium_Atypia

label_protocol: cDNA synthesis, amplification, and labeling: The Ovation® FFPE WTA System (NuGEN San Carlos, CA) was used to prepare amplified cDNA from FFPE-derived total RNA because amplification is initiated at the 3´ end as well as randomly throughout the whole transcriptome in the sample which makes this system ideal for amplification of RNA obtained from FFPE samples.  50 ng of RNA was used to prepare the cDNA according to the manufactures instructions. The cDNA was then purified using columns from the QIAquick PCR Purification kit (Qiagen). Buffer PB from the purification kit was added to the cDNA reaction, loaded on to the column, and centrifuged for 1 min at 13,000xg. The flow through was discarded and 80% EtOH was added to the column and centrifuged for 1 min at 13,000xg. The 80% EtOH wash step was repeated and the purified cDNA was eluted with nuclease free water.  An aliquot containing 5 g of cDNA was fragmented and labeled using the Encore Biotin Module (NuGEN) according to the manufacturer’s instructions. The biotin labeled cDNA was hybridized to Affymetrix 1.0 ST microarrays by Genome Explorations.

growth_protocol: Samples microdissected from H&E stained FFPE tissue samples

extract_protocol: Microdissection and RNA isolation: The H&E stained sections of the atypical hyperplasias (AH) samples were used to estimate the total area for microdissection. A minimum area of 10 x 106 μm2 was required to ensure a minimum of 50 ng total RNA.  Consecutive tissue sections  (8-μm thick) were cut using RNase-free conditions and mounted on membrane slides (MMI). The first and every 10th section were H&E stained for microscopic evaluation of AH tissue. The AH lesion and benign glandular tissue were marked by a breast pathologist (GMC) for microdissection. The benign glandular areas were selected to be at least 1 cm away from the AH lesion. The tissues on membrane slides were deparaffinized in 3 changes of Xylene, and allowed to air dry under a vacuum in a desiccator for 30 min prior to the LCM procedure. The unstained sections were oriented for microdissection aided by landmarks defined on the H& stained slides. Using MMI Cell Tools software (Version Celltools-4.4 #261, Rockledge FL), areas to be microdissected were circumscribed on the monitor using the MMI system stylus. Microdissected AH and benign tissues were collected separately onto caps using the MMI Cell Cut laser capture system (MMI Inc., Rockledge FL). The microdissected tissue was collected in 150 l digestion buffer containing 10 l proteinase K (miRNeasey FFPE Kit, Qiagen), was kept overnight at 55C and stored at -80C until further processing.  Total RNA was isolated from LCM tissue using the miRNeasey FFPE Kit (Qiagen) according to the manufacturer’s instructions and quantified using a NanoDrop1000 (Thermo Fisher Scientific).

treatment_protocol: Microscopic evaluation: Atypical hyperplasias (AH) arise in the terminal duct lobular units of the breast and are divided into ductal and lobular subtypes based on cytomorphologic characteristics. Ductal lesions included in the study are atypical ductal hyperplasia (ADH) and flat epithelial atypia (FEA); lobular lesions included atypical lobular hyperplasia (ALH) and lobular carcinoma in situ (LCIS). Patients with either ductal or lobular atypia were included in the analysis to assess differences in transcriptional features. To assure consistency of diagnoses, the specimens were reviewed by a single breast pathologist (GMC) and marked for microdissection. Sufficient RNA was obtained from 21 AH lesions (from 20 patients).  The tissues included 8 lobular lesions (ALH and/or LCIS), 11 ductal lesions (ADH and/or FEA), and 2 that were a mixture of ductal and lobular lesions (sampled separately). The mean age was 51.9 years (SD=7.9 years).

tag: gender

tag: patient age

tag: r/l breast

value: R

tag: histology

value: Atypia

tag: copathology report

value: ADH, FEA


title: JJN3_control_1

value: JJN3 plasma cell leukemia cell line


title: JJN3_control_2


title: 2_4_hls/hls: Small RNAs from ovaries of 2.4 spn-E/spn-E transgenic strain

data_processing:
smallRNA-seq: Reads with clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG) were passed through length (>18 nt), quality (80% of nt should contain >=20 Phred score) and artefacts filters, and mapped by bowtie2 to dm3 genome assembly and transgene sequences.
GRO-seq: Reads were clipped 3'-adapter (5'-TGGAATTCTCGGGTGCCAAGG), reads smaller than 19 nt were discarded. Reads were mapped to the dm3/R5 genomic assembly of transgene sequence by bowtie2 and deduplexed. Only single-mapped reads were used for the construction the genomic profiles.
Genome_build: dm3
Supplementary_files_format_and_content: smallRNA-seq: Tab-delimited file include the raw counts of clipped read occurrences.  GRO-seq: Genomic profiles of RPM-normalized single-mapped reads.

value: 2.4 spn-E/spn-E

value: small RNAs


title: WT-0h

city: Daejeon

first: Bu-Yeo

last: Kim

address: 1672 Yuseongdae-ro, Yuseong-gu

department: Herbal Medicine Research Division

country: South Korea

institute: Korea Institute of Oriental Medicine

data_processing:
RNA sequencing was performed using a NovaSeq 6000 Sequencing system (Illumina). QuantSeq reads were aligned to a reference genome (genome assembly version of hg19) using Bowtie2 to estimate the amount of transcripts. Read count data were then normalized to obtain fragments per kilobase of million reads mapped (FPKM) using the edgeR R package.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include read count values for each sample.

source_name: induced pluripotent stem cells (iPSCs)

growth_protocol: We used human induced pluripotent stem cells (iPSCs) which have been established from human foreskin fibroblasts (CRL-2429; American Tissue Culture Collection (ATCC), Manassas, VA, USA). iPSCs were maintained on mitomycin C-treated STO feeder cells (mouse embryo fibroblasts; CRL-1503; ATCC) or on hESC-qualified Matrigel Matrix (#354277; Corning, Bedford, MA, USA)-coated culture plates with mTeSR1 medium (Stem Cell Technologies, Vancouver, BC, Canada). iPSCs were gently detached by treatment with ReLeSR (Stem Cell Technologies). STO cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS; Gibco), 100 Units/ml penicillin/100 μg/ml streptomycin (Gibco), 0.1 mM β-mercaptoethanol (β-ME; Gibco), and 1% non-essential amino acid (NEAA; Gibco).

extract_protocol:
Total RNAs from BV-untreated and –treated iPSCs were extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. After quality assessment of the RNA by 2100 Bioanalyzer Instrument (Agilent, Santa Clara, CA, USA), only samples with an RNA integrity number >7.0 were included in the QuantSeq analysis.
From 500 ng total RNA, double-stranded cDNA libraries were prepared using a TruSeq Stranded Total RNA LT Sample Prep Kit with Rico-zero Gold (Illumina, San Diego, CA, USA). The sequencing library is prepared by random fragmentation of the cDNA sample, followed by 5’ and 3’ adapter ligation. Adapter-ligated fragments are then PCR amplified and gel purified.

treatment_protocol: Purified BV was purchased from Chung-Jin Biotech (Asan, Korea) and dissolved in phosphate buffered saline (PBS). iPSCs were seeded on 12-well culture plates, incubated overnight, and then treated with BV (2.5 μg/mL) for 1 and 4 hrs.

tag: origin

value: iPSCs established from human foreskin fibroblasts

value: Human Induced Pluripotent Stem Cells


title: WT-1h


title: WT-4h


title: Piwi-KD

description:
4 days knockdown
siPiwi-4days

value: Drosophila ovarian somatic cell

tag: knockdown

value: piwi 4days


title: BL_CT_4M_SL_3

tag: Stage

value: postharvest

value: cv. Blanquilla


title: BL_CT_4M_SL_2

tag: cultivar


title: Donor 12 Control

city: Denver

first: Satria

last: Sajuthi

state: Colorado

address: 1400 Jackson St.

institute: National Jewish Health

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_37_S78_L002

data_processing:
Raw FASTQ files were trimmed with skewer
Trimmed reads were aligned to human transcriptome hg38 with HiSAT2
Gene counting were performed with HTSEQ-count
Individual count table were combined with R statistical software to create a raw count matrix
Raw count matrix was then normalized by size factor with DESEQ2
Genome_build: Hg38
Supplementary_files_format_and_content: Raw gene count matrix and normalized gene count matrix in tab separated value file format

source_name: Nasal brushing

growth_protocol: Expansion and differentiation of nasal airway epithelial cells at air-liquid interface (ALI) in vitro was conducted according to established protocols (Everman et al., Methods Mol Bio, 2018).

extract_protocol:
RNA was purified from sample lysates using the Quick-RNATM MiniPrep kit (Zymo Research). Lysates were centrifuged at 16,000xg for 2 minutes in a QIAshredder (Qiagen) to homogenize sample and remove insoluble debris before beginning standard manufacturer protocol with inclusion of optional DNase step. RNA was eluted in 30 mL of DNase/RNase free water and eluent was passed through the column one additional time to ensure maximum RNA recovery from filter.
KAPA Biosystems mRNA HyperPrep whole transcriptome libraries (Roche) were constructed with 250 ng RNA per sample and 12 cycles of library amplification. Libraries were barcoded using Illumina Dual-Index adapters (Integrated DNA Technologies) and paired-end sequenced using the Illumina NovaSeq® 6000 system.

treatment_protocol: Upon mucociliary differentiation (day 28-32), ALI cultures were washed with PBS and then apically treated with mock extract or PM2.5 extract in a final volume of 20 µL media. PBS wash and stimulation were repeated at 24h, followed by on-membrane lysis using RNA lysis buffer (Zymo Research) containing 40 mM dithiothreitol for total RNA collection after an additional 24h of culture incubation.

tag: tissue

value: Nasal airway epithelium

tag: age

value: ALI day 28-32

value: OECtrl

tag: asthma status

value: Healthy


title: 2_4_hls/+: Small RNAs from ovaries of 2.4 spn-E/+ transgenic strain

value: ovaries

tag: strain

tag: molecule subtype


title: Donor 12 High dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_40_S106_L002

tag: treatment


title: BL_CT_4M_SL_1


title: BL_1MCP_4M_SL_3


title: 1_9_mat_GROseq: GRO-seq from ovaries of 1.9 mat transgenic strain

value: 1.9 mat

value: nascent RNAs


title: Donor 12 Low dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_38_S82_L002


title: 1_9_pat: Small RNAs from ovaries of 1.9 pat transgenic strain

value: 1.9 pat


title: 1_9_mat: Small RNAs from ovaries of 1.9 mat transgenic strain


title: BL_1MCP_4M_SL_2


title: 3_6I: Small RNAs from ovaries of 3.6I transgenic strain


title: Donor 11 Control

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
AirPolAMP4_1_S87_L001


title: Donor 11 Moderate dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
AirPolAMP4_2_S88_L001


title: BL_1MCP_4M_SL_1


title: 3_6R: Small RNAs from ovaries of 3.6R transgenic strain


title: CLD-rep4

city: Ames

first: Andrew

middle: J

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were qulaity checked with fastqc, mapped to Agam 4.7 whole genome using STAR v2.5.2b
FeatureCounts from subread was used to estimate read counts for genes
Genome_build: AgamP4.7
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample ...

organism: Anopheles gambiae

source_name: Approximately 5 day old adult female An. gambiae abdominal carcass tissues (internal organs removed).

extract_protocol:
Following treatment with liposomes, mosquitoes were challenged with P. berghei. ~24hrs post-infection, mosquitoes were dissected to remove digestive and reproductive organs, then the remaining abdomen was processed for RNA isolation. Samples were prepared from ~15 mosquitoes and processed in TRIzol reagent. RNA was evaluated for quality using an Agilent 2100 Bioanalyzer. Samples were sent to the DNA Facility at Iowa State University for library construction and stranded mRNA-Seq. Gene expression analysis was performed the Genome Informatics Facility at Iowa State University.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Keele

tag: developmental stage

tag: Sex

value: female

tag: condition

value: injected with clodronate liposomes (experimental) one day prior to malaria parasite challenge.


title: 2_4I: Small RNAs from ovaries of 2.4I transgenic strain

value: small RNAs


title: Donor 12 Moderate dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_39_S93_L002


title: CLD-rep3

value: Approximately 5 day old adult female An. gambiae abdominal carcass tissues (internal organs removed).


title: 2_4R: Small RNAs from ovaries of 2.4R transgenic strain


title: Donor 10 Water Extract Control for NIST

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_33_S108_L002

value: WECtrl


title: Donor 10 Control

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_29_S104_L002


title: Donor 10 NIST

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_36_S67_L002

value: NIST


title: CLD-rep1


title: 2_1I: Small RNAs from ovaries of 2.1I transgenic strain


title: 2_1R: Small RNAs from ovaries of 2.1R transgenic strain


title: Donor 10 High dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_32_S105_L002


title: LP-rep4

value: injected with control liposomes (experimental) one day prior to malaria parasite challenge.


title: Donor 10 Moderate dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_31_S81_L002


title: Donor 10 Low dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_30_S103_L002


title: 1_9R: Small RNAs from ovaries of 1.9R transgenic strain


title: LP-rep2


title: LP-rep3


title: Donor 9 Water Extract Control for NIST

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_13_S95_L002


title: LP-rep1


title: X5_SC

city: Baltimore

first: Yun

last: Guan

state: Maryland

address: Ross 350, 720 Rutland Ave

department: Anesthesiology and Critical Care Medicine

institute: Johns Hopkins University

data_processing:
reads aligned to rn6 genome with HiSat2
count table was generated using featureCounts
differential gene expression performed using DESeq2
Genome_build: rn6
Supplementary_files_format_and_content: count table was generated using featureCounts

organism: Rattus norvegicus

source_name: Ipsilateral spinal cord

growth_protocol: Adult male rats weighing 350-400g

extract_protocol:
Tissue dounce homogenized in Trizol & RNA extracted from aqueous phase with Quick-RNA Plus kit (Zyno) with on-column DNAseI digestion
1ug total RNA used as input to NEBNext Ultra II Directional RNA Library Prep kit for Illumina after poly(A_ selection by the NEBNext poly(A) mRNA Isolation Module and barcoded using the NEBNext Multiplex Oligos

treatment_protocol: Paclitaxel given intraperiotoneally 1.5 mg/kg on days 1,3,5,7. SCS administered at 50Hz, 0.2ms, constant current, 608 hours/session daily at 80% MoT

value: Ipsilateral spinal cord

tag: group

value: PTX+Sham SCS

value: male


title: Donor 9 Control

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_9_S79_L002

value: Nasal airway epithelium

value: ALI day 28-32

value: OECtrl


title: X4_SC


title: Donor 9 NIST

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_16_S77_L002

value: Healthy


title: Mi-2-KD

description:
4 days knockdown
siMi2-4days

tag: cell type

value: Drosophila ovarian somatic cell

value: mi-2 4days


title: Donor 9 High dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_12_S89_L002


title: X2_SC


title: 1_9I: Small RNAs from ovaries of 1.9I transgenic strain

value: ovaries


title: CLD-rep2

value: Keele

value: female


title: X3_SC


title: Donor 9 Moderate dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_11_S72_L002


title: Patient 6 B3_wufsh

city: CHANG SHA

first: FU

middle: YUN

last: FENG

state: HUNAN

address: No. 138 Tonglu Road, Yuelu District, Hexi Distric

department: Blood

country: China

institute: The Third Xiangya Hospital of Central South University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 3 out of 6 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.Differentially expressed circRNAs with statistical significance between two samples or two groups were identified using fold change cutoff or through Volcano Plot filtering respectively.The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.        .

source_name: MM samples

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: subject status

value: multiple myeloma patient

value: 55 years

tag: tissue source

value: multiple myeloma

value: bone marrow


title: Patient 5 B2_xjx

value: 48 years


title: X1_SC

value: Ipsilateral spinal cord


title: Donor 9 Low dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_10_S113_L002


title: Patient 4 B1_dzhzh

value: 35 years


title: S5_SC

value: PTX+SCS

value: male


title: Patient 3 A3_hlm

source_name: normal liver samples

value: 58 years

value: normal liver


title: Donor 8 Control

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_1_S84_L002

value: Nasal airway epithelium

value: ALI day 28-32

value: OECtrl

value: Healthy


title: Donor 8 NIST

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_8_S70_L002

value: NIST


title: S1_SC


title: Donor 8 High dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_4_S76_L002


title: N3_SC

value: Naive


title: N2_SC


title: Series14_FerretTrachea_IAV_d3_6

city: New York

first: Daniel

last: Blanco Melo

state: NY

address: One Gustave L. Levy Place, Box 1124

department: Microbiology

institute: Icahn School of Medicine at Mount Sina

description:
Mf-trachea-H3N2-3d-F533-2
processed data file: RawReadCounts_Ferret.tsv

data_processing:
cDNA libraries were sequenced using an Illumina NextSeq 500 platform
Raw sequencing reads were aligned to the human genome (hg19) or Ferret genome (MusPutFur1.0) using the RNA-Seq Alignment App (v2.0.1) on Basespace (Illumina, CA)
Differential gene expression analysis was performed using DESeq2 (implemented in the RNA Express App (v1.1.0) on Basespace (Illumina, CA)) comparing Infected samples to their correspondent mock treated sample, for each virus/cell type.
Genome_build: human (hg19), Ferret (MusPutFur1.0)
Supplementary_files_format_and_content: Tab separated value (tsv) matrix of raw read counts per gene for each sample.

molecule: polyA RNA

organism: Mustela putorius furo

source_name: IAV infected 4 month old Ferret

extract_protocol:
TruSeq Stranded mRNA LP
Total RNA was extracted using RNeasy Mini Kit (Qiagen)

tag: tissue/cell type

value: Trachea

value: IAV infected (1E5 PFU)

tag: time after treatment

value: 3 days


title: S2_SC


title: Donor 8 Water Extract Control for NIST

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_5_S98_L002

value: WECtrl


title: Donor 8 Moderate dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_3_S94_L002


title: N1_SC


title: Patient 2 A2_chchl

value: 45 years

value: bone marrow


title: Series14_FerretTrachea_IAV_d3_5

description:
Mf-trachea-H3N2-3d-F533-1
processed data file: RawReadCounts_Ferret.tsv


title: Donor 8 Low dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_2_S111_L002


title: Patient 1 A1_gzhx

value: 32 years


title: CI-AKI Rep3_mRNA

city: Fuzhou

first: Zhiqing

last: Wang

state: Fujian

address: NO. 156, North Xierhuan Road

department: Department of Cardiology

institute: 900 Hospital of the Joint Logistics Team

data_processing:
Raw reads were preprocessed with Seqtk to filter out adapter sequences in reads, bases near 3'-end with quality value lower than 20, and reads of length smaller than 25, and reads of ribosome RNA.
Clean reads were aligned to reference genome (rn6) by Hisat2 (Ver2.0.4) with default parameters.
Gene expression was quantified and then normalized as FPKM(Fragments Per Kilobase of exon model per Million mapped reads). In this step, fragments of each gene were counted with Stringtie(version 1.3.0) and normalized into trimmed mean of M values (TMM), after which FPKM values of every gene were calculated by Perl scripts.
Genome_build: rn6
Supplementary_files_format_and_content: text file with FPKM and read count

source_name: kidney

growth_protocol: Rats were pretreated with water dehydration for 48 hours before the experiment, and were allowed to recover with free access to tap water after surgical procedure. Standard chow was allowed throughout the study.

extract_protocol:
Total RNA was extracted with mirVana miRNA Isolation Kit (Cat #. AM1561, Austin TX, US) and its Standard Operating Protocol(SOP), which then experienced quality control with 2100 Bioanalyzer (Agilent Technologies Santa Clara, US). Afterwards, the total RNA was purified with RNAClean XP Kit (Cat A63987, Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Cat #79254, QIAGEN, GmBH, Germany).
Library was constructed in steps: rRNA removal, fragmentation, synthesis of 1st and 2nd strand of cDNA, end repairment, poly-A appending at 3'-end, adapter ligation, and enrichment. These steps were completed with VAHTS Total RNA-Seq Library Prep Kit for Illumina (Vazyme), Agencourt AMPure XP Beads (Beckman), SuperScript II Reverse Transcriptase (Invitrogen), Qubit dsDNA HS Array Kit (Invitrogen), and Agilent High Sensitivity DNA Kit (Agilent).

treatment_protocol: Rats were pretreated with intravenous injection of indomethacin (10mg/kg) and N-ω nitro-L-arginine methyl ester (10mg/kg) before contrast medium administration.

value: Sprague-Dawley

value: kidney

value: three-month-old

tag: disease state

value: contrast-induced acute kidney injury (CI-AKI)


title: Donor 7 Water Extract Control for NIST

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_25_S92_L002

value: Nasal airway epithelium


title: Series14_FerretTrachea_IAV_d3_4

description:
Mf-trachea-H3N2-3d-F532-2
processed data file: RawReadCounts_Ferret.tsv


title: H460 Resistant vs Sensitive

type: genomic

city: Madrid

first: Carlos

last: Rodriguez Antolin

address: Paseo de la Castellana

department: Genetics

institute: Hospital La Paz Institute for Health Research

description: Microarray data from resistant and sensitive cisplatin H460 lung cancer cell line

hyb_protocol: After probe denaturation and pre-annealing with Cot-1 DNA, hybridization was performed at 65ºC with rotation for 24 h.

scan_protocol: After two washing steps, the microarray was then scanned by the Agilent Microarray Scanner and analyzed with Feature Extraction software (v9.1 Agilent Technologies) and Agilent Cytogenomic 3.0.1.1.

data_processing: The analysis and visualization of the microarray data was performed using Agilent Cytogenomic 3.0.1.1.

molecule: genomic DNA

source_name: Resistan phenotype

label_protocol: After heat inactivation of the enzymes at 65ºC for 20 min, each digested sample was labeled by random priming (Genomic DNA Enzymatic Labeling Kit Agilent) for 2 h using Cy5-dUTP for patient DNAs and Cy3-dUTP for reference DNAs. Labeled products were column purified (Microcon Ym-30 filters, Millipore Corporation).

growth_protocol: Growth protocols were the standard indicated  from the ATCC (Manassas, USA) and ECACC (Sigma-Aldrich, Spain) cells were  cultured as recommended

extract_protocol: DNA (500 ng) from the resistant and the sensitive (used as reference) subtypes of each cell line were double-digested with RsaI and AluI for 2h at 37ºC

treatment_protocol: Cisplatin resistant variant was established from the parental sensitive cell line treated with increasing doses of cisplatine. (Farma Ferrer, Spain)

tag: cell line

value: Lung

tag: chemoterapy drug

value: Cisplatin

tag: phenotype

value: Resistant

source_name: Sensitive phenotype

value: Sensitive


title: OVCAR3 Resistant vs Sensitive

description: Microarray data from resistant and sensitive cisplatin OVCAR3 ovarian cancer cell line

tag: tissue

value: Ovarian


title: leaf_slug_24h_rep3

city: Nijmegen

first: Onno

middle: Wouter

last: Calf

address: Heyendaalseweg 135

department: Molecular Interaction Ecology

country: Netherlands

institute: Radboud University

hyb_protocol: 600 ng of the cRNA were hybridised using the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) following the manufacturer’s protocol at 65°C for 17 h.

scan_protocol: Fluorescence signals were detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron per pixel.

data_processing: Microarray data were analysed using the “limma” software packages from Bioconductor in “R” (R Core Team, 2015; Ritchie et al., 2015). The uploaded data were background-corrected using the “normexp” method and normalized between microarrays using the “quantile” method and Log2-transformed.All raw data were background-corrected and normalized across all arrays.

organism: Solanum dulcamara

source_name: leaf, slug damaged, 24h

label_protocol: Fluorescent cyanine 3-CTP-labelled cRNA was generated using the Low Input QuickAmp Labeling Kit (Agilent Technologies) using oligo-dT primer following the manufacture’s protocol.

growth_protocol: Solanum dulcamara plants were grown from seeds in a greenhouse at a 16 h photoperiod with minimum temperatures of 20/17°C (day/night) and a photon irradiance ~280 µmol m-2 s-1

extract_protocol: The total leaf area that was covered by the clip cage was collected for analyses of gene expression. Total RNA extraction and purification were performed on ground fresh leaf material using the RNeasy® Plant Mini kit (Qiagen) and DNAse I (Fermentas, RNAse-free) following the manufacturer’s instructions. Quality and quantity of the RNA were estimated using a NanoDrop 1000 device (Thermo Fisher Scientific, Waltham, MA, USA) and 1.5 % agarose gel electrophoresis. Equal quantities of total RNA from the four plants of a single plant population at each time point were pooled, resulting in four total RNA samples per treatment (control or induced).

treatment_protocol: The tip of leaf 10 from the apex was fitted with a clip cage to prevent the consumption of the whole leaf in the feeding treatments. Clip cages were left empty or received one adult GFS to initiate feeding exposure for 24 h.This exposure to slugs, that are mostly active at night, includes both locomotion mucus application and feeding. We did not assess when the slugs were actually feeding, but plants in the slug treatments showed substantial feeding damage (estimated by eye, > 1 cm2).

value: leaf

value: slug damaged, 24h

tag: location

value: Goeree


title: leaf_slug_24h_rep4

value: Siethen


title: A2780 Resistant vs Sensitive

description: Microarray data from resistant and sensitive cisplatin A2780 ovarian cancer cell line


title: EGFP-KD

city: Tokyo

first: Kaoru

last: Sato

address: 35-2 Sakae-cho, Itabashi-ku

institute: Tokyo Metropolitan Institute of Gerontology

description:
4 days knockdown
siEGFP-4days

data_processing:
adaptors were trimmed in BGI
depletion of dm6 ribosomal RNAs by bowtie2 v2.2.4
mapped to dm6 transcriptome by bowtie2 v2.2.4
culculating FPKM
Genome_build: Drosophila melanogaster dm6
Supplementary_files_format_and_content: siMi2-genes-FPKM.csv
Supplementary_files_format_and_content: siMi2-TE-FPKM.csv

source_name: OSC

extract_protocol: RNA libraries were raised using TruSeq RNA Library Prep Kit (illunima) according to the manufacturer’s instructions in BGI.

value: Drosophila ovarian somatic cell

tag: knockdown

value: egfp 4days


title: leaf_slug_24h_rep2

tag: treatment

value: Friesland


title: CI-AKI Rep2_mRNA

tag: strain

value: Sprague-Dawley

tag: age

value: male


title: Donor 7 Control

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_21_S68_L002

value: ALI day 28-32

value: OECtrl

tag: asthma status

value: Healthy


title: CI-AKI Rep1_mRNA

value: kidney

value: three-month-old

tag: Sex

value: contrast-induced acute kidney injury (CI-AKI)


title: leaf_slug_24h_rep1

value: Erkner


title: Series14_FerretTrachea_IAV_d3_2

description:
Mf-trachea-H3N2-3d-F531-2
processed data file: RawReadCounts_Ferret.tsv

value: Trachea

value: IAV infected (1E5 PFU)

value: 3 days


title: H23 Resistant vs Sensitive

description: Microarray data from resistant and sensitive cisplatin H23 lung cancer cell line

value: Lung

value: Cisplatin

value: Resistant

value: Sensitive


title: Series14_FerretTrachea_IAV_d3_3

description:
Mf-trachea-H3N2-3d-F532-1
processed data file: RawReadCounts_Ferret.tsv


title: Control Rep3_mRNA

value: control


title: Series14_FerretTrachea_IAV_d3_1

description:
Mf-trachea-H3N2-3d-F531-1
processed data file: RawReadCounts_Ferret.tsv


title: leaf_control_24h_rep4

source_name: leaf, undamaged control, 24h

value: leaf

value: undamaged control, 24h

value: Siethen


title: Control Rep2_mRNA

value: Sprague-Dawley

value: male


title: Series14_FerretTrachea_SARS-CoV-2_d3_4

description:
Mf-Tr-19
processed data file: RawReadCounts_Ferret.tsv

source_name: SARS-CoV-2 infected 4 month old Ferret

value: SARS-CoV-2 infected (5E4 PFU)


title: Donor 7 Moderate dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_23_S58_L002

value: Nasal airway epithelium

value: ALI day 28-32

value: Healthy


title: Donor 7 High dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_24_S62_L002


title: leaf_control_24h_rep3

value: Goeree


title: Donor 7 Low dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_22_S112_L002


title: Series14_FerretTrachea_SARS-CoV-2_d3_3

description:
Mf-Tr-18
processed data file: RawReadCounts_Ferret.tsv

value: Trachea


title: leaf_control_24h_rep2

value: Friesland


title: Series14_FerretTrachea_SARS-CoV-2_d3_1

description:
Mf-Tr-16
processed data file: RawReadCounts_Ferret.tsv

value: 3 days


title: Series14_FerretTrachea_SARS-CoV-2_d3_2

description:
Mf-Tr-17
processed data file: RawReadCounts_Ferret.tsv


title: Donor 6 Control

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
AirPolAMP4_7_S82_L001

value: OECtrl

value: Asthma


title: Donor 7 NIST

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_28_S107_L002

value: NIST


title: Series14_FerretTrachea_Ctl_d3_4

description:
Mf-trachea-naive-3d-F752
processed data file: RawReadCounts_Ferret.tsv

source_name: Mock treated 4 month old Ferret

value: Mock treatment


title: Control Rep1_mRNA

value: kidney

value: three-month-old

value: control


title: leaf_control_24h_rep1

value: leaf

value: undamaged control, 24h

value: Erkner


title: leaf_slug_0h_rep4

source_name: leaf, slug damaged, 0h

value: slug damaged, 0h

value: Siethen


title: hepar tissues circRNA of 12h after liver transplantation-3

city: Zhengzhou

first: chen

last: sanyang

state: erqi

address: No.1, East Jian She Road

department: Department of Hepatobiliary and Pancreatic Surgery

institute: The First Affiliated Hospital of Zhengzhou University

description: circRNA

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Rat circRNA Microarray V2.0, and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, circRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed circRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed circRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: hepar tissues 12h after liver transplantation

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: Hepar tissues of 12h after brain death donor liver transplantation and matched non-brain death donor liver transplantation

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

treatment_protocol: Tissues from liver transplantation and propmptly frozen in the liquid nitrogen

value: liver

tag: gender

value: male


title: leaf_slug_0h_rep2


title: leaf_slug_0h_rep3

value: Goeree


title: hepar tissues circRNA of 12h after liver transplantation-1

description: circRNA


title: Donor 4 Control

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_19_S71_L002

value: Nasal airway epithelium

value: ALI day 28-32


title: leaf_slug_0h_rep1


title: Donor 4 Moderate dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_20_S64_L002


title: Series14_FerretTrachea_Ctl_d3_1

description:
Mf-trachea-mock-3d-F751
processed data file: RawReadCounts_Ferret.tsv

value: Trachea

value: 3 days


title: hepar tissues circRNA of 12h after liver transplantation-2

description: circRNA


title: leaf_control_0h_rep3

source_name: leaf, undamaged control, 0h

value: undamaged control, 0h


title: Donor 5 Moderate dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
AirPolAMP4_6_S92_L001

source_name: Nasal brushing

value: Asthma


title: Donor 6 Moderate dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
AirPolAMP4_8_S83_L001


title: leaf_control_0h_rep2

value: Friesland


title: Donor 3 Control

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_17_S110_L002

value: OECtrl


title: Series13_FerretNW_SARS-CoV-2_d14_2

description:
USA-WA1-2020-F877-14dpi-indexE9
processed data file: RawReadCounts_Ferret.tsv

extract_protocol:
TruSeq RNA Library Prep Kit v2
Total RNA was extracted using RNeasy Mini Kit (Qiagen)

value: Nasal Wash

value: SARS-CoV-2 infected (5E4 PFU)

value: 14 days


title: Series14_FerretTrachea_Ctl_d3_3

description:
Mf-trachea-naive-3d-F751
processed data file: RawReadCounts_Ferret.tsv

value: Mock treatment


title: Series14_FerretTrachea_Ctl_d3_2

description:
Mf-trachea-mock-3d-F752
processed data file: RawReadCounts_Ferret.tsv


title: Series13_FerretNW_SARS-CoV-2_d14_1

description:
USA-WA1-2020-F876-14dpi-indexE7
processed data file: RawReadCounts_Ferret.tsv


title: Donor 3 Moderate dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_18_S88_L002


title: Series13_FerretNW_Ctl_d14_2

description:
Naive-F873-B-14dpi-indexF7
processed data file: RawReadCounts_Ferret.tsv


title: Donor 2 Control

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
AirPolAMP4_3_S89_L001


title: hepar tissues circRNA of 12h after brain death donor liver transplantation-2

description: circRNA

source_name: hepar tissues 12h after brain death donor liver transplantation


title: Series13_FerretNW_Ctl_d14_1

description:
Naive-F873-14dpi-indexF9
processed data file: RawReadCounts_Ferret.tsv


title: CD14+ CD16++ donors 1

city: Montpellier

first: Isabelle

last: DUROUX-RICHARD

address: 80 av Augustin Fliche

country: France

description:
Test
SAMPLE 4

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package:expression suite
For the normalization it uses the average of MammU6 values.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_mean Mamm U6)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (i.e., CD14++ CD16-/CD14+ CD16++) ratios.

label: FAM

source_name: Freshly isolated monocyte CD14+CD16++

label_protocol: Total 100 ng RNA per sample were reverse transcribed to cDNA with Megaplex Human Pool A  stem loop RT primers (version 3.0) (Termofisher)and TaqMan MicroRNA RT kit (Invitrogen) as per manufacturer´s instructions for TLDA,), following preamplification containing MegaPlex Human Pool A PreAmp primers (ThermoFisher)

extract_protocol: Total RNA was extracted with miRNeasy Mcroi Kit (Qiagen)

tag: cell type

value: monocyte


title: Donor 2 Moderate dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
AirPolAMP4_4_S90_L001


title: CD14+ CD16++ donors 2

description:
Test
SAMPLE 5


title: Donor 5 Control

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
AirPolAMP4_5_S91_L001


title: leaf_control_0h_rep4

value: leaf

value: Siethen


title: hepar tissues circRNA of 12h after brain death donor liver transplantation-3

description: circRNA

value: liver

value: male


title: Root_oil_history_oil_rep3

city: Durham

first: Claudia

last: Gunsch

state: NC

address: 100 Science Dr

institute: Duke University

hyb_protocol: labeled DNA and universal standard mixed with hybridization buffer (Agilent) and 10% formamide; hyb 22 hr at 68C

scan_protocol: Scanned on a Nimblegen MS400, images were quantified using Agilent Feature Extraction Software (version 12.1.1.1).

data_processing:
Data normalized using the Microarray Data Manager at http://www.ou.edu/ieg/tools/data-analysis-pipeline
signal to noise ratio of > 2, the signal >200 and >1.3 times the background

organism: uncultured bacterium

source_name: Root of Spartina alterniflora, oil history, oil added

label_protocol: amplified product labeled with cy3 using klenow and random primers at 37C

growth_protocol: The plants were germinated in the spring of 2016 and the experiment begun on May 1, 2016.  It was sampled every 6 months for the next two years, and completely harvested in June 2018. Of 10 replicates for each treatment, only three replicates from June 2018 were anlyzed with GeoChip. Spartina alterniflora seeds were collected in November 2015 in southern Louisiana and placed at 4 °C to stratify.  In February 2016 the microbial community on the surface of the seeds was reduced by subjecting them to a 95% EtOH bath for 3 minutes, then 30%min in 0.825% bleach and rinsed in sterile DI water for 10 seconds.   The seeds were then germinated in DI water and transplanted to trays in a Conviron Model GR48 Plant Grow Room (Controlled Environments Ltd., Winnipeg, Canada).  The growing substrate was a 1:1 mixture of organic humus and vermiculite that was autoclaved three times at 121 °C for 60 min to reduce the microbial community in the substrate.  Seedlings were grown under conditions meant to mimic conditions in southern Louisiana, after the methods of Krauss et al. (1998).  Seedlings were watered with deionized water and given 1 tablespoon of Osmocote fertilizer (14:14:14 NPK).  In April 2016 the plantlets were transferred to the greenhouse and allowed to acclimate to greenhouse conditions for about three weeks.  On May 1st the plantlets were planted into pots filled with inoculum soil.  The inoculum soil was collected from Bay Jimmy, LA at sites that had been heavily oiled (Google maps: 29.44464, -89.88959) or relatively unoiled (Google maps: 29.44006, -89.88583) in the DWH oil spill (Zengel et al., 2015).  Within 60 hours of collection the soil was sieved through a 1cm screen, placed in 1-gallon trade pots and either planted or left unplanted.  The pots were randomized in 5 blocks on an approximate East-West axis on 4 tables oriented approximately North-South.  The plants grew in the inoculum for one month and then the entire plant-soil plug was placed in a 5-gallon mesocosm. Each mesocosm consisted of a 3-gallon trade pot nested in a water-filled 5-gallon bucket.  The soil/plant plug was placed inside of the 3-gallon trade pot containing 2.5 gallons of a 2:3 organic humus to sand mixture. Half of the mesocosms also received 1.6 L of oil naturally weathered oil skimmed off the ocean during the DWH oil spill and distributed by the Gulf of Mexico Research Initiative (GoMRI). To reduce sporefall germination, 0.5 gallons of clean sand were placed in an even layer around the top of the plant. Three weeks after mesocosm construction, 8 grams of Scott’s Osmocote Plus (Marysville, Ohio) was added to the surface and covered with an additional 0.25 gal sand layer. The fertilizer is a patterned-release complete nutrient fertilizer containing 15% N, 9% P, and 12% K (releasing at maximum 1.00 g·m-2 nitrate per month). Drip irrigation supplied water to the surface of each pot, and pots were inserted into buckets in order to maintain a high water table. Drainage tubes were installed near the top of each bucket, allowing some flow through. To prevent reactivity to oil, the 3-gallon trade pots were lined with Teflon bags (P-00113, Welch Flurocarbon, Inc, Dover, NH, USA). The bottom of each bag was punctured to permit drainage. Over the course of the experiment, plants received water from a timer-based drip irrigation, so that some portion of the water would turn over every day.  If necessary, during hot summer months the watering was augmented by hand to maintain the height of the water table.  Once a month, the mesocosms received 1 liter of 5 ppt solution of Instant Ocean salt (Instant Ocean Spectrum Brands, Blacksburg, VA).  Every two months mesocosms were augmented with an additional 4 grams of fertilizer and 1 liter of inoculum, a soil slurry from the same marsh sites used in the original inoculation.  Whenever salt built up on the plant leaves, mesocosms (planted and unplanted) were misted to wash salt off the leaves.

extract_protocol:
RNA was isolated from root and leaf samples using liquid nitrogen grinding and QIAGEN RNEasy PowerSoil Total RNA kit (Qiagen, Germantown, MD). The extracted RNA was converted immediately into cDNA using High Capacity cDNA Reverse Transcription Kit (ThermoFisher, Waltham, MA). cDNA was then sent to Glomics Inc. (Norman, OK) for GeoChip analysis. Glomics Inc. amplified samples using whole community genomic amplification.
Kandalepas, D., Blum, M.J., and Van Bael, S.A. (2015). Shifts in Symbiotic Endophyte Communities of a Foundational Salt Marsh Grass following Oil Exposure from the Deepwater Horizon Oil Spill. PLoS One 10, e0122378.  Krauss, K.W., Chambers, J.L., and Allen, J.A. (1998). Salinity effects and differential germination of several half-sib families of baldcypress from different seed sources. New Forests 15, 53-68.  Zengel, S., Bernik, B.M., Rutherford, N., Nixon, Z., and Michel, J. (2015). Heavily Oiled Salt Marsh following the Deepwater Horizon Oil Spill, Ecological Comparisons of Shoreline Cleanup Treatments and Recovery. PLoS ONE 10, e0132324.

treatment_protocol: Leaves: Approximately 5g of whole, healthy leaves were collected, placed into a clean Ziploc bag and kept in refrigeration. All subsequent processing occurred within 12 hours of collection. Edges were removed from leaves and leaves chopped into smaller chunks.  Leaves were treated with bleach and ethanol to reduce the presence of microbes on the outside of the tissue. Using sterile technique in a biosafety cabinet and following the methods of Kandalepas et al. (2015), leaf pieces were submerged for 10 seconds in 95% ethanol, 2 minutes in 0.525% sodium hypochlorite (10% bleach) followed by 2 minutes in 70% ethanol and frozen in a CTAB buffer (2% CTAB, 0.02M EDTA, 0.1M Tris, 1.4M NaCl final concentrations) at -20 °C until DNA  extraction. Roots: Roots were processed similarly to leaves, however the treatment to remove external microbes was slightly different.  Root pieces were submerged for 10 seconds in 70% ethanol, 2 minutes in 2.625% sodium hypochlorite (50% bleach), followed by 3 rinses in sterile DI water.

tag: source

value: Spartina alterniflora root microbiome

tag: growth

value: oil history, oil added

organism: synthetic construct

tag: reference

value: Synthetic oligonucleotides complementing GeoChip-specific probes for signal normalization.


title: hepar tissues circRNA of 12h after brain death donor liver transplantation-1

description: circRNA


title: Root_oil_history_oil_rep1


title: Series12_FerretNW_IAV_d7_1

description:
pH1N1-d7-nw-F5572
processed data file: RawReadCounts_Ferret.tsv

tag: tissue/cell type

value: IAV infected (1E5 PFU)

value: A/California/04/2009 (pH1N1)

tag: time after treatment

value: 7 days


title: Series12_FerretNW_SARS-CoV-2_d7_2

description:
Mf_NL_Gr3_d7_877
processed data file: RawReadCounts_Ferret.tsv


title: CD14++ CD16- donors 2

description:
Test
SAMPLE 2

source_name: Freshly isolated monocyte CD14++CD16-


title: Donor 1 Moderate dose OE

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_46_S97_L002

value: Nasal airway epithelium

value: ALI day 28-32

value: Asthma


title: Z83 8h

city: Harbin

first: Jian

address: 600 Changjiang Road

institute: Northeast Agricultural University

data_processing:
BGI500 own software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12). The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni .
Genome_build: NCBI_GCF_000188115.3_SL2.50
Supplementary_files_format_and_content: Excels include FPKM values for each Sample

organism: Solanum lycopersicum

source_name: Micro-TOM-EX

extract_protocol:
RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard BGI500 protocols

treatment_protocol: Micro-TOM and Micro-TOM-EX were sown into pots filled with soil and grown under controlled conditions (16h light，NaCl treated) in a greenhouse at the Horticultural station of Northeast Agricultural University

tag: cultivar

value: Micro-TOM-EX


title: LY6Clow mouse 3

description:
Test
SAMPLE 6

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package:expression suite
For the normalization it uses the average of MammU6 values.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_mean Mamm U6)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control (i.e.,LY6Chigh/Ly6Clow) ratios.

organism: Mus musculus

source_name: Freshly isolated monocyte Ly6Clow

label_protocol: Total 10 ng RNA per sample were reverse transcribed to cDNA with Megaplex rodent Pool A  stem loop RT primers (version 2.1) (Termofisher)and TaqMan MicroRNA RT kit (Invitrogen) as per manufacturer´s instructions for TLDA,), following preamplification containing MegaPlex rodent Pool A PreAmp primers (ThermoFisher)


title: Series12_FerretNW_IAV_d7_2

description:
pH1N1-d7-nw-F5576
processed data file: RawReadCounts_Ferret.tsv

source_name: IAV infected 4 month old Ferret

value: Nasal Wash


title: LY6Clow mouse 2

description:
Test
SAMPLE 5


title: Root_oil_history_oil_rep2


title: Series12_FerretNW_SARS-CoV-2_d7_1

description:
Mf_NL_Gr3_d7_376
processed data file: RawReadCounts_Ferret.tsv

value: SARS-CoV-2 infected (5E4 PFU)


title: Z82 8h


title: Root_oil_history_no_oil_rep2

source_name: Root of Spartina alterniflora, oil history, no oil added

value: oil history, no oil added


title: LY6Clow mouse 1

description:
Test
SAMPLE 4

value: monocyte


title: CD14++ CD16- donors 1

description:
test
SAMPLE 1


title: Series12_FerretNW_Ctl_d7_2

description:
Mf_NL_Gr4_d7_873
processed data file: RawReadCounts_Ferret.tsv

value: Mock treatment


title: Root_oil_history_no_oil_rep1


title: Root_oil_history_no_oil_rep3


title: Z81 8h

value: leaf


title: Root_no_oil_history_oil_rep2

source_name: Root of Spartina alterniflora, no oil history, oil added

value: no oil history, oil added


title: Root_no_oil_history_oil_rep3

value: Spartina alterniflora root microbiome


title: Series11_FerretNW_SARS-CoV-2_d3_2

description:
MfNL_Gr3_d3_877
processed data file: RawReadCounts_Ferret.tsv

value: 3 days


title: Series12_FerretNW_Ctl_d7_1

description:
Mf_NL_Gr4_d7_870
processed data file: RawReadCounts_Ferret.tsv


title: LY6Chigh mouse 3

description:
Test
SAMPLE 3

source_name: Freshly isolated monocyte Ly6Chigh


title: Z23 2h


title: Series11_FerretNW_SARS-CoV-2_d3_1

description:
MfNL_Gr2_d3_872
processed data file: RawReadCounts_Ferret.tsv


title: Z21 2h


title: LY6Chigh mouse 2

description:
Test
SAMPLE 2


title: LY6Chigh mouse 1

description:
test
SAMPLE 1


title: Z22 2h


title: Z03 0h


title: White-light-Somatic Replicate C

city: Tabriz

first: Soulmaz

last: Ekhtari

address: 29 Bahman Blvd

country: Iran

institute: Tabriz university

description: White-light-Somatic-C

data_processing:
Illumina HiSeq-2500 used for basecalling.
The adapter contamination was checked, trimmed and reads and then, unknown or low quality bases were trimmed.
Reads of 12 samples were aligned onto V. carteri genome assembly V2 (available in Phytozome; https://phytozome.jgi.doe.gov) using TopHat2 (v2) software using -N 1 --coverage-search --read-realign-edit-dist 0 -g 1 parameters.
Assembly of the transcripts per each sample was made employing Cufflinks software (v2.0.1) with parameters of -p 2 --max-frag-multihits 1.
The assembled transcripts were merged using cuffmerge. Cuffdiff software (v2) was used to test statistically significant differences in transcript abundance between control and treatment groups of both cell-types.
Genome_build: V. carteri genome assembly V2 reference sequence used for read alignment.
Supplementary_files_format_and_content: *-fpkm.txt: Tab-delimited text files include FPKM values for each Sample.

organism: Volvox carteri

source_name: somatic cells

growth_protocol: Cultures were grown synchronously under vegetative conditions using Standard Volvox Medium 29 at 28°C under a 16-8 hour light to dark cycle 30, with average illumination of ~100 μmol photons m-2 s-1 photosynthetically-active irradiation.

extract_protocol:
Three biological replicates per treatment and cell types were used for RNA extraction using Trizol reagent. Total RNA of 12 samples were submitted to the GATC Biotech (Konstanz, Germany) for Illumina-based polyA library preparation and sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Ultraviolet B irradiation treatment (for one hour) was performed using narrowband UV-B lamp (Philips TL40W/12RS) with a light intensity of 0.056 mw/cm-2.

tag: strain/background

tag: genotype/variation

value: wild type

tag: developmental stage

value: After the maturation/before the embryogenesis

value: somatic cells

value: White light


title: Series11_FerretNW_Ctl_d3_1

description:
MfNL_Gr4_d3_870
processed data file: RawReadCounts_Ferret.tsv


title: Series11_FerretNW_Ctl_d3_2

description:
MfNL_Gr4_d3_873
processed data file: RawReadCounts_Ferret.tsv


title: Z02 0h

tag: tissue


title: White-light-Somatic Replicate A

description: White-light-Somatic-A

tag: treatment


title: Series10_FerretNW_SARS-CoV-2_d1_2

description:
MfNL_Gr3_d1_877
processed data file: RawReadCounts_Ferret.tsv

source_name: SARS-CoV-2 infected 4 month old Ferret

tag: strain

value: 1 day


title: UVB-treated-Somatic Replicate C

description: UVB-treated-Somatic-C

value: UVB


title: Root_no_oil_history_oil_rep1

value: Synthetic oligonucleotides complementing GeoChip-specific probes for signal normalization.


title: CD14++ CD16- donors 3

description:
Test
SAMPLE 3


title: Series10_FerretNW_Ctl_d1_2

description:
MfNL_Gr4_d1_873
processed data file: RawReadCounts_Ferret.tsv

source_name: Mock treated 4 month old Ferret


title: CK83 8h

source_name: Micro-TOM

value: Micro-TOM


title: Series10_FerretNW_SARS-CoV-2_d1_1

description:
MfNL_Gr2_d1_872
processed data file: RawReadCounts_Ferret.tsv

value: Nasal Wash


title: leaf_control_0h_rep1

value: undamaged control, 0h

tag: location

value: Erkner


title: UVB-treated-Somatic Replicate B

description: UVB-treated-Somatic-B


title: Root_no_oil_history_no_oil_rep1

source_name: Root of Spartina alterniflora, no oil history, no oil added

value: no oil history, no oil added


title: CK82 8h


title: Leaf_oil_history_oil_rep3

source_name: Leaf of Spartina alterniflora, oil history, oil added

value: Spartina alterniflora leaf microbiome

value: oil history, oil added


title: White-light-Somatic Replicate B

description: White-light-Somatic-B


title: Root_no_oil_history_no_oil_rep2


title: Series10_FerretNW_Ctl_d1_1

description:
MfNL_Gr4_d1_870
processed data file: RawReadCounts_Ferret.tsv

value: Mock treatment


title: UVB-treated-Somatic Replicate A

description: UVB-treated-Somatic-A


title: CK81 8h

value: leaf


title: White-light-Gonidi Replicate C

description: White-light-Gonidi-C

source_name: reproductive cells

value: reproductive cells


title: Z01 0h

value: Micro-TOM-EX


title: mrna-seq Gc

city: Nanjing

first: Shaowu

last: Yin

state: jiangsu

address: College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road,  210023, China.

institute: Nanjing Normal University

data_processing:
The library for sequencing was generated using an Illumina TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) analysis.
Transcriptome sequencing was carried out on an Illumina HiSeq 2500 platform that generated approximately 125-bp paired-end (PE) raw reads by LC Sciences (Houston, TX, USA).
After removing adaptor sequences, ambiguous ‘N’ nucleotides (with the ratio of ‘N’ greater than 5%) and low quality sequences (with quality score less than 20), the remaining clean reads were assembled using trinity software as described for de novo transcriptome assembly without a reference genome. The quality of the assembly was critically assessed by LC Sciences before subsequent
The high-quality trimmed sequences were used for further mapping to the T. fasciatus genome (unpublished data) with Hisat 2.0.4.
Supplementary_files_format_and_content: The expression level of each transcript was measured as the number of clean reads mapped to its sequence. The mapped clean read number was normalized to RPKM (reads per kilo of per million mapped reads) with RSEM 1.2.3. We used DESeq to determine the FDR threshold. FDR < 0.05 and fold change > 2 were considered to indicate significant expression abundance.

organism: Takifugu fasciatus

source_name: liver

growth_protocol: A total of 120 juvenile T. fasciatus (13 ± 1.76 cm in length, 22 ± 2.85 g in weight), supplied from Zhongyang Group Co., Ltd. (Jiangsu Province, China), were randomly transferred to six aquaria with biofiltered water recirculation systems (equipped with cooling and heating functions; volume 200 L; flow rate 5 L/min), and were divided into the control group (G1, G2 and G3; total of 60 individuals) and the experimental group (Ga, Gb and Gc; total of 60 individuals). These individuals were acclimated at 26 ± 1 °C for 2 weeks. During the acclimation period, the commercial fish diet (including 42% w/w protein and 8.0% w/w fat, supplied by Zhenjiang Jiaji Feed Co. Ltd.) was given twice a day until 24 h before the experimental treatments (Figure 1).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s protocol. The total RNA quantity and purity were analysed with a Bioanalyzer 2100 and an RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number > 7.0.
For constructing six cDNA library, approximately 5 μg of total RNA per sample was used for the RNA sample preparations. The library for sequencing was generated using an Illumina TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). Transcriptome sequencing was carried out on an Illumina HiSeq 2500 platform that generated approximately 125-bp paired-end (PE) raw reads by LC Sciences (Houston, TX, USA). After removing adaptor sequences, ambiguous ‘N’ nucleotides (with the ratio of ‘N’ greater than 5%) and low quality sequences (with quality score less than 20), the high-quality trimmed sequences were used for further mapping to the T. fasciatus genome (unpublished data) with Hisat 2.0.4.

treatment_protocol: The water temperature of the CG was maintained at 26 ± 1 °C until the sampling was completed. The water temperature of the three experimental tanks (EG) decreased from 26°C to 19°C at a rate of 0.85 °C /1 h, and then maintained at 19°C for 12h, before decreasing from 19°C to 12°C at the same rate. After the EG was maintained at 12°C for 24 h, both the experimental and control fish were quickly removed for liver dissection.

tag: development stage

value: juvenile fish

value: liver

tag: sample type

value: Experimental


title: CK23 2h


title: Leaf_oil_history_oil_rep2


title: Leaf_oil_history_oil_rep1


title: Leaf_oil_history_no_oil_rep1

source_name: Leaf of Spartina alterniflora, oil history, no oil added

value: oil history, no oil added


title: Leaf_oil_history_no_oil_rep2


title: Leaf_oil_history_no_oil_rep3


title: Leaf_no_oil_history_oil_rep3

source_name: Leaf of Spartina alterniflora, no oil history, oil added

value: no oil history, oil added


title: CK22 2h


title: mrna-seq Gb


title: mrna-seq Ga


title: White-light-Gonidi Replicate B

description: White-light-Gonidi-B

value: wild type

value: After the maturation/before the embryogenesis

value: White light


title: UVB-treated-Gonidi Replicate B

description: UVB-treated-Gonidi-B

value: UVB


title: CK03 0h

value: Micro-TOM


title: mrna-seq G3

value: Control


title: White-light-Gonidi Replicate A

description: White-light-Gonidi-A


title: UVB-treated-Gonidi Replicate A

description: UVB-treated-Gonidi-A


title: Donor 1 Control

description:
AirPol_raw_counts.txt
AirPol_norm_counts.txt
APM5_45_S69_L002

source_name: Nasal brushing

value: Nasal airway epithelium

tag: age

value: ALI day 28-32

value: OECtrl

tag: asthma status

value: Asthma


title: mrna-seq G2


title: mrna-seq G1


title: CK01 0h

value: leaf


title: UVB-treated-Gonidi Replicate C

description: UVB-treated-Gonidi-C

tag: cell type

value: reproductive cells


title: CK02 0h


title: Leaf_no_oil_history_oil_rep1

tag: source

value: Spartina alterniflora leaf microbiome

tag: growth

value: Synthetic oligonucleotides complementing GeoChip-specific probes for signal normalization.


title: Leaf_no_oil_history_no_oil_rep1

source_name: Leaf of Spartina alterniflora, no oil history, no oil added

value: no oil history, no oil added

tag: reference


title: CK21 2h


title: Leaf_no_oil_history_no_oil_rep3


title: Leaf_no_oil_history_no_oil_rep2


title: vhp-1 RNAi injured, bio rep 3

status: Public on Apr 09 2020

city: Dallas

first: Peter

middle: M

last: Douglas

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UT Southwestern Medical Center

description:
vhp1_12
PolyA RNA
processed data file: RNAseq_Processed_matrix_file.xlsx

data_processing:
Basecalling and trimming were performed using CLC Genomics Workbench ver. 9.5.
Sequences were mapped to the whole Caenorhabditis elegans genome using CLC 9.5.
Expression values and Reads per kilobase million (RPKM) were calculated according to default CLC settings.
Genome_build: WBcel235
Supplementary_files_format_and_content: RNAseq_Processed_matrix_file.xlsx: Excel file contains counts, RPKM, TPM, and CPM values for each transcript.

organism: Caenorhabditis elegans

source_name: All tissues

growth_protocol: 25 C on HT115 bacteria and NGM plates supplemented with IPTG and Carbenicillin.

extract_protocol:
Whole worm RNA was extracted using Trizol with freeze/thawing and vortexing. RNA was later enriched for mRNA using oligo(dt) beads.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Blunt force trauma by paralytic agitation in a Precellys Evolution. Collected 1 hour post treatment.

tag: genotype

value: Day 1 adult

value: All tissues

value: Blunt force trauma injury

tag: RNAi

value: vhp-1 RNAi


title: EV injured, bio rep 2

description:
vhp1_5
PolyA RNA
processed data file: RNAseq_Processed_matrix_file.xlsx


title: vhp-1 RNAi uninjured, bio rep 2

description:
vhp1_8
PolyA RNA
processed data file: RNAseq_Processed_matrix_file.xlsx

value: Uninjured


title: vhp-1 RNAi uninjured, bio rep 3

description:
vhp1_9
PolyA RNA
processed data file: RNAseq_Processed_matrix_file.xlsx


title: EV injured, bio rep 3

description:
vhp1_6
PolyA RNA
processed data file: RNAseq_Processed_matrix_file.xlsx


title: EV uninjured, bio rep 3

description:
vhp1_3
PolyA RNA
processed data file: RNAseq_Processed_matrix_file.xlsx


title: EV injured, bio rep 1

description:
vhp1_4
PolyA RNA
processed data file: RNAseq_Processed_matrix_file.xlsx


title: EV uninjured, bio rep 1

description:
vhp1_1
PolyA RNA
processed data file: RNAseq_Processed_matrix_file.xlsx


title: CD14+ CD16++ donors 3

description:
Test
SAMPLE 6

source_name: Freshly isolated monocyte CD14+CD16++

value: monocyte


title: Leaf_no_oil_history_oil_rep2

value: no oil history, oil added


title: 36-L-061-Myom-1_S36

city: Lexington

first: Barry

middle: A.

last: Ball

state: Kentucky

address: 108 Gluck Equine Research Center,

department: Veterinary Scinece

institute: University of Kentucky

description: Stranded

data_processing:
The Fastq files were evaluated for read quality using FastQC 0.11.4.
Trim Galore 0.4.1 was used for adapter and read quality trimming (Phred score threshold of 30).
Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using STAR 2.5.3a (Dobin, Davis et al. 2013).
Reads were annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1.
Fragments per kilobase per million (FPKM) were used to determine the expression level of genes.
Cuffdiff 2.2.1 was used to calculate differentially expressed genes (DEG) between samples from the control and urea groups.
Significance level was set at FDR-adjusted p-value of the test statistic < 0.05 using a Benjamini-Hochberg correction.
Genome_build: EquCab 3.0
Supplementary_files_format_and_content: *_fpkm_tracking.fpkm_tracking: Normalized abundance measurements - Cufflink Gene.FPKM.Tracking

organism: Equus caballus

source_name: Uterus

extract_protocol:
Total RNA was isolated from all myometrial samples using RNeasy Mini Kit (#74104; Qiagen), and DNA digestion was performed on-column using RNase-free DNase I (#79254: Qiagen), followed by cleanup procedures. All procedures were performed according to the manufacturer’s instructions. After extraction, RNA concentration and quality were analyzed using Nanodrop 2000 spectrophotometer (#ND-2000; Thermo Fisher Scientific) and Agilent 2100 Bioanalyzer® (Agilent, Santa Clara, CA, USA). All samples had a 260/280 ratio >2.0 and RNA integrity number (RIN) > 8.0.
A TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA) was used to prepare libraries for mRNA sequencing. Libraries were loaded onto an Agilent DNA 1000 chip and validated on an Agilent 2100 Bioanalyzer (Agilent). Quantitation was performed with the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems. Libraries were run on a NextSeq 500 v2 (Illumina) 300cycles High Output kit in a 2x150 base pairs with paired-end reads.

treatment_protocol: Placentitis was induced in five mares at approximately 290d of gestation (placentitis group), four mares with gestationally age-matched (290 d) pregnancies did not receive any treatment (control group), and the remaining three mares were maintained until approximately 330 d of gestation (prepartum group). For induction of placentitis in the former group, Streptococcus equi subsp. zooepidemicus was introduced intracervically.

value: Myometrium

tag: group

value: Prepartum


title: Healthy gender-matched control

city: Cambridge

first: Adrian

last: Liston

address: Babraham Research Campus

institute: The Babraham Institute

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline (V.3.1.0). Step1: Cellranger mkfastq demultiplexed libraries based on sample indices and converted the barcode and read data to FASTQ files. The conversion into FASTQ files were done using Illumina bcl2fastq (v2.19.0.316).
Step2:  Cellranger count took FASTQ files from cellranger mkfastq and performed alignment, filtering, barcode counting, and UMI counting.  A post sorted genome BAM file and a feature-barcode matrix was generated for each sample using this pipeline.
Step 3: Quality control of the generated matrices (genes expressed in >= 5 cells, cells with gene count more than 200 and less than 5000, cells with less than 20% mitochondrial genes) was performed using Seurat V2.2.
Genome_build: Human reference (GRCh38)
Supplementary_files_format_and_content: A matrix of UMI counts for each feature (i.e. gene; row) that are detected in each cell (column)  in each sample

source_name: Bone marrow

growth_protocol: Not applicable

extract_protocol:
RBC depletion using EasySep™ RBC Depletion Reagent (StemCell Technologies)
Single cell RNAseq libraries were generated using a commercial droplet platform (Chromium system; 10X Genomics). Briefly, the EasySep™ RBC Depletion Reagent (StemCell Technologies) was used to deplete erythrocytes from whole bone marrow samples collected in heparinised tubes according to manufacturer’s instructions. The cell count and the viability of the bone marrow cells were assessed using LUNA dual florescence cell counter (Logos Biosystems) and as per the 10X recommendations (Single cell 3’ reagent kits v2 user guide; CG00052 Rev B), we aimed at a target recovery of 6000 cells for all the samples. Post cell count and QC, the samples were immediately loaded individually onto the Chromium Controller. Single cell RNAseq libraries were prepared using manufacturers recommendations, and at the different check points the library quality was assessed using Qubit (ThermoFisher) and Bioanalyzer (Agilent). With a sequencing coverage target of 50,000 reads per cell, single cell libraries were sequenced on Illumina HiSeq4000 platform using paired-end sequencing workflow and with recommended 10X; v3 read parameters (28-8-0-91 cycles).
R1 fastq file: 10x barcode +UMI; R2 fastq file: mRNA
scRNA-Seq

treatment_protocol: Collection of whole bone marrow aspirate in heparanized tubes

value: Bone marrow

tag: disease state

value: healthy


title: SEC61A1 patient

value: severe congenital neutropenia with a de novo mutation in SEC61A1


title: vhp-1 RNAi injured, bio rep 1

description:
vhp1_10
PolyA RNA
processed data file: RNAseq_Processed_matrix_file.xlsx


title: 34-H-034-Myom-1_S34

description: Stranded


title: N641MR2

city: Athens

first: Wentao

last: Li

state: GA

address: 500 D. W Brooks Drive

department: Environmental Health Science

institute: University of Georgia

library_source: genomic

data_processing:
adaptor trimming
alignment
reads filtering
deduplication
strand separation
gene coverage count
Genome_build: hg19

source_name: newborn foreskin

growth_protocol: Celles were cultured in Dulbecco's Modified Eagle's Medium (DMEM, Gibco, USA) supplemented with 10% fetal bovine serum (FBS, Sigma-Aldrich, USA) at 37 ºC in a 5% CO2 humidified incubator.

extract_protocol:
Cells were lysed gently and small molecular weight DNA, consisting mostly of excised 26-27 mers was separated from chromosomal high molecular weight DNA by centrifugation
Briefly, the excision products were isolated by TFIIH immunoprecipitation following gentle cell lysis and non-chromatin fraction separation, and ligated with adaptors. The ligated excision products were then further purified by immunoprecipitation with anti-(6-4)PP antibody and repaired by (6-4)PP photolyase before the library amplification by PCR. Libraries were sequenced on an Illumina HiSeq 4000 platform.
XR-seq

treatment_protocol: Briefly, the 80% confluent NHF1 cells were irradiated for 20 s under a 250 nm UV lamp (1 J/m2/s) after removing the culture medium and incubated at 37 °C in a 5% CO2 humidified chamber for 1 min or 2 min with 37 °C culture medium. Then, the cells were put on ice immediately and washed one time with ice-cold PBS before being harvested by a cell scarper in 10 ml ice-cold PBS. In each replicate of (6-4)PP XR-seq experiment, 50 and 30 petri dishes (150mm x 15mm) containing NHF1 cells were used at 1 min and 2 min timepoints respectively.

value: UVC

tag: treatment time (m)


title: N641MR1


title: N642MR1


title: 32-L60--Myom-1_S32

description: Stranded

tag: tissue

value: Control


title: 35-L-045-Myom-1_S35

description: Stranded


title: N642MR2

tag: treatment


title: EV uninjured, bio rep 2

description:
vhp1_2
PolyA RNA
processed data file: RNAseq_Processed_matrix_file.xlsx

tag: strain


title: 29-M74--Myom-1_S29

description: Stranded

value: Placentitis


title: 30-K56--Myom-1_S30

description: Stranded


title: 28-L63--Myom-1_S28

description: Stranded


title: 27-L50--Myom-1_S27

description: Stranded


title: 31-L53--Myom-1_S31

description: Stranded


title: 26-L48--Myom-1_S26

description: Stranded


title: ChSP KLF13 input 1

city: Ann Arbor

first: Robert

last: Denver

state: Michigan

address: 1105 North University Ave

department: MCDB

institute: University of Michigan

data_processing:
Reads were quality checked using FastQC v0.11.3 and quality trimmed with bbduk v37.09.
QC processed reads were aligned reads to the reference (GRCm38) using BWA mem v0.7.17-r1188 with default parameters.
Peaks were identified and annotated using PePr v1.1.18 and ChIPseeker v1.16.1 respectively.
Motif enrichment was performed using HOMER v4.9.1.
Genome_build: GRCm38
Supplementary_files_format_and_content: called peaks, bed file

growth_protocol: We cultured HT22 cells in high-glucose DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Corning) and penicillin G (100 U/ ml) + streptomycin (100 µg/ml; Gibco) at 37 °C under an atmosphere of 5 % CO2. We created a cell line to express a biotin tag KLF13 fusion protein that is biotinylated in vivo by the biotin ligase BirA.

extract_protocol:
Cells were washed, crosslinked with 1 % paraformaldehyde and chromatin extracted and sonicated using an M220 Focused-Ultrasonicator (Covaris) for 20 min with a 5 % duty factor. The chromatin shearing (200-600 bp) was confirmed by agarose gel electrophoresis.
DNA libraries were prepared by the University of Michigan DNA Sequencing Core.

treatment_protocol: To identify regions of the genome where KLF13 associates in chromatin, we engineered the mouse hippocampus-derived neuronal cell line HT22  to stably express the biotin ligase BirA. Cells were then transfected with pTO-Klf13Bio plasmid to express a biotinylated form of KLF13. Chromatin streptavidin precipitation was applied to chromatin extracted from cells 24 hr after transfection and subjected to deep sequencing.

tag: cell line

value: neuronal cell line HT22

tag: transfection

tag: ip protocol


title: ChSP KLF13 input 2

value: pTO-Klf13Bio plasmid to express a biotinylated form of KLF13


title: ChSP KLF13 input 3


title: ChSP KLF13 sample 4

value: Chromatin streptavidin precipitation


title: ChSP KLF13 input 4


title: 25-K51--Myom-1_S25

description: Stranded


title: ChSP KLF13 sample 2


title: Dox treatment 3

data_processing:
Reads were quality checked using FastQC v0.11.3
QC processed reads were aligned to the reference (GRCm38) using Hisat2 v2.1.0, with default parameter settings, with the exception of: “--dta”.
Stringtie v1.3.3 was used for gene and isoform-level quantification, using the “-e -G” and option which quantifies transcripts based upon an input GTF file
Data were pre-filtered to remove genes with 0 counts in all samples. Normalization and differential expression was performed with DESeq2, using a negative binomial generalized linear model
Genome_build: GRCm38
Supplementary_files_format_and_content: raw abundance counts; differential expression data

growth_protocol: To create stably transfected cell lines we cultured the HT22 parent line in high-glucose DMEM (Invitrogen) supplemented with 10% fetal bovine serum (Corning) and penicillin G (100 U/ ml) + streptomycin (100 µg/ml; Gibco) at 37 °C under an atmosphere of 5 % CO2. We created a cell line to express V5KLF13 under control of the tet repressor.

extract_protocol:
We extracted total RNA from HT22 cells using the TRIzol Reagent (Invitrogen) following the manufacturer’s instructions.
Total RNA libraries were prepared by the University of Michigan DNA Sequencing Core.

treatment_protocol: We treated cells with doxycyline (1 µg/ml) for 8 hr

value: Dox


title: ChSP KLF13 sample 3


title: 33-L-056-Myom-1_S33

description: Stranded


title: Vehicle treatment 3

value: Vehicle


title: ChSP KLF13 sample 1


title: Dox treatment 2


title: Dox treatment 1


title: Vehicle treatment 2


title: Vehicle treatment 1


title: mp_MHC_4.3: EAE infiltrating monocytes/macrophages MHC+ROS- Replicate 3

city: San Francisco, CA

first: Katerina

last: akassoglou

address: 1650 Owens st

institute: Gladstone Institutes

data_processing:
All FASTQ files  were trimmed of known adapters and low-quality regions of reads using Fastq-mcf and sequence QC was assessed using FastQC and RSeQC. Reads were aligned to the mm9 mouse genome assembly using Tophat 2.0.13. Mapped reads were counted using featureCounts from Subread suite and then differential gene analysis was performed using edgeR. The data set was filtered by including all genes with minimum of two replicates with CPM (counts per million) between 0.5 and 5000. The remaining genes were normalized using calcNormFactors weighted trimmed mean of M-values and the differential expression between samples was used to calculate P-values in edgeR. The R function "p.adjust" was used to calculate the FDR (false discovery rate) for each P-value using the Benjamini-Hochberg method. GO Elite was used to identify differentially expressed genes that were overrepresented in existing annotated genes . Clustering was performed by k-means clustering with 100 clusters on log transform expression levels then by Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) on the k-means clusters to prune highly similar clusters.
Genome_build: mm9

source_name: spinal cord

extract_protocol:
Mice were perfused with ice-cold phosphate-buffered saline (PBS) and spinal cords were flushed out from the spinal column with PBS. Tissues were incubated in HBSS with 0.2% collagenase, type 3 (Worthington) gently shaking for 30 min at 37 °C, and then mechanically dissociated and passed through a 40-um strainer (Falcon). Cells were collected in complete RPMI-1640 medium (without phenol red supplemented with 25 mM HEPES pH 7.4, 1% Penicillin/Streptavidin and 10% heat-inactivated fetal bovine serum (FBS; Thermo Fisher Scientific)) and myelin was depleted following the myelin removal beads II manufactures guidelines (Miltenyi Biotec). Myelin-depleted cell suspensions were treated for 5 min at 4 °C with Fc-block in BSA staining buffer (BD Biosciences) and then incubated for 30 min at 4 °C with CD11b APC-Cy7 (M1/70) and MHC II (30-F11) antibodies. Surfaced stained cells were stained for intracellular ROS in vitro using membrane permeable, fluorescent reagent 2′,7′–dichlorofluorescein diacetate (DCFDA; Abcam). Cells were incubated with 10 uM DCFDA in PBS supplemented with 2% FBS, 2 mM EDTA (Gibco) for 30 min at 37 °C, and directly analyzed by flow cytometry. For bulk RNA-seq cell sorting, CompBeads Compensation Particles (BD Biosciences) were used for color compensation controls. In each experiment, the maximal cell number of sorted microglia and macrophages was assessed based on CD11b and CD45 signal intensities. ROS+ (DCFDA) cells were gated based on FITC signals (cut-off 2 × 103), and MHC II+ cells gated based on PE-Cy7 signal (cut-off 3 × 103) compared to the unstained cells. Microglia and macrophage subpopulations were classified into MHC II+ ROS+, MHC II– ROS– (baseline), MHC II– ROS+ and MHC II+ROS–. In each sorting experiment, eight distinct cell populations were collected separately on ice. After centrifugation at 300g and 4°C for 6 min, cell pellets were stored at -80°C in 150 ul RLT buffer (Qiagen) with 1% 2-mercaptoethanol (Gibco) prior to RNA isolation. Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s instructions.
cDNA was generated from full-length RNA and uniformly sheared with the NuGEN Ovation RNA-seq V2 kit and Covaris S2 Sonicator, respectively. Libraries were purified using Agencourt XP magnetic beads and quantified by KAPA qPCR (Illumina).  Four libraries per lane were pooled for a single-end 50bp run on the Illumnia HiSeq 4000.

tag: condition

value: Onset EAE

value: spinal cord


title: mp_base_3.3: EAE infiltrating monocytes/macrophages MHC-ROS- Replicate 3


title: mp_healthy_1: Healthy bone-marrow derived macrophages replicate 1

source_name: bone marrow

value: Healthy

value: bone marrow


title: mp_MHCTox_1.3: EAE infiltrating monocytes/macrophages MHC+ROS+ Replicate 3


title: MG_MHC_4.2: EAE Microglia MHC+ROS- Replicate 2


title: MG_Tox_2.3: EAE Microglia MHC-ROS+ Replicate 3


title: mp_MHC_4.2: EAE infiltrating monocytes/macrophages MHC+ROS- Replicate 2


title: MG_base_3.3: EAE Microglia MHC-ROS- Replicate 3


title: MG_MHCTox_1.3: EAE Microglia MHC+ROS+ Replicate 3


title: mp_base_3.2: EAE infiltrating monocytes/macrophages MHC-ROS- Replicate 2


title: MG_base_3.2: EAE Microglia MHC-ROS- Replicate 2


title: mp_MHCTox_1.2: EAE infiltrating monocytes/macrophages MHC+ROS+ Replicate 2


title: mp_Tox_2.2: EAE infiltrating monocytes/macrophages MHC-ROS+ Replicate 2


title: MG_MHCTox_1.2: EAE Microglia MHC+ROS+ Replicate 2


title: MG_Tox_2.2: EAE Microglia MHC-ROS+ Replicate 2


title: MG_MHC_4.1: EAE Microglia MHC+ROS- Replicate 1


title: mp_base_3.1: EAE infiltrating monocytes/macrophages MHC-ROS- Replicate 1


title: mp_Tox_2.1: EAE infiltrating monocytes/macrophages MHC-ROS+ Replicate 1


title: MG_healthy_1: Healthy Microglia replicate 1


title: MG_Tox_2.1: EAE Microglia MHC-ROS+ Replicate 1


title: mp_Tox_2.3: EAE infiltrating monocytes/macrophages MHC-ROS+ Replicate 3


title: MG_base_3.1: EAE Microglia MHC-ROS- Replicate 1


title: MG_MHCTox_1.1: EAE Microglia MHC+ROS+ Replicate 1


title: EAE CD11b+ ROS+ replicate 2

data_processing:
All FASTQ files were aligned to the mm10 reference assembly using the 10x Genomics CellRanger count version 2.0.1, and then each sample was combined into one dataset using the 10x Genomics Cell Ranger Aggr with default parameters
The R toolkit Seurat v3 was used for quality control (QC) processing, graph-based clustering, visualizations, and differential gene expression analyses of single cell RNA-seq data and performed in R version 3.4.2. Cellranger Aggr aggregated dataset of 9,079 cells were filtered with QC parameters 200 – 5,000 nFeature_RNA per cell, > 5% and > 25% mitochondrial and ribosomal genes, respectively. The percent of mitochondrial (percent.mito) and ribosomal (percent.ribo) genes were regressed out. All remaining variable genes were used for downstream analyses, including immediate early response genes induced by cell isolation procedure. Following QC, 17,814 genes across 8,701 single cells were analyzed with Seurat default parameters unless otherwise stated. To determine statistically significant principal components (PC), JackStraw was performed with num.replicate = 100. For clustering analysis, FindNeighbors and FindClusters were used with the first 20 significant PC and a resolution = 0.8, respectively. For subclustering analysis, monocyte/macrophage or microglia clusters were separately re-clustered by running through the Seurat pipeline as described above. FindClusters was implemented at a resolution = 0.4 for monocyte/macrophages or resolution = 0.3 for microglia subcluster analysis.
Genome_build: mm10

extract_protocol:
Mice were perfused with ice-cold phosphate-buffered saline (PBS) and spinal cords were flushed out from the spinal column with PBS. Tissues were incubated in HBSS with 0.2% collagenase, type 3 (Worthington) gently shaking for 30 min at 37 °C, and then mechanically dissociated and passed through a 40-um strainer (Falcon). Cells were collected in complete RPMI-1640 medium (without phenol red supplemented with 25 mM HEPES pH 7.4, 1% Penicillin/Streptavidin and 10% heat-inactivated fetal bovine serum (FBS; Thermo Fisher Scientific)) and myelin was depleted following the myelin removal beads II manufactures guidelines (Miltenyi Biotec). Myelin-depleted cell suspensions were treated for 5 min at 4 °C with Fc-block in BSA staining buffer (BD Biosciences) and then incubated for 30 min at 4 °C with CD11b APC-Cy7 (M1/70) antibodies. Live cells isolated from spinal cord were stained for intracellular ROS in vitro using membrane permeable, fluorescent reagent 2′,7′–dichlorofluorescein diacetate (DCFDA; Abcam). Cells were incubated with 10 uM DCFDA in PBS supplemented with 2% FBS without EDTA at 4 °C for 30 min prior to cell sorting. Cells were incubated for 5 min at 4°C with 1 uM sytox blue live/dead stain and then sorted using FACSAria II. Sorted cells were kept on ice until all samples were collected and then resuspended in cold PBS supplemented with 2% FBS at 233 cells/uL and immediately processed for single cell RNA-sequencing.
Libraries were prepared following manufactures instructions for the Chromium Single Cell 3′ v2 Reagent Kit (10X Genomics)

tag: age

value: 10 weeks old


title: EAE CD11b+ ROS+ replicate 1


title: Healthy CD11b+ ROS- replicate 2


title: EAE CD11b+ ROS- replicate 1