title: 17-0602_4-WT5

status: Public on Mar 31 2021

type: SRA

city: Columbus

first: John

last: Gunn

state: Ohio

address: 700 Children’s Drive

department: Center for Microbial Pathogenesis

country: USA

institute: Abigail Wexner Research Institute at Nationwide Children’s Hospital

library_source: transcriptomic

data_processing:
Samples were aligned to the GCF_000022165.1 assembly of the Salmonella typhimurium reference from NCBI (https://www.ncbi.nlm.nih.gov/assembly/GCF_000022165.1/) using v0.7.15 of the BWAMEM aligner.
Features were identified from the GFF files that came with the assembly from NCBI.
Feature coverage counts were calculated using version 0.6.1p1 of HTSeq -count
Differentially expressed features were calculated using DESeq2.
Genome_build: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Supplementary_files_format_and_content: Excel spreadsheet and CSV files containing read counts for each sample and differential expression data for each feature.

molecule: total RNA

source_name: Biofilm

growth_protocol: Overnight (O/N) cultures were grown in TSB at 37°C with aeration. These were normalized to OD600=0.8, diluted 1:10 into M9 + 5mM or 40mM L-arabinose, and 0.1 mL was dispensed into every well of a non-treated polystyrene 96-well plate (Corning) (one plate per strain). The plates were incubated for 4 days at 25˚C on a GyroMini nutating mixer (LabNet International, Inc.) at 24rpm. Media was replenished daily.

extract_protocol: The biofilm was washed with 100 μL phosphate-buffered saline (PBS) twice to remove planktonic cells, scraped for 2 minutes with a 200 μL pipette tip, transferred to a microcentrifuge tube, and centrifuged at 10,000 × g for 3 min. RNA was extracted using the hot phenol method. Briefly, the supernatant was removed, and pellets were resuspended in 475 μl AE buffer (50 mM sodium acetate [NaOAc], 10 mM EDTA, pH 5.2). Forty microliters of 20% SDS and 475 μl of phenol were added and incubated for 10 min at 65°C, shaking every minute. Samples were put on ice for 5 min and centrifuged for 15 min at 10,000 rpm at 4°C. Supernatants were transferred to new microcentrifuge tubes and 475 μL of chloroform was added, mixed, and centrifuged for 10 min at 2,000 rpm at 4°C. The top aqueous layer was placed in a new microcentrifuge tube, and RNA was precipitated by adding 500 μL isopropanol and 50 μL sodium acetate (2 M), centrifuging for 20 min (12,000 rpm, 4°C), and washing with 250 μL 70% cold ethanol. Finally, samples were treated with DNase (12.5% of total reaction volume, catalog number M0303L; New England BioLabs, Ipswich, MA, USA) for 45 min. RNA isolation was performed in quadruplicate.

tag: genotype

value: Wild-type

tag: treatment

value: L-arabinose, 5mM

tag: tissue

value: Biofilm


title: 17-0598_2-delta40

organism: Salmonella enterica subsp. enterica serovar Typhimurium

value: {delta}araE

value: L-arabinose, 40mM


title: 17-0594_1-WT40


title: 17-0600_3-WT40


title: 17-0599_3-WT5


title: 17-0601_3-delta40


title: 17-0596_2-WT5


title: 17-0604_4-delta40


title: 17-0597_2-WT40


title: 17-0603_4-WT40


title: 17-0595_1-delta40


title: repo_Rpl10_TBI_D6_ZT00-3

city: Evanston

first: Ravi

last: Allada

state: IL

address: 2205 Tech Drive

department: Neurobiology

institute: Northwestern University

data_processing:
Sequence reads were processed to calculate TPM and estimated counts by kallisto
Transcripts values for each gene were summed to gene level using R library "tximport".
Genome_build: dmel-all-transcript-r6.14
Supplementary_files_format_and_content: summarized csv file containing TMP values for genes for each sample

organism: Drosophila melanogaster

source_name: Glials

growth_protocol: Flies were raised at 25°C,12:12 LD cycle on standard sucrose-yeast (SY) food

extract_protocol:
Adult fly heads were separated at certain ages and time points. Affinity Purification of Ribosomes and Isolation of Ribosome-Bound mRNAs were carried out as previously described (Huang, et al., 2013; Ng, et al., 2016). mRNAs were then amplified and convereted to cDNAs as previously described (Kula-Eversole, et al., 2010; Nagoshi, et al., 2010; Xu, et al., 2019). The cDNA was submitted to HGAC at the University of Chicago for library preparation and sequencing.
Library construction and sequencing floowed the protocol at HGAC at University of Chicago

tag: cell type

value: Glials

tag: gender

value: Female

value: TBI

tag: time point


title: repo_Rpl10_nonTBI_D6_ZT00-3


title: repo_Rpl10_nonTBI_D3_ZT00-3


title: repo_Rpl10_TBI_D10_ZT00-2


title: 17-0593_1-WT5


title: repo_Rpl10_nonTBI_D10_ZT00-3


title: repo_Rpl10_nonTBI_D10_ZT00-2


title: repo_Rpl10_TBI_D3_ZT00-3


title: repo_Rpl10_TBI_D6_ZT00-2


title: repo_Rpl10_nonTBI_D6_ZT00-2


title: repo_Rpl10_nonTBI_D3_ZT00-2


title: repo_Rpl10_TBI_D3_ZT00-2


title: repo_Rpl10_TBI_D3_ZT00-1


title: repo_Rpl10_TBI_D10_ZT00-1


title: repo_Rpl10_nonTBI_D10_ZT00-1


title: WT_control_Ler_chipseq_rep2

city: NORWICH

first: Robert

last: Sablowski

state: Norfolk

address: The John Innes Centre

department: CDB

country: United Kingdom

institute: JIC

library_source: genomic

data_processing:
Reads aligned against the TAIR10 Col-0 reference sequence with Bowtie2 (v2-2.1.0)
Data were sorted and indexed with Samtools to generate .bam files
MACS 2.0.10 was used to call peaks and calculate q-values
Filtering: to select peaks that were consistently detected across replicates, peak calling with MACS 2.0.10 was applied to individual replicates and overlapping peak regions were accepted if they had q-values of 10-3 or lower in each ATH1-GFP replicate, were not detected in any of the wt controls and the overlapping region was at least 50 nucleotides long.
Association with gene models: filtered peaks were attributed to gene models within 3 kb upstream or 1.5 kb downstream of the corresponding coding sequence, without intervening coding sequences.
Genome_build: TAIR10
Supplementary_files_format_and_content: _peaks.narrowPeak files: produced by MACS2.0.10, used to display peaks in genome browser, contain peak names, genomic location, peak enrichment, p-values and q-values; Summary table
Supplementary_files_format_and_content: _peaks.txt files: produced by MACS2.0.10, contain peak names, genomic location, peak lenghts, enrichment, p-values and q-values
Supplementary_files_format_and_content: ATH1_ChIP-seq_targets.txt is a tab-delimited text file with information about genes associated with filtered peaks: AGI name, Gene start, Gene end, Number of overlapping MACS peaks, Fold enrichment, log10 q-value, Short_description, Computational_description.

molecule: genomic DNA

organism: Arabidopsis thaliana

growth_protocol: Plants were grown for two weeks in a controlled environment room at 20-22 °C, 16 h light (100 µE).

extract_protocol:
ChIP was performed as described in Schiessl et al. 2014, PNAS 111, 2830-2835.
Illumina TruSeq ChIP-Seq libraries were constructed as described in Kaufmann et al, 2009, PLoS Biology 7, e90.
ChIP-seq: 50 bp single-end reads sequenced with Illumina HiSeq 2500 (Rapid-Run mode) as described by the manufacturer.

treatment_protocol: Three biological replicates were used for each treatment. Each replicate was prepared from 1-2 g of seedlings; immediatey after harvesting, leaves and roots were removed and the remaining shoot tissues were processed.

tag: genotype/variation

value: wild-type control (Landsberg-erecta)

value: seedling shoots with leaves removed

tag: chip antibody

value: anti-GFP µMACS Microbeads (Milteyi Biotec)


title: ATH1-GFP_chipseq_rep1

value: ath1-3 mutant transformed with genomic contruct expressing a fusion between ATH1 and GFP (pATH1:ATH1-GFP)


title: WT_control_Ler_chipseq_rep3


title: repo_Rpl10_TBI_D6_ZT00-1


title: ATH1-GFP_chipseq_rep2


title: ATH1-GFP_chipseq_rep3


title: repo_Rpl10_nonTBI_D6_ZT00-1


title: WT_control_Ler_chipseq_rep1


title: CL1-0 cells treated FSTL1 antibody for 6 hours

type: RNA

city: Taipei

first: Jean

last: Chiou

address: No. 128, Academia Road, Section 2, Nankang,

country: Taiwan

institute: Genomics Research Center, Academia Sinica

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

organism: Homo sapiens

source_name: CL1-0 6hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with puromycin for two weeks.  Stably transduced cells were use for this experiment.

tag: disease state

value: Lung  adenocarcinoma

tag: cell line

value: CL1-0 lung cancer cell line

value: type II alveolar cell

value: FSTL1 antibody

tag: time

value: 6 hours


title: T24-DDP2

city: Hangzhou

first: Baiye

last: Jin

state: Zhejiang

address: Qinchun Road No.17

department: Urology

country: China

institute: Zhejiang University

data_processing:
Base-calling using Illumina Casava1.7 software
Data filting step:Remove the reads with adapter;  Remove the reads containing n (n means the base information cannot be determined);  Remove the low quality reads (the base number of qphred < = 20 accounts for more than 50% of the whole read length).
HISTA2 version 2.0 for Read alignment
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: Mix genes matrix with raw count or FPKM in six samples

source_name: human bladder cancer cell line T24

growth_protocol: T24 cells were cultured in 1640 medium containing 10% fetal bovine serum. The culture conditions were 37 ℃, 5% CO2.

extract_protocol:
TRIzol (Thermo Fisher Scientific, Inc.) was used for cells total RNA extraction according to manufacturer's protocol. Then different groups of RNA were used for RNA-seq or qRT-PCR.
Strand specific library construction: the method of reverse transcription synthesis of the first strand of cDNA is the same as that of NEB, but the difference is that when the second strand is synthesized, the dTTP in dNTPs is replaced by dUTP, and then the cDNA ends are repaired, A-tail is added, sequencing connector is connected, and length screening is carried out. Then the second strand of cDNA containing u is degraded by user enzyme, and then PCR amplification is carried out to obtain the library. Chain specific library has many advantages, such as obtaining more effective information under the same amount of data; obtaining more accurate gene quantitative, positioning and annotation information; providing the expression level of antisense transcripts and single exon in each isoform. The kit used to build the library was NEBNEXT® Ultra ™ Directional RNA Library Prep Kit for Illumina®。After the construction of the library, qubit2.0 fluorometer was used for preliminary quantification, and the library was diluted to 1.5ng/ul. Then the insert size of the library was detected by Agilent 2100 Bioanalyzer. After the insert size met the expectation, the effective concentration of the library was accurately quantified by QRT PCR (the effective concentration of the library was higher than 2nm) to ensure the quality of the library.

treatment_protocol: Both T24 cells were cultured at 37 ℃ and 5% CO2. 24 hours before RNA collection, 1 ug / ml cisplatin was added to T24 DDP groups, and PBS was added to controled T24 groups. Total RNA was extracted with Trizol after 24 hours of treatment.

value: bladder

value: cisplatin


title: T24-DDP1


title: CL1-0 cells treated FSTL1 antibody for 0 hours

source_name: CL1-0 0hr

value: 0 hours


title: T24-DDP3


title: T24-NC3

value: PBS


title: T24-NC2


title: T24-NC1


title: A2C

city: Brasília

first: Taina

last: Raiol

state: DF

address: Av. L3 Norte, Campus Universitário Darcy Ribeiro

department: Fiocruz Brasília (GEREB)

country: Brazil

institute: Oswaldo Cruz Foundation - Fiocruz

description: de-CxI.xls

data_processing:
Illumina reads were analyzed for quality control by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Filtered reads were aligned simultaneously to the human (Ensembl GRCh38.87) and Trypanosoma cruzi (Ensembl Protists ASM20906v1) reference genomes using HISAT2 v2.0.6 (Kim et al., 2015).
Aligned files were ordered and indexed using Samtools v0.1.18 (Li et al., 2009) followed by read count using the human genome annotation files of Ensembl genome build GRCh38.87 and the software HTSeq-count v0.6.0 (-m intersection-nonempty) (Anders et al., 2015).
Differential expression analysis was performed using DEseq2 package v2.14 from R/Bioconductor (Love et al., 2014), comparing Infected and Control samples (padj ≤ 0.05).
All the analyses were performed after exclusion of outliers, leaving at least one representative sample of each donor.
Genome_build: Ensembl GRCh38.87 for human and Ensembl Protists ASM20906v1 for T. cruzi
Supplementary_files_format_and_content: de-CxI.xls

source_name: Blood monocyte-derived dendritic cells

growth_protocol: Mo-DCs were cultured in RPMI 1640, 10% FSB, IL-4 and GM-CSF were used for differentiation. Metacyclic trypomastigotes were obtained in TAU and TAU3AAG media.

extract_protocol:
Infected and Control MoDCs were harvested, and RNA was extracted by Trizol reagent (Ambion) as suggested by the manufacturer's recommendations.
Oligo d(T) beads were used to perform mRNA enrichment, which were fragmented randomly and converted in cDNA. Then, poly(A) tails were added and enriched by PCR to generate a cDNA library. Illumina HiSeq 2500 was used to perform the paired-end sequencing of 150bp reads.

treatment_protocol: T. cruzi-infected Mo-DCs were in contact with the metacyclic trypomastigote forms during 12 h after differentiation. Control mo-DCs were cultured without parasites 12 h after differentiation.

value: Control Mo-DCs

tag: donor

value: A

tag: replicate


title: B1C

description: de-CxI.xls

value: B


title: C2C

description: de-CxI.xls

value: C


title: C1C

description: de-CxI.xls


title: A1C

description: de-CxI.xls


title: CTRL siRNA G766R mut DIS3 rep 1

city: Warsaw

first: Anna

middle: Maria

last: Hojka-Osinska

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute of Molecular and Cell Biology

data_processing:
Illumina Casava1.7 software used for basecalling
Sequencing reads were quality filtered using Cutadapt, to remove Illumina adapter sequences, trim low-quality fragments (min. Q score was set to 20), and remove reads shorter than 30 nt after trimming. Reads were mapped to human genome (hg38) using STAR.
Alternative splicing (AS) events were analysed using JUM.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files

source_name: HEK293 FLP-In T-Rex stable cell line

growth_protocol: Stably transfected derivates of HEK293 FLP-In T-Rex cells expressing wild type DIS3 or catatonically inactive version (G766R) of DIS3 were cultured for transfection in 6-well format in Dulbecco's modified Eagle's medium, supplemented with 10% fetal bovine serum without antibiotics.

extract_protocol:
Total RNA was isolated with the TRI Reagent according to the manufacturer’s instructions.
Following DNase treatment, strand-specific RNA libraries were prepared using a KAPA Stranded RNA-seq Library Preparation Kit according to the manufacturer’s protocol.
dUTP, stranded

treatment_protocol: Expression of transgenes coding for sh-miRNA-EGFP cassettes for silencing of the endogenous DIS3 and sh-miRNA-insensitive FLAG-tagged exogenous DIS3 protein was induced with tetracycline at a final concentration of 25 ng/mL, 24 hours before siRNA transfection. For siRNA mediated SF3A1 depletion, tetracycline induced cells were subjected to Silencer Select siRNA s20118 transfection (Ambion). Scrambled Silencer Select Negative Control siRNA  (Ambion) was used as a negative control. Transfections were performed using Lipofectamine RNAiMAX  and 20 nM siRNA according to the manufacturer’s recommendations

value: HEK293 FLP-In T-Rex

value: expressing G766R mut DIS3

value: 25 ng/mL tetracycline

tag: sirna treatment

value: CTRL siRNA


title: SF3A1 siRNA G766R mut DIS3 rep 2

value: SF3A1 siRNA


title: SF3A1 siRNA G766R mut DIS3 rep 1


title: SF3A1 siRNA WT DIS3 rep 2

value: expressing WT DIS3


title: repo_Rpl10_nonTBI_D3_ZT00-1

value: Glials

value: Female


title: CTRL siRNA WT DIS3 rep 1


title: H_E1: Mutant 1

city: Rochester

first: Zachary

middle: C

last: Murphy

state: NY

address: 601 Elmwood Ave box 703

institute: University of Rochester

data_processing:
Sequencing platform HiSeq 2500
Data cleaning: Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35
Genome alignment: STAR_2.6.0c, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification 1: subread-1.6.1, featurecounts, -s 0 -t exon -g gene_name
Genome_build: GRCh37.p13 GENOCDOE v19: Hg19

growth_protocol: HUDEP2 cells grown in serum free erythroid medium with erythropoietin, stem cell factor, and dexamethasone per published protocols

extract_protocol:
RNA was extracted using Qiagen RNeasy per manufacterurs protocol
1ng of total RNA was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech, Mountain View, CA) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Flourometer (Life Technnologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA). Single end reads of 100nt were generated for each sample.

value: Codanin-1 Mutant


title: SF3A1 siRNA WT DIS3 rep 1


title: CTRL siRNA WT DIS3 rep 2


title: H_E5: Control 1

value: Control


title: CTRL siRNA G766R mut DIS3 rep 2


title: H_C3: Mutant 2


title: NRF2SFN IP sulforaphane (SFN)

city: Manchester

first: Svitlana

last: Kurinna

address: Dover Street

institute: University of Manchester

description: activated transcription factor

data_processing:
Bowtie 2, default parameters
reads were mapped to GRChg38
Peak calling was done using MASC2
MACS2 default parameters and band width of 300bp
only the peaks with p value < 0.05 were requested
Genome_build: GRChg38
Supplementary_files_format_and_content: wig files

source_name: human keratinocytes

growth_protocol: primary human keratinocytes were isolated from human foreskin after separation of the dermis and dissociation of the epidermis by the dispase/trypsin/EDTA treatment, seeded on fibroblast feet layers and passaged without the feeder for further expansion and treatment

extract_protocol:
Lysates were clarified from sonicated nuclei and NRF2-DNA complexes were isolated with an antibody against total NRF2 (Active Motif; ChIP-grade, 10μl/IP).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: 5μM SFN or vehicle (DMSO) in the growth factors free KSF medium stabilised with ethanolamine/phosphoethanolamine

value: human epidermis

value: SFN

tag: group

value: sulforaphane treatment (activation)


title: H_E2: Mutant 3


title: H_C5: Control 2


title: H_C2: Control 3


title: NRF2 IP control (vehicle)

description: transcription factor

value: DMSO

value: control treatment


title: NRF2SFN input

description: activated transcription factor


title: NRF2 input

description: transcription factor


title: AI010_2D_PRBveh_48h_rep2

city: Minneapolis

first: Carol

last: Lange

state: MN

address: 2231 6th ST SE

department: Masonic Cancer Center

institute: University of Minnesota

data_processing:
RNA sequencing data analysis was performed using Artificial Intelligene’s (AI, www.artificialintelligene.com) RNAseq analysis platform. Briefly, short reads were aligned to the hg19 human genome using STAR. Subsequently cufflinks packages were used to perform transcript assemblies. Downstream differential gene expression calling on the reference and experimental groups of interest was performed using DESeq2. To perform clustering analyses on a group of samples, a union of all the genes and their expression RPKM values within that group was generated to build a read count matrix for the group of interest. Various unsupervised and other machine learning techniques were applied to this composite read count matrix of interest. The sample-sample correlation heatmaps represent the correlation observed between any two samples. The sample-feature heatmaps represent the signal intensity of a feature for any given sample. ggplot2, heatmap.2 and Pheatmap packages in R were used to build various heatmaps. Functional analysis was performed using gene set enrichment analyses.
Genome_build: HG19
Supplementary_files_format_and_content: AI010_ReadCounts.csv: RPKM values from DESeq

growth_protocol:
Protocol name: Progestin in FTE_2017run
Fallopian Tube Epithelial (FTE) cells expressing the PRA or PRB isoforms or EV were treated with progestins and RNA-seq analyses performed.

extract_protocol:
The RNA extraction was done using the Qiagen RNasy kits.
Illumina TruSeq Stranded mRNA Library Prep kit was used to prepare the libraries.

treatment_protocol: Cell lines were cultured in adherent conditions and treated with 10 nM R5020 for 6h prior to RNA isolation

value: fallopian tube epithelium

value: vehicle

tag: mutation

tag: plenti

value: PR-B

tag: clones


title: AI010_2D_PRB_R50_48h_rep1

tag: treatment


title: AI010_2D_PRBveh_48h_rep3


title: AI010_2D_PRB_R50_48h_rep3


title: AI010_2D_PRA_R50_48h_rep3

value: PR-A


title: AI010_2D_PRBveh_48h_rep1


title: AI010_2D_EVveh_48h_rep2


title: AI010_2D_PRAveh_48h_rep2


title: AI010_2D_PRAveh_48h_rep3


title: AI010_2D_PRA_R50_48h_rep2


title: AI010_2D_PRA_R50_48h_rep1


title: AI010_2D_EVveh_48h_rep1


title: AI009_2D_PRB_R50_6h_rep2


title: AI009_2D_PRB_R50_6h_rep3


title: AI009_2D_PRBveh_6h_rep3


title: AI010_2D_PRB_R50_48h_rep2


title: AI010_2D_EVveh_48h_rep3


title: AI009_2D_PRBveh_6h_rep1


title: AI009_2D_PRA_R50_6h_rep1


title: AI009_2D_PRAveh_6h_rep3


title: AI009_2D_PRAveh_6h_rep2


title: AI009_2D_PRB_R50_6h_rep1


title: AI009_2D_PRBveh_6h_rep2


title: AI009_2D_PRA_R50_6h_rep2


title: AI010_2D_PRAveh_48h_rep1


title: AI009_2D_EVveh_6h_rep2


title: AI009_2D_EVveh_6h_rep3


title: AI009_2D_EVveh_6h_rep1


title: RCS_12

city: Cleveland

first: Chase

last: Neumann

state: OH

address: 99089 Carnegie Ave

institute: CCF

data_processing:
Trim Galore
FastQC
Star aligner
EdgeR differential expression
Genome_build: Mus Musculus Mm10
Supplementary_files_format_and_content: GEO_RCS_adipose_de.csv, normalized counts with P-values, logFC of transcripts

organism: Mus musculus

source_name: Adipose mRNA from High Fat Diet mouse treated with IMC

extract_protocol:
Qiagen Rneasy Lipid Columns
Illumina TruSeq Directional Library Kit

treatment_protocol: Vehicle vs. IMC

tag: strain

tag: tissue

value: Adipose Tissue

value: Iodomethylcholine (IMC)


title: RCS_11


title: RCS_8


title: RCS_7


title: AI009_2D_PRA_R50_6h_rep3

tag: cell type


title: AI009_2D_PRAveh_6h_rep1


title: RCS_9


title: RCS_6

source_name: Adipose mRNA from High Fat Diet mouse treated with Vehicle

value: Vehicle


title: RCS_5


title: RCS_10


title: P0_KO_Brain_2_Ribosome_contained_mRNA_HiSeq

city: Kumamoto City

first: Takeshi

last: Chujo

state: Kumamoto prefecture

address: 1-1-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

description: Brain ribosome-contained mRNA fragments

data_processing:
Library strategy: Ribo-seq
A-site mRNA codon counting procedure: Using MiSeq data, mRNA codon situated in ribosomal A-site was extracted and counted. 1) 3' Adaptor sequences were trimmed using Galaxy. 2) Sequences were aligned to mouse ribosomal RNAs using Bowtie2 to remove ribosomal RNA sequences. 3) Remaining sequences were aligned to mouse mRNAs to extract mRNA sequences. 4) Ribosome-contained mRNA sequences were analyzed using Ribogalaxy Triplet Periodicity software and Metagene analysis to determine the position of mRNA A-site codons. 5) 30-nt mRNA fragments were selected, and trimmed to leave A-site codons (nucleotides 17-19). Read numbers were counted using the Count function in Galaxy.
Total or ribosomal mRNA counting procedure: Using HiSeq data, mRNA read number was counted: 1) 3' adaptor sequence was trimmed. 2) Sequences were mapped to mouse transcriptome using HISAT2 and mm10 GTF file from UCSC Table Browser. 3) mRNA reads were counted using Htseq-count.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Excel files: 1. A-site codon numbers (brain, liver). 2. mRNA read numbers (brain)

source_name: Ftsj1 KO mouse 2

growth_protocol: Neonate mice were sacrificed at P0.5.

extract_protocol:
Brains or livers were disected and snap-frozen in liquid nitrogen. Brains or livers were lysed and subjected to ribosome-profiling, or  to total RNA purification followed by PolyA+ RNA selection.
Library was constructed using a 3' adaptor (5App/CTGTAGGCACCATCAAT/3ddC).

treatment_protocol: None.

value: Brain

tag: genotype

value: Ftsj1 KO


title: P0_KO_Brain_1_Ribosome_contained_mRNA_HiSeq

description: Brain ribosome-contained mRNA fragments

source_name: Ftsj1 KO mouse 1


title: P0_KO_Brain_2_Total_mRNA_HiSeq

description: Brain total mRNA fragments

data_processing:
A-site mRNA codon counting procedure: Using MiSeq data, mRNA codon situated in ribosomal A-site was extracted and counted. 1) 3' Adaptor sequences were trimmed using Galaxy. 2) Sequences were aligned to mouse ribosomal RNAs using Bowtie2 to remove ribosomal RNA sequences. 3) Remaining sequences were aligned to mouse mRNAs to extract mRNA sequences. 4) Ribosome-contained mRNA sequences were analyzed using Ribogalaxy Triplet Periodicity software and Metagene analysis to determine the position of mRNA A-site codons. 5) 30-nt mRNA fragments were selected, and trimmed to leave A-site codons (nucleotides 17-19). Read numbers were counted using the Count function in Galaxy.
Total or ribosomal mRNA counting procedure: Using HiSeq data, mRNA read number was counted: 1) 3' adaptor sequence was trimmed. 2) Sequences were mapped to mouse transcriptome using HISAT2 and mm10 GTF file from UCSC Table Browser. 3) mRNA reads were counted using Htseq-count.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Excel files: 1. A-site codon numbers (brain, liver). 2. mRNA read numbers (brain)


title: P0_KO_Liver_1_Ribosome_contained_mRNA_MiSeq

description: Liver ribosome-contained mRNA fragments

value: Liver


title: P0_Ctrl_Brain_3_Ribosome_contained_mRNA_HiSeq

description: Brain ribosome-contained mRNA fragments

source_name: WT mouse 3

value: WT


title: P0_Ctrl_Brain_1_Ribosome_contained_mRNA_HiSeq

description: Brain ribosome-contained mRNA fragments

source_name: WT mouse 1


title: P0_KO_Brain_3_Total_mRNA_HiSeq

description: Brain total mRNA fragments

source_name: Ftsj1 KO mouse 3


title: P0_Ctrl_Brain_1_Total_mRNA_HiSeq

description: Brain total mRNA fragments


title: RCS_2


title: P0_KO_Liver_3_Ribosome_contained_mRNA_MiSeq

description: Liver ribosome-contained mRNA fragments


title: RCS_4


title: P0_Ctrl_Brain_2_Total_mRNA_HiSeq

description: Brain total mRNA fragments

source_name: WT mouse 2


title: 8_wk_KO_Brain_3_Total_mRNA_HiSeq

description: Brain total mRNA

data_processing:
A-site mRNA codon counting procedure: Using MiSeq data, mRNA codon situated in ribosomal A-site was extracted and counted. 1) 3' Adaptor sequences were trimmed on Galaxy. 2) Sequences were aligned to mouse ribosomal RNAs using Bowtie2 to remove ribosomal RNA sequences. 3) Remaining sequences were aligned to mouse mRNAs to extract mRNA sequences. 4) Ribosome-contained mRNA sequences were analyzed using Ribogalaxy Triplet Periodicity software and Metagene analysis software to determine the position of mRNA A-site codons. 5) 30-nt mRNA fragments were selected, and trimmed to leave A-site codons (nucleotides 17-19). Read numbers were counted using the Count function in Galaxy.
Total or ribosomal mRNA counting procedure: Using HiSeq data, mRNA read number was counted: 1) 3' adaptor sequence was trimmed. 2) Sequences were mapped to mouse transcriptome using HISAT2 and mm10 GTF file from UCSC Table Browser. 3) mRNA reads were counted using Htseq-count.
Genome_build: mm10
Supplementary_files_format_and_content: 8wk_MiSeq_Asite_Codon_processed_data
Supplementary_files_format_and_content: 8wk_HiSeq_mRNA_processed_data

growth_protocol: Mice were grown to 8 weeks.

extract_protocol:
Brains were disected and snap-frozen in liquid nitrogen. Brains were lysed and subjected to ribosome-profiling, or  to total RNA purification followed by PolyA+ RNA selection.
Library was constructed using a 3' adaptor (5App/CTGTAGGCACCATCAAT/3ddC).


title: 8_wk_KO_Brain_2_Ribosome_contained_mRNA_HiSeq

description: Brain ribosome-contained mRNA fragments

data_processing:
Library strategy: Ribo-seq
A-site mRNA codon counting procedure: Using MiSeq data, mRNA codon situated in ribosomal A-site was extracted and counted. 1) 3' Adaptor sequences were trimmed on Galaxy. 2) Sequences were aligned to mouse ribosomal RNAs using Bowtie2 to remove ribosomal RNA sequences. 3) Remaining sequences were aligned to mouse mRNAs to extract mRNA sequences. 4) Ribosome-contained mRNA sequences were analyzed using Ribogalaxy Triplet Periodicity software and Metagene analysis software to determine the position of mRNA A-site codons. 5) 30-nt mRNA fragments were selected, and trimmed to leave A-site codons (nucleotides 17-19). Read numbers were counted using the Count function in Galaxy.
Total or ribosomal mRNA counting procedure: Using HiSeq data, mRNA read number was counted: 1) 3' adaptor sequence was trimmed. 2) Sequences were mapped to mouse transcriptome using HISAT2 and mm10 GTF file from UCSC Table Browser. 3) mRNA reads were counted using Htseq-count.
Genome_build: mm10
Supplementary_files_format_and_content: 8wk_MiSeq_Asite_Codon_processed_data
Supplementary_files_format_and_content: 8wk_HiSeq_mRNA_processed_data


title: RCS_3


title: P0_Ctrl_Liver_2_Ribosome_contained_mRNA_MiSeq

description: Liver ribosome-contained mRNA fragments


title: P0_Ctrl_Brain_2_Ribosome_contained_mRNA_HiSeq

description: Brain ribosome-contained mRNA fragments


title: 8_wk_KO_Brain_3_Ribosome_contained_mRNA_HiSeq

description: Brain ribosome-contained mRNA fragments


title: P0_KO_Liver_2_Ribosome_contained_mRNA_MiSeq

description: Liver ribosome-contained mRNA fragments


title: P0_KO_Brain_1_Total_mRNA_HiSeq

description: Brain total mRNA fragments


title: P0_Ctrl_Brain_3_Total_mRNA_HiSeq

description: Brain total mRNA fragments


title: 8_wk_Ctrl_Brain_2_Ribosome_contained_mRNA_HiSeq

description: Brain ribosome-contained mRNA fragments


title: 8_wk_Ctrl_Brain_1_Ribosome_contained_mRNA_HiSeq

description: Brain ribosome-contained mRNA fragments


title: P0_Ctrl_Liver_1_Ribosome_contained_mRNA_MiSeq

description: Liver ribosome-contained mRNA fragments


title: P0_KO_Brain_3_Ribosome_contained_mRNA_HiSeq

description: Brain ribosome-contained mRNA fragments


title: P0_Ctrl_Liver_3_Ribosome_contained_mRNA_MiSeq

description: Liver ribosome-contained mRNA fragments


title: 8_wk_KO_Brain_2_Total_mRNA_HiSeq

description: Brain total mRNA


title: 8_wk_KO_Brain_1_Ribosome_contained_mRNA_HiSeq

description: Brain ribosome-contained mRNA fragments


title: 8_wk_Ctrl_Brain_3_Ribosome_contained_mRNA_HiSeq

description: Brain ribosome-contained mRNA fragments


title: FGF1 variant rep3 [T4]

city: Wenzhou

first: Dezhong

last: Wang

address: Chashan town

department: ILS

institute: Wenzhou Univsersity

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

source_name: cardiac tissues

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The treatment group were received FGF1 variant (every other day, i.p, 0.5mg/kg) for 16 weeks since the db/db mice were 10-week old. For the model group, mice were received same amount saline as control.

value: heart

value: lepr-/-

tag: agent

value: FGF1 variant

tag: age

value: 26 weeks


title: FGF1 variant rep1 [T1]


title: 8_wk_KO_Brain_1_Total_mRNA_HiSeq

description: Brain total mRNA


title: Model rep2 [M3]


title: FGF1 variant rep2 [T2]


title: Model rep3 [M4]


title: Model rep1 [M2]


title: 8_wk_Ctrl_Brain_2_Total_mRNA_HiSeq

description: Brain total mRNA


title: srsf1-hko_1m_rep-1

city: Urbana

first: Waqar

last: Arif

address: 506 S. Mathews Avenue

department: Biochemistry

institute: UIUC

description:
SRSF1KO_5wk_1_ACAGTGAT_L00M
1 month srsf1 hko replicate 1
processed data file:
srsf1_hko_1m_deseq2_output.csv
transcript_tpm_kallisto_table.csv

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Sequenced reads were trimmed for adaptor sequence and transcript abundances were computed using kallisto v0.46.0
kallisto index was generated using Gencode annotation, GRCm38_vM19
Differential gene expression analysis was performed with the kallisto abundance tables using tximport and DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Table of TPM values of annotated transcripts and DESeq2 output of differential gene expression

source_name: 1 month srsf1 hko_hepatocytes

growth_protocol: Organisms were housed in flow cages, following the standard 12 hour light/dark cycle

extract_protocol:
Purified hepatocytes were flash frozen in liquid nitrogen, and RNA was harvested using Qiagen RNAeasy Kit. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols for “TruSeq Stranded mRNAseq Sample Prep kit”

treatment_protocol: Acute knock-out model was achieved by injection of AAV8 viral vectors expressing iCRE (SRSF1 acHKO) or GFP (Controls)  into SRSF1 f/f mice at 8 weeks of age. Viral vector gene expression was driven by TBG promoter, allowing for hepatocyte-specific expression.

tag: strain background

value: 1 month

value: hepatocytes


title: ctrl_1m_rep-1

description:
Cre_5wk_1_CAGATCAT_L00M
1 month control replicate 1
processed data file:
srsf1_hko_1m_deseq2_output.csv
transcript_tpm_kallisto_table.csv

source_name: 1 month control_hepatocytes

value: albcre+/-


title: 8_wk_Ctrl_Brain_1_Total_mRNA_HiSeq

description: Brain total mRNA


title: srsf1-hko_10d_rep-1

description:
SRSF1KO_p10_1_ATGTCAGA_L00M
10 day srsf1 hko replicate 1
processed data file:
srsf1_hko_pn10_deseq2_output.csv
transcript_tpm_kallisto_table.csv

source_name: 10 day srsf1 hko_hepatocytes

value: post natal day 10


title: srsf1-hko_1m_rep-2

description:
SRSF1KO_5wk_2_GCCAATAT_L00M
1 month srsf1 hko replicate 2
processed data file:
srsf1_hko_1m_deseq2_output.csv
transcript_tpm_kallisto_table.csv


title: ctrl_1m_rep-2

description:
Cre_5wk_2_ACTTGAAT_L00M
1 month control replicate 2
processed data file:
srsf1_hko_1m_deseq2_output.csv
transcript_tpm_kallisto_table.csv


title: ctrl_10d_rep-1

description:
Cre_p10_1_AGTCAACA_L00M
10 day control replicate 1
processed data file:
srsf1_hko_pn10_deseq2_output.csv
transcript_tpm_kallisto_table.csv

source_name: 10 day control_hepatocytes


title: Soft_9d_2

city: Boulder

first: Cierra

last: Walker

state: CO

address: 3415 Colorado Ave

institute: University of Colorado Boulder

data_processing:
Trimmed with bbduk version 38.05 to discard low quality reads
Aligned to susScr11.1 genome with hisat2 (version 2.1.0)
Sam converted to bam using samtools (v 1.8)
PCR duplicates removed using Sambamba ( version 0.6.6 )
Made bigwig files using deepTools bamCoverage (version 3.0.1)
Genome_build: susScr11.1
Supplementary_files_format_and_content: bigWig files, regular or scaled to fly-genome (internal control)

organism: Sus scrofa

source_name: Aortic valve leaflets

growth_protocol: Media was replenished every other day

extract_protocol:
The omni ATAC libraries were prepared following the original omni-ATAC protocol (Corces 2017) with the following modifications. Cells were grown on hydrogels with each replicate having been grown and processed at different dates. Approximately 50,000 cells per well were used for each transposition reaction, with each reaction taking place while the cells were still attached onto their hydrogel substrate. A 300 μL total volume per 12-well plate well reaction was prepared as follows: 150 μL Tagment DNA Buffer (Illumina Ref 15027866), 7.5 μL Tagment DNA Enzyme 1 (Illumina Ref 15027865), 3 μL digitonin (Promega Ref G944A, diluted 1:1 with water), 30 μL Tween-20, 10.5 μL water, 89 μL PBS, 10 μL S2 Drosophila melanogaster nuclei; incubating for 50 minutes at 37°C. The Drosophila spike-in was added for the first replicate for a total of 500 nuclei (1% of total nuclei), and for the second replicate pair it was added for a total of 2,500 nuclei (5% of total nuclei). The pre-amplified transposed fragments were extracted from the hydrogel-attached cells with a phenol/chloroform/isoamyl alcohol (25:24:1) DNA precipitation.
The post-amplified ATAC-libraries were cleaned-up with DNA Clean and Concentrator-5 Kit (Zymo Research Ref D4014). The qPCR amplification was done using NEBNext Ultra II Q5 Master Mix (NEB Ref M0544S), SYBR Gold (Life Tech Ref S11494), and Nextera DNA CD Indices (Illumina Ref 20015882). The libraries were size-selected to remove DNA fragments greater than 1000 bp with a Sage Science BluePippin. The ATAC-seq libraries were quantified with Qubit HS DNA assay and their fragment size-distributions determined with Agilent HS D5000 ScreenTape. Libraries were pooled and sequenced as paired-end 2x37 reads with a NextSeq sequencer at the University of Colorado Boulder BioFrontiers Next Generation Sequencing Core.

treatment_protocol: Primary porcine aortic valvular interstitial cells were isolated and seeded onto PEGdiPDA hydrogels (G' = 4 kPa (stiff) or 2 kPa (soft)). The cells were cultured in Media 199 (Life Technologies) supplemented with 1% human serum, 50 U/mL penicillin, 50 μg/mL streptomycin, and 1 μg/mL amphotericin B for 3 days or 9 days.

tag: biological replicate

tag: phenotype

value: fibroblast

value: Valvular interstitial cells

tag: drosophila spike in included

value: yes


title: B2C

description: de-CxI.xls

source_name: Blood monocyte-derived dendritic cells

value: Control Mo-DCs

tag: donor

value: B

tag: replicate


title: Soft_3d_2


title: Soft_3d_3


title: Stiff_9d_4

value: persistent myofibroblast


title: Soft_9d_1

value: no


title: Soft_3d_1


title: Stiff_9d_2


title: 8_wk_Ctrl_Brain_3_Total_mRNA_HiSeq

description: Brain total mRNA

value: Brain


title: Soft_9d_3


title: srsf1-hko_10d_rep-2

description:
SRSF1KO_p10_2_CCGTCCCG_L00M
10 day srsf1 hko replicate 2
processed data file:
srsf1_hko_pn10_deseq2_output.csv
transcript_tpm_kallisto_table.csv


title: ctrl_10d_rep-2

description:
Cre_p10_2_AGTTCCGT_L00M
10 day control replicate 2
processed data file:
srsf1_hko_pn10_deseq2_output.csv
transcript_tpm_kallisto_table.csv


title: Stiff_9d_1


title: Stiff_3d_4

value: transient myofibroblast


title: Stiff_3d_3


title: M9 + amino acids replicate 2

city: Stanford

first: Markus

last: Covert

state: CA

address: 443 Via Ortega

department: Bioengineering

institute: Stanford University

description: Sample 8

data_processing:
Code to process the raw data is available at bitbucket.org/derekmacklin/sequenceprocessing
bbmap version 34.33 was used to pre-process the raw reads (e.g., quality-trim reads, remove adapter sequences, remove reads that map to rRNA or tRNA)
expression values computed using RSEM 1.2.19 (with bowtie2 2.2.3)
note: mapped Ecocyc's gene annotation (start/stop positions) to U00096.2 and used that as the reference
Genome_build: U00096.2

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli culture

extract_protocol:
Cells were harvested at OD 0.4. RNA was purified using the Qiagen RNeasy Protect Bacteria Mini Kit and rRNA was depleted using Epicentre Ribo-Zero rRNA Removal Kits (Gram-Negative Bacteria).
Library prep was performed by the Stanford Functional Genomics Facility (SFGF) using the TruSeq Stranded Total RNA Sample Preparation guide. Paired-end sequencing was performed by the SFGF on an Illumina NextSeq 500.

tag: growth medium

value: M9 + amino acids


title: Stiff_9d_3


title: M9 + amino acids replicate 3

description: Sample 13


title: Drought_0.3MPa

city: Bikaner

first: PN

last: Sivalingam

address: Beechwal

country: India

institute: ICAR - Central Institute for Arid Horticulture

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to de novo assembled transcriptome using bowtie2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Ziziphus nummularia

source_name: seedling

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CIAHZN-J

value: Whole seedling

tag: condition

value: drought (-0.3MP)


title: Control_0MPa

value: control (0MPa)


title: M9 + amino acids replicate 1

description: Sample 3


title: Stiff_3d_1


title: M9 minimal replicate 3

description: Sample 11

value: M9 minimal


title: day7-input-3

city: Nanjing

first: Chuanxi

last: Yang

state: China

address: 300 Guangzhou Road, 210029, Nanjing, PR China

department: Department of Cardiology

institute: School of Medicine, Southeast University

data_processing:
HISAT2 software used for Clean reads.
After mapping to transcriptomes, significantly enriched m6A modification sites were detected by using exomePeak (version 2.8.0, an exome-based peak-calling algorithm) with default parameters (P < 1 x 10-5, FDR < 1 x 10-3, Fold Enrichment ≥ 2).
HOMER software (version 4.10) was used to de novo identify consensus motifs from the enriched m6A modification sites.
For differential methylation analysis, peaks overlapping or unique for treated and control samples were detected using exomepeak software and fold changes with adjusted p values were calculated for the hypo- and hypermethylated peaks.
Genome_build: rat(rn5)
Supplementary_files_format_and_content: tab-delimited text files include fold changes and p values

organism: Rattus norvegicus

source_name: heart tissue

extract_protocol:
Total RNA isolation from tissue and NRCMs was performed using the TRIzol reagent and a Qiagen RNeasy kit, following the manufacturer’s instructions. RNA was reversed using random hexamer priming (Applied Biosystems).
Ribosomal RNA was removed from the products, and the first strand of cDNA was synthesized by SMART. PCR amplification and library purification were used to obtain an ultramicro-RNA methylated m6A library. Bioptic QseP70 Analyzer was used to conduct quality control over the library.
RNA-Seq,meRIP-seq

value: post natal day 7

value: Sprague Dawley


title: day0-input-3

value: post natal day 0


title: day7-input-1


title: day7-input-2


title: day7-IP-3

description: m6A-IP RNA

tag: meip antibody

value: Abcam, cat. no. ab151230


title: day7-IP-2

description: m6A-IP RNA


title: day0-IP-3

description: m6A-IP RNA


title: day0-input-2


title: day7-IP-1

description: m6A-IP RNA


title: day0-input-1


title: day0-IP-2

description: m6A-IP RNA


title: Stiff_3d_2

value: Valvular interstitial cells

value: yes


title: day0-IP-1

description: m6A-IP RNA


title: 4C_SKNMC

city: Chicago

first: Feng

last: Yue

address: 303 E Chicago Ave. Simpson Querrey 7-518

department: Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
library strategy: 4C-seq
Raw sequencing reads were mapped to hg38 with BWA mem (version 0.7.15)
Duplicated reads were filtered with Picard Markduplicates (version 2.23.9)
Bigwig files were generated using bedGraphToBigWig tool
Genome_build: hg38
Supplementary_files_format_and_content: bigwig, binary format for visualization of 1D genomic data

source_name: Askin’s tumor metastatic site

growth_protocol: SK-N-MC cell line were grown in Gibco Minimum Essential Media media with 10% fetal bovine serum (cat# 1500-500), following ATCC's protocol: https://www.atcc.org/products/all/HTB-10#culturemethod

extract_protocol:
4C was performed to construct the library: 10 million SK-N-MC cells in cell culture were harvested, resuspended in 8.75ml 1X complete medium, and immediately crosslinked in 2% formaldehyde for 10 minutes. Nuclei were isolated from fixed cells and digested by restriction enzyme DpnII (NEB, #R0543) overnight.  Digested DNA was ligated using T4 DNA ligase (NEB, #M2020) and decrosslinked by incubating in proteinase K overnight (Qiagen, #19133). DNA was then purified and selected by weight that is over 30K Dolton, and DNA was digested by the second restriction enzyme Csp6i (Thermo, #ER0211) overnight. DNA was religated using DNA ligase (1U/ul, Invitrogen, #15224017) in low concentration.
DNA was further purified and DNA fragments that contain Myc promoter were amplified by PCR reaction with 30 cycles: We chose a transcription start site of Myc gene that is flanked by DPNII and CSP6I cutting site at each end as an anchor (chr8: 127735189-127735615), and we use a pair of primers that contain Truseq indices to amplify regions located to the upstream and downstream of the anchor. The PCR products were further purified, underwent size selection to remove small DNA fragments, and sent for sequencing on Illumina HiSeq 2500 with a depth of 2 million reads. Myc-upstream-SK-N-MC: CAAGCAGAAGACGGCATACGAGAGATGTAGCCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGTTGCCTGCTCTCTGCCAGT. Myc-downstream:  AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTCCACTCTCCCTGGGACTCT

treatment_protocol: No treatment was applied

value: SKNMC cells

tag: assay


title: M9 minimal replicate 2

description: Sample 6


title: LLRC8aLL3

city: Iowa City

first: Chad

last: Grueter

state: Iowa

address: 285 Newton Rd, 4332 PBDB, 285 Newton Rd

institute: University of Iowa

data_processing:
Illumina basespace used for analysis
Base trimming to 125 bp was performed using Fastq toolkit (V2.2.0)  10 bases were trimmed from the 5' end, and 16 bases were trimmed from the 3' end
Alignment was performed using RNAseq Alignment (v1.1.0) and Bowtie2 to align to Homo Sapiens (par-masked)/HG19 (refseq)
Transcripts were assembled and differential gene expression was performed using Cufflinks Assembly and DE (Version 2.1.0)
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: HUVECs

extract_protocol:
Endothelial cells were scraped from plates in Trizol and RNA was extracted using RNA miniprep kit (Zymo)
RNA libraries were prepared for sequencing using TruSeq RNA Library prep kit  V2

value: HUVEC

tag: knockdown


title: LLRC8aSC2

value: scramble


title: M9 minimal replicate 1

description: Sample 1

tag: strain


title: LLRC8aLL1


title: LLRC8aSC1


title: C2I

description: de-CxI.xls

data_processing:
Illumina reads were analyzed for quality control by FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Filtered reads were aligned simultaneously to the human (Ensembl GRCh38.87) and Trypanosoma cruzi (Ensembl Protists ASM20906v1) reference genomes using HISAT2 v2.0.6 (Kim et al., 2015).
Aligned files were ordered and indexed using Samtools v0.1.18 (Li et al., 2009) followed by read count using the human genome annotation files of Ensembl genome build GRCh38.87 and the software HTSeq-count v0.6.0 (-m intersection-nonempty) (Anders et al., 2015).
Differential expression analysis was performed using DEseq2 package v2.14 from R/Bioconductor (Love et al., 2014), comparing Infected and Control samples (padj ≤ 0.05).
All the analyses were performed after exclusion of outliers, leaving at least one representative sample of each donor.
Genome_build: Ensembl GRCh38.87 for human and Ensembl Protists ASM20906v1 for T. cruzi
Supplementary_files_format_and_content: de-CxI.xls

organism:
Trypanosoma cruzi
Homo sapiens

value: T. cruzi-Infected Mo-DCs

value: C


title: LLRC8aLL2


title: B2I

description: de-CxI.xls

value: B


title: B1I

description: de-CxI.xls


title: C1I

description: de-CxI.xls


title: A1I

description: de-CxI.xls

value: A


title: Homo sapiens with Chagas disease treated with Benznidazole [114030113]

type: genomic

city: Sao Paulo

first: Roberta

last: Martins

address: Av. Dr. Eneas Carvalho de Aguiar, 470

institute: FMUSP

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
affymetrix-algorithm-name = AxiomGT1
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Axiom_InCor_BB
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: cy3, cy5

source_name: Benzidazole adverse reaction_No

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cryopreserved buffy-coat of peripheral blood

extract_protocol: Genomic DNA was extracted from cryopreserved buffy-coat obtained from peripheral blood using the Qiagen DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

treatment_protocol: The patients received Benznidazole (5mg/Kg/day) for 60 days, maximum of 300mg/day.

tag: subject status

value: Chagas disease patient treated with Benznidazole

tag: adverse reaction to benznidazole

value: No

tag: tissue

value: buffy-coat of peripheral blood collection


title: Homo sapiens with Chagas disease treated with Benznidazole [114030114]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030112]

source_name: Benzidazole adverse reaction_Yes

value: Yes


title: Homo sapiens with Chagas disease treated with Benznidazole [114030116]


title: LLRC8aSC3

tag: cell type


title: Homo sapiens with Chagas disease treated with Benznidazole [114030106]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030103]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030111]


title: Homo sapiens with Chagas disease treated with Benznidazole [11403033]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030100]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030095]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030094]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030102]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030098]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030097]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030099]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030086]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030096]


title: A2I

description: de-CxI.xls

extract_protocol:
Infected and Control MoDCs were harvested, and RNA was extracted by Trizol reagent (Ambion) as suggested by the manufacturer's recommendations.
Oligo d(T) beads were used to perform mRNA enrichment, which were fragmented randomly and converted in cDNA. Then, poly(A) tails were added and enriched by PCR to generate a cDNA library. Illumina HiSeq 2500 was used to perform the paired-end sequencing of 150bp reads.


title: Homo sapiens with Chagas disease treated with Benznidazole [114030085]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030092]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030117]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030084]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030093]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030091]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030115]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030109]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030105]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030081]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030083]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030080]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030082]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030107]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030078]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030077]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030076]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030074]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030087]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030073]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030066]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030071]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030067]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030061]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030072]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030058]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030069]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030055]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030054]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030068]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030050]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030051]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030048]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030053]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030052]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030047]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030049]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030046]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030044]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030043]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030042]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030045]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030038]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030039]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030037]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030036]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030034]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030028]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030027]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030023]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030022]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030018]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030019]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030014]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030013]


title: Homo sapiens with Chagas disease treated with Benznidazole [113050010]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030024]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030020]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030011]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030026]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030016]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030015]


title: Homo sapiens with Chagas disease treated with Benznidazole [113050009]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030017]


title: Homo sapiens with Chagas disease treated with Benznidazole [113050008]


title: Homo sapiens with Chagas disease treated with Benznidazole [113050003]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030029]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030012]


title: Homo sapiens with Chagas disease treated with Benznidazole [113050006]


title: Homo sapiens with Chagas disease treated with Benznidazole [113050001]


title: Homo sapiens with Chagas disease treated with Benznidazole [113050004]


title: Homo sapiens with Chagas disease treated with Benznidazole [114030021]


title: Homo sapiens with Chagas disease treated with Benznidazole [113050007]


title: Homo sapiens with Chagas disease treated with Benznidazole [113050002]


title: Homo sapiens with Chagas disease treated with Benznidazole [113050005]


title: A549 cells, pH1N1 infected at MOI: 0.5, indirect BMdEos exposure, biological replicate 2

city: Memphis

first: Robert

last: Rooney

state: TN

address: 50 N. Dunlap, Room 366R, LeBonheur CFRC

department: Pediatrics

institute: University of Tennessee Health Science Center

description: Gene expression data from human A549 cells, infected with influenza strain pH1N1 (MOI: 0.5), indirect eosinophil exposure for 3 days

hyb_protocol: Following fragmentation, 5.5ug of cDNA were hybridized for 16 hr at 45degreeC on Clariom™ S Human arrays (GPL26157). GeneChip arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip arrays were scanned using the Affymetrix GCS 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the SST-RMA-Gene algorithm using Affymetrix Expression Console software.

source_name: A549 aveolar epithelial cells

label_protocol: Sense target cDNA was prepared from 100ng of total RNA, fragmented, and biotin-labeled using the Clariom™ S Human Assay Kit (GPL26157).

growth_protocol: Eosinophils were derived from female C57BL/6 bone marrow by culturing for 14 days in eosinophil growth media. A549 (ATCC) were seeded in 24-well plates and incubated for 24 h at 37ºC with 5% CO2.

extract_protocol: BMdEos cells were separated out and RNA was isolated from A549 cells with the RNeasy Mini RNA extraction kit (Qiagen, Hilden, Germany) per the manufacturer’s recommended procedure, and eluted into RNase-free water.

treatment_protocol: A549 (ATCC) were seeded in 24-well plates and incubated for 24 h at 37ºC with 5% CO2. Confluent monolayers of A549 cells were infected with 0.5 MOI of pH1N1 and cells were incubated at 37ºC with 5% CO2 in the presence of 1 µg/mL of TPCK-trypsin. Mock-infected cells received infection media instead of virus. Mature BMdEos suspended in growth media were added at 1:1 ratio to A549 cells directly or indirectly by using Transwell® permeable supports (0.4 µM permeable membrane) (Castor, Kennebunk, ME). Non-exposed A549 cells received eosinophil growth media.

value: isolated from carcinoma originating in human lung aveolar epithelia

tag: eosinophil exposure

value: Indirect

tag: influenza strain


title: A549 cells, pH1N1 infected at MOI: 0.5, direct BMdEos exposure, biological replicate 1

description: Gene expression data from human A549 cells, infected with influenza strain pH1N1 (MOI: 0.5), direct eosinophil exposure for 3 days

value: Direct


title: A549 cells, mock infected, direct BMdEos exposure, biological replicate 2

description: Gene expression data from human A549 cells, mock infected, direct eosinophil exposure for 3 days

value: Mock


title: A549 cells, pH1N1 infected at MOI: 0.5, no BMdEos exposure, biological replicate 4

description: Gene expression data from human A549 cells, infected with influenza strain pH1N1 (MOI: 0.5), mock eosinophil exposure


title: A549 cells, pH1N1 infected at MOI: 0.5, indirect BMdEos exposure, biological replicate 4


title: A549 cells, mock infected, indirect BMdEos exposure, biological replicate 3

description: Gene expression data from human A549 cells, mock infected, indirect eosinophil exposure for 3 days


title: A549 cells, mock infected, direct BMdEos exposure, biological replicate 1


title: A549 cells, mock infected, indirect BMdEos exposure, biological replicate 4


title: A549 cells, pH1N1 infected at MOI: 0.5, no BMdEos exposure, biological replicate 1


title: A549 cells, mock infected, no BMdEos exposure, biological replicate 4

description: Gene expression data from human A549 cells, mock infected, mock eosinophil exposure


title: A549 cells, pH1N1 infected at MOI: 0.5, direct BMdEos exposure, biological replicate 2


title: A549 cells, pH1N1 infected at MOI: 0.5, no BMdEos exposure, biological replicate 2


title: A549 cells, pH1N1 infected at MOI: 0.5, indirect BMdEos exposure, biological replicate 1


title: Peritoneal macrophage Control, LPS 12 hr

city: Nagoya

first: Kento

last: Kurita

state: Aichi

address: Furo-cho

department: Department of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine

institute: Nagoya University

hyb_protocol: Following fragmentation, aRNA were hybridized on Mouse Genome 430 2.0 using Hybridization oven 640.   Gene Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Chip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: peritoneal macrophages cultured in serine/glycine-depleted medium and treated with LPS for 12 hr

label_protocol: Biotinylated aRNA were prepared according to Gene Chip 3' IVT Express Kit aRNA amplification procedure and Gene Chip 3' IVT Express KitUse Manual p/N 702646 Rev.1

growth_protocol: Peritoneal macrophages were cultured in Dulbecco's Modified Eagle Medium with 10% FBS for 6 days and then cultured in control or serine/glycine-depleted medium for 24 hr.

extract_protocol: Total RNA was prepared using Sepasol(nacalai-tesque). Cleanup and concentration was performed by Rneasy MinElute Cleanup Kit.

treatment_protocol: After culturing in control or serine/glycine-depleted medium for 24 hr, peritoneal macrophages were stimulated with LPS (10 ng/ml) for 6 or 12 hr.

value: peritoneal macrophages

tag: gender

value: male


title: A549 cells, pH1N1 infected at MOI: 0.5, direct BMdEos exposure, biological replicate 4


title: Peritoneal macrophage Control, Veh 12 hr

source_name: peritoneal macrophages cultured in control medium and treated with vehicle for 12 hr


title: A549 cells, pH1N1 infected at MOI: 0.5, direct BMdEos exposure, biological replicate 3


title: A549 cells, mock infected, indirect BMdEos exposure, biological replicate 2


title: A549 cells, mock infected, indirect BMdEos exposure, biological replicate 1


title: A549 cells, mock infected, no BMdEos exposure, biological replicate 3


title: A549 cells, mock infected, no BMdEos exposure, biological replicate 2


title: Peritoneal macrophage Serine/glycine-depleted, LPS 6 hr

source_name: peritoneal macrophages cultured in control medium and treated with LPS for 6 hr


title: RelA 5 rep1

city: Copenhagen

first: Kristoffer

middle: Skovbo

last: Winther

address: Ole Maaloesvej 5

department: Department of Biology

country: Denmark

institute: University og Copenhagen

data_processing:
Library strategy: CRAC
fastq_quality_filter -q 30 -Q 33 -i<(Sequencingfile.fastq.bz2 | bunzip2 -c) -o Filteredsequencingfile.fastq #quality filtering
pyBarcodeFilter.py -f Filteredsequencingfile.fastq -b barcodes.txt #demultiplex in respect to 5' barcode
cutadapt NNNCACTAGC_rela_0_rep1.fastq -a TGGAATT -m 12 -o rela_0_1.trimmed.fastq #trimming of 3'end linker
pyFastqDuplicateRemover.py -f rela_0_1.trimmed.fastq -o rela_0_1.trimmed.collapsed.fasta #removal of PCR duplicates
bowtie2-build ecoli_masked.fa ecoli bowtie2 -x ecoli -f rela_0_1.trimmed.collapsed.fasta > rela_0_1.sam #alignment using masked genome file
Genome_build: NC_000913.3
Supplementary_files_format_and_content: mapped read coordinates in GTF format

organism: Escherichia coli

source_name: Bacterial cells replicate 1

growth_protocol: Bacterial cells were grown in MOPS (morpholinepropanesulfonic acid) minimal medium at 30C supplemented with 0.2% glucose and with all nucleobases (10 µg ml-1 of each).

extract_protocol:
The cells were subsequently UV-C crosslinked and harvested by centrifugation, washed in ice-cold phosphate buffered saline (PBS) and snap frozen in liquid nitrogen. The pellets were stored at -80C. The HTF tagged proteins were then purified, linkers ligated to crosslinked RNA, cDNA synthesized and DNA libraries generated as described in Winther et al. 2018.
Libraries were constructed as per, Sinha and Winther 2020

treatment_protocol: Non-starved cultures were collected at OD600= 0.2 and isoleucine starved cultures were collected after incubation with 500μg/mL L-Valine for 5 or 30 min (samples indicated 0,5 or 30)

tag: strrain

value: MG1655 relA::HTF


title: P0_KO_Brain_1_Ribosome_contained_mRNA_MiSeq

description: Brain ribosome-contained mRNA fragments

data_processing:
Library strategy: Ribo-seq
A-site mRNA codon counting procedure: Using MiSeq data, mRNA codon situated in ribosomal A-site was extracted and counted. 1) 3' Adaptor sequences were trimmed using Galaxy. 2) Sequences were aligned to mouse ribosomal RNAs using Bowtie2 to remove ribosomal RNA sequences. 3) Remaining sequences were aligned to mouse mRNAs to extract mRNA sequences. 4) Ribosome-contained mRNA sequences were analyzed using Ribogalaxy Triplet Periodicity software and Metagene analysis to determine the position of mRNA A-site codons. 5) 30-nt mRNA fragments were selected, and trimmed to leave A-site codons (nucleotides 17-19). Read numbers were counted using the Count function in Galaxy.
Total or ribosomal mRNA counting procedure: Using HiSeq data, mRNA read number was counted: 1) 3' adaptor sequence was trimmed. 2) Sequences were mapped to mouse transcriptome using HISAT2 and mm10 GTF file from UCSC Table Browser. 3) mRNA reads were counted using Htseq-count.
Genome_build: Mouse mm10
Supplementary_files_format_and_content: Excel files: 1. A-site codon numbers (brain, liver). 2. mRNA read numbers (brain)

source_name: Ftsj1 KO mouse 1

value: Brain

tag: genotype

value: Ftsj1 KO


title: RelA 0 rep2

source_name: Bacterial cells replicate 2


title: A121E 30 rep2

value: MG1655 relAA121E::HTF


title: A121E 5 rep1


title: A121E 0 rep1


title: P0_KO_Brain_3_Ribosome_contained_mRNA_MiSeq

description: Brain ribosome-contained mRNA fragments

source_name: Ftsj1 KO mouse 3


title: P0_Ctrl_Brain_3_Ribosome_contained_mRNA_MiSeq

description: Brain ribosome-contained mRNA fragments

source_name: WT mouse 3

value: WT


title: RelA 30 rep2


title: A121E 0 rep2


title: P0_KO_Brain_2_Ribosome_contained_mRNA_MiSeq

description: Brain ribosome-contained mRNA fragments

source_name: Ftsj1 KO mouse 2


title: RelA 0 rep1


title: A549 cells, pH1N1 infected at MOI: 0.5, indirect BMdEos exposure, biological replicate 3


title: Peritoneal macrophage Serine/glycine-depleted, LPS 12 hr


title: A549 cells, pH1N1 infected at MOI: 0.5, no BMdEos exposure, biological replicate 3


title: A121E 30 rep1


title: RelA 30 rep1


title: Peritoneal macrophage Serine/glycine-depleted, Veh 12 hr


title: Peritoneal macrophage Control, LPS 6 hr


title: A549 cells, mock infected, no BMdEos exposure, biological replicate 1


title: Peritoneal macrophage Control, Veh 6 hr

source_name: peritoneal macrophages cultured in control medium and treated with vehicle for 6 hr


title: P0_Ctrl_Brain_1_Ribosome_contained_mRNA_MiSeq

description: Brain ribosome-contained mRNA fragments

source_name: WT mouse 1


title: Cpeb1 siRNA

city: Hirakata

first: Souichi

last: Oe

state: Osaka

address: 2-5-1 Shinmachi

institute: Kansai Medical University

description: Gene expression data from CPEB1-depleted Neuro2a cells.

hyb_protocol: Biotin-labeled cRNA (12.5 ug) were hybridized for 16 hr on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the GeneChip®Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip®Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) by using AGCC (Affymetrix®GeneChip®Command Console®Software), and Affymetrix®Expression Console™ .

source_name: Neuro2a cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA by using 3’IVT PLUS Reagent Kit (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mouse neuroblastoma Neuro2a cells (ATCC, Manassas, VA, USA) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Thermo Fisher, Waltham, MA, USA) supplemented with 10% fetal bovine serum (FBS) (GE Healthcare, San Ramon, CA, USA) and 2% GlutaMAX-I (Thermo Fisher).

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

treatment_protocol: For siRNA transfection, stealth RNAi siRNAs (Thermo Fisher) targeting Cpeb1 mRNA were designed based on their coding regions (accession number, NM_001252525). siRNA transfection was performed using Lipofectamine RNAiMAX (Thermo Fisher) following the manufacturer’s protocols.

value: Neuro2a cells

tag: treatment

value: Cpeb1 siRNA for 24 hours


title: 8_wk_KO_Brain_3_Total_tRNA_fragment_MiSeq

description: Brain total tRNA fragments

data_processing:
Adaptor sequence was removed.
Sequences were mapped to tRNA sequences (retreived from the Genomic tRNA database) using Bowtie2.
Read numbers were counted using position information in BAM files and Group function in Galaxy.
Genome_build: Genomic tRNA database mouse tRNAs
Supplementary_files_format_and_content: Excel file containing tRNA read numbers and tRNA fragment read numbers

extract_protocol:
Brains were disected and snap-frozen in liquid nitrogen. Brains were subjected to ribosome-profiling for the "ribosome-contained tRNA" samples. Total RNA was collected from brain lysates for "total tRNA" and "total tRNA fragment" samples. tRNAs and tRNA fragments were collected from total RNA by gel excision of corresponding sized bands.
Library was constructed using a 3' adaptor (5App/CTGTAGGCACCATCAAT/3ddC). AlkB treatment was performed before reverse transcription to remove RT-blocking tRNA modifications.


title: A549 cells, mock infected, direct BMdEos exposure, biological replicate 3


title: Peritoneal macrophage Serine/glycine-depleted, Veh 6 hr


title: Ro

city: Seoul

first: Joo Hyun

last: Kim

address: 50 Irwon-dong

country: South Korea

institute: Sungkyunkwan University

description: Gene expression data from SNK6 cell lines

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

source_name: NKT cell lymphoma

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: SNK6 cells were cultured in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 500 U/ml interleukin-2 (IL-2).

extract_protocol: Total RNA was prepared using a Qiagen RNA extraction kit. cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer.

treatment_protocol: SNK6 cells were treated with romidepsin in the presence or absence of sildenafil for 72hr.

tag: cell line


title: control siRNA

description: Gene expression data from control Neuro2a cells.

value: control siRNA for 24 hours


title: P0_Ctrl_Brain_2_Ribosome_contained_mRNA_MiSeq

description: Brain ribosome-contained mRNA fragments

source_name: WT mouse 2

extract_protocol:
Brains or livers were disected and snap-frozen in liquid nitrogen. Brains or livers were lysed and subjected to ribosome-profiling, or  to total RNA purification followed by PolyA+ RNA selection.
Library was constructed using a 3' adaptor (5App/CTGTAGGCACCATCAAT/3ddC).


title: 8_wk_KO_Brain_2_Total_tRNA_fragment_MiSeq

description: Brain total tRNA fragments


title: 8_wk_KO_Brain_1_Ribosome_contained_tRNA_MiSeq

description: Brain ribosome-contained tRNA

data_processing:
Library strategy: Ribo-tRNA-seq
Adaptor sequence was removed.
Sequences were mapped to tRNA sequences (retreived from the Genomic tRNA database) using Bowtie2.
Read numbers were counted using position information in BAM files and Group function in Galaxy.
Genome_build: Genomic tRNA database mouse tRNAs
Supplementary_files_format_and_content: Excel file containing tRNA read numbers and tRNA fragment read numbers


title: Ro_plus_Via


title: 8_wk_Ctrl_Brain_2_Total_tRNA_fragment_MiSeq

description: Brain total tRNA fragments


title: 8_wk_KO_Brain_2_Ribosome_contained_tRNA_MiSeq

description: Brain ribosome-contained tRNA


title: 8_wk_KO_Brain_1_Total_tRNA_fragment_MiSeq

description: Brain total tRNA fragments


title: 8_wk_Ctrl_Brain_3_Total_tRNA_fragment_MiSeq

description: Brain total tRNA fragments


title: 8_wk_Ctrl_Brain_1_Total_tRNA_fragment_MiSeq

description: Brain total tRNA fragments


title: 8_wk_KO_Brain_2_Total_tRNA_MiSeq

description: Brain total tRNA


title: 8_wk_Ctrl_Brain_2_Total_tRNA_MiSeq

description: Brain total tRNA


title: 8_wk_Ctrl_Brain_1_Ribosome_contained_tRNA_MiSeq

description: Brain ribosome-contained tRNA


title: 8_wk_KO_Brain_3_Total_tRNA_MiSeq

description: Brain total tRNA


title: 8_wk_Ctrl_Brain_1_Total_tRNA_MiSeq

description: Brain total tRNA


title: 8_wk_KO_Brain_1_Total_tRNA_MiSeq

description: Brain total tRNA


title: 8_wk_Ctrl_Brain_3_Total_tRNA_MiSeq

description: Brain total tRNA


title: 8_wk_KO_Brain_2_Ribosome_contained_mRNA_MiSeq

description: Brain ribosome-contained mRNA fragments

data_processing:
Library strategy: Ribo-seq
A-site mRNA codon counting procedure: Using MiSeq data, mRNA codon situated in ribosomal A-site was extracted and counted. 1) 3' Adaptor sequences were trimmed on Galaxy. 2) Sequences were aligned to mouse ribosomal RNAs using Bowtie2 to remove ribosomal RNA sequences. 3) Remaining sequences were aligned to mouse mRNAs to extract mRNA sequences. 4) Ribosome-contained mRNA sequences were analyzed using Ribogalaxy Triplet Periodicity software and Metagene analysis software to determine the position of mRNA A-site codons. 5) 30-nt mRNA fragments were selected, and trimmed to leave A-site codons (nucleotides 17-19). Read numbers were counted using the Count function in Galaxy.
Total or ribosomal mRNA counting procedure: Using HiSeq data, mRNA read number was counted: 1) 3' adaptor sequence was trimmed. 2) Sequences were mapped to mouse transcriptome using HISAT2 and mm10 GTF file from UCSC Table Browser. 3) mRNA reads were counted using Htseq-count.
Genome_build: mm10
Supplementary_files_format_and_content: 8wk_MiSeq_Asite_Codon_processed_data
Supplementary_files_format_and_content: 8wk_HiSeq_mRNA_processed_data

extract_protocol:
Brains were disected and snap-frozen in liquid nitrogen. Brains were lysed and subjected to ribosome-profiling, or  to total RNA purification followed by PolyA+ RNA selection.
Library was constructed using a 3' adaptor (5App/CTGTAGGCACCATCAAT/3ddC).


title: 8_wk_Ctrl_Brain_2_Ribosome_contained_mRNA_MiSeq

description: Brain ribosome-contained mRNA fragments


title: 8_wk_Ctrl_Brain_3_Ribosome_contained_mRNA_MiSeq

description: Brain ribosome-contained mRNA fragments


title: 8_wk_KO_Brain_1_Ribosome_contained_mRNA_MiSeq

description: Brain ribosome-contained mRNA fragments


title: 8_wk_Ctrl_Brain_1_Ribosome_contained_mRNA_MiSeq

description: Brain ribosome-contained mRNA fragments


title: 8_wk_KO_Brain_3_Ribosome_contained_mRNA_MiSeq

description: Brain ribosome-contained mRNA fragments


title: RNA-Seq PT70_1

city: New York

first: Sagar

last: Chhangawala

address: 1300 York Ave.

department: PBSB

institute: Weill Cornell Medical College

description: ribodepleted RNA

data_processing:
fastq files were aligned using STAR (v2.5.0b, default parameters)
Read counting was performed using htseq-count (v0.9.1, parameters: --stranded=no -t exon)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file that contains gene IDs and read counts for each sample

source_name: PDAC EpCAM+ primary tumor

extract_protocol:
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 631-800ng of total RNA with an RNA integrity number varying from 2.8 to 9.4 underwent ribosomal depletion
library preparation was done using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR.

tag: tumor differentiation

value: poorly diff

tag: margin status

value: Positive

tag: tumor stage

value: T3 N1

tag: adjuvant therapy

tag: radiotherapy

value: No

tag: recurrence status

value: unknown


title: RNA-Seq PT9_1

description: ribodepleted RNA

value: moderately diff

value: T3 N0

value: Yes


title: RNA-Seq PT62_1

description: ribodepleted RNA

value: Free


title: RNA-Seq PT63_1

description: ribodepleted RNA


title: RNA-Seq PT65_1

description: ribodepleted RNA


title: RNA-Seq PT7_1

description: ribodepleted RNA


title: RNA-Seq PT66_1

description: ribodepleted RNA

value: moderately to poorly diff


title: RNA-Seq PT67_1

description: ribodepleted RNA


title: RNA-Seq PT69_1

description: ribodepleted RNA


title: RNA-Seq PT64_1

description: ribodepleted RNA


title: RNA-Seq PT61_1

description: ribodepleted RNA


title: RNA-Seq PT6_1

description: ribodepleted RNA


title: RNA-Seq PT58_1

description: ribodepleted RNA


title: RNA-Seq PT55_1

description: ribodepleted RNA


title: 8_wk_KO_Brain_3_Ribosome_contained_tRNA_MiSeq

description: Brain ribosome-contained tRNA

tag: strain

value: Brain


title: RNA-Seq PT59_1

description: ribodepleted RNA


title: RNA-Seq PT60_1

description: ribodepleted RNA


title: RNA-Seq PT53_1

description: ribodepleted RNA


title: EOs_Skin_2

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

description: Gene expression for skin of gilthead sea bream fed 0.5% EOs diet pool 2

hyb_protocol: The hybridization protocol was carried out according to Agilent's instructions. Briefly, 1.65 μg of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/mg cRNA) was fragmented at 60°C for 30 min in a total reaction volume of 55 µl containing 25X Agilent fragmentation buffer and 10X Agilent blocking agent. On completion of the fragmentation reaction, 55 µl of 2X GEx hybridization buffer was added to the fragmentation mixture and hybridized to S. aurata array (ID 024502, Agilent) at 65°C and 10 rpm for 17 hours in a rotating hybridization oven.

scan_protocol: After hybridization, microarrays were washed 1 min at room temperature (RT) with GEWash Buffer 1 (Agilent), 1 min with GE Wash buffer 2 (Agilent) pre-incubated at 37°C, 45 s at RT with Acetonitrile (Sigma, St Louis, MO, USA), and 30 s at RT with stabilization and drying solution (Agilent). Slides were scanned immediately afterwashing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area: 61 x21.6 mm; Scan resolution: 5 µm; Dye channel set to green; Green PMT: 100%). Spot intensities and other quality control features were extracted with Feature Extraction software version 10.4.0.0 (Agilent).

data_processing: For microarray analysis, a percentile shift normalization was carried out and then data were filtered by expression (standard deviation) among groups. Then, gene-level analysis was conducted in order to obtain the median of signal intensities from spots within a probe set. Statistical test (t-test unpaired) was done with GeneSpring software GX 14.3 to obtain the differentially expressed genes (p-value < 0.05) between control and treatments.

organism: Sparus aurata

label_protocol: One-color microarray was carried out according to manufacturer’s protocols. Briefly, 200 ng of total RNA was reversed transcribed along with spike-in (Agilent One-Color RNA Spike-In kit, Agilent Technologies, USA). Then, the solution was used as template for Cyanine-3 (Cy3) labeled cRNA synthesis and amplification with the Low Input Quick Amp Labelling kit (Agilent).  Samples of cRNA were purified using the RNeasy micro kit (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from skin using  the RNeasy® Mini Kit (Qiagen, Germany). Total RNA was eluted in a final volume of 35 μL nuclease-free water and treated with DNAse using the DNA-freeᵀᴹ DNA Removal Kit according to manufacturer’s instructions (Invitrogen, Thermo Fisher Scientific, Lithuania). Total RNA concentration and purity were quantified using a Nanodrop-2000® spectrophotometer (Thermo Scientific, USA) and stored at -80 °C until analysis. Prior to hybridization with microarrays, samples were diluted to 133.33 ng/µL concentration and checked for integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies, Spain). All the RNA analysed in this study were selected by the criteria of a RIN value > 8.5.

treatment_protocol:
Gilthead sea bream (Sparus aurata) were obtained from an aquaculture company (Valencia, Spain) and transported to the on-grown facilities of IRTA in Sant Carles de La Ràpita (Tarragona, Spain).
All animal experimental procedures were conducted in compliance with the experimental research protocol approved by the Committee of Ethics and Animal Experimentation of the Institut de Recerca i Tecnologia Agroalimentàries (IRTA) and in accordance with the Guidelines of the European Union Council (86/609/EU) for the use of laboratory animals. After transport, fish received three treatments with hydrogen peroxide and two treatments with formaldehyde (150 ppm, during one hour each) to treat injuries and avoid the presence of any parasite. After the on-growing period of 105 days, 150 fish (BW = 40.26 ± 0.14 g) were randomly distributed in six aerated 450 L square-shaped tanks with smoothed corners, using an IRTAmar® recirculation system (5-10 % water replacement per day) under natural photoperiod. Water temperature (21-28 °C), oxygen (6.8 ± 1.7 mg/L) and pH (7.5 ± 0.01) were daily controlled, whereas salinity (35‰) as well as ammonia (0.13 ± 0.1 mg NH4+ L−1) and nitrite (0.18 ± 0.1 mg NO2- L−1) levels were weekly monitored.The nutritional assay was carried out in triplicate tanks with an initial density of 2 kg/m3 (25 fish per tank). Fish were fed both diets two times per day at the daily rate of 3.0% of the stocked biomass, which approached apparent satiation.  At day 65 of feeding, four fish were randomly selected from each tank, euthanized with anaesthetic (MS-222, Sigma-Aldrich) and a section from the skin was sampled and stored in RNAlater™, incubated overnight at 4 °C, and stored at -80 °C until analysed.

value: Skin

tag: age

value: juveniles, 155 g

value: EOs diet


title: RNA-Seq PT52_1

description: ribodepleted RNA


title: RNA-Seq PT50_1

description: ribodepleted RNA


title: Control_Skin_3

description: Gene expression for control group pool 3

tag: tissue

value: control


title: Control_Skin_1

description: Gene expression for control group pool 1


title: Control_Skin_2

description: Gene expression for control group pool 2


title: EOs_Skin_3

description: Gene expression for skin of gilthead sea bream fed 0.5% EOs diet pool 3


title: RNA-Seq PT71_1

description: ribodepleted RNA


title: RNA-Seq PT51_1

description: ribodepleted RNA


title: 8_wk_Ctrl_Brain_2_Ribosome_contained_tRNA_MiSeq

city: Kumamoto City

first: Takeshi

last: Chujo

address: 1-1-1 Honjo, Chuo-ku

institute: Kumamoto University

description: Brain ribosome-contained tRNA

value: WT


title: RNA-Seq PT49_1

description: ribodepleted RNA


title: RNA-Seq PT46_1

description: ribodepleted RNA


title: RNA-Seq PT44_1

description: ribodepleted RNA


title: RNA-Seq PT47_1

description: ribodepleted RNA


title: RNA-Seq PT4_1

description: ribodepleted RNA


title: RNA-Seq PT43_1

description: ribodepleted RNA


title: RNA-Seq PT5_1

description: ribodepleted RNA


title: RNA-Seq PT39_1

description: ribodepleted RNA


title: RNA-Seq PT45_1

description: ribodepleted RNA


title: EOs_Skin_1

description: Gene expression for skin of gilthead sea bream fed 0.5% EOs diet pool 1


title: RNA-Seq PT35_1

description: ribodepleted RNA

value: T2 N1


title: RNA-Seq PT36_1

description: ribodepleted RNA


title: RNA-Seq PT37_1

description: ribodepleted RNA


title: RNA-Seq PT32_1

description: ribodepleted RNA


title: RNA-Seq PT25_1

description: ribodepleted RNA


title: RNA-Seq PT23_1

description: ribodepleted RNA

value: poorly diff


title: RNA-Seq PT33_1

description: ribodepleted RNA


title: RNA-Seq PT21_1

description: ribodepleted RNA

value: Positive


title: RNA-Seq PT17_1

description: ribodepleted RNA

value: T3 N1


title: RNA-Seq PT16_1

description: ribodepleted RNA

value: No


title: RNA-Seq PT34_1

description: ribodepleted RNA


title: RNA-Seq PT24_1

description: ribodepleted RNA

value: unknown


title: RNA-Seq PT18_1

description: ribodepleted RNA


title: RNA-Seq PT20_1

description: ribodepleted RNA


title: RNA-Seq PT13_1

description: ribodepleted RNA


title: RNA-Seq PT10_1

description: ribodepleted RNA


title: RNA-Seq PT12_1

description: ribodepleted RNA


title: Cd36 KO

city: La Jolla

first: Susan

last: Kaech

address: 10010 N Torrey Pines Rd

institute: Salk InstituteSalk Institute for Biological Studies

data_processing:
fastq files were generated for the Read1 for cell barcode and UMI and Read2 for transcript applying cellranger mkfastq
The Read2 was aligned to the mouse genome (GRCm38/mm10) with cell ranger count (with default parameters, version 2.1.1 from 10x genomics)
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger output files

source_name: tumor infiltrating leukotyctes

extract_protocol:
10X genomics
Droplets and libraries were prepared using Chromium Single Cell 3' Reagent Kits v2 according to manufacturer's protocol (10X genomics).

tag: markers for facs sort

value: CD45+ CD3+ and CD45+ CD11b+

tag: cell type

value: mixed sample (non-demultiplexed) representing CD4+ T cells, CD8+ T cells


title: Cd36 WT


title: 5i inguinal lymph node (i-Tcells)

city: Munich

first: Thomas

last: Korn

state: Bavaria

address: Ismaninger Str. 22

department: Neurology

country: Germany

institute: Technical University of Munich

data_processing:
library was created using the NEB UltraII FS kit
bcl files were demultiplexed using bcl2fastq v2.20.0.422
fastq files were mapped to the mm10 genome using STAR (version 2.7.5b)
final raw count matrix was obtain using Drop-seq_tools-1.12
Genome_build: mm10
Supplementary_files_format_and_content: raw count matrix text file

source_name: inguinal lymph node

extract_protocol:
Cells were sorted on a BD Aria III into TCL buffer and frozen at -80°C. Total RNA was isolated using the RNAeasy Plus micro kit (Qiagen, #74034).
Quality and integrity of total RNA was controlled on a Bioanalyzer 2100 (Agilent Technologies). Library preparation for bulk-sequencing of poly(A)-RNA was done as described previously (Parekh et al., 2016). Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher, #EP0742) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adaptor. Ends of the cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. NEB UltraII FS kit was used to fragment cDNA. After end repair and A-tailing a TruSeq adapter was ligated and 3'-end-fragments were finally amplified using primers with Illumina P5 and P7 overhangs. In comparison to Parekh et al. (2016), the P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 67 cycles for the cDNA in read1 and 16 cycles for the barcodes and UMIs in read2. Data was processed using the published Drop-seq pipeline (v1.0) to generate sample- and gene-wise UMI tables (Macosko et al., 2015). Reference genome (GRCm38) was used for alignment. Transcript and gene definitions were used according to GENCODE version M25

value: inguinal lymph node

value: 38 days

value: CD4+CD44high T cell


title: 8i inguinal lymph node (i-Tcells)

value: 37 days


title: 2m spleen (m-T cells)

source_name: spleen

value: spleen

value: 36 days


title: 6i inguinal lymph node (i-Tcells)


title: 5i spleen (i-Tcells)


title: 4m spleen (m-T cells)

value: 35 days


title: 3m spleen (m-T cells)


title: 2m mesenteric lymph node (m-T cells)

source_name: mesenteric lymph node

value: mesenteric lymph node


title: 1m spleen (m-T cells)


title: 3m mesenteric lymph node (m-T cells)


title: 7i inguinal lymph node (i-Tcells)


title: 1m mesenteric lymph node (m-T cells)


title: RNA-Seq PT14_1

description: ribodepleted RNA

value: Free

value: Yes


title: 4m mesenteric lymph node (m-T cells)


title: 8i spleen (i-Tcells)


title: 6i spleen (i-Tcells)


title: iNKTDay14_1

city: Boston

last: Gensollen

address: 77 Avenue Louis Pasteur

department: Gastroenterology

institute: Brigham and Women's Hospital/Harvard Medical School

data_processing: Reads were aligned to the mouse genome (GRCm38/mm10) with STAR and expression counts were estimated with HTseq using Partek Flow software v10. Differential transcript expression analysis was performed comparing invariant NKT cells purified from colon lamina propria at day 14 versus day 56 after birth in SPF mice or comparing macrophages purified from colon lamina propria of SPF and GF mice at day 9 or SPF mice at day 8 or 14 using the following parameters. Differential expression of transcripts was determined by using the R package DESeq2. Differentially expressed transcripts in each cell population were selected with the threshold of log2|FoldChange| > 1 and Padj < 0.05 and then subjected to gene ontology pathway analysis using Metascape website.

source_name: colon

extract_protocol:
Between 300-3000 sorted cells were collected directly in RLT Plus Buffer (Qiagen) and RNA was isolated according to manufacturer’s instructions.
Library construction was performed using the SMART-seq v4 Ultra Low Input RNA Kit (Takara) according to the manufacturer’s instruction. Single-end (50bp) sequencing was performed using Illumina NextSeq500 sequencing platform.

value: iNKT

value: colon

tag: microbiota

value: Specific Pathogen Free

value: 14 day old


title: iNKTDay56_2

value: 56 day old


title: iNKTDay56_1


title: MacGF_3

value: Macrophages

value: Germ free

value: 9 day old


title: iNKTDay14_2


title: MacGF_4


title: iNKTDay56_3


title: MacGF_2


title: iNKTDay14_3


title: MacGF_1


title: MacSPF_2


title: iNKTDay56_4


title: MacSPF_1


title: 7i spleen (i-Tcells)


title: HSC-MFs-7d-2

city: PARIS

first: Axelle

last: Cadoret

address: 27 rue de Chaligny

department: UMRS938 CRSA

country: France

institute: INSERM

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads with following parameters : cutoff: '20' leading: '10' minlen: '50' slidingwindow: '4' trailing: '10'
Star v2.5.3a has been used to align reads on  reference genome using standard options
Quantification of gene and isoform abundances has been done with rsem 1.2.28
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including expecting counts, TPM and FPKM

source_name: Liver

extract_protocol:
Total RNA was extracted from harvested cells following Rneasy Micro Kit (Qiagen) protocol.
Libraries were prepared from the extracted RNA using the KAPA Stranded mRNA-Seq Kit

value: Liver

value: Hepatic stellate cell-derived myofibroblasts


title: HSC-MFs-7d-3


title: HSC-MFs-7d-1


title: HSC-MFs-7d-4


title: HSCs-4

value: Hepatic stellate cells


title: HSCs-2


title: PMSC-MFs-7d-1

value: Portal mesenchymal stem cell-derived myofibroblasts-7d


title: PMSC-MFs-7d-4


title: HSCs-3


title: HSCs-1


title: PMSCs-4

value: Portal mesenchymal stem cells


title: PMSC-MFs-3d-2

value: Portal mesenchymal stem cell-derived myofibroblasts-3d


title: PMSC-MFs-7d-3


title: PMSC-MFs-7d-2


title: PMSC-MFs-3d-3


title: MacDay8_2

value: 8 day old


title: MacDay8_3


title: MacDay8_4


title: MacDay14_3


title: MacDay8_1


title: MacDay14_4


title: MacDay14_2


title: PMSC-MFs-3d-4


title: PMSCs-3


title: PMSCs-2


title: MacDay14_1


title: PMSCs-1


title: 8_wk_Ctrl_Brain_3_Ribosome_contained_tRNA_MiSeq

description: Brain ribosome-contained tRNA

value: Brain

value: WT


title: PMSC-MFs-3d-1