title: MM.1S 5 nM bortezomib 24 h mRNA replicate 1

description: juncbase_tables_DMSO_vs_Bortezomib_jcn272.tsv

data_processing:
Alignment: four libraries from timecourse study were aligned with Bowtie v0.12.8 allowing for up to two mismatches.  Aligned rRNA and tRNA reads were discarded.  Remaining transcripts were aligned to known canonical transcripts to human genome draft GRCh37/hg19 .  All other libraries were aligned with HISAT v2.1.0.
Compression: The mapped reads were converted from sequence alignment map format to binary alignment map format using Samtools (v1.3.1 for timecourse samples and v0.1.19 for all others).
Assembly and Expression: transcriptome assembled and abundance quantified for four libraries from timecourse study by in-house C++ scripts, which assign and count unique reads mapping to canonical hg19 transcripts. Only uniquely mapping reads were used for analysis.  All other binary alignment mapped reads were quantified for gene-level expression with HTSeq-0.7.2
Differential Expression: Differential gene expression analysis for single timepoint response study was performed in R with DESeq2
Alternative splicing analysis: For all mapped reads, except for the timecourse study, alternative splicing events were quantified through JuncBASE v1.2-beta using default parameters.  Intron-exon junction database was created from hg19 annotations.  T-test was used to compare number of inclusion and exclusion reads and p-values were adjusted with Benjamini-Hochberg correction.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: "delink_c2g_fw5rv_xpr.txt" in-house C++ scripts output with UCSC Gene ID, raw reads, and normalized RPKM.  Conversion tables available from UCSC through the kgXref function were used  to convert UCSC gene ID to HUGO gene nomenclature and to UniProt accession number for further analysis
Supplementary_files_format_and_content: "juncbase_tables…tsv" JuncBASE alternative splicing output with gene symbols, Known annotated or Novel splice site, splicing event type, chromosome number, strand, junction coordinates, percent spliced in (PSI) value for each sample replicate, comparison sample set medians, the difference in percent spliced in between the medians of two comparison sets, statistical T-test p-value, and B-H corrected p-value.  Each JuncBASE file compares two conditions and is associated with six samples from the two conditions (exccept "AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz" which pools 24 samples from AMO1_parent, WT, SD, and SA for both DMSO and 15 nM cfz").  Set1_med and Set2_med are median PSI for samples in each condition.  Extraneous columns for other conditions not associated with the JuncBASE file were processed together and left in the table, but do not participate in the comparison.
Supplementary_files_format_and_content: "deseq2_counts.csv" DESEQ2 output tables with Gene Symbol, log2(fold change) for each gene between two comparing conditions, the standard error for the log2 change and the statistical p-value for that comparison and the multiple comparison adjusted p-value.

growth_protocol: Heat shock experiment and Timecourse MM.1S cultures were grown in RPMI-1640, 10% FBS, 1% Pencillin-Streptomycin.  Single time point MM.1S and AMO-1 cultures were used for concurrent global proteomics and phosphoproteomics analysis and grown in SILAC media with dialyzed FBS, 1% pencillin streptomycin and supplemented with either Lysine and Arginine (for drug treated samples) or Lys8 and Arg10 (for isotopically heavy labeled protein DMSO) samples.  AMO-1 SRSF1 samples were engineered to overexpress either wildtype SRSF1 (WT) or phosphomimetic (SD) or phosphodead (SA) RS domain mutants and were grown in RPMI-1640, 10% FBS, 1% Penicillin-Streptomycin.  All cells were passaged every 2-3 days and disposed after 50 passages.

treatment_protocol: For heat shock samples, MM.1S cultures were incubated at 42C for 4 h in 3 biological replicates.  Timecourse MM.1S cultures were treated with 30 nM carfilzomib and harvested after 0, 8, 16, or 24 h treatment in a single biological replicate.  Single timepoint cultures were harvested after 24 h of drug (or DMSO) treatment) in 3 biological replicates.  AMO-1 SRSF1 expressing cultures were also treated with either 15 nM carfilzomib or DMSO for 24 h and harvested in 3 biological replicates.

tag: cell type

tag: experiment

value: single timepoint response alternative splicing

tag: timepoint

tag: drug

value: 5 nM bortezomib


title: MM.1S 5 nM bortezomib 24 h mRNA replicate 3

status: Public on Feb 18 2020

type: SRA

city: San Francisco

first: Hector

middle: Han-Li

last: Huang

state: CALIFORNIA

address: 185 Berry St, Ste 290/Rm 2410

department: Laboratory Medicine

country: USA

institute: University of California San Francisco

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

source_name: MM.1S myeloma cell line

extract_protocol:
Total RNA was extracted by standard RNA extraction kit (RNeasy, Qiagen) and cleaned up with RNA clean & concentrator columns (Zymo).  For all except the timecourse samples, polyA-mRNA was enriched from total RNA with polyA-binding magnetic bead protocol (NEB).
RNA libraries were prepared for sequencing using standard Illumina protocols and Hyper Prep RNA sequencing kit (Kapa, with RiboErase for timecourse samples to remove abundant rRNA).  Protocol aimed at generating 200-300 bp fragments.  Reverse-transcribed cDNA was ligated to TruSeq barcode adapters for Illumina platform.  200-400 bp cDNA libraries were selected by PAGE extraction and purification, or AMPure bead size selection in the case of SRSF1 overexpression samples.  Four samples were multiplexed in a single lane for sequencing for the timecourse samples, seven samples were multiplexed for the single timepoint samples, and 9 samples were multiplexed for the SRSF1 overexpression samples.


title: MM.1S 5 nM bortezomib 24 h mRNA replicate 2


title: MM.1S heat shock 4 h mRNA replicate 2

description: juncbase_tables_DMSO_vs_heatshock_jcn272.tsv

value: heat shock induced intron retention

value: 4 h


title: MM.1S heat shock 4 h mRNA replicate 3


title: Astrocyte1

city: Columbus

first: Pearlly

last: Yan

state: Ohio

department: Comprehensive Cancer Center

institute: The Ohio State University

description: Replicates of mouse DG Astrocyte cells

data_processing:
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterRemoval v2.2.0 to remove sequencing adapters
Reads were aligned against the mouse genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts using GENCODE release M14
Genome_build: GRCm38p4
Supplementary_files_format_and_content: TSV Counts tables generated using Subread FeatureCounts, Unfiltered

organism: Mus musculus

source_name: Mouse Dente Gyrus

extract_protocol:
Cells were resuspended in PBS without calcium/magnesium and filtered through a 35µm nylon filter before staining with the following antibodies: O4-APC (1:100, R&D FAB1326A), O1-eFluor660 (1:100, Thermo Fisher/eBioscience, Pittsburgh, PA, 5065082), GLAST-PE (1:50, Miltenyi Biotec, Bergisch Gladbach, Germany, 130-098-804), CD45-APC (1:100, BD Biosciences, Franklin Lakes, NJ, 561018), CD31-APC (1:100, BD Biosciences, Franklin Lakes, NJ, 561814). Cells were incubated with antibodies on ice for 30 minutes. During the last 10 minutes of staining, Hoechst dye (1:10,000, Thermo Fisher, Pittsburgh, PA, 33342) was added for live/dead discrimination. All cells were washed twice following staining and immediately sorted as stem, progenitor, or astrocyte populations based on fluorescent markers with the FACSAria III (BD Biosciences, Franklin Lakes, NJ). CD31, CD45, O1, and O4 negative live cells were designated as stem cells if double positive for GLAST and GFP, progenitors if only GFP positive, and astrocytes if only GLAST positive. For cells in the limited cell number study, 50 cells were sorted into 96 well format plate for downstream lcRNA-seq library generation.
The Clontech SMARTer v4 kit (Takara Bio USA, Inc., Mountain View, CA) was used for direct global preamplification in FACS-derived murine DG cell types prior to library generation at triplicate with the Nextera XT DNA Library Prep kit (Illumina, Inc., San Diego, CA).
Low Input RNA-Seq

value: Astrocyte


title: MM.1S 0 h control mRNA replicate 3

description:
juncbase_tables_DMSO_vs_heatshock_jcn272.tsv
juncbase_tables_DMSO_vs_Bortezomib_jcn272.tsv

value: 0 h (untreated)


title: Astrocyte3

description: Replicates of mouse DG Astrocyte cells


title: NaNO2.EDTA_2

city: Vancouver

first: Erin

last: Gill

state: British Columbia

address: 2259 Lower Mall

country: Canada

institute: University of British Columbia

description: ribosomally depleted RNA

data_processing:
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq 2500
fastq file quality control was performed using FastQC v0.11.5 and MultiQC v0.8.dev0
fastq files were aligned to the PA14 genome using STARv2.5.2b
read count tables were generated using htseq-count v.2.5
Genome_build: PAO1 NC_002516 (GenBank gene annotations)
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads per gene for each sample

molecule: total RNA

organism: Pseudomonas aeruginosa PAO1

source_name: bacterial culture (LBN media)

growth_protocol: Bacteria were grown aerobically overnight in LB at 37oC. The next day, bacteria were diluted 100-fold into 20 ml of fresh LBN 6.5 then aliquoted into 4 tubes containing 5 ml each. Tubes were incubated anaerobically at 37oC under static conditions for 3 hr. Final concentrations of 1 mM EDTA and/or 15 mM NaNO2 were added to each tube. Then, cells were incubated for an additional 2.5 hr.

extract_protocol:
Qiagen Bacteria Protect Rneasy Mini kit, Epicentre Ribo-Zero rRNA removal kit
mRNA reverse transcribed using Illumina TruSeq stranded mRNA library preparation kit. Libraries barcoded with 8bp oligos then amplified for 15 cycles

tag: media additive(s)

value: NaNO2 + EDTA


title: MM.1S 0 h control mRNA replicate 2


title: MM.1S heat shock 4 h mRNA replicate 1


title: EDTA_3

description: ribosomally depleted RNA

value: EDTA


title: MM.1S 0 h control mRNA replicate 1


title: NaNO2.EDTA_1

description: ribosomally depleted RNA


title: Progenitor3

description: Replicates of mouse DG Progenitor cells

value: Progenitor


title: NaNO2.EDTA_3

description: ribosomally depleted RNA


title: 4-month-old_leaf 1

city: Kusatsu, Shiga

first: Midori

last: Tabara

address: 1-1-1, Noji-Higashi

country: Japan

institute: Ritsumeikan University

data_processing:
Illumina Casava ver.1.8.2 software was used for base calling.
Sequenced reads were mapped to the petunia genome using TopHat ver. 2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19 (Trapnell et al., 2009). Since the genome of Petunia hybrida was amphidiploid of Petunia axillaris and Petunia inflata, genome data was prepared to merge these genome datasets (P. axillaris, v1.0.1; P. inflata, v1.6.2; Sol Genomic Network https://solgenomics.net/).
The number of fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm ver. 2.2.1 (Trapnell et al., 2010).
Genome_build: P. axillaris, v1.0.1; P. inflata, v1.6.2; Sol Genomic Network https://solgenomics.net/
Supplementary_files_format_and_content: FPKM

organism: Petunia x hybrida

extract_protocol:
Total RNAs were extracted by using the Trizol reagent following the manufacturer’s protocol (Thermo Fisher Scientific, MA).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

tag: cultivar

value: Rondo Rose-star

tag: age

tag: tissue

value: leaf


title: EDTA_2

description: ribosomally depleted RNA


title: Healthy Subject.1

city: Naples

first: Mario

last: Galgani

address: via S. Pansini, 5

country: Italy

institute: IEOS Istituto per l'endocrinologia e l'oncologia sperimentale

data_processing:
Raw data were processed by Bcl2Fastq 2.0.2 version of the Illumina pipeline for both format conversion and de-multiplexing and lower quality bases and adapters were removed by ERNE and Cutadapt software.
On average 30M of reads were produced per sample (min 29.1M, max 32.5M). Reads were then deduplicated based on unique molecular identifier (UMI) composed of 8 random bases for unambiguous identification of unique library molecules.
Reads were aligned on reference GRCh38 genome/transcriptome with STAR.
Full-length transcripts representing multiple spliced variants for each gene locus were assembled and quantified by Stringtie and RNA-Seq data was preprocessed by counting the overlap of reads with genes through htseq-count.
DESeq2 was used to perform comparisons between expression levels of genes and transcripts. Normalization was performed using the median-of-ratios method.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

source_name: TR3-56 cells

extract_protocol:
TR3-56 cells were flow sorted, a cell suspension was prepared and RNA was extracted using the RNeasy Micro Kit from QIAGEN, according to manufacturer’s instructions. RNA samples were then quantified and quality tested by Agilent 2100 Bioanalyzer RNA assay (Agilent technologies, Santa Clara, CA) or Caliper (PerkinElmer, Waltham, MA).
Libraries were prepared by the ‘Ovation SoLo RNA-seq Library Preparation kit’ (NuGEN, San Carlos, CA), following the manufacturer’s instructions and checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay or Caliper (PerkinElmer, Waltham, MA).
Libraries were then processed and sequenced on single-end 1x75 mode on NextsSeq500 (Illumina, San Diego, CA) following the manufacturer’s instructions.

tag: subject ethnicity

value: Caucasian

tag: subject status

value: Healthy Subject

value: Flow sorted TR3-56 cells


title: DM4.WGBS.BRAF.Rep2

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

country: United Kingdom

institute: University of Glasgow

library_source: genomic

data_processing:
The quality of sequenced reads was first tested using FastQC (version 0.10.0). Thereafter, adapters and low-quality sequence tails were excluded using trim-galore (version 0.3.0). Alignment of sequence reads to UCSC (hg19) genome was performed using Bismark (version 0.10.1) based on the Bowtie2 aligner (version 2.1.0) (Krueger and Andrews, 2011).
The methylation status of each aligned sequence tag was then inferred by comparison to the unconverted reference genome. Potential duplicate reads (defined as those reads for which both ends of a given fragment align to the same genomic position on the same strand) were then removed to control for PCR bias. Furthermore, the exclusion of reads with >3 methylated cytosines in a non-CpG context controlled for incomplete bisulfite-conversion. Methylated cytosines were then identified by aggregation of processed reads on a per CpG basis, followed by the collapsing of CpG dyads into a single score for the cytosine on the forward strand.
Differentially-methylated CpGs were then identified using a two-tailed Fisher’s exact test. Only those CpGs with ≥10 reads within each condition tested were considered for statistical analysis. False-positives were controlled at a rate of 5% by means of FDR-correction of p-values using the Benjimini-Hochberg FDR function.
Global percentage methylation was determined by division of the total number of methylated counts by the total number of methylated and unmethylated counts in the entire data set, followed by multiplication by 100 for each biological condition. Differentially-methylated regions (DMRs) were identified using 500bp sliding-windows. At each window, DMR significance was determined using Fisher’s exact test, together with a χ2 test of heterogeneity between biological replicates for each condition tested. Multi-sample correction was performed using the Benjimini-Hochberg FDR function, and DMRs defined as those windows with an FDR-corrected p-value < 0.05 and nonsignificant heterogeneity between biological replicates (χ2 test p >0.05).
Genome_build: hg19
Supplementary_files_format_and_content: TSV Matrix of Bismark Meth/Unmeth Calls

molecule: genomic DNA

growth_protocol: Human fetal lung fibroblasts (IMR-90) were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine, 10units/mL Penicillin G and 10μg/ml streptomycin. Cells were cultured in 10cm plates in a humidified atmosphere with 3% O2 and 5% CO2. Passaging of cells was performed at 70-80% confluency. Culture media were aspirated, and the cells lavaged twice with sterile phosphate-buffered saline to remove remaining traces of culture media. Trypsinisation was then performed with 1mL of 1% trypsin in phosphate-buffered EDTA solution for 3 minutes at 37°C. With cell detachment confirmed by visual inspection with a microscope, the trypsin solution was neutralised by the addition of fresh culture media (supplemented with FBS) to the plate. Cells were then resuspended in culture media, passaged to fresh plates, and returned to the incubator.

extract_protocol:
Bisulfite-conversion was then performed using the Zymo EZ DNA methylation-Gold kit, which converts unmethylated cytosines to uracils. Bisulfite-treated DNA was then subjected to 90bp paired-end sequencing using an Illumina HiSeq-4000 machine.
The WGBS analysis pipeline has been described previously, and is summarised in Cruickshanks et al., 2013.

treatment_protocol: 12x106 HEK-293T cells were seeded in 25 mL of culture medium to TC175 flasks 20 hours prior to transfection. Cells were approximately 70% confluent for transfection. Immediately prior to transfection, 13mL of culture medium was aspirated from flasks, and the cells returned to the incubator. Lipofectamine 2000 was selected as a transfection agent for all lentivirus production. 120μL of transfection agent were added dropwise to 1.5mL of sterile DMEM in a 15mL centrifuge tube, gently agitated and incubated for five minutes at room temperature. Concurrently, packaging plasmids (5μg plpVSVG and 8μg psPAX2) were combined with 20μg of vector genome in 1.5mL of sterile DMEM in a separate 15mL centrifuge tube. Thereafter the DNA and transfection reagent solutions were combined, gently agitated and incubated for 20 minutes at room temperature. The transfection solution was then added to the prepared HEK-293T flasks to yield a total final transfection volume of 15mL. Following transfection, HEK-293T cells were returned to the incubator for six hours, following which the transfection solution was aspirated, and a fresh 15mL of culture medium added to the flask. For all transfections, a separate green fluorescent protein (GFP) control transfection was performed in parallel to confirm transfection efficiency. After a period of twenty hours following transfection, GFP controls were examined to confirm transfection efficiency. Lentiviral supernatant was then aspirated from transfected HEK-293T cells, reserved and stored at 4°C. A further 15mL of culture medium was added to the HEK-293T cells and returned to the incubator for a further twenty hours. The second lentiviral supernatant fraction was then combined with the first, centrifuged at 3000RPM in a table-top centrifuge, and filtered through a 0.45μM low-protein binding PVDF filter prior to concentration. Filtered viral supernatants were transferred to sterile 38.5mL polypropylene centrifuge tubes (Beckman 326823) and weights equalised by the addition of sterile PBS. Ultracentrifugation was performed at 47,000 x g in an SW-28 Beckman- Coulter ultracentrifuge for two hours at 10°C. Following centrifugation, the supernatant was discarded by gentle inversion, and the viral pellet resuspended in 100μL of sterile PBS overnight at 4°C, prior to being aliquoted and stored at -80°C. The multiplicity of infection (MOI) for lentiviral preparations was calculated empirically by seeding cells to a 6-well plate twenty-four hours prior to transduction. Culture medium was then aspirated from each well, replaced with 1mL of fresh culture medium supplemented with polybrene at a final concentration of 8μg/mL, and the cells returned to the incubator for four hours prior to transduction. Concentrated lentivirus was then added to each well at 0, 1, 2, 4, 8 and 16 μL/mL, and returned to the incubator for sixteen hours. Following transduction, the infection medium was removed from each well, and replenished with 2mL of fresh culture medium supplemented with the appropriate drug selection as determined by the construct design. The minimum volume of lentiviral construct required to yield 100% cell survival following drug-selection was then employed for all subsequent experiments. All experiments involving lentivirus were performed in their entirety under drug selection.

value: Human Fetal Lung Fibroblasts

tag: passages

value: BRAF v600E


title: NaNO2_3

description: ribosomally depleted RNA


title: EDTA_1

description: ribosomally depleted RNA


title: DM3.WGBS.BRAF.Rep1


title: DM2.WGBS.vector.Rep2

value: Empty vector control


title: Control_3

description: ribosomally depleted RNA


title: AMO-1 SRSF1mSA 15 nM carfilzomib mRNA replicate 3

description:
SA 15cfz_3
juncbase_tables_WT_DMSO_vs_SA_DMSO.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv

data_processing:
Alignment: four libraries from timecourse study were aligned with Bowtie v0.12.8 allowing for up to two mismatches.  Aligned rRNA and tRNA reads were discarded.  Remaining transcripts were aligned to known canonical transcripts to human genome draft GRCh37/hg19 .  All other libraries were aligned with HISAT v2.1.0.
Compression: The mapped reads were converted from sequence alignment map format to binary alignment map format using Samtools (v1.3.1 for timecourse samples and v0.1.19 for all others).
Assembly and Expression: transcriptome assembled and abundance quantified for four libraries from timecourse study by in-house C++ scripts, which assign and count unique reads mapping to canonical hg19 transcripts. Only uniquely mapping reads were used for analysis.  All other binary alignment mapped reads were quantified for gene-level expression with HTSeq-0.7.2
Differential Expression: Differential gene expression analysis for single timepoint response study was performed in R with DESeq2
Alternative splicing analysis: For all mapped reads, except for the timecourse study, alternative splicing events were quantified through JuncBASE v1.2-beta using default parameters.  Intron-exon junction database was created from hg19 annotations.  T-test was used to compare number of inclusion and exclusion reads and p-values were adjusted with Benjamini-Hochberg correction.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: "delink_c2g_fw5rv_xpr.txt" in-house C++ scripts output with UCSC Gene ID, raw reads, and normalized RPKM.  Conversion tables available from UCSC through the kgXref function were used to convert UCSC gene ID to HUGO gene nomenclature and to UniProt accession number for further analysis
Supplementary_files_format_and_content: "juncbase_tables…tsv" JuncBASE alternative splicing output with gene symbols, Known annotated or Novel splice site, splicing event type, chromosome number, strand, junction coordinates, percent spliced in (PSI) value for each sample replicate, comparison sample set medians, the difference in percent spliced in between the medians of two comparison sets, statistical T-test p-value, and B-H corrected p-value.  Each JuncBASE file compares two conditions and is associated with six samples from the two conditions (exccept "AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz" which pools 24 samples from AMO1_parent, WT, SD, and SA for both DMSO and 15 nM cfz").  Set1_med and Set2_med are median PSI for samples in each condition.  Extraneous columns for other conditions not associated with the JuncBASE file were processed together and left in the table, but do not participate in the comparison.
Supplementary_files_format_and_content: "deseq2_counts.csv" DESEQ2 output tables with Gene Symbol, log2(fold change) for each gene between two comparing conditions, the standard error for the log2 change and the statistical p-value for that comparison and the multiple comparison adjusted p-value.

source_name: AMO-1 myeloma cell line

growth_protocol: Timecourse MM.1S cultures were grown in RPMI-1640, 10% FBS, 1% Pencillin-Streptomycin.  Single time point MM.1S and AMO-1 cultures were used for concurrent global proteomics and phosphoproteomics analysis and grown in SILAC media with dialyzed FBS, 1% pencillin streptomycin and supplemented with either Lysine and Arginine (for drug treated samples) or Lys8 and Arg10 (for isotopically heavy labeled protein DMSO) samples.  AMO-1 SRSF1 samples were engineered to overexpress either wildtype SRSF1 (WT) or phosphomimetic (SD) or phosphodead (SA) RS domain mutants and were grown in RPMI-1640, 10% FBS, 1% Penicillin-Streptomycin.  All cells were passaged every 2-3 days and disposed after 50 passages.

treatment_protocol: Timecourse MM.1S cultures were treated with 30 nM carfilzomib and harvested after 0, 8, 16, or 24 h treatment in a single biological replicate.  Single timepoint cultures were harvested after 24 h of drug (or DMSO) treatment) in 3 biological replicates.  AMO-1 SRSF1 expressing cultures were also treated with either 15 nM carfilzomib or DMSO for 24 h and harvested in 3 biological replicates.

tag: cell line

value: exogenous SRSF1mSA effect alternative splicing

value: 15 nM carfilzomib


title: AMO-1 SRSF1mSA 15 nM carfilzomib mRNA replicate 2

description:
SA 15cfz_2
juncbase_tables_WT_DMSO_vs_SA_DMSO.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv


title: Control_1

description: ribosomally depleted RNA


title: AMO-1 SRSF1mSD 15 nM carfilzomib mRNA replicate 2

description:
SD 15cfz_2
juncbase_tables_WT_DMSO_vs_SD_DMSO.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv

value: exogenous SRSF1mSD effect alternative splicing


title: AMO-1 SRSF1mSA 15 nM carfilzomib mRNA replicate 4

description:
SA 15cfz_4
juncbase_tables_WT_DMSO_vs_SA_DMSO.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv


title: AMO-1 SRSF1mSD 15 nM carfilzomib mRNA replicate 3

description:
SD 15cfz_3
juncbase_tables_WT_DMSO_vs_SD_DMSO.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv


title: DSMD_QKO_day2_rep2

city: Shanghai

first: Qing

last: Li

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

country: China

institute: Chinese Academy of Science

description:
D3_1
PRKM.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling
the preprocessed reads were aligned to the protein encoding gene of mouse reference genome (NCBI Mus musculus assembly GRCm38.p5) using hisat2 (version 2.0.5).
adaptors as well as low quality base pairs were trimmed.
Transcriptome profiling was determined in units of RPKM (Reads Per Kilobase per Million mapped reads) using locally developed Perl script.
Genome_build: NCBI Mus musculus assembly GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ..

source_name: fiber'

growth_protocol: T cell conditional medium and differentiation medium

extract_protocol:
RNA was extracted using TRIZOL Reagent according to manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissure

value: muscle

value: 4 month old

tag: genotype/variation

value: DM1 mutant


title: DSMD_QKO_day2_rep1

description:
C3_1
PRKM.xlsx


title: Control_2

description: ribosomally depleted RNA


title: DSMD_QKO_day0_rep2

description:
D1_1
PRKM.xlsx

source_name: Muscle stem cell


title: DSMD_QKO_day1_rep1

description:
C2_1
PRKM.xlsx

source_name: fiber


title: AMO-1 SRSF1 WT 15 nM carfilzomib mRNA replicate 3

description:
WT 15cfz_3
juncbase_tables_WT_DMSO_vs_WT_15cfz.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv

value: exogenous SRSF1 WT effect alternative splicing


title: DSMD_QKO_day0_rep1

description:
C1_1
PRKM.xlsx


title: AMO-1 SRSF1mSD 15 nM carfilzomib mRNA replicate 4

description:
SD 15cfz_4
juncbase_tables_WT_DMSO_vs_SD_DMSO.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv


title: AMO-1 SRSF1 WT 15 nM carfilzomib mRNA replicate 4

description:
WT 15cfz_4
juncbase_tables_WT_DMSO_vs_WT_15cfz.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv


title: DM1.WGBS.vector.Rep1


title: NaNO2_1

description: ribosomally depleted RNA


title: AMO-1 SRSF1mSA DMSO mRNA replicate 3

description:
SA DMSO_3
juncbase_tables_WT_DMSO_vs_SA_DMSO.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv

value: 24 h (untreated)

value: DMSO


title: DSM_TKO_day2_rep1

description:
B3_1
PRKM.xlsx


title: DSMD_QKO_day1_rep2

description:
D2_1
PRKM.xlsx


title: DSM_TKO_day2_rep2

description:
B6_1
PRKM.xlsx


title: AMO-1 SRSF1mSA DMSO mRNA replicate 2

description:
SA DMSO_2
juncbase_tables_WT_DMSO_vs_SA_DMSO.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv


title: AMO-1 SRSF1mSA DMSO mRNA replicate 4

description:
SA DMSO_4
juncbase_tables_WT_DMSO_vs_SA_DMSO.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv


title: DSM_TKO_day0_rep2

description:
B4_1
PRKM.xlsx


title: AMO-1 SRSF1mSD DMSO mRNA replicate 3

description:
SD DMSO_3
juncbase_tables_WT_DMSO_vs_SD_DMSO.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv


title: DSM_TKO_day1_rep1

description:
B2_1
PRKM.xlsx


title: WT_day2_rep2

description:
A6_1
PRKM.xlsx

value: wild type


title: AMO-1 SRSF1mSD DMSO mRNA replicate 2

description:
SD DMSO_2
juncbase_tables_WT_DMSO_vs_SD_DMSO.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv


title: AMO-1 SRSF1 WT DMSO mRNA replicate 3

description:
WT DMSO_3
juncbase_tables_WT_DMSO_vs_WT_15cfz.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv


title: DSM_TKO_day1_rep2

description:
B5_1
PRKM.xlsx


title: DSM_TKO_day0_rep1

description:
B1_1
PRKM.xlsx


title: AMO-1 SRSF1 WT DMSO mRNA replicate 4

description:
WT DMSO_4
juncbase_tables_WT_DMSO_vs_WT_15cfz.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv


title: WT_day1_rep2

description:
A5_1
PRKM.xlsx


title: AMO-1 SRSF1 WT DMSO mRNA replicate 2

description:
WT DMSO_2
juncbase_tables_WT_DMSO_vs_WT_15cfz.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv


title: WT_day0_rep2

description:
A4_1
PRKM.xlsx


title: AMO-1 SRSF1 WT 15 nM carfilzomib mRNA replicate 2

description:
WT 15cfz_2
juncbase_tables_WT_DMSO_vs_WT_15cfz.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv


title: AMO-1 15 nM carfilzomib mRNA replicate 7

description:
AMO-1 15cfz_7
juncbase_tables_AMO1_parent_DMSO_vs_AMO1_parent_15cfz.csv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv
ctrl_AMO1_vs_15_cfz_AMO1_results_deseq2_counts.csv

value: single timepoint response alternative splicing


title: WT_day2_rep1

description:
A3_1
PRKM.xlsx


title: WT_day1_rep1

description:
A2_1
PRKM.xlsx


title: AMO-1 15 nM carfilzomib mRNA replicate 8

description:
AMO-1 15cfz_8
juncbase_tables_AMO1_parent_DMSO_vs_AMO1_parent_15cfz.csv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv
ctrl_AMO1_vs_15_cfz_AMO1_results_deseq2_counts.csv


title: AMO-1 15 nM carfilzomib mRNA replicate 4

description:
AMO-1 15cfz_4
juncbase_tables_AMO1_parent_DMSO_vs_AMO1_parent_15cfz.csv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv
ctrl_AMO1_vs_15_cfz_AMO1_results_deseq2_counts.csv


title: AMO-1 DMSO mRNA replicate 7

description:
AMO-1 DMSO_7
juncbase_tables_AMO1_parent_DMSO_vs_AMO1_parent_15cfz.csv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv
ctrl_AMO1_vs_15_cfz_AMO1_results_deseq2_counts.csv


title: AMO-1 DMSO mRNA replicate 8

description:
AMO-1 DMSO_8
juncbase_tables_AMO1_parent_DMSO_vs_AMO1_parent_15cfz.csv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv
ctrl_AMO1_vs_15_cfz_AMO1_results_deseq2_counts.csv


title: AMO-1 DMSO mRNA replicate 4

description:
AMO-1 DMSO_4
juncbase_tables_AMO1_parent_DMSO_vs_AMO1_parent_15cfz.csv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv
ctrl_AMO1_vs_15_cfz_AMO1_results_deseq2_counts.csv


title: AMO-1 10 nM E7107 mRNA replicate 4

description:
AMO-1 10E7107_4
ctrl_AMO1_vs_10_E7107_AMO1_results_deseq2_counts.csv


title: AMO-1 SRSF1mSD DMSO mRNA replicate 4

description:
SD DMSO_4
juncbase_tables_WT_DMSO_vs_SD_DMSO.tsv
juncbase_tables_AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz.tsv


title: AMO-1 10 nM E7107 mRNA replicate 3

description:
AMO-1 10E7107_3
ctrl_AMO1_vs_10_E7107_AMO1_results_deseq2_counts.csv


title: AMO-1 10 nM E7107 mRNA replicate 1

description:
AMO-1 10E7107_1
ctrl_AMO1_vs_10_E7107_AMO1_results_deseq2_counts.csv


title: MM.1S 10 nM E7107 mRNA replicate 3

description:
MM.1S 10E7107_3
juncbase_tables_MM1S_DMSO_vs_MM1S_10E7107.tsv
ctrl_MM1s_vs_10_E7107_MM1s_results_deseq2_counts.csv


title: MM.1S 10 nM E7107 mRNA replicate 4

description:
MM.1S 10E7107_4
juncbase_tables_MM1S_DMSO_vs_MM1S_10E7107.tsv
ctrl_MM1s_vs_10_E7107_MM1s_results_deseq2_counts.csv


title: MM.1S 10 nM E7107 mRNA replicate 1

description:
MM.1S 10E7107_1
juncbase_tables_MM1S_DMSO_vs_MM1S_10E7107.tsv
ctrl_MM1s_vs_10_E7107_MM1s_results_deseq2_counts.csv


title: A1_nonLRC_A

first: Jacob

middle: Cameron

last: Kimmel

state: CA

department: Biochemistry and Biophysics

institute: UCSF

description: Aged nonLRCs, activated, mouse 1

data_processing:
Reads were demultiplexed using bcl2fastq.
Reads were aligned, assigned to cell barcodes, UMIs collapsed, and cell barcodes were filtered using 10X cellranger 2.
Reads were aggregated using cellranger 2 to account for differences in sequencing depth by subsampling reads.
Genome_build: mm10
Supplementary_files_format_and_content: Rdata, containing a Seurat object of cell counts and metadata.

source_name: Aged 1 Activated nonLRC

growth_protocol: MuSCs were cultured for 0 hr or 18 hr in 10% horse serum, DMEM + pen/strep on sarcoma derived ECM (Sigma) at 37C and 5%CO2.

extract_protocol:
Muscle stem cells were isolated by FACS using a triple negative CD31-/CD45-/Sca1- and double positive VCAM+/α7- integrin+ strategy. Mononuclear cell suspensions were generated by mincing muscle tissue with scissors and digesting in collagenase II (2 mg/mL, DMEM) for 90 minutes, then dispase II + collagenase II for 30 minutes, then filtering with 40 um and 20 um filters.
10X Single Cell 3' v2

treatment_protocol: Mice were treated with 2 mg/mL DOX from E10.5 to E16.5 in the maternal drinking water.

value: muscle stem cells from limb muscle

value: 18 hours

tag: label retaining

value: nonLRC

value: 20 months

tag: activated

value: activated


title: A2_nonLRC_Q

description: Aged nonLRCs, freshly isolated, mouse 2

source_name: Aged 2 Quiescent nonLRC

tag: cell type

value: 0 hours

value: quiescent


title: MM.1S 10 uM melphalan mRNA replicate 10

description:
MM.1S 10melph_10
juncbase_tables_MM1S_DMSO_vs_MM1S_10melph.tsv
ctrl_MM1s_vs_10_melph_MM1S_results_deseq2_counts.csv

tag: experiment

value: 10 uM melphalan


title: A2_LRC_A

description: Aged LRCs, activated, mouse 2

source_name: Aged 2 Activated LRC

tag: timepoint

value: LRC


title: A2_LRC_Q

description: Aged LRCs, freshly isolated, mouse 2

source_name: Aged 2 Quiescent LRC


title: myoblast lncRNA 1

type: RNA

city: Guangzhou

first: Rui

last: Chen

address: 466 Xin Gang Zhong Road

department: Guangdong Traditional Medical and Sports Injury Rehabilitation Research Institute

institute: Guangdong Second Provincial General Hospital

description: Gene expression

hyb_protocol: 1 μg of  Cy3-labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: The scanned images were analyzed with Agilent feature extraction software (version 11.0.1.1).

source_name: cell line C2C12

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from cells using TRIZOL reagent (Life Technologies, Grand Island, NY, USA) in accordance with the manufacturer’s protocol. RNA quantity and quality were measured by NanoDrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA). RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: The mouse myoblast cell line C2C12 was cultured in DMEM high glucose supplemented with 10% fetal bovine serum, 100 U/mL of penicillin, and 100 μg/mL of streptomycin in 5% CO2 at 37°C. When the cells reached 80–90% confluence, they were differentiated by incubation in DMEM containing 2% horse serum.

tag: differentiation

value: myoblast


title: myotube lncRNA 2

description: Gene expression after differentiation

source_name: cell line C2C12,incubation in DMEM containing 2% horse serum

value: myotube


title: myoblast lncRNA 2

description: Gene expression


title: MM.1S 10 uM melphalan mRNA replicate 1

description:
MM.1S 10melph_1
juncbase_tables_MM1S_DMSO_vs_MM1S_10melph.tsv
ctrl_MM1s_vs_10_melph_MM1S_results_deseq2_counts.csv

tag: drug


title: WT_day0_rep1

description:
A1_1
PRKM.xlsx

value: muscle

value: 4 month old


title: myotube lncRNA 1

description: Gene expression after differentiation


title: MM.1S DMSO mRNA replicate 8

description:
MM.1S DMSO_8
juncbase_tables_MM1S_DMSO_vs_MM1S_18cfz.tsv
juncbase_tables_MM1S_DMSO_vs_MM1S_10melph.tsv
juncbase_tables_MM1S_DMSO_vs_MM1S_10E7107.tsv
ctrl_MM1s_vs_18_cfz_MM1s_results_deseq2_counts.csv
ctrl_MM1s_vs_10_melph_MM1S_results_deseq2_counts.csv
ctrl_MM1s_vs_10_E7107_MM1s_results_deseq2_counts.csv

value: 24 h (untreated)


title: Y2_nonLRC_Q

description: Young nonLRCs, freshly isolated, mouse 2

source_name: Young 2 Quiescent nonLRC

value: 3 months


title: A1_LRC_A

description: Aged LRCs, activated, mouse 1

source_name: Aged 1 Activated LRC


title: MM.1S DMSO mRNA replicate 4

description:
MM.1S DMSO_4
juncbase_tables_MM1S_DMSO_vs_MM1S_18cfz.tsv
juncbase_tables_MM1S_DMSO_vs_MM1S_10melph.tsv
juncbase_tables_MM1S_DMSO_vs_MM1S_10E7107.tsv
ctrl_MM1s_vs_18_cfz_MM1s_results_deseq2_counts.csv
ctrl_MM1s_vs_10_melph_MM1S_results_deseq2_counts.csv
ctrl_MM1s_vs_10_E7107_MM1s_results_deseq2_counts.csv

value: DMSO


title: MM.1S DMSO mRNA replicate 3

description:
MM.1S DMSO_3
juncbase_tables_MM1S_DMSO_vs_MM1S_18cfz.tsv
juncbase_tables_MM1S_DMSO_vs_MM1S_10melph.tsv
juncbase_tables_MM1S_DMSO_vs_MM1S_10E7107.tsv
ctrl_MM1s_vs_18_cfz_MM1s_results_deseq2_counts.csv
ctrl_MM1s_vs_10_melph_MM1S_results_deseq2_counts.csv
ctrl_MM1s_vs_10_E7107_MM1s_results_deseq2_counts.csv

value: single timepoint response alternative splicing


title: plu100R3 #2

description:
100pg of total RNA from CD5- cells was processed.
unfiltered_100pg_counts.txt

data_processing:
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterRemoval v2.2.0 to remove sequencing adapters
Reads were aligned against the mouse genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts using GENCODE release 25
Genome_build: GRCh38p7
Supplementary_files_format_and_content: TSV Counts tables generated using Subread FeatureCounts, Unfiltered

source_name: Human CLL B Cells

extract_protocol:
Cells were stained and sorted by FACS Aria (BD Biosciences, San Jose, CA, USA). Live CLL B cells (CD5+CD19+) and normal B cells (CD5-CD19+) were sorted from the patient sample. Briefly, cells for FACS were resuspended in PBS without calcium/magnesium and filtered through a 35µm nylon filter and then stained for PE-conjugated CD45 (HI30), PerCp Cy-5.5-conjugated CD19 (HIB19), and Alexa Fluor 700-conjugated CD3 (UCHT1) monoclonal antibodies. Nonviable cells were excluded by the LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit (Life Technologies, Carlsbad, CA, USA). Appropriate fluorescence minus one controls were used to determine nonspecific background staining. Single-cell gates were used to exclude the possibility of doublet cells.
Total RNA quantified using the Invitrogen Qubit RNA HS Assay kit (Invitrogen, Carlsbad, CA) was serially diluted to masses characteristic of single- and low cell number RNA-Seq (10-, 100-, and 1000-pg). The Clontech SMARTer v4 kit (Takara Bio USA, Inc., Mountain View, CA) was used for global preamplification in serially diluted CD5+/CD5- RNA.
Low Input RNA-Seq

tag: input rna mass (pg)

tag: cd5 sorting status

value: CD5 Positive


title: A1_LRC_Q

description: Aged LRCs, freshly isolated, mouse 1

source_name: Aged 1 Quiescent LRC

value: muscle stem cells from limb muscle

tag: age


title: plu100R3 #1

description:
10pg of total RNA from CD5- cells was processed.
unfiltered_10pg_counts.txt


title: Y1_nonLRC_A

description: Young nonLRCs, activated, mouse 1

source_name: Young 1 Activated nonLRC

value: 18 hours

value: nonLRC


title: A1_nonLRC_Q

description: Aged nonLRCs, freshly isolated, mouse 1

source_name: Aged 1 Quiescent nonLRC

value: 20 months


title: myoblast lncRNA 3

description: Gene expression


title: myotube lncRNA 3

description: Gene expression after differentiation


title: Y2_LRC_Q

description: Young LRCs, freshly isolated, mouse 2

source_name: Young 2 Quiescent LRC

value: 0 hours


title: Y1_LRC_A

description: Young LRCs, activated, mouse 1

source_name: Young 1 Activated LRC

value: activated


title: Y2_nonLRC_A

description: Young nonLRCs, activated, mouse 2

source_name: Young 2 Activated nonLRC


title: MM.1S 18 nM carfilzomib mRNA replicate 1

description:
MM.1S 18cfz_1
juncbase_tables_MM1S_DMSO_vs_MM1S_18cfz.tsv
ctrl_MM1s_vs_18_cfz_MM1s_results_deseq2_counts.csv

source_name: MM.1S myeloma cell line

value: 18 nM carfilzomib


title: Y1_LRC_Q

description: Young LRCs, freshly isolated, mouse 1

source_name: Young 1 Quiescent LRC

value: LRC

value: quiescent


title: MM.1S 18 nM carfilzomib mRNA replicate 3

description:
MM.1S 18cfz_3
juncbase_tables_MM1S_DMSO_vs_MM1S_18cfz.tsv
ctrl_MM1s_vs_18_cfz_MM1s_results_deseq2_counts.csv


title: plu100R1 #1


title: plu100R1 #2


title: MH4-3L

city: Shijiazhuang

first: Linyi

last: Shu

state: Hebei

address: 348 Heping West Road

department: Department of Endocrinology

institute: Hebei General Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse GRCm38.91 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: liver

extract_protocol:
livers were removed, flash frozen on dry ice, and 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

tag: diet

value: High fat feed and 200mg/kg/day metformin gastrointestinal administration (gavage)

tag: tissue

value: liver

value: post natal day 21


title: plu1000R3

description:
1000pg of total RNA from CD5- cells was processed.
unfiltered_1000pg_counts.txt


title: plu100R2 #2


title: MH8-4L


title: RH6-3L

value: High fat feed and 100mg/kg/day resveratrol gastrointestinal administration (gavage)


title: plu1000R1


title: MH6-5L


title: plu1000R2


title: min10R3

description:
10pg of total RNA from CD5+ cells was processed.
unfiltered_10pg_counts.txt

value: CD5 Negative


title: RH3-3L


title: min100R3

description:
100pg of total RNA from CD5+ cells was processed.
unfiltered_100pg_counts.txt


title: MM.1S 10 uM melphalan mRNA replicate 2

description:
MM.1S 10melph_2
juncbase_tables_MM1S_DMSO_vs_MM1S_10melph.tsv
ctrl_MM1s_vs_10_melph_MM1S_results_deseq2_counts.csv

value: 10 uM melphalan


title: plu100R2 #1


title: min10R2


title: RH1-2L


title: RH1-4L


title: H7-3L

value: High fat feed


title: min100R1


title: H7-5L


title: MH8-2L


title: H7-2L


title: H7-4L


title: min1000R2

description:
1000pg of total RNA from CD5+ cells was processed.
unfiltered_1000pg_counts.txt


title: min1000R1


title: C2-2L

value: Ordinary feed


title: C1-5L


title: min10R1


title: A2_nonLRC_A

description: Aged nonLRCs, activated, mouse 2

source_name: Aged 2 Activated nonLRC

value: muscle stem cells from limb muscle


title: C1-1L


title: C1-4L


title: min100R2


title: min1000R3


title: Third instar larval testis cleaned of fat body with papain rep 8.

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

description: Pool of 25 pseudo-testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.

data_processing:
We used RTA v1.13 (Illumina, San Diego, CA) for base calling and bcl2fastq v1.8 (Illumina, San Diego, CA) to de-multiplex and convert BCL to FASTQ format.
We created a reference by concatenating the Drosophila melanogaster genome assembly release 6 plus ISO1 MT (GCA_000001215.4) and ERCC (SRM2374) from NIST and processed as described in (Jiang et al. 2011. PMID: 21816910 and Lee et al. 2016 PMID: 27512518). We generated a set of known splice sites using FlyBase r6.16 and aligned reads with Hisat2 v2.1.0 (Kim et al. 2015. PMID: 25751142) using default settings except --max-introlen 300000 and --known-splicesite-infile. Multi-mapping reads and low quality alignments were removed using Samtools v1.7 (Li et al. 2009. PMID: 19505943) -q 20 prior to calculating gene coverage.
We created a set of gene level counts using featureCounts v1.6.1 (Liao et al., 2014. PMID: 24227677) with default options except (-s 2) to create strand specific read counts using the FlyBase r6.16 GTF concatenated with a GTF generated for ERCC. We also generated unstranded (-s 0) intergenic counts by using a custom GTF based on intergenic regions in FlyBase r6.16.
Finally, strand specific browser tracks (BigWigs) were created using DeepTools v3.0.2 (Ramírez et al. 2016. PMID: 27079975) with --minMappingQuality 20, --ignoreDuplicates, --smoothLength 10, --normalizeUsing RPKM, and --filterRNAstrand forward or --filterRNAstrand reverse.
Genome_build: Drosophila melanogaster Release 6 plus ISO1 MT (GCA_000001215.4).
Supplementary_files_format_and_content: *.pos.bigwig: Is a first strand bigWig file generated using DeepTools v3.0.2 using options ( --minMappingQuality 20, --ignoreDuplicates, --smoothLength 10, --normalizeUsing RPKM, and --filterRNAstrand forward)    *.neg.bigwig: Is a second strand bigWig file generated using DeepTools v3.0.2 using options ( --minMappingQuality 20, --ignoreDuplicates, --smoothLength 10, --normalizeUsing RPKM, and --filterRNAstrand reverse)    *.featurecounts.txt: Contains gene level + ERCC level raw counts generated using featureCounts v1.6.1 with options (-s 2)    *.featurecounts.intergenic.txt: Contains intergenic level raw counts generated using featureCounts v1.6.1 with options (-s 0)

organism: Drosophila melanogaster

source_name: tissue

growth_protocol: We grew w1118 flies (FBst0005905; Bloomington stock center, Bloomington, IN) on Fly food A (LabExpress Ann Arbor, MI) at 25°C in constant light and 60% relative humidity. We collected eggs from six mated females every 8-16 hr, and allowed them to develop until the late third instar larval stage, just after they are immobilized and prior to larval anterior spiracle extension. Additionally, we monitored for gut clearance by providing second and third instar larvae with yeast/water paste containing 0.5 mg/ml Sulforhodamine B sodium salt (Sigma-Aldrich, Cat. No. S1402-25G. St. Louis, MO), and selected individuals with mostly cleared guts with the food only in mid and hindgut.

extract_protocol:
We dissected late third instar larvae in PBS at 22°C (Gibco Life Technologies, Carlsbad, CA). Each sample was collected in 350 μl RLT buffer (Qiagen, Cat. No. 79216. Valencia, CA), vortexed two times for 30 sec with a 30 sec interval and quick frozen in a dry ice ethanol bath and stored at -80°C until RNA extraction. We collected testes with the fatbody attached just around the gonads (pool of 10 testes). We collected testes without fatbody by enzymatically removing fatbody by treating with 0.075 mg/ml Papain (Sigma-Aldrich, St. Louis, MO) and 0.075 mg/ml Collagenase enzymes (Sigma-Aldrich, St. Louis, MO) in PBS in 1.5ml eppendorf tube for 3 min with gentle vortexing by flicking the tube with a forefinger (pool of 15 testes). We collected fatbody alone by dissecting the fatbody around the gonads (pool from 10 testes). We dissociated testes after removing the fatbody either by treating with 0.5% Trypsin (ThermoFisher, Walkersville, MD) and 2 mg/ml Collagenase (Sigma-Aldrich, St. Louis, MO) in PBS for 30 min at 22°C or with 2 mg/ml Papain and 2 mg/ml Collagenase enzymes (pools of 15 testes). To obtain maximum dissociation, testes were teased apart with tungsten needles (Fine Scientific Tools, Foster City, CA) and pipetted several times. We pelleted cells using a table top centrifuge at 0.9 g for 5 min and resuspended in 350 μl RLT buffer.       We extracted total RNA using RNeasy 96 kit (Qiagen, Cat. No. 1019545. Valencia, CA) and followed the manufacturer’s protocol. RNA was quantified using Quant-iT RiboGreen quantification kit (Life Technologies, Cat. No. R11490. Carlsbad, CA). RNA was stored in -80°C until the library preparation.
We used 200 ng of total RNA and performed RNA-seq library preparation  according to Lee et al (doi:10.1101/032920 and Gene Expression Omnibus GSE73920). Briefly, PolyA+ selection was done using Dynabeads Oligo(dT)25 (Life technologies, Grand Island, NY). Selected mRNA was fragmented, RT was performed with the second strand synthesis by incorporating dUTPs. We used External RNA control consortium spike-ins pools 78A and 78B (SRM2374, Zook et al., 2012. PMID: 22859977) transcribed from standard reference. We used barcoded adaptors for indexing the libraries (Qiagen, 98 TruSeq v2 kit barcoded adaptors, Valencia, CA). We sequenced stranded 42 multiplexed libraries using a single-ended 50 bp strategy on one lane using a HiSeq Illumina 2500 (Illumina, San Diego, CA).

tag: Sex

value: male

tag: developmental stage

value: Late third instar larval stage:immobilized, partial gut clearance as dyed yeast paste exist partly in midgut and hindgut, prior to anterior spiracle eversion.

value: 25degree C

tag: spike-in

value: ERCC (SRM2374) 78B

value: A


title: Third instar larval testis cleaned of fat body with papain rep 7.

description: Pool of 15 testes with fatbody removed by enzymatically treating with Papain and Collagenase enzymes.

tag: strain

value: ERCC (SRM2374) 78A


title: Third instar larval testis cleaned of fat body with papain rep 5.


title: Third instar larval testis cleaned of fat body with papain rep 6.


title: HCA2 (MJ90) cells, module2-2 weeks

city: Minato-ku

first: Yoshikazu

last: Johmura

state: Tokyo

address: 4-6-1, Shirokanedai

department: Institute of Medical Science

institute: University of Tokyo

description:
module2.count.xlsx
2-2week_S4_R1.count.txt

data_processing:
The libraries were paired-end sequenced on a Hiseq2500 platform
The sequeincing data were aligned to huan genome using Bowtie2
Genome_build: shRNA reference barcode sequence (Cellecta)
Supplementary_files_format_and_content: counts

source_name: 16 days after shRNA library infection

growth_protocol: Cells were cultured in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
conventional genome DNA purufication method
Pooled Barcorded Lentiviral shRNA library kit v5 (Cellecta)  according to the manufacturer’s instructions.

treatment_protocol: RO3306 (9 uM) + Nutlin3a (10 uM) for 48 hrs

tag: cell line

value: HCA2 (MJ90)

value: skin fibroblast

tag: treatment

value: shRNA library infection (Module 2)

tag: time

value: 16 days after shRNA library infection

tag: stimuli

value: nutlin3a + RO3306.


title: HCA2 (MJ90) cells, module3-2 weeks

description:
module3.count.xlsx
3-2week_S6_R1.count.txt

tag: cell type

value: shRNA library infection (Module 3)


title: usp15ko_sm_3

city: Tsukuba

first: Fuminori

last: Tsuruta

address: 1-1-1 Tennodai

institute: University of Tsukuba

hyb_protocol: DNA samples were hybridized at 45°C for 17 hours on Mouse Exon 1.0 ST arrays and the samples were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Gene Spring 12.6 software.

label: Biotin

label_protocol: Biotinylated fragmented DNA were prepared according to the GeneChip WT Terminal Labeling and Hybridization kit protocol (Affymetrix).

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

treatment_protocol: The tissues were collected after dissecting mice according to the university guidelines for animal care and use.

tag: genotype

tag: tissues

value: Skeletal muscle


title: usp15ko_sm_1


title: usp15ko_sm_2


title: wt_sm_3

value: wildtype


title: HKO2

city: Ann Arbor

first: Liangyou

last: Rui

state: Michigan

address: 1137 Catherine Street

department: Molecular and Integrative Physiology

institute: University of Michigan

description: Gene expression data from liver tissue of SlugHKO fed HFD

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on Mouse Gene 2.1 ST, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267).

scan_protocol: Peg Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267).

data_processing: RMA was used to fit log2 expression values to the data using the oligo bioconductor package in R version 3.3.0

label: biotin

source_name: HKO2 mouse

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 400 ng total RNA.

growth_protocol: C57BL/6J males were housed on a 12-h light-dark cycle in the Unit for Laboratory Animal Medicine at the University of Michigan and fed ad libitum either a chow diet (9% fat in calories; TestDiet, St. Louis, MO) or a HFD (60% fat in calories)

extract_protocol: Total RNAs  were extracted from the same parts of liver tissues by  using TRIzol reagent according to the manufacturer's instructions.

treatment_protocol: Slugf/f mice were crossed with albumin-CreERT2 drivers to generate hepatic specific Slug knockout mice (HKO) and their littermates (Con). All the mice at 8 weeks old were fed a HFD for 11 weeks.

value: Liver

value: SlugHKO

value: high fat diet


title: HKO3

source_name: HKO3 mouse


title: HKO1

source_name: HKO1 mouse


title: Con1

description: Gene expression data from liver tissue of Slug f/f fed HFD

source_name: Con1 mouse

value: Slug f/f


title: Con2

source_name: Con2 mouse


title: wt_sm_1


title: Con3

source_name: Con3 mouse


title: usp15ko_cb_3

value: Cerebellum


title: HCA2 (MJ90) cells, module2-0day

description:
module2.count.xlsx
2-0day_S3_R1.count.txt

source_name: 2days after shRNA library infection

value: 2 days after shRNA library infection

value: nutlin3a + RO3306


title: HCA2 (MJ90) cells, module1-2 weeks

description:
module1.count.xlsx
1-2week_S2_R1.count.txt

value: shRNA library infection (Module 1)


title: 3D7

first: Yilong

last: Zhang

address: No.800 Xiangying road, Yangpu Dirtrict, Shanghai, China.

department: Department of Tropical diseases,

institute: Second Military Medical University, Shanghai, China.

data_processing:
Raw data (raw reads) were processed using Seqtk(https://github.com/lh3/seqtk). The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome (http://plasmodb.org/common/downloads/release-35/Pfalciparum3D7/PlasmoDB-35_Pfalciparum3D7_Genome.fasta))using TopHat.
FPKM value of each gene was calculated using cufflinks.
and the read counts of each gene were obtained by Hisat2.
DEGs were identified using the edgeR R package functions estimate Size Factors and nbinomTest.
Genome_build: PlasmoDB-35_Pfalciparum3D7
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values

organism: Plasmodium falciparum

source_name: Red blood cell

growth_protocol: The P.falciparum lines 3D7, PfSWIB and PfSWIB∆ were first thawed and established for continuous cultivation: thawed isolates were cultured in the RPMI 1640 medium (Invitrogen) containing 25 mM Hepes, 2 mM L-glutamine, 0.1 mM hypoxanthine (Sigma), 20 mg/ml gentamicin (Sigma), 0.5% Albumax II and 2% human serum (type AB+). Cultures were grown in media with type O+ erythrocytes at a 3% hematocrit under 2% O2, 5.5% CO2, 92.5% N2 at 37℃.

extract_protocol:
Total RNAs of synchronous parasite culture was extracted using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Shiled1 (Clontech, soluble in ethanol, 0.5mM) was added into the culture medium (final concentration: 0.5μM), to induce the degradation of PfSWIB.

value: Red blood cell

value: wild type (Blank-control)


title: HCA2 (MJ90) cells, module1-0day

description:
module1.count.xlsx
1-0day_S1_R1.count.txt

source_name: 2 days after shRNA library infection

value: HCA2 (MJ90)

value: skin fibroblast


title: HCA2 (MJ90) cells, module3-0day

description:
module3.count.xlsx
3-0day_S5_R1.count.txt


title: wt_cb_2


title: PfSWIB

value: wild type (Self-control)


title: usp15ko_cb_1


title: usp15ko_cb_2


title: PfSWIB∆

value: shiled1 induced (PfSWIB KD)


title: wt_cb_3


title: Prostate cancer cell line

city: Charlottesville

first: Pankaj

last: Kumar

state: VA

address: JPA, 1312A Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

data_processing: Paired end reads were mapped to the hg38 genome build using bwa-mem (Li and Durbin, 2009) with default setting. The split reads (reads not mapped in contiguous manner) were collected using tool samblaster (Faust and Hall, 2014). If one tag of a paired read is mapped contiguously (one entry in mapped file) and other tag is mapped in a split manner (two entries in mapped file) then the particular read id will have three entries in alignment file. We therefore collected all the read pair IDs that mapped to three unique sites in the genome from the alignment file. Next we collected the split reads that mapped uniquely at two positions on the same chromosome and in the same orientation. Returning to the list of paired end IDs that mapped uniquely to three sites in the genome, we identified paired end IDs where the contiguously mapped read is between the two split reads and on the opposite strand. From this list we annotate a circle if we find at least one junctional sequence. For karyotype and box plot we considered at least two junctional reads.

growth_protocol: complete medium

extract_protocol:
ATAC-seq for cell lines was performed as per the OMNI-ATAC-seq protocol
Nuclear pellet was then subjected to transposition reaction using Nextera DNA Sample Preparation kit (Illumina #FC-121-1030) in the presence of 0.01% digitonin and 0.1% Tween-20 at 37°C for 30 minutes and cleaned up with DNA Clean and Concentrator-5 Kit (Zymo #D4014). For qPCR, 3 to 6 additional cycles of PCR amplification was performed using NEBNext High-Fidelity 2X PCR Master Mix (NEB #M0541L) and Nextera Index Kit (Illumina #15055289). Cleaned up libraries were quantified and pooled for sequencing by Novogene.

treatment_protocol: Briefly, C4-2 and OVCAR8 cells were grown in RPMI-1640 (Corning #10-040) supplemented with 10% FBS to ~80% confluence. 50,000 viable cells were lysed in 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.1% Tween-20.

value: WT

tag: passage


title: wt_cb_1


title: wt_sm_2

value: Skeletal muscle


title: MM.1S 18 nM carfilzomib mRNA replicate 4

description:
MM.1S 18cfz_4
juncbase_tables_MM1S_DMSO_vs_MM1S_18cfz.tsv
ctrl_MM1s_vs_18_cfz_MM1s_results_deseq2_counts.csv

extract_protocol:
Total RNA was extracted by standard RNA extraction kit (RNeasy, Qiagen) and cleaned up with RNA clean & concentrator columns (Zymo).  For all except the timecourse samples, polyA-mRNA was enriched from total RNA with polyA-binding magnetic bead protocol (NEB).
RNA libraries were prepared for sequencing using standard Illumina protocols and Hyper Prep RNA sequencing kit (Kapa, with RiboErase for timecourse samples to remove abundant rRNA).  Protocol aimed at generating 200-300 bp fragments.  Reverse-transcribed cDNA was ligated to TruSeq barcode adapters for Illumina platform.  200-400 bp cDNA libraries were selected by PAGE extraction and purification, or AMPure bead size selection in the case of SRSF1 overexpression samples.  Four samples were multiplexed in a single lane for sequencing for the timecourse samples, seven samples were multiplexed for the single timepoint samples, and 9 samples were multiplexed for the SRSF1 overexpression samples.

tag: experiment

value: single timepoint response alternative splicing

tag: timepoint

tag: drug

value: 18 nM carfilzomib


title: F7672.GFP.CL5

city: São Paulo

first: Karina

middle: Griesi

last: Oliveira

state: SP

address: Rua Brentano, 292, Ap. 61

country: Brazil

institute: Hospital Albert Einstein

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 hg19 genome using TopHat2 v2.0.11.
Read counts per gene were summarized using HTSeq
Genes with FPKM<1 in more than a half of the samples were excluded from the next steps
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq files (.out) contains the count numbers sumarized per gene

source_name: neuron

growth_protocol: iPSC-derived NPC were cultured in NB media (DMEM/F12, N2 and B27 supplement) with 20ng/ml of FGF and EGF and replated/expanded every 2-3 days; for neuron generation, NPCs were plated in a low density and then cultured for 4 weeks with NB media with 1uM of retinoic acid

extract_protocol:
RNA was harvested using NucleoSpin RNA extraction kit (Macherey-Nagel). 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: iPSC-derived

tag: disease status

value: Control

value: neuron


title: F7672.CL5

source_name: mixed neuronal cells

value: mixed neuronal cells


title: F7672.CL6


title: F7672.GFP.CL6


title: F5618.CL6


title: Narcissus_D632-ZX01-T08

city: Zhangzhou

first: Yansen

last: He

state: Fujian

address: No.1499 Jiulong Avenue

institute: Institute of Subtropical Agriculture, Fujian Academy of Agricultural Sciences

data_processing:
Sequence reads with adapters or low-quality bases were removed from the raw data to generate clean reads. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated.
All the downstream analyses were based on clean data with high quality. The clean reads were then used de novo transcriptome assembly using Trinity software [78]. Trinity combined reads with overlaps to form contigs, which were then clustered to generate unigenes.
Gene function was annotated based on the following databases: NCBI non-redundant protein sequences (NR); Protein family (Pfam); Clusters of Orthologous Groups of proteins (KOG/COG/eggNOG); A manually annotated and reviewed protein sequence database (Swiss-Prot); Kyoto Encyclopedia of Genes and Genomes (KEGG); Gene Ontology (GO).
Differentially expressed genes (DEGs) analysis was performed using the DEGSeq R package and analyzed using Bowtie [79]. Expression levels were calculated according to the RSEM method [80]. The fragments per kilobase of transcript per million mapped reads (FPKM) method was used to calculate the rate of DEGs [81], and the false discovery rate (FDR) was used to correct the P-value thresholds via multiple testing [82]. Genes with an adjusted P value ≤ 0.05 and a foldchange (log2FC) ≥ 1 were assigned as significantly differential expressed.
Genome_build: Narcissus.Unigene.fa

organism: Narcissus tazetta subsp. chinensis

source_name: Petal of the full-bloom stage on the seventh day

growth_protocol: They were grown in a plantation under natural conditions

extract_protocol:
One point to five grams sample tissues were used for total RNA extraction by a Quick RNA Isolation Kit according to the manufacturer’s protocol (Bioteke Corporation, RP3202, Beijing, China). Total RNA degradation and contamination were monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). In addition, RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
A total of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease / polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2000 platform and paired-end reads were generated.

treatment_protocol: Narcissus petal and corolla tissues of samples were collected at the first day of the early flowering stage (Day1) and the seventh day of the full-bloom stage (Day7)

tag: cultivar

value: cv Jinzhanyintai

value: full-bloom stage

tag: time point

tag: tissue

value: petal tissues


title: Narcissus_D632-ZX01-T06

source_name: Corolla of the full-bloom stage on the seventh day

tag: developmental stage

value: corolla tissues


title: Narcissus_D632-ZX01-T07


title: Narcissus_D632-ZX01-T05


title: Narcissus_D632-ZX01-T04

source_name: Petal of the early flowering stage on the first day

value: early flowering stage


title: F7647.CL1


title: Narcissus_D632-ZX01-T03


title: F5618.GFP.CL6


title: F5618.CL3


title: Narcissus_D632-ZX01-T02

source_name: Corolla of the early flowering stage on the first day


title: Ovarian cancer cell line


title: ACTsh

description: Gene expression  of wild type (Blank-control)

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: strain

value: Red blood cell

value: wild type (Blank-control)


title: Narcissus_D632-ZX01-T01


title: ACT

description: Gene expression of wild type (Self-control)

value: wild type (Self-control)


title: F7647.CL3


title: Y2_LRC_A

description: Young LRCs, activated, mouse 2

source_name: Young 2 Activated LRC

value: muscle stem cells from limb muscle

value: 18 hours

tag: label retaining

value: LRC

tag: age

value: 3 months

tag: activated

value: activated


title: F6281.CL4

value: iPSC-derived

value: ASD


title: F6281.GFP.CL1

value: neuron


title: F7511.CL2

value: mixed neuronal cells


title: 307G7

description: Gene expression of shiled1 induced (PfSWIB KD)

value: shiled1 induced (PfSWIB KD)


title: F6136.CL4


title: F2735.GFP.CL2


title: F5541.GFP.CL2

value: Control


title: F2735.CL2


title: F2688.CL6


title: F5541.CL2


title: F2688.CL4


title: F2613.CL1


title: Donor sample 4

first: Weiguo

last: Fu

address: 180 Fenglin Road

department: Department of Vascular Surgery

institute: Zhongshan Hospital Fudan University

description: Control 4

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: abdominal aorta

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

growth_protocol: Samples were stored at -80℃ until assayed.

extract_protocol: Total RNA of the aortic samples were isolated using Trizol Reagent (Invitrogen, Carlsbad, CA, USA). NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA) was utilized to assess the quality and quantification of the total RNA.

tag: gender

value: female

value: abdominal aorta


title: F7672.cl4

source_name: NPC

tag: cell type

value: NPC


title: Donor sample 3

description: Control 3

value: male


title: F2613.GFP.CL1


title: F2735.CL3


title: Abdominal aortic aneurysm sample 1

description: AAA 1

source_name: full thickness abdominal aortic aneurysm tissue


title: F7647.cl3


title: Donor sample 2

description: Control 2


title: Abdominal aortic aneurysm sample 3

description: AAA 3


title: Abdominal aortic aneurysm sample 2

description: AAA 2


title: Donor sample 1

description: Control 1


title: F7647.cl2


title: Abdominal aortic aneurysm sample 4

description: AAA 4


title: Day_7_Chondro_donor#3_replicate#2

city: Davos Platz

first: Martin

middle: J

last: Stoddart

address: Clavadelerstrasse 8

country: Switzerland

institute: AO Research Institute Davos

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

source_name: Human mesenchymal stromal cells from bone marrow (vertebra)

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000

growth_protocol: MSCs were seeded at an initial cell density of 3x103 cells/cm2 and grown until passage 2 in α-MEM with 10% MSC-qualified FBS, 100 U/mL penicillin, 100 μg/mL streptomycin and 5 ng/ml basic Fibroblast Growth Factor. Cultures were maintained at 37°C/5% CO2, and the medium was refreshed every second day.

extract_protocol: Total RNA was isolated with TRIreagent following manufacturer's instructions. Briefly, 100 µl of 1-Bromo-3-chloropropane (Sigma-Aldrich, St. Louis, MO, USA) were added to TRIreagent, mixed thoroughly and the samples were centrifuged at 12000 g for 15 min at 4°C. The recovered aqueous phase was mixed with 500 µl of 2-propanol (Sigma-Aldrich) and precipitation of RNA was carried out overnight at -20°C for enhanced recovery of small RNA species. RNA pellet was then washed with 75% EtOH (Sigma-Aldrich) and resuspended in 20 µl of DEPC-treated H2O. Total RNA concentration was measured with NanoDrop 1000 (Thermo Fisher) and purity was assessed by evaluation of the A260/280 and A260/230 ratios.

treatment_protocol: At passage 3, cells were seeded for the induction of osteogenic or chondrogenic differentiation. For osteogenic differentiation, cells were seeded at a density of 1.5x104 cells/cm2 in 6-well plates. After cell attachment the medium was changed: control (CRL) samples were kept in DMEM 1g/l glucose (Gibco), 10% heat inactivated FBS (Gibco), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco). Osteogenic differentiation was induced by the addition of 50 µg/mL ascorbic acid 2-phosphate, 5 mM β-glycerol phosphate and 10 nM dexamethasone (all from Sigma-Aldrich) to the control medium. Samples were prepared in triplicate for each donor and each condition.   For chondrogenic differentiation, cells were seeded into pellet culture, using 2x105 cells/pellet. Cell were directly seeded into either control (CRL) or chondrogenic medium. Control medium was composed by DMEM 4.5 g/l glucose, 100 U/mL penicillin, 100 μg/mL streptomycin, 1% ITS+, and 1% NEAA. Chondrogenic medium was with the addition of 50 µg/mL ascorbic acid 2-phosphate, 100 nM dexamethasone, and 10 ng/ml TGF-β1 (Fitzgerald Industries). The medium was refreshed every second day to ensure to keep stable levels of differentiation factors in the media and samples were collected at day 7 for RNA isolation.

tag: age of donor

value: 55 years

tag: sex of donor

value: Female

tag: cell treatment

value: Chondrogenic differentiation in pellet (day 7)


title: F7315.cl4


title: Day_7_Chondro_donor#2_replicate#2

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

value: 80 years

value: Male


title: Day_7_Chondro_donor#1_replicate#2

value: 59 years


title: F7315.cl5


title: Day_7_Chondro_donor#1_replicate#1


title: Day_7_Chondro_donor#2_replicate#1


title: Y1_nonLRC_Q

city: San Francisco

description: Young nonLRCs, freshly isolated, mouse 1

source_name: Young 1 Quiescent nonLRC

value: muscle stem cells from limb muscle

value: 0 hours

value: nonLRC

value: 3 months

value: quiescent


title: Day_7_CRL_pellet_donor#3_replicate#2

value: Pellet culture control (day 7)


title: F6119.cl1

value: iPSC-derived

value: Control


title: Day_7_Chondro_donor#3_replicate#1


title: F5618.cl3


title: F5618.cl6


title: F7647.cl1


title: F5541.cl5


title: F6281.cl4

value: ASD


title: F5541.cl2

value: NPC


title: Day_7_CRL_pellet_donor#1_replicate#2


title: Day_7_CRL_pellet_donor#2_replicate#2


title: Day_7_CRL_pellet_donor#2_replicate#1


title: Day_7_CRL_pellet_donor#3_replicate#1


title: Day_7_CRL_pellet_donor#1_replicate#1


title: Day_7_Osteo_donor#3_replicate#2

value: Osteogenic differentiation in monolayer (day 7)


title: Day_7_Osteo_donor#3_replicate#1

value: 55 years


title: F5541.cl1


title: F6281.cl2


title: F6119.cl7


title: F6281.cl1


title: F7511.cl3


title: Day_7_Osteo_donor#2_replicate#2


title: F7511.cl2


title: Day_7_Osteo_donor#2_replicate#1


title: Day_7_Osteo_donor#1_replicate#2


title: Day_7_CRL_monolayer_donor#3_replicate#2

value: Female

value: Monolayer culture control (day 7)


title: Day_7_Osteo_donor#1_replicate#1


title: F7511.cl1


title: Day_7_CRL_monolayer_donor#3_replicate#1


title: F6136.cl1


title: F2735.cl3


title: No_Add_Glu_CB1_KO_FA20

city: Mainz

first: Prof. Beat

last: Lutz

state: Rheinland

address: Duesbergweg 6

department: Institute of Physiological Chemistry

country: Germany

institute: University Medical Center of the Johannes Gutenberg University Mainz

data_processing:
Quality of individual samples were checked using Fastqc version v0.10.5
Quality check was followed by alignment using TopHat version v2.1.1 to the mouse genome (mm9) with default parameters
Mapped reads were considered for read count per gene using HTSeq version 0.9.1
Differential expression analysis was performed using Deseq, R package.

extract_protocol:
mPFC was isolated and flash frozen on dry ice. RNA was extracted using a miRNA Mini kit (Quiagen, #217004). Total RNA (750-1000 ng/sample) was rRNA depleted by Ribo-Zero rRNA removal kit from Illumina.
RNA library was prepared for sequencing using NEBNExt Ultra II Directional RNA library kit.

tag: strain background

value: 2-4 months

tag: genotype/variation

tag: mouse group

value: non-addicted

value: Brain, Prefrontal Cortex


title: No_Add_Glu_CB1_KO_FA19


title: mutant mpeg1+ 1

city: Planegg-Martinsried

first: Jovica

last: Ninkovic

state: Bayern

address: Großhaderner Straße 9

department: Department for Cell Biology

institute: LMU München

data_processing:
Base call was performed via RTA Version 2.7.7
Sequences were aligned to the annotated zebrafish genome (GRCz10) with STAR, using default parameters as described in Dobin et al, Current protocols in bioinformatics, 2015
Normalised gene counts were internally generated via Deseq2 (release 3.9) pipeline in R, as described in in Love et al, Genome biology, 2014
Genome_build: GRCz10
Supplementary_files_format_and_content: Excel tables (.xlsx) containing normalised gene counts for each sample (including ENSEMBL gene I.D.)

organism: Danio rerio

source_name: FACS-isolated cells from telencephalon

extract_protocol:
For samples obtained from whole telencephalon, RNeasy Mini Kit (QIAGEN) was used. For samples obtained from FACS-isolated cells, PicoPure RNA Isolation Kit (Thermo Fischer Scientific) was used.
RNA libraries were prepared with a SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Clontech) and a MicroPlex Library Preparation kit v2 (Diagenode)

value: telencephalon

value: 5 months

tag: genotype

value: grna-/-;grnb-/-


title: No_Add_Glu_CB1_KO_FA18


title: mutant mpeg1+ 2


title: wildtype mpeg1+ 3

value: wildtype


title: F2688.cl6

tag: disease status


title: mutant mpeg1+ 4


title: mutant mpeg1+ 3


title: F2735.cl1


title: F2688.cl5


title: No_Add_Glu_CB1_KO_FA17


title: wildtype mpeg1+ 2


title: Day_7_CRL_monolayer_donor#2_replicate#2

value: 80 years

value: Male


title: F2688.cl4

value: iPSC-derived


title: Day_7_CRL_monolayer_donor#1_replicate#1

value: 59 years


title: mutant olig2+ 4


title: F2613.cl3

value: ASD


title: Day_7_CRL_monolayer_donor#2_replicate#1


title: Day_7_CRL_monolayer_donor#1_replicate#2


title: F2613.cl2

value: NPC


title: wildtype mpeg1+ 1


title: Add_Glu_CB1_KO_FA15

value: food addicted


title: F2735.cl2


title: Add_Glu_CB1_KO_FA14


title: No_Add_Glu_CB1_KO_FA16


title: mutant olig2+ 3


title: F2613.cl1


title: Add_Glu_CB1_KO_FA13


title: mutant olig2+ 2


title: No_add_Glu_CB1_WT_FA11

value: WT


title: mutant olig2+ 1


title: wildtype olig2+ 4


title: Add_Glu_CB1_KO_FA12


title: No_add_Glu_CB1_WT_FA9


title: No_add_Glu_CB1_WT_FA10


title: wildtype olig2+ 2


title: wildtype olig2+ 3


title: No_add_Glu_CB1_WT_FA8


title: Add_Glu_CB1_WT_FA6


title: No_add_Glu_CB1_WT_FA7


title: Add_Glu_CB1_WT_FA5


title: old mutant 4

source_name: Whole telencephalon

value: 18 months


title: old mutant 2


title: old mutant 5


title: Add_Glu_CB1_WT_FA4


title: old mutant 3


title: old mutant 1


title: Add_Glu_CB1_WT_FA2


title: young mutant 5


title: Add_Glu_CB1_WT_FA1


title: sh_417587_S15

city: Lausanne

first: Delphine

last: Grun

address: route Cantonale

institute: EPFL

description: organoids (KD)

data_processing:
hisat2 -k 5 --rna-strandness RF --seed 42 -p 7 -x
featureCounts -p -s 2 -T 4 -t exon -g gene_id -Q 10 -a
Genome_build: hg19
Supplementary_files_format_and_content: The .txt.gz.gz files contain read counts on genes

source_name: brain organoids

growth_protocol: STEMdiff™ Cerebral Organoid Kit - STEMCELL Technologies #08570

extract_protocol:
TruSeq stranded mRNA sample preparation kit (Illumina)
High pure RNA isolation kit (Roche)
As recommended by illumina (TruSeq stranded mRNA sample preparation kit)

treatment_protocol: transduced cells were puromycin selected

tag: culture

tag: shRNA

value: KZFPs


title: wildtype olig2+ 1

tag: tissue


title: PolII ChIP-Seq P60 replicate 2

city: Vassilika Vouton, Herakleion

first: Iannis

last: Talianidis

state: Crete

address: 100 N. Plastira Str

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology - Hellas

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer as well as standard Illumina base callers (bcl2fastq).
The RNA-Seq FASTQ files were mapped on the UCSC mm9 reference genome using tophat2 , with default settings and using additional transcript annotation data for the mm9 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html). The ChIP-Seq FASTQ files were also mapped to the mm9 genome using bwa  with standard parameters. The resulting BAM files were visualized in the UCSC Genome Browser using bedtools  and tools provided by the UCSC Genome Browser toolkit. Prior to any alignment or further analysis, the quality all the FASTQ files and the reads contained therein was inspected with the FastQC package.
The raw bam files were summarized to an exon read counts table and the exon read counts were filtered for artifacts as follows: if an annotated gene had up to 5 exons, read presence was required in at least 2 of the exons, else if an annotated gene had more than 5 exons, then read presence was required in at least 0.2x⌈E⌉ exons, where ⌈.⌉ is the ceiling mathematical function. After exon filtering, the final read counts for each gene model were calculated as the sums of their exon reads, creating a gene counts table where each row corresponded to an Ensembl gene model and each column corresponded to an RNA-Seq sample. The gene counts table was normalized using the Bioconductor package DESeq after removing genes that had zero counts over all samples. Genes presenting any of the following were excluded from further analysis: i) genes with length less than 500, ii) genes whose average reads per 100 bp was less than the 25th quantile of the total normalized distribution of average reads per 100bp, iii) genes with read counts below the median read counts of the total normalized count distribution. The resulting gene counts table was subjected to differential expression analysis using the Bioconductor package DESeq. Differentially expressed genes were identified with an FDR threshold of 0.05 and a fold change threshold of -1 and 1 (log2) scale for up and down regulated genes respectively. All the analyses and reporting  were performed within the Bioconductor package metaseqR.  For the transcription factor data (CEBPα, HNF4α), the two biological replicates for each developmental stage and their respective DNA input samples were subjected to peak calling using MACS 1.4  with the default settings for mouse genome. Prior to peak calling and in order to compensate for differences in library sizes between ChIP and Input DNA sequencing samples, the total number of reads of each sample was equalized by uniformly downsampling reads relatively to the sample with the lower number of reads. The putative binding sites returned by MACS were further filtered for artifacts by i) imposing an additional MACS FDR threshold of 0.1%, ii) excluding peaks demonstrating a fold enrichment less than 1 in log2 scale (where fold enrichment is the ratio of reads under a peak area in the ChIP sample to the respective number of reads in the Input DNA sample).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene for RNA-Seq data. BED files with peak coordinates for ChIP-Seq data. BigWig signal files for ChIP-Seq data.

source_name: PolII ChIP-Seq P60

growth_protocol: Mice were maintained in grouped cages in a temperature-controlled, pathogen-free facility on a 12-hr light/dark cycle and fed by a standard chow diet (Altromin 1324; 19% protein, 5% fat) or High Fat Diet (34% crude Fat, 23% crude Protein, 5% crude fiber by Mucedola s.r.l.) and water ad libitum. All animal experiments were approved by the Prefecture of Attica and were performed in accordance with the respective national and European Union regulations. All the experiments were performed in randomly chosen age-matched male mice. No blinding was used in this study.

extract_protocol:
RNA preparation: Total RNA was prepared by homogenizing liver pieces in 10 volumes of Trizol reagent followed by the addition of 2 volumes of chlorophorm and centrifugation at 12000 g for 15 minutes. The aqueous phases were precipitated with isopropanol. Following resuspension in water RNAs were subjected to additional precipitation with ethanol. The RNA samples were digested with 10 units of DNase I for 10 min at 37 0C, followed by purification with phenol/chlorophorm extraction and ethanol precipitation. Chromatin immunoprecipitation: Liver tissue was minced to small pieces in PBS and after addition of formaldehyde to a 1% final concentration immediately was subjected to 10 strokes of dounce homogenization. Cross-linking was continued for 10 min and stopped by the addition of glycine at 0.125 M final concentration. Cross-linked cells were treated with a buffer containing 50 mM HEPES pH 7.5, 0.14 M NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40 and 0.25% Triton-X100, for 10 minutes and then with a buffer containing 0.2 M NaCl, 1 mM EDTA, 0.5 mM EGTA and 10 mM Tris-HCl pH 8.0 for 5 minutes. The nuclei were resuspended up to 4 ml with sonication buffer containing 10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate and 0.5% N-lauroylsarcosine and sonicated for 12 minutes in Covaris Sonicator instrument. After sonication, samples were supplemented with 400 μl of 10% Triton X-100 and centrifuged for 10 minutes at 20.000 rcf. After centrifugation, the extracted chromatin was incubated overnight with Dynabeads Protein G, that were prebound by 10 ug of the respective antibodies. The beads were washed six times with a buffer containing 50 mM Hepes pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, and 0.7% Na-deoxycholate, and then once with a buffer containing 20 mM Tris-HCl pH 7.6 and 150 mM NaCl. Immunoprecipitated chromatin was eluted from the beads and reverse crosslinked by overnight incubation with a buffer containing 50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1 % SDS, at 65 0C. Following incubation, samples were diluted by addition of one volume of TE. RNAs and proteins were removed by incubation with 20 ug/ml RNAse A for 30 minutes at 37 C, followed by incubation with 20 ug/ml Proteinase-K for 2 hours at 55 0C. DNA was extracted by phenol/chlorophorm and precipitated with ethanol. About 10 ng of the immunoprecipitated DNA and input DNA was used for library preparation.
Libraries were prepared using TruSeq or NEBNext Adaptors, depending on whether less or more than 6 indexes were included. In all cases, 25 μl of immunoprecipitated DNA was purified using the MinElute columns (Qiagen, 28604) and eluted with 10 ul elution buffer. The concentration of the eluted DNA was measured in Qubit using the dsDNA HS Assay Kit (Invitrogen Q32851). Subsequently, ten ng of ChIP or input DNA were subject to end repair, in a mix containing T4 DNA polymerase (NEB M0203L), Klenow fragment (NEB M0210L), T4 DNA PNK (NEB M0201L) and dNTPs in T4 DNA Ligase Buffer (NEB, B02025) at 20 °C for 30 min. Following end repair, samples were purified using the Agentcourt AMPURE XP system (Agentcourt A63881) and subject to A addition by incubation with dATP and Klenow 3’-->5’ exo- 37 °C for 30 min. Another AMPURE XP purification was performed and then Truseq or NEBNext adaptors were ligated using Quick Ligase in Quick Ligase Buffer. Following adaptor ligation, samples were incubated with 1.5 ul USER enzyme at 37 °C for 15 minutes, to cleave the adaptor hairpin loop. Purification and size selection was performed again by AMPURE XP and PCR amplification was performed using Truseq or NEBnext Primers in Kapa Hifi Hotstart mix. A final purification was performed and libraries were ready for Bioanalyzer assessment and sequencing.

treatment_protocol: The mice were not treated.

tag: strain

value: F1 mice (C57Bl6/CBA)

value: 60 days postnatal

value: Wild type

value: liver

tag: chip antibody

value: RNA-Pol-II

tag: chip antibody vendor

value: Euromedex

tag: chip antibody cat. #

tag: chip antibody lot #


title: young mutant 3

value: telencephalon

tag: age

value: 5 months

value: grna-/-;grnb-/-


title: usp15ko_sm_2 [exon-level]

description:
ko_sm_2.cel
Exon analysis data from wt and usp15 deficient mice

tag: tissues

value: Skeletal muscle


title: PolII ChIP-Seq P60 replicate 1


title: shE_S6

description: organoids (Ctrl)

value: STEMdiff™ Cerebral Organoid Kit - STEMCELL Technologies #08570

value: control lentivector


title: young mutant 1


title: sh_417587_S13

description: organoids (KD)


title: Add_Glu_CB1_WT_FA3

value: 2-4 months

value: Brain, Prefrontal Cortex


title: usp15ko_sm_3 [exon-level]

description:
ko_sm_3.cel
Exon analysis data from wt and usp15 deficient mice


title: young mutant 4


title: PolII ChIP-Seq P0.5 replicate 1

source_name: PolII ChIP-Seq P0.5

value: 0.5 days postnatal


title: shE_S5

description: organoids (Ctrl)


title: young mutant 2


title: PolII ChIP-Seq e18.5 replicate 2

source_name: PolII ChIP-Seq e18.5

value: 18.5 days embryonic


title: wt_cb_1 [exon-level]

description:
wt_cb_1.cel
Exon analysis data from wt and usp15 deficient mice

value: wildtype

value: Cerebellum


title: old wildtype 5

value: 18 months


title: wt_cb_2 [exon-level]

description:
wt_cb_2.cel
Exon analysis data from wt and usp15 deficient mice


title: shE_S4

description: organoids (Ctrl)


title: wt_cb_3 [exon-level]

description:
wt_cb_3.cel
Exon analysis data from wt and usp15 deficient mice


title: usp15ko_cb_1 [exon-level]

description:
ko_cb_1.cel
Exon analysis data from wt and usp15 deficient mice


title: old wildtype 4


title: usp15ko_sm_1 [exon-level]

description:
ko_sm_1.cel
Exon analysis data from wt and usp15 deficient mice


title: old wildtype 3


title: wt_sm_1 [exon-level]

description:
wt_sm_1.cel
Exon analysis data from wt and usp15 deficient mice


title: usp15ko_cb_3 [exon-level]

description:
ko_cb_3.cel
Exon analysis data from wt and usp15 deficient mice


title: old wildtype 2


title: iN-STINGi-ShZ_S23

description: Neuron STINGi (KD)

data_processing:
hisat2 -k 5 --rna-strandness RF --seed 42 -p 4 -x
featureCounts -p -s 2 -T 4 -t exon -g gene_id -Q 10 -a
Genome_build: hg19
Supplementary_files_format_and_content: The .txt.gz files contain read counts on genes

source_name: iN

growth_protocol: mTESRI

treatment_protocol: w puromycin, w/wo STING inhibitor, with doxycyclin

value: mTESRI

tag: agent

value: STING

value: Neuron

tag: sirna

value: KZFPs genes (KD)


title: wt_sm_3 [exon-level]

description:
wt_sm_3.cel
Exon analysis data from wt and usp15 deficient mice


title: usp15ko_cb_2 [exon-level]

description:
ko_cb_2.cel
Exon analysis data from wt and usp15 deficient mice


title: wt_sm_2 [exon-level]

description:
wt_sm_2.cel
Exon analysis data from wt and usp15 deficient mice


title: old wildtype 1

value: telencephalon


title: HNF4a ChIP-Seq P14 replicate 2

source_name: HNF4a ChIP-Seq P14

value: F1 mice (C57Bl6/CBA)

value: 14 days postnatal

value: Wild type

value: liver

value: Santa Cruz Biotech/Aviva


title: PolII ChIP-Seq e18.5 replicate 1

value: RNA-Pol-II

value: Euromedex


title: iN-STINGi-ShL_S22

description: Neuron STINGi (Ctrl)

value: Luciferease gene


title: iN-STINGi-ShL_S21

description: Neuron STINGi (Ctrl)


title: young wildtype 5

value: 5 months


title: HNF4a ChIP-Seq P0.5 replicate 2

source_name: HNF4a ChIP-Seq P0.5

value: 0.5 days postnatal


title: HNF4a ChIP-Seq e18.5 replicate 2

source_name: HNF4a ChIP-Seq e18.5

value: 18.5 days embryonic


title: young wildtype 3

value: wildtype


title: young wildtype 4


title: HNF4a ChIP-Seq P0.5 replicate 1


title: iN-Ctrl-ShZ_S15

description: Neuron untreated (KD)

value: mTESRI


title: iN-Ctrl-ShZ_S16

description: Neuron untreated (KD)


title: HNF4a ChIP-Seq P14 replicate 1


title: HNF4a ChIP-Seq e18.5 replicate 1


title: iN-Ctrl-ShL_S14

description: Neuron untreated (Ctrl)


title: young wildtype 2


title: iN-Ctrl-ShL_S13

description: Neuron untreated (Ctrl)


title: CEBPa ChIP-Seq P14 replicate 2

source_name: CEBPa ChIP-Seq P14

value: C/EBPa

value: Santa Cruz Biotech


title: young wildtype 1


title: CEBPa ChIP-Seq P14 replicate 1


title: 200078650240_R04C02

status: Public on Feb 17 2020

type: genomic

city: Brisbane

first: Jacob

last: Gratten

address: 37 Kent Street

department: Mater Research Institute

country: Australia

institute: University of Queensland

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Genome Studio using standard recommended Illumina scanner setting

data_processing: Genome Studio software

label: Cy3, Cy5

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from SGPD samples using ??? according to standard instructions

tag: gender

value: Male

tag: disease-state

value: Parkinson's disease

value: whole blood


title: 200078650258_R02C01

value: Female

value: Control


title: 200078650240_R06C01


title: 200078650240_R04C01


title: 200078650240_R03C01


title: iN-STINGi_ShZ_S24

description: Neuron STINGi (KD)

value: STING

value: Neuron

value: KZFPs genes (KD)


title: 200078650258_R06C01


title: 200078650258_R04C01


title: 200078650258_R03C02


title: 200078650240_R05C02


title: 200078650258_R04C02


title: 200078650240_R06C02


title: 200078650258_R01C01


title: 200078650240_R02C02


title: 200078650240_R05C01


title: 200078650258_R06C02


title: 200078650240_R03C02


title: 200078650258_R05C01


title: 200078650258_R03C01


title: 200078650240_R01C02


title: 200078650258_R05C02


title: 200078650240_R02C01


title: 200078650240_R01C01


title: 200078650237_R06C02


title: 200078650258_R01C02


title: 200078650237_R05C02


title: 200078650237_R03C02


title: 200078650237_R02C02


title: 200078650237_R01C02


title: 200078650237_R06C01


title: 200078650232_R05C02


title: 200078650232_R05C01


title: 200078650232_R04C02


title: 200078650232_R02C02


title: 200078650232_R06C01