title: [WT3, Wild_Type]

description: circular RNAs

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Arrays v2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

label_protocol: A random primer-based labeling system is coupled with RNase R-based sample pretreatment to efficiently remove linear RNAs, and specifically label circular RNAs.

growth_protocol: Adult mouse stiatum

extract_protocol: Trizol

treatment_protocol: RNA immunoprecipitation (RIP) from HuD transgenic overexpressing (HuD-OE)mice vs. WT or vs. IgG controls

tag: antibody

value: anti-myc tag antibody (9B11; Cell Signalling Technology Inc.)


title: [WT2, Wild_Type]

status: Public on Jun 28 2020

type: RNA

city: Albuquerque

first: Nora

last: Perrone-Bizzozero

state: NM

address: 1 University of New Mexico MSC08 4740

department: Neurosciences

country: USA

institute: University of New Mexico

description: circular RNAs

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

data_processing: A series of data processing including quantile normalization were performed using the R software limma package.

molecule: total RNA

organism: Mus musculus

source_name: striatum

tag: genotype/variation

value: wild type


title: Control_2

type: SRA

city: Vienna

first: Johannes

middle: A.

last: Schmid

address: Schwarzspanierstr. 17

department: Vascular Biology and Thrombosis Research

country: Austria

institute: Med. Univ. Wien

library_source: transcriptomic

data_processing:
fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) (version 0.11.5) was used to check the quality of reads.
Sequence reads were aligned to UCSC mouse genome version mm10 using STAR version 2.7.0e.
Differential expression analysis was performed using DEseq2 version 1.22.2 package in R.
Gene annotation with biomaRt_2.40.5.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: caIKK2EC_vs_WT_DESeq2results.tsv: Tab-delimited text file containing differential expression (DE) analysis performed using DEseq2 version 1.22.2; Gene Symbol, ensembl gene ID, Entrez, gene_biotype;baseMean,log2FoldChange,lfcSE,stat,pvalue,padj, normalized counts for each sample.
Supplementary_files_format_and_content: caIKK2EC_vs_WT_DESeq2results_rlog_counts.tsv: Tab-delimited text file containing differential expression (DE) analysis performed using DEseq2 version 1.22.2; Gene Symbol, ensembl gene ID, Entrez, gene_biotype;baseMean,log2FoldChange,lfcSE,stat,pvalue,padj, rlog transformed counts for each sample.
Supplementary_files_format_and_content: all_samples_counts.txt: Tab-delimited text file containing gene counts for each sample obtained from the output of STAR aligner version 2.7.0e using the parameter --quantMode GeneCounts.

source_name: Aorta

growth_protocol: Mice with a constitutive active form of IKK2 (caIKK2(+/+)) and a co-translationally expressed EGFP downstream of a loxP-flanked STOP-cassette, were crossed with BMX-CreERT2(+/-) ApoE(-/-) mice, which express an inducible Cre recombinase only in arterial endothelial cells (obtained from Christian Weber, Munich, Germany) to generate caIKK2(+/+) BMXCreERT2(+/-) ApoE(-/-) mice (designated as caIKK2EC). BMX-Cre-negative, caIKK2(+/+) BMXCreERT2(-/-) ApoE(-/-) littermates were referred to as control (control) mice. MRNA profile of whole aortas was generated by deep sequencing, using Illumina HiSeq3000/4000 instrument.

extract_protocol:
For RNA isolation, aortas were homogenized in lysis buffer using a Precellys® homogenizer (VWR®, Randnor, Pennsylvania), RNA was isolated with the PeqGOLD total RNA isolation Kit (c-line, Thermo Fisher Scientific, Waltham, MA, US) according to the manufacture’s protocol and the RNA concentration was measured by NanoDrop (VWR®, Vienna, Austria).
Sequencing libraries were prepared at the Core Facility Genomics, Medical University of Vienna using the NEBNext Poly(A) mRNA MagneticIsolation Module and the NEBNext Ultra™ Directional RNA Library Prep Kitfor Illumina according to manufacturer's protocol (New EnglandBiolabs). Libraries were QC‑checked on a Bioanalyzer 2100 (Agilent) using a HighSensitivity DNA Kit for correct insert size and quantitated using QubitdsDNA HS Assay (Invitrogen). Pooled libraries had an average length of 330‑360 bp and were sequenced on a HiSeq3000/4000 instrument (Illumina) in 1x50bp sequencing mode.

treatment_protocol: Tamoxifen (1 mg/20 g mouse) was injected intraperitoneally (i.p.) at five consecutive days. Both experimental groups (Control and caIKK2EC mice) were injected to exclude potential off-target effects of the drug. To induce the development of atherosclerotic plaques, mice were fed a Western-type diet containing 21,2% fat and 2070 mg/kg cholesterol (TD88137 mod, ssniff, Germany) ad libitum for 12 weeks.

tag: genotype

value: Control

tag: tissue

value: aorta

tag: Sex

value: Female

tag: age (weeks)


title: AQRsi1 BT549 Rep1

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

data_processing:
De-multiplex with bcl2fastq-1.8.4
Aligned/quantified with Tophat 2.1.1
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited counts tables

molecule: polyA RNA

organism: Homo sapiens

source_name: Cancer cells

extract_protocol:
Qiagen RNeasy Kit
Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit

tag: cell line

tag: sirna


title: BRCA1si1 BT549 Rep1


title: [WT1, Wild_Type]

description: circular RNAs


title: C4_normal_Bisulfite-seq

city: Nanjing

first: Zhen

last: Zhou

state: Jiangsu

address: 22th,Hankou Road

department: School of Lifesciences

country: China

institute: Nanjing University

library_source: genomic

data_processing:
All bisulfite sequencing reads were first trimmed to remove adaptors and lowquality bases using trim_galore (version 0.3.3) (parameters: --quality 20 --phred33 --length 50 --paired). Next, reads that passed quality control were mapped to the Mouse reference genome (mm10) using Bismark with paired-end alignment mode (parameters: --non-directional --fastq).
To recover additional sequencing reads, unmapped reads were realigned to the same reference genome in single-end alignment mode. Only reads with a unique mapping location in the genome were retained for further analysis.
All genomic DNA sequencing reads were also stripped of their adaptor sequences using the trim galore tool and then mapped to the mm10 reference genome using BWA31 with long-reads ‘Mem’ mode, resulting in an average of 14.98% mapping efficiency (7.07–28.48% range).
After alignment, reads were further deduplicated using the ‘samtools rmdup’ command (Borgel et al., 2010). For each cytosine site (or guanine corresponding to a cytosine on the opposite strand) in the reference genome sequence, the DNA methylation level was determined by the ratio of the number of reads supporting C (methylated) to that of total reads (methylated and unmethylated). Notably, in this study, the DNA methylation level of any given sample or region was referred to as the DNA methylation level of the CpG sites of this sample or region, unless specified elsewhere. A bin approach (10Kbp/bin) was used to estimate the methylation rate in consecutive regions.
We also estimated the DNA methylation level of different genomic regions that were annotated in the UCSC genome table and other databases, including CGIs, exons, introns, intergenic regions, intragenic regions, and repetitive regions (Bird, 2002). The DNA methylation level of these genomic regions was calculated on the basis of the average methylation level of all covered CpG sites within these regions.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include analysis resultf of differentially methylated regions for each group.

molecule: genomic DNA

source_name: embryos

growth_protocol: sRNAs isolated from normal or depressed mice sperm with a concentration of 2 ng/μl were microinjected in to fertilized eggs of C57BL/6 background. The zygotes were then cultured in M16 medium (Sigma) at 37 °C in 5% CO2. At the second day, the 2-cell embryos were transferred to potassium-supplemented simplex optimized medium (KSOM, Millipore). Embryos at E4.5 stage were collected at approximately 108 h after microinjection, respectively.

extract_protocol:
Single E4.5-stage embryo was subjected to extraction of the genomic DNA using the Genomic DNA Clean and Concentrator kit (VisTech, Dayton, OH) according to the manufacturer’s instructions.
A single embryo was seeded into lysis buffer by mouth pipette. DNA was released after proteinase treatment at 50 °C and then subjected to bisulfite conversion. After column-based purification, DNA was complemented with the biotinylated random primer Bio-P5-N9 and 50 units of Klenow polymerase (3' to 5' exo–, New England BioLabs, Beverly, MA). This random priming was repeated five times in total. Second strands were synthesized using another random primer, P7-N9, and final libraries were generated after 8 to 12 cycles of PCR amplification with the Illumina universal PCR primer and Illumina indexed primer.Sequencing data were generated on the Illumina HiSeq 4000 platform (sequenced by Novogene).

value: embryos

tag: Stage

tag: strain

tag: injected with sperm srna from

value: Normal mice


title: WT-1

description: lncRNA-mRNAs

hyb_protocol: The labeled cRNAs were hybridized onto the Mouse LncRNA Array v3.0 (8 x 60K, Arraystar).

label_protocol: Arraystar Flash RNA Labeling Kit was used for sample labeling.

growth_protocol: Adult mice

extract_protocol: Trizol. mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a mixture of oligo(dT) and random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

treatment_protocol: HuD KO mice vs. WT

value: Adult striatum


title: [IgG3, IgG]

description: circular RNAs

value: IgG


title: [IgG2, IgG]

description: circular RNAs


title: AQRsi1 MDA231 Rep2


title: AQRsi1 MDA231 Rep1


title: HuD-KO-1

description: lncRNA-mRNAs

value: HuD KO (Elalvl4-/-)


title: C1_normal_Bisulfite-seq


title: WT-2

description: lncRNA-mRNAs


title: [IgG1, IgG]

description: circular RNAs


title: HuD-KO-2

description: lncRNA-mRNAs


title: [HuDoe2, HuD_transgenic]

description: circular RNAs

value: HuD transgenic


title: U87_3T3_scRNAseq [PJ0707172]

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway

institute: Columbia University

data_processing:
Read 1 and read 2 fastq files were generated on basespace.
16-nt cell barcodes (CBs) were extracted from position 3-10 and 13-20, and 8-nt unique molecular identifiers (UMIs) were extracted from position 1-2, 11-12 and  21-24 of Read 1.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read.
Trimmed reads were then aligned to the reference human or(and) mouse genome using STAR v.2.7.0 with parameters "-- sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. A digital gene expression matrix was then generated from the corrected barcode-UMI-gene triplets.
Genome_build: GRCh38 and GRCm38 (sample 1)
Genome_build: GRCh38  (sample 2)
Supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression level of each individual cell.

organism:
Homo sapiens
Mus musculus

source_name: Brain and embyro

growth_protocol: U87 cells and 3T3 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplimented with 10% (v/v) Fetal Bovine Serum (FBS).

extract_protocol:
mRNA molecues were captured using bead-bound oligo dT(30).
Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.


title: [HuDoe1, HuD_transgenic]

description: circular RNAs


title: T3: R. mucilaginosa + 0.2mM SA

status: Public on Jun 27 2020

city: Zhenjiang

first: Solairaj

last: Dhanasekaran

address: Jiangsu University

department: School of Food and Biological Engineering

institute: Jiangsu University

data_processing:
After sequencing segmentation and quality control of the offline file was done using the reference genome reference genome version：GCF_000317415.1_Csi_valencia_1.0 reference genome site ads：https: //www.ncbi.nlm.nih.gov/genome/?term=Citrus+sinensis
To correct the significant P-value obtained from the original hypothesis test from the false discovery rate (FDR), the Benjamini-Hochberg correction method was used. The log2(fold change) I≥ 1 and FDR < 0.05 screening criteria was used to obtained the differentially expressed genes (DEGs). The function of the (DEGs) were annotated using gene database such as gene ontology (GO) (Young et al. 2010), cluster of original groups of protein (COG) (Darren et al. 2000), Kyoto encyclopaedia of genes and genes (KEGG) (Altermann et al. 2005), Swiss Prot (Pasquier et al. 1999) and National Center for Biotechnology Information (NCBI) (O’Leary et al. 2016).
Genome_build: Csi_valencia_1.0
Supplementary_files_format_and_content: FPKMs

organism: Citrus sinensis

source_name: Citrus sinensis (L.) Osbeck

extract_protocol:
Using Illumina HiSeq 2500, subsequent sequencing was carried out after RNA extraction, library construction and sequencing, double-strand cDNA synthesis, terminal repair and ligation, and library quality control.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Albedo

value: excised Albedo

tag: age

value: 3 days after innoculation

tag: treatment

value: R. mucilaginosa + 0.2mM SA


title: C2_normal_Bisulfite-seq


title: T1: R. mucilaginosa + 0.2mM SA


title: T2: R. mucilaginosa + 0.2mM SA


title: CK1: R. mucilaginosa

value: R. mucilaginosa


title: CK3: R. mucilaginosa


title: CK2: R. mucilaginosa


title: WT Rep4

city: Aurora

first: Srinivas

last: Ramachandran

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
Paired-end sequencing was performed on a HiSeq 2500 (Illumina) with 50 cycles for each read. Raw data from the sequencer was demultiplexed and FASTQ files were generated using bcl2fastq Conversion Software (Illumina).
Paired-end reads were aligned to mm10 version of the mouse genome using bowtie2 with following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant -I 10 -X 700.
The fraction of reads mapped at each nucleotide was multiplied by the total number of nucleotides mapped genome-wide, which was arbitrarily chosen as approximate size of the genome (2.8x10^9), to give a normalized count at that position.
The reads were then aggregated to 25 base-pair windows, and only paired-end reads of length 40 to 120bp were used in the analysis as they usually represent areas of transcription factor binding.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files of coverage of paired end reads with insert size between 40 and 120 bp

source_name: WT MEFs

extract_protocol:
ATAC-seq was performed according to Buenrostro et al. (Nature Methods 2013) with 50,000 cultured WT MEFs and JMJD5 KO MEF cells. Cells were lysed to extract nuclei. Nuclei were resuspended in 50 μL 1× TD buffer containing 2.5 μL transposase (Nextera, Illumina). The transposase reaction was conducted for 40 min at 37 °C.
Library amplification and barcoding were performed using Illumina compatible index primers purchased from IDTdna. PCR was conducted for 12-15 cycles. Library purification was performed with the MinElute PCR Purification Kit (Qiagen) and size selection was using AMPureXP beads (Beckman Coulter). Libraries were quantified and size distribution was assessed using the Bioanalyzer High Sensitivity DNA Kit (Agilent).

value: WT


title: WT Rep3


title: WT Rep2


title: WGBS_PL-NSC2

city: Los Angeles

first: Andrew

last: King

state: CA

address: Gonda Bldg Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

data_processing:
Fastq files were trimmed using Trim Galore version 0.4.1 with options --paired, --trim1, --clip_R2 10, and --phred33.
Paired-end reads were mapped to mm9 genome using Bismark version 0.17.0 specifying --phred33-quals.
Mapped reads were deduplicated and filtered for non-conversion. Methylation state of individual CpGs were then determined using bismark_methylation_extractor.
Genome_build: mm9
Supplementary_files_format_and_content: Bismark coverage output containing chr, start position, end position, methylation percentage, methylated counts, and unmethylated counts respectively.

source_name: ES-derived Neural stem cell (NSC)

growth_protocol: Mouse embryonic stem cells (mESCs) were grown on irradiated mouse embryonic fibroblasts and maintained in DMEM supplemented with 15% fetal bovine serum, 1 mM GlutaMAX, 1X Non-essential amino acids, 1X Penicillin/Streptomycin, mLIF, and 0.001% β-mercaptoethanol. Neural induction was performed by adapting mESCs to feeder-free conditions and seeded at low densities (5,000-10,000 cells/cm2) on gelatinized plates. Induction was performed as a monolayer in defined default medium (DDM) for 10 days with addition of 1uM cyclopamine starting on day 2. Progenitor intermediates were replated on poly-D-lysine and laminin coated culture dishes on day 10. Neural stem cells were expanded in DMEM-F12-based medium supplemented with N-2, hEGF, and bFGF.

extract_protocol:
Genomic DNA was purified from mESCs and NSCs using standard phenol-chloroform-isoamyl alcohol extraction followed by ethanol precipitation. Genomic DNA was spiked with 0.5% lambda DNA, fragmented to 250-350 bp using Bioruptor (Diagenode), and concentrated by ethanol precipitation. 500 ng of fragmented DNA was used for bisulfite conversion using EZ DNA Methylation-Direct Kit (Zymo).
WGBS libraries were constructed using Accel-NGS Methyl-Seq DNA Library Kit (Swift) according to manufacturer’s recommendations. WGBS libraries were quantified using Qubit Fluorometer and Agilent 2200 TapeStation (Agilent). Libraries were pooled and sequenced using the Illumina HiSeq 4000 as 150-bp paired-end sequencing reads.

tag: cell type

value: J1 NSC

tag: background strain

value: Dnmt3a P900L


title: JMJD5 KO Rep4

source_name: JMJD5 KO MEFs

value: JMJD5 KO


title: JMJD5 KO Rep1


title: WT Rep1


title: WGBS_PL-NSC1


title: JMJD5 KO Rep3


title: WGBS_MK-NSC2

value: Dnmt3a M544K


title: [HuDoe3, HuD_transgenic]

description: circular RNAs

value: anti-myc tag antibody (9B11; Cell Signalling Technology Inc.)


title: WGBS_MK-NSC1


title: WGBS_GS-NSC1

value: Dnmt3a G528S


title: WGBS_KO-NSC

value: Dnmt3a KO


title: WGBS_J1-NSC2


title: WGBS_J1-NSC1


title: WGBS_KO-ESC

source_name: Embryonic stem cell (ESC)

value: J1 ESC


title: WGBS_J1-ESC


title: WGBS_IN-NSC1

value: Dnmt3a I306N


title: WGBS_IN-NSC2


title: WGBS_GS-NSC2


title: S1BKOS1ADS_ChIP_Pol2_2

city: Chicago

first: Ali

last: Shilatifard

address: 303 East Superior Street

institute: Northwestern University

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output and bcl2fastq v.2.19.1 for NovaSeq output .
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC mm9 using Bowtie version 1.1.2.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC mm9 using Tophat version 2.1.0.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

source_name: embryonic stem cell

growth_protocol: ESCs were grown in N2B27 media supplemented with MEK inhibitor, GSK3 inhibitor, and LIF (2i/LIF).

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions. For ChIP, ESCs were fixed in 1% formaldehyde, followed by quenching and cell lysis before chromatin sonication using a E220 focused-ultrasonicator (Covaris). Sheared chromatin was then subjected to immunoprecipitation, and immunoprecipitated DNA was then washed, eluted, reverse cross-linked, and purified prior to submission for library preparation.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit.

value: embryonic stem cell

tag: chip antibody

value: Rpb1 (CST, D8L4Y)


title: Mll1KO_ChIP_H3K4me3_1

value: H3K4me3 (Homemade, #519)


title: S1BS1ADSMll2DS_ChIP_Pol2_1


title: S1BS1ADSMll2DS_RNA_1


title: S1BS1ADSMll2DS_ChIP_Pol2_2


title: S1BKOS1ADS_ChIP_H3K4me3_3


title: S1BS1ADSMll1KO_ChIP_H3K4me3_1


title: S1BS1ADSMll2DS_RNA_4


title: Mll2DS_ChIP_Pol2_2


title: WT_ChIP_Pol2_2

value: Wildtype/WT


title: WT_ChIP_H3K4me3_2


title: Mll2DS_ChIP_H3K4me3_1


title: S1BS1ADSMll2DS_ChIP_H3K4me3_1


title: WT_RNA_6


title: Mll2DS_RNA_1


title: WT_ChIP_Pol2_3


title: WT_RNA_5


title: S1BS1ADSMll2DS_RNA_3


title: WT_RNA_7


title: Mll2DS_ChIP_Pol2_1


title: S1BS1ADSMll2DS_RNA_2


title: WT_RNA_4


title: S1BKOS1ADSshMll2_ChIP_H3K4me3_2

tag: shRNA

value: Mll2 shRNA


title: Mll2DS_RNA_2


title: S1BKOS1ADSshNT_ChIP_H3K4me3_2

value: non-targeting shRNA


title: WTshMll2_ChIP_H3K4me3_2


title: WTshNT_ChIP_H3K4me3_2


title: S1BKO_RNA_2


title: S1BKO_RNA_3


title: S1BKO_RNA_1


title: S1BKOS1ADS_RNA_4


title: WT_RNA_2


title: S1BKOS1ADS_RNA_3


title: WT_RNA_3


title: S1BKOS1ADS_RNA_6


title: SU_MB002_TGP_NEG_B

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

description:
Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-TGP-N-B

data_processing:
Raw sequence data were exported to FASTQ format and were filtered based on quality scores.
Next the reads were mapped to  the GRCh38/hg38 reference version using HISAT.
The counts were obtained by using ht-seq count with the “intersection-strict” option.
Counts were transformed with TMM transformation and then normalized with VOOM.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data file contains a matrix containing data from all samples.

source_name: pediatric medulloblastoma

extract_protocol:
Total RNA was extracted using the Norgen Total RNA isolation kit and quantified using a NanoDrop Spectrophotometer ND-1000.
The RNA was sequenced using single-end 50 bp reads on the Illumina HiSeq platform (Illumina, San Diego CA, USA).

value: pediatric medulloblastoma

tag: molecular subgroup

value: Group 3


title: S1BKOS1ADS_RNA_5

tag: genotype/variation


title: S1BKO_ChIP_H3K4me3_2


title: S1BKOS1ADS_ChIP_H3K4me3_1


title: WT_RNA_1


title: ICB1299_PBS_C

description:
Singh_HISAT_USCS_VOOM_TMM.csv
ICB1299-PBS-C

value: Group 4


title: ICB1299_L807mts_B

description:
Singh_HISAT_USCS_VOOM_TMM.csv
ICB1299-L807-B


title: S1BKOS1ADS_RNA_1


title: ICB1299_L807mts_A

description:
Singh_HISAT_USCS_VOOM_TMM.csv
ICB1299-L807-A


title: S1BKOS1ADS_RNA_2


title: SU_MB002_TGP_POS_B

description:
Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-TGP-P-B


title: lir35 mutant

first: Takuya

last: Sakaguchi

address: 9500 Euclid Ave.

institute: Cleveland Clinic Foundation

description: Whole body of 20 larvae at 5 dpf.

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Zv9 whole genome using bowtie
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for wt and lri35 mutant larvae

organism: Danio rerio

source_name: Whole body of 20 larvae at 5 dpf

extract_protocol:
Total RNA was isloated by the Rneasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: AB/TL

value: whole body

value: 5 dpf

tag: genotype

value: lir35 mutant


title: SU_MB002_TGP_POS_A

description:
Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-TGP-P-A

tag: tissue


title: S1BKO_ChIP_H3K4me3_1


title: SU_MB002_TGP_POS_C

description:
Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-TGP-P-C


title: SU_MB002_TGP_NEG_C

description:
Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-TGP-N-C


title: WT_ChIP_H3K4me3_1


title: ICB1299_PBS_B

description:
Singh_HISAT_USCS_VOOM_TMM.csv
ICB1299-PBS-B


title: WT siblings

description: Whole body of 20 larvae at 5 dpf.

value: WT


title: ICB1299_PBS_A

description:
Singh_HISAT_USCS_VOOM_TMM.csv
ICB1299-PBS-A


title: ICB1299_L807mts_C

description:
Singh_HISAT_USCS_VOOM_TMM.csv
ICB1299-L807-C


title: SU_MB002_TGP_NEG_A

description:
Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-TGP-N-A


title: S1BKOS1ADS_ChIP_H3K4me3_2


title: S1BKOS1ADS_ChIP_Input_2


title: SU_MB002_L807mts_A

description:
Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-L807-A


title: SU_MB002_PBS_C

description:
Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-PBS-C


title: S1BKOS1ADS_ChIP_Input_1


title: ICB1299_C

description:
Singh_HISAT_USCS_VOOM_TMM.csv
ICB1299-C


title: S1BKO_ChIP_Input_2


title: ICB1299_B

description:
Singh_HISAT_USCS_VOOM_TMM.csv
ICB1299-B


title: S1BKO_ChIP_Input_1


title: SU_MB002_PBS_A

description:
Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-PBS-A


title: WT_ChIP_Input_1


title: SU_MB002_L807mts_C

description:
Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-L807-C


title: SU_MB002_C

description:
Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-C


title: SU_MB002_B

description:
Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-B


title: S1BS1ADSMll1KO_RNA_4


title: S1BKO_ChIP_Pol2_2


title: SU_MB002_PBS_B

description:
Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-PBS-B


title: S1BKO_ChIP_Pol2_1


title: SU_MB002_L807mts_B

description:
Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-L807-B


title: S1BS1ADSMll1KO_RNA_2


title: ICB1299_A

description:
Singh_HISAT_USCS_VOOM_TMM.csv
ICB1299-A


title: S1BS1ADSMll1KO_RNA_3


title: S1BKOS1ADS_ChIP_Pol2_1


title: S1BS1ADSMll1KO_RNA_1


title: SU_MB002_A

description:
Singh_HISAT_USCS_VOOM_TMM.csv
SU-MB002-A


title: BT853_C

description:
Singh_HISAT_USCS_VOOM_TMM.csv
BT853-C

value: Wnt


title: WT_ChIP_Pol2_1


title: BT853_B

description:
Singh_HISAT_USCS_VOOM_TMM.csv
BT853-B


title: S1BKOS1ADSshMll2_ChIP_H3K4me3_1


title: WT_ChIP_Mll2_1

value: Mll2 (Homemade, #9173)


title: BT853_A

description:
Singh_HISAT_USCS_VOOM_TMM.csv
BT853-A


title: H3K36me3 DKO [nfki-1(cer1); ikb-1(nr2070)]

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

data_processing:
ChIPseq data analysis: Illumina pipeline analyzed short reads were uniquely aligned using  the program BOWTIE (version 2)  (Langmead 2009) allowing at most two mismatches against C. elegans genome version WBcel235. Using bedTools (genomecov) we have prepared bedGraph tagdensity from read aligned BAM files.
Genome_build: WBcel235
Supplementary_files_format_and_content: bedgraph

organism: Caenorhabditis elegans

source_name: frozen whole worms

growth_protocol: Worms were synchronized and grown at 25oC on 150 mm plates with OP50 as food source. 40 hours after seeding worms were collected with M9 buffer, harvested and washed until the supernatant appeared clear of bacteria. Worms were then washed with FA buffer (50mM HEPES/KOH pH 7.5, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate and 150mM NaCl) with proteases and phosphatases inhibitors (Roche, Cat. No. 1187350001) and pellet resuspended with twice it volume of FA buffer. Worms were then released into a mortar full of nitrogen in a drop wise manner, to form pearls that would be stored to -80oC prior to grinding.

extract_protocol: CHIPseq libraries were prepared following the protocol from NEBNext Ultra DNA Library Prep kit for Illumina (Ref.:#7370) starting from 10ng of DNA of each sample. And the extraction protocol is the standard using RIPA buffer.

value: H3K36me3 (Abcam, ab9050)

value: whole worms


title: S1BKOS1ADSshNT_ChIP_H3K4me3_1

value: embryonic stem cell


title: WTshNT_ChIP_H3K4me3_1

value: H3K4me3 (Homemade, #519)


title: JMJD5 KO Rep2

value: JMJD5 KO


title: WTshMll2_ChIP_H3K4me3_1

value: Wildtype/WT

value: Mll2 shRNA


title: H3K36me3 ikb-1(nr2070)


title: H3K36me3 nfki-1(cer1)


title: H3K27me3 nfki-1(cer1)

value: H3K27me3 (Millipore #07-449)


title: H3K27me3 ikb-1(nr2070)


title: H3K36me3 WT


title: INPUT ikb-1(nr2070)


title: H3K27me3 DKO [nfki-1(cer1); ikb-1(nr2070)]


title: INPUT nfki-1(cer1)


title: INPUT DKO [nfki-1(cer1); ikb-1(nr2070)]


title: INPUT WT


title: 25 ug/ml DRB-treated A549 cells_1

city: Moscow

first: Dmitri

middle: D

last: Pervouchine

address: Bolshoy Bul'var, 30, str 1

department: Skoltech Center for Molecular and Cellular Biology

country: Russia

institute: Skolkovo Institute of Science and Technology

data_processing:
Alignment with STAR version 2.7.3a at default parameters
Splice junction calling with IPSA pipeline v3.2
Filtering out non-GT/AG splice junctions
PSI computation by IPSA pipeline v3.2 by pooling two bioreplicates
Genome_build: Human genome GRCh37 (hg19), GENCODE annotation v19
Supplementary_files_format_and_content: The change of exon inclusion (deltaPSI) was computed as PSI(treatment) – PSI(control)

source_name: Lung adenocarcinoma

growth_protocol: A549 cell line was maintained in DMEM/F-12 medium containing 10% fetal bovine serum, 50 U/ml penicillin, and 0.05 mg/ml streptomycin (all products from Thermo Fisher Scientific) at 37°C in 5% CO2

extract_protocol:
Total RNA was isolated using PureLink RNA Mini Kit (Thermo Fisher Scientific). Poly(A)+ mRNA was purified using Dynabeads Oligo(dT) 25 (Thermo Fisher Scientific) following the manufacturer’s instructions
Illumina cDNA libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England BioLabs) following the manufacturer’s protocol with the only modification - the change of fragmentation time from 15 to 10 minutes. cDNA libraries were sequenced using the NextSeq500 (Illumina, San Diego, CA USA) instrument; 33–41 million raw reads were obtained for each sample with a 75 bp read length.

treatment_protocol: Alpha-amanitin (Sigma) treatments 1 and 2 μg/mL of α-amanitin was added to cells at 50-70% confluency. After 24h of treatment, cells were harvested

value: 25 ug/ml DRB

tag: replicate


title: 1 ug/ml a-amanitin-treated A549 cells_2

value: 1 ug/ml a-amanitin


title: 1 ug/ml a-amanitin-treated A549 cells_1


title: DMSO-treated A549 cells_1

value: DMSO


title: 2 ug/ml a-amanitin-treated A549 cells_1

value: 2 ug/ml a-amanitin


title: 10 ug/ml DRB-treated A549 cells_2

value: 10 ug/ml DRB


title: 25 ug/ml DRB-treated A549 cells_2


title: H3K27me3 WT


title: AS-109692-LR-16203

city: Heidelberg

first: Konstantin

last: Okonechnikov

state: Germany

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center

data_processing:
Reads were aligned to mm10 reference using STAR 2.4.1d
Gene expression counts were computed with htseq-count tool 0.6.1
Quality control was performed with Qualimap v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: gene expression raw counts

source_name: Granule precursor cells P7

extract_protocol:
The cells were prepared from P7 cerebella using percoll density gradient centrifugation
Cells were captured the using the C1 Fluidigm systems with 96-well chips. The total RNAs were extracted from single sorted cells and the library was prepared for for Illumina sequencing

value: brain


title: 2 ug/ml a-amanitin-treated A549 cells_2


title: AS-109690-LR-16203


title: AS-109688-LR-16203


title: AS-109686-LR-16203


title: DMSO-treated A549 cells_2


title: AS-109684-LR-16203


title: 10 ug/ml DRB-treated A549 cells_1


title: AS-109682-LR-16203


title: AS-109680-LR-16203


title: AS-109678-LR-16203


title: AS-109676-LR-16203


title: AS-109672-LR-16203


title: AS-109670-LR-16203


title: AS-109674-LR-16203


title: AS-109668-LR-16203


title: AS-109666-LR-16203


title: PLS-DMII-NPDR-rep1

type: other

city: Davis

first: Zeljka

last: Smit-McBride

address: One Shields Ave, Tupper Hall #2403

department: Ophthalmology & Vision Science

institute: University of California, Davis Eye Center

hyb_protocol: Standard Affymetrix labeling protocol

scan_protocol: Standard Affymetrix labeling protocol

data_processing: The data sets in .cel files were analyzed with the Expression Console and Transcriptome Analysis Console (Affymetrix, Santa Clara).  The analysis was done separately for each sample of ocular fluid and plasma.  After importing .cel and .arr files, RMA-DABG summarization algorithm was applied using Expression Console with applied “only Homo sapiens” default data analysis settings.

label: biotin

molecule: other

source_name: PLS-DMII-NPDR

label_protocol: Probe labeling was done from 10 ng of aqueous, 20ng of vitreous and 20ng of plasma miRNA samples using FlashTag (Affymetrix) procedure.

extract_protocol: RNA was isolated using Exiqons’ modification of Qiagen’s microRNeasy kit. Quantification and quality check of isolated miRNA was performed on BioAnalyzer (Agilent) with Small RNA microfluidics Chips.

tag: disease state

value: DM Type II with nonproliferative diabetic retinopathy

value: Plasma


title: AS-109662-LR-16203


title: AS-109660-LR-16203


title: AS-109657-LR-16202


title: PLS-DMII-PDR-rep5

source_name: PLS-DMII-PDR

value: DM-Type II with proliferative diabetic retinopathy


title: PLS-DMII-NPDR-rep2


title: PLS-DMII-PDR-rep3


title: PLS-DMII-PDR-rep4


title: AS-109655-LR-16202


title: PLS-DMII-NPDR-rep4


title: PLS-DMII-PDR-rep1


title: PLS-DMII-PDR-rep6


title: PLS-DMI-PDR-rep2

source_name: PLS-DMI-PDR

value: DM-Type I with proliferative diabetic retinopathy


title: PLS-DMI-PDR-rep5


title: PLS-DMI-PDR-rep4


title: PLS-DMI-PDR-rep1


title: PLS-CON-rep10

source_name: PLS-CON

value: control


title: PLS-CON-rep9


title: PLS-CON-rep8


title: PLS-DMII-PDR-rep2


title: AS-109651-LR-16202


title: PLS-DMI-PDR-rep3


title: PLS-CON-rep7


title: AS-109664-LR-16203


title: AS-109653-LR-16202


title: AS-109649-LR-16202


title: PLS-CON-rep6


title: PLS-CON-rep5


title: AS-109647-LR-16202


title: AS-109645-LR-16202


title: AS-109643-LR-16202


title: AS-109641-LR-16202


title: AS-109639-LR-16202


title: PLS-CON-rep4


title: PLS-CON-rep3


title: AS-109637-LR-16202


title: AS-109633-LR-16202


title: AS-109635-LR-16202


title: AS-109629-LR-16202


title: AS-109631-LR-16202


title: AS-109625-LR-16202


title: PLS-CON-rep1


title: AS-109627-LR-16202


title: VIT-DMII-NPDR-rep3

source_name: VIT-NDMII-PDR

value: Vitreous


title: AS-109623-LR-16202


title: AS-109620-LR-16314


title: AS-109618-LR-16314


title: PLS-CON-rep2


title: AS-109616-LR-16314


title: AS-109614-LR-16314


title: AS-109612-LR-16314


title: VIT-DMII-NPDR-rep1


title: VIT-DMII-PDR-rep3

source_name: VIT-DMII-PDR

value: DM Type II with proliferative diabetic retinopathy


title: AS-109694-LR-16203


title: AS-109606-LR-16314


title: VIT-DMII-PDR-rep5


title: VIT-DMII-PDR-rep2


title: VIT-DMII-PDR-rep4


title: AS-109608-LR-16314


title: AS-109610-LR-16314


title: VIT-DMI-PDR-rep4

source_name: VIT-DMI-PDR


title: VIT-DMII-PDR-rep1


title: VIT-DMII-NPDR-rep4


title: VIT-DMII-NPDR-rep2


title: VIT-DMI-PDR-rep2


title: VIT-DMI-PDR-rep1


title: VIT-DMII-PDR-rep6


title: VIT-DMI-PDR-rep3


title: AS-109600-LR-16314


title: VIT-CON-rep10

source_name: VIT-CON


title: AS-109596-LR-16314


title: VIT-CON-rep8


title: VIT-CON-rep6


title: VIT-CON-rep7


title: AS-109594-LR-16314


title: VIT-CON-rep5


title: AS-109592-LR-16314


title: VIT-CON-rep4


title: VIT-CON-rep9


title: VIT-CON-rep3


title: AS-109590-LR-16314


title: AS-109602-LR-16314


title: AS-109588-LR-16314


title: AS-109586-LR-16314


title: AS-109598-LR-16314


title: AQC-DMII-NPDR-rep4

source_name: AQC-DMII-NPDR

value: Aqueous


title: AQC-DMII-NPDR-rep3


title: AS-109583-LR-16313


title: AS-109581-LR-16313


title: AS-109577-LR-16313


title: AQC-DMII-NPDR-rep1


title: AQC-DMII-PDR-rep6

source_name: AQC-DMII-PDR


title: VIT-CON-rep1


title: AQC-DMII-PDR-rep5


title: AS-109579-LR-16313


title: AQC-DMII-PDR-rep3


title: AQC-DMII-PDR-rep4


title: AQC-DMII-NPDR-rep2


title: AQC-DMI-PDR-rep4

source_name: AQC-DMI-PDR


title: AS-109573-LR-16313


title: AQC-DMII-PDR-rep1


title: VIT-CON-rep2


title: B16F10 Plumbagin-treated 2

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array (430 2.0 ). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009).
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files ).
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HT_MG-430_PM
program-name = Expression Console
program-version = 1.4.1.46
program-company = Affymetrix

source_name: B16F10 treated with plumbagin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: The B16F10 cells were used for this experiement

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added and the cell suspensions were centrifuged for 5 minutes at 500 g and the pellet was stored at -80°C until use.

treatment_protocol: The cells were treated with 0 and 2 µM plumbagin for 24 h

value: plumbagin for 24hrs


title: AQC-DMI-PDR-rep1


title: AQC-DMI-PDR-rep3


title: AQC-DMI-PDR-rep2


title: PLS-DMII-NPDR-rep3


title: AQC-CON-rep10

source_name: AQC-CON


title: B16F10 Plumbagin-treated 1


title: B16F10 untreated control 2

source_name: B16F10 treated with MilliQ

value: MilliQ


title: AQC-DMII-PDR-rep2


title: HH-Sq2_IN+ HH-Sq-treated

city: Tsukuba

first: Munkhzul

last: Ganbold

state: Ibaraki Prefecture

institute: AIST-University of Tsukuba Open Innovation Laboratory for Food and Medicinal Resource Engineering (FoodMed-OIL)

description:
Gene expression data from adipocyte-induced dADSC treated with HH-Sq at D14
HH-Sq2

hyb_protocol: Following fragmentation, 9.4 µg of cRNA were hybridized for 16 hr at 45°C on GeneChip Human Genome Array (HG-U219). GeneChip was washed and stained in the Gene Atlas Fluidics Station

scan_protocol: GeneChip was scanned three times for technical replicates using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out by Transcriptome Analysis Console (TAC) v4.0 (Affymetrix, Japan).
Expression console signal intensity. For calculating average value, fold change, and Anova p-value of signal intensity of replicates, we used Transcriptome Analysis Console (TAC) v4.0 (Affymetrix, Japan).  Algorithm: RMA

source_name: IN + HH-Sq treated, technical rep-2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA

growth_protocol: ADSCs from a donor with T2D (dADSCs) was purchased from Lonza (Walkersville, MD). dADSCs were isolated from donated tissue of 74-year old Caucasian female (BMI = 25, Donor 29752) lipoaspirates collected during elective surgical liposuction procedures, after obtaining permission by informed consent. Cells were cultured in ADSC growth medium (ADSC-GM BulletKit™) obtained from Lonza (Walkersville, MD) containing ADSC basal medium supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, and gentamicin-amphotericin B (GA-1000) according to the manufacturer’s instruction at 37°C in 5% CO2 humidified incubator. Cells are subcultured 5000 cells per cm2 as recommended by the provider.

extract_protocol: Total RNA was extracted at the D14 after adipocyte differentiation using Isogen (Nippon Gene Co. Ltd., Toyama, Japan). The total RNA was resuspended in Tris-EDTA and stocked at -80°C until use.

treatment_protocol: Human adipose-derived stem cells from type 2 diabetics (dADSC) obtained from Lonza (Walkersville, MD) were induced adipocyte differentiation using adipocyte differentiation medium (PGM™-2 Bulletkit, Lonza, Walkersville, MD) for 14 days without any treatment as control (IN), treated with 1 µM of Squalene (Sq), and treated with 1 µM of Squalene derivative (HH-Sq).

value: Adipose-derived stem cells after adipocyte differentiation

value: donor diagnosed with T2D


title: AS-109571-LR-16313


title: AS-109575-LR-16313


title: AQC-CON-rep7


title: AQC-CON-rep8


title: B16F10 untreated control 1


title: AQC-CON-rep9


title: HH-Sq3_IN+ HH-Sq-treated

description:
Gene expression data from adipocyte-induced dADSC treated with HH-Sq at D14
HH-Sq3

source_name: IN + HH-Sq treated, technical rep-3


title: AQC-CON-rep6


title: AS-109567-LR-16313

source_name: Granule precursor cells P7


title: AS-109565-LR-16313


title: AQC-CON-rep5


title: AQC-CON-rep2


title: AS-109563-LR-16313


title: 7393

city: Brussels

first: Grégoire

last: de Streel

state: Woluwe-Saint-Lambert

address: 75 Avenue Hippocrate

department: de Duve Institute

country: Belgium

institute: UCLOUVAIN

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to the human reference genome using Hisat2 version 2.0.5 with parameters  -p 20 --dta -t --un-conc
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using stringtie version 1.3.3
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample

source_name: Skin

extract_protocol:
Fragments of surgically resected or biopsied tumors were snap frozen on dry ice, and RNA was harvested using GITC and CsCl-gradient separation.
Illumina TruSeq RNA Sample Prep Kit  was used with poly-A RNA purified from 1 ug of total RNA for the construction of cDNA sequencing libraries.

value: Cutaneous melanoma metastasis

value: melanoma of the eye

tag: gender

value: F

tag: cell line

value: Not Known


title: AQC-CON-rep4


title: 7102

value: melanoma of the skin

value: M


title: AS-109604-LR-16314

value: brain


title: 7090


title: AQC-CON-rep1


title: AS-109561-LR-16313


title: Sq3_IN+ Sq-treated

description:
Gene expression data from adipocyte-induced dADSC treated with Sq at D14
Sq3

source_name: IN + Sq treated, technical rep-3


title: 7130


title: AS-109559-LR-16313


title: AS-109569-LR-16313


title: 7316


title: 7074


title: AQC-CON-rep3


title: 7387

value: surgery, vemurafenib, ipilimumab


title: S1BS1ADSMll1KO_ChIP_H3K4me3_2

source_name: embryonic stem cell

value: embryonic stem cell

value: H3K4me3 (Homemade, #519)


title: Sq2_IN+ Sq-treated

description:
Gene expression data from adipocyte-induced dADSC treated with Sq at D14
Sq2

source_name: IN + Sq treated, technical rep-2


title: Sq1_IN+ Sq-treated

description:
Gene expression data from adipocyte-induced dADSC treated with Sq at D14
Sq1

source_name: IN + Sq treated, technical rep-1


title: IN3_Adipocyte-induced control

description:
Gene expression data from adipocyte-induced dADSC at D14
IN3

source_name: Adipocyte-induced control, technical rep-3


title: P0 tooth

city: SENDAI

first: Kan

last: Saito

state: Miyagi

address: 4-1 Seiryo-machi

department: Oral Health and Development Sciences

institute: Tohoku University

description: Gene expression of tooth

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Fragmentation Buffer and 10x Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE Microarray 8 x 60K(G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner(G2505C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: P0 WT tooth

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit

value: tooth


title: P0 skin

description: Gene expression of skin

source_name: P0 WT skin

value: skin


title: AS-109557-LR-16313


title: AS-109555-LR-16313


title: IN1_Adipocyte-induced control

description:
Gene expression data from adipocyte-induced dADSC at D14
IN1

source_name: Adipocyte-induced control, technical rep-1


title: HH-Sq1_IN+ HH-Sq-treated

description:
Gene expression data from adipocyte-induced dADSC treated with HH-Sq at D14
HH-Sq1

source_name: IN + HH-Sq treated, technical rep-1


title: 7132


title: 7067


title: AS-109553-LR-16313


title: 7149


title: S1BS1ADSMll2DS_ChIP_H3K4me3_2


title: 7123


title: AS-109551-LR-16313


title: IN2_Adipocyte-induced control

description:
Gene expression data from adipocyte-induced dADSC at D14
IN2

source_name: Adipocyte-induced control, technical rep-2


title: 7101


title: Mll2DS_ChIP_H3K4me3_2


title: 7270


title: Mll1KO_ChIP_H3K4me3_2


title: AS-109549-LR-16313


title: 7124


title: S1BKOS1ADS_ChIP_H3K4me3_4


title: AS-109546-LR-16312


title: 7105


title: 7300


title: 7220


title: WT_ChIP_H3K4me3_3

value: Wildtype/WT


title: WT_ChIP_H3K4me3_4


title: AS-109542-LR-16312


title: 7057


title: T357-2

city: Wuhan

first: xiao

last: wang

address: No.1 Shizishan street, Hongshan district, Wuhan City, Hubei Province

institute: Huazhong Agricutural University

description: rRNA-depleted RNA

data_processing:
Data filtered of the raw data  using FASTX-Toolkit tools(version 0.0.13.2) and tested the results using FastQC(version0.10.1).
Read mapped to the published genome of Prunus persica (verde et al 2013) using Bowtie2(version 2.1.0) and TopHat(version 2.0.10), Samtools(version 0.1.18),.
Fragments Per Kilobase of exon per  Million Fragments Mapped(FPKM) were calculated using a series of Cufflinks software(version 2.1.1).
Genome_build: Prunus_persica_NCBIv2
Supplementary_files_format_and_content: csv files include FPKM values for each Sample ...

organism: Prunus persica

source_name: flesh cells

extract_protocol:
Extract total RNA from each sample,then use Ribo-Zero Magnetic Kit to delete rRNA.
RNA libraries were prepared using Directional RNA Library Prep Kit for Illumina. Libraries were sequenced on Illumina HiSeq 2500.

treatment_protocol: Postharvest peach fruit were pre-stored on 5℃ for 2 d, and divided into two random groups under 2 different temperatures of 25℃, 35℃

tag: stored temperature(℃）

tag: stored times(day)

value: flesh cells


title: AS-109540-LR-16312

tag: strain


title: AS-109538-LR-16312

tag: age


title: T357-1

description: rRNA-depleted RNA


title: T356-1

description: rRNA-depleted RNA


title: T355-2

description: rRNA-depleted RNA


title: AS-109536-LR-16312


title: WT Sample_17

city: Munich

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

department: Research Unit Apoptosis in Hematopoietic Stem Cells

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to the concatenated Human (hg38) and Mouse (mm10) Genome with STAR 2.6.0a
Quantification was done with ENSEMBL gene models (GRCh38.84/GRCm38.75)
Genome_build: Human: hg38, Ensembl 84; Mouse: mm10, Ensembl 75
Supplementary_files_format_and_content: sample (columns) and gene (rows) -wise UMI expression table

source_name: WT Sample_17

growth_protocol: ALL-265 PDX cells transgenic for rtTA3 and tet-R and either mock-, wtKLF4 or mutKLF4 Dox-inducible vectors and injected into mice. Tumor growth was monitored by in vivo imaging. When mice displayed signs of overt leukemia, Dox was added to the drinking water of mice and mice were euthanized 3 days later. PDX cells were re-isolated from spleens and mock-, wtKLF4 and mutKLF4-expressing cells sorted based on subpopulation-specific fluorochromes.

extract_protocol:
ALL PDX cells were re-isolated from murine spleen using a mortar and pistil, washed twice in PBS. PDX cells were sorted for mTagBFP, mCherry and according to the subpopulation-specific fluorochromes T-Sapphire for the mock subpopulation and iRFP720 for either the mutKLF4 or wtKLF4 subpopulation.
Libraries were constructed using a bulk adjusted SCRB-seq protocol.

treatment_protocol: Tumor-bearing mice received Doxycycline in their drinking water to induce transgene expression from day 18 onwards

tag: treatment

value: wt


title: WT Sample_18

source_name: WT Sample_18


title: AS-109532-LR-16312


title: WT Sample_16

source_name: WT Sample_16


title: WT_ChIP_Input_2

tag: cell type


title: 7148


title: WT Sample_14

source_name: WT Sample_14


title: AS-109544-LR-16312

source_name: Granule precursor cells P7


title: WT Sample_15

source_name: WT Sample_15


title: T353-2

description: rRNA-depleted RNA


title: T355-1

description: rRNA-depleted RNA


title: Donor 4 Vehicle 4h

city: London

first: Joseph

middle: J

last: Boyle

address: Du Cane Rd

department: NHLI

country: United Kingdom

institute: Imperial College London

hyb_protocol: Manufacturers recommended

scan_protocol: Manufacturers recommended

data_processing: Manufacturers recommended

source_name: Stratagene human reference RNA

label_protocol: Agilent 4x44k

growth_protocol: 10% autologous serum Iscove's Modified Eagle's Medium; for 24h from isolation. Isolated from 45mL blood, aseptically collected, purified by Histopaque 1077 followed by washing and adherence to culture plastic for 2h; represents CD14+CD16-, CD14-CD16+ and CD14+CD16+ subpopulations.

extract_protocol: Qiagen RLT buffer

treatment_protocol: Metfromin 10uM (10-5 mol/L) (10 micromolar) diluted from 1mM stock in PBS, from Sigma-Aldrich (D150959-5G), filter-sterilised,

value: Stratagene human reference RNA

source_name: Donor 4 human monocyte-derived macrophages, vehicle -treated, 4h

value: adult

value: male

value: peripheral blood


title: AS-109530-LR-16312


title: Donor 4 Metformin 4h

source_name: Donor 4 human monocyte-derived macrophages, metformin-treated, 4h


title: WT Sample_13

source_name: WT Sample_13


title: Donor 3 Metformin 4h

source_name: Donor 3 human monocyte-derived macrophages, metformin-treated, 4h


title: T353-1

description: rRNA-depleted RNA


title: WT Sample_12

source_name: WT Sample_12


title: Donor 3 Vehicle 4h

source_name: Donor 3 human monocyte-derived macrophages, vehicle -treated, 4h


title: AS-109528-LR-16312


title: Donor 2 Vehicle 4h

source_name: Donor 2 human monocyte-derived macrophages, vehicle -treated, 4h


title: NSrp70 Conditional KO CD69+ DP thymocytes

city: Gwangju

first: Chang-Hyun

last: Kim

address: 123, Cheomdangwagi-ro, Buk-gu

department: School of Life Sciences

country: South Korea

institute: Gwangju Institute of Science and Technology (GIST)

data_processing:
HCS 2.2.70 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSC mm 10 whole genome using HISAT2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using StringTie program. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM and TMM values for each Sample.

source_name: thymocytes

extract_protocol:
Thymocytes were purified from the mouse thymus. Total RNA was harvested using Trizol reagent from sorted CD69+ thymocytes.
TruSeq RNA Sample Prep Kit v2 (Part # 15026495 Rev. F Sequencing) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: strain/background

value: NSRP1f/fCD4Cre (NSrp70 conditional KO)

value: CD69+ DP thymocytes

value: 6 weeks


title: Donor 2 Metformin 4h

source_name: Donor 2 human monocyte-derived macrophages, metformin-treated, 4h


title: T351-2

description: rRNA-depleted RNA

source_name: flesh cells


title: Donor 1 Metformin 4h

source_name: Donor 1 human monocyte-derived macrophages, metformin-treated, 4h


title: Donor 1 Vehicle 4h

source_name: Donor 1 human monocyte-derived macrophages, vehicle -treated, 4h


title: AS-109534-LR-16312


title: AS-109526-LR-16312


title: WT CD69+ DP thymocytes

value: NSRP1f/f (wild type)


title: T257-1

description: rRNA-depleted RNA


title: AS-109524-LR-16312

value: brain


title: AS-109522-LR-16312


title: T253-2

description: rRNA-depleted RNA


title: T356-2

description: rRNA-depleted RNA


title: T352-1

description: rRNA-depleted RNA


title: T352-2

description: rRNA-depleted RNA


title: WT Sample_9

source_name: WT Sample_9


title: WT Sample_7

source_name: WT Sample_7


title: AS-109520-LR-16312

source_name: Granule precursor cells P7


title: WT Sample_10

source_name: WT Sample_10


title: WT Sample_11

source_name: WT Sample_11


title: AS-109518-LR-16312


title: WT Sample_8

source_name: WT Sample_8


title: wild type WT 2

city: Albuquerque

first: Nora

last: Perrone-Bizzozero

address: 1 University of New Mexico MSC08 4740

department: Neurosciences

institute: University of New Mexico

description: circRNAs

data_processing: A series of data processing including quantile normalization were performed using the R software limma package.

source_name: striatum

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: Trizol

treatment_protocol: HuD-OE vs Wild type littermates

value: WT

tag: Sex


title: Mock Sample_6

source_name: Mock Sample_6

value: mock


title: wild type WT 3

description: circRNAs


title: AS-109516-LR-16312


title: T257-2

description: rRNA-depleted RNA


title: Mock Sample_5

source_name: Mock Sample_5


title: wild type WT 1

description: circRNAs


title: T351-1

description: rRNA-depleted RNA


title: AS-109514-LR-16312


title: AS-109512-LR-16312


title: HuD_OE_3

description: circRNAs

value: HuD OE


title: Mock Sample_4

source_name: Mock Sample_4


title: T256-1

description: rRNA-depleted RNA


title: HuD_OE_2

description: circRNAs


title: Mock Sample_3

source_name: Mock Sample_3


title: AS-109509-LR-16311


title: Mock Sample_2

source_name: Mock Sample_2


title: T255-2

description: rRNA-depleted RNA


title: T255-1

description: rRNA-depleted RNA


title: AS-109507-LR-16311


title: T253-1

description: rRNA-depleted RNA


title: AS-109505-LR-16311


title: Mock Sample_1

source_name: Mock Sample_1


title: AS-109503-LR-16311


title: T252-2

description: rRNA-depleted RNA


title: HuD_OE_1

description: circRNAs


title: T256-2

description: rRNA-depleted RNA


title: T252-1

description: rRNA-depleted RNA


title: AS-109501-LR-16311


title: High Altitude Day 21 (4,111m, Kyrgyz) Sample 20

city: North Delhi

first: PRIYA

last: GAUR

state: Delhi

address: DIPAS, DRDO, Lucknow Road, Timarpur, (Near vishwavidyalaya metro station),Delhi

country: India

institute: Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization

data_processing:
Homo sapiens HG19 genome as reference and use STAR RNA aligner for mapping the QC passed reads (trim_galore) onto the reference genome
After removing the PCR and optical duplicate reads from the alignment using picardtools the read counts for the genes were extracted using featureCounts software
edgeR, a R package for performing differential expression analysis tests with the normalized expression counts.
Genes with absolute log2FoldChange ≥±0.58 and multiple test adjusted pvalue < 0.05 will be considered as statistically significant
Followed by enrichment analysis of Gene Ontology and KEGG pathways terms for the significantly differentially expressed genes.
Genome_build: HG19
Supplementary_files_format_and_content: Read counts at gene level in tab delimited text file

source_name: Whole Blood

extract_protocol:
Venous blood samples from individuals at basal and at different altitude time points was collected in PAX gene Blood RNA Tubes (PAXgene, PreAnalytix, Hombrehtikon, Switzerland, distributed by Qiagen, catalogue no. 762165). PAX contains 6.5 ml of RNA stabilizing solution in which 2.5 ml of whole blood is added using a blood collection accessory at room temperature. After blood collection, PAX tube was inverted 8-10 times, were kept upright at room temperature (18-25°C) for 2 hours than transferred to freezer (-20°C) for 24 hours and finally stored at -80°C. Isolation of total cellular RNA was done using PAX gene blood RNA Kit (PreAnalytix) as per manufacturer’s protocol. DNase digestion was carried out for the removal of DNA using RNase free DNase set (Qiagen) on the RNA spin column. Purified RNA was immediately chilled on ice. RNA concentration and quality was evaluated by measuring absorbance at 260 and 280 nm using a spectrophotometer (NanoDrop, USA) before being stored at -80°C.
RNA libraries were prepared for sequencing using NEB Next RNA II library preperation kit for Illumina protocol

treatment_protocol: Study started at basal (≤800 m) at Bishkek, Kyrgyzstan and sample was collected. Subjects were inducted by road to ~ 3000m for acclimatization. After that, subjects were moved to 4,111m by road where they stayed for 21 days and throughout the altitude stay temporal analysis was performed at high altitude 3rd day, 7th day, 14th day, and 21st day and sample were collected

value: Whole blood


title: High Altitude Day 21 (4,111m, Kyrgyz) Sample 19


title: High Altitude day 21 (4,111m, Indian) Sample 18


title: wild type WT_3

description: circRNAs

treatment_protocol: HuD KO (Elavl4 -/-) vs Wild type littermates


title: AS-109499-LR-16311


title: wild type WT_2

description: circRNAs


title: T251-2

description: rRNA-depleted RNA

source_name: flesh cells


title: AS-109497-LR-16311


title: High Altitude day 21 (4,111m, Indian) Sample 17


title: T251-1

description: rRNA-depleted RNA


title: wild type WT_1

description: circRNAs


title: HuD_KO_3

description: circRNAs

value: HuD KO


title: High Altitude Day 14 (4,111m, Kyrgyz) Sample 16


title: AS-109495-LR-16311


title: High Altitude Day 14 (4,111m, Kyrgyz) Sample 15


title: AS-109493-LR-16311


title: HuD_KO_1

description: circRNAs


title: A549 siSNRPD3_rep2

city: Amsterdam

first: Victor

middle: W

last: van Beusechem

address: De Boelelaan 1117

department: Medical Oncology

country: Netherlands

institute: Amsterdam UMC

description:
A549 NSCLC cells treated with siRNA targeting SNRPD3
SNRPD3_DE.csv
siSNRPD3_A3SS.MATS.JunctionCountOnly.txt
siSNRPD3_A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
siSNRPD3_A5SS.MATS.JunctionCountOnly.txt
siSNRPD3_A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
siSNRPD3_MXE.MATS.JunctionCountOnly.txt
siSNRPD3_MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
siSNRPD3_RI.MATS.JunctionCountOnly.txt
siSNRPD3_RI.MATS.ReadsOnTargetAndJunctionCounts.txt
siSNRPD3_SE.MATS.JunctionCountOnly.txt
siSNRPD3_SE.MATS.ReadsOnTargetAndJunctionCounts.txt

data_processing:
Raw reads were first subjected to a quality control using FastQC version 0.11.4 with default settings and visualized with MultiQC version 0.9 with default parameters.
Adapters were trimmed, reads were processed to 120 nt and mapped to the human genome (USCS RefSeq hg19 annotation) using STAR 2.5.0
Differential expression was analyzed using DESeq2 version 1.10
Alternative splicing was detected using the rMATS algorithm version 3.2.5
Genome_build: USCS RefSeq hg19 annotation
Supplementary_files_format_and_content: CSV files contain the results of the differential expression analyses. Headers include "BaseMean", "log2FoldChange",  "lfcSE", "pvalue" and "padj"
Supplementary_files_format_and_content: Text files contain the results of alternative splicing analyses; alternative 3' or 5' splice site usage (A3SS and A5SS), mutually exclusive exons (MXE), retained introns (RI) and skipped exons (SE). Headers include "ID", "GeneID", "geneSymbol", "chr" (location on the chromosome), "strand", "exonStart_0base" (location of the alternatively spliced exon), "exonEnd" (location of the alternatively spliced exon), "upstreamES" (location of the upstream exon on the chromosome), "upstreamEE" (location of the upstream exon on the chromosome), "downstreamES" (location of the downstream exon on the chromosome), "downstreamEE" (location of the downstream exon on the chromosome), "IC_SAMPLE_1" (inclusion counts sample 1 siNT), "SC_SAMPLE_1" (skipping counts sample 1 siNT), "IC_SAMPLE_2" (skipping counts sample 2 siRNA), "SC_SAMPLE_2" (skipping counts sample 2 siRNA), "IncFormLen" (length of the product with alternatively spliced exon included), "SkipForLen" (length of the product with alternatively spliced exon excluded), "PValue", "FDR", "IncLevel1" (inclusion level sample 1 siNT), "IncLevel2" (inclusion level sample 2 siRNA), "IncLevelDifference" (difference between inclusion level sample 1 minus inclusion level sample 2)

source_name: A549 NSCLC cells

growth_protocol: A549 NSCLC cells were maintained in DMEM + 10%FCS and 1%pen-strep and subcultured every 48 hours.

extract_protocol:
Total RNA was extracted from A549 NSCLC cells using the miRNeasy Mini Kit from Qiagen.
Sequencing libraries were prepared using the TruSeq Stranded mRNA Sample Preparation kit from Illumina.
125 bases paired end RNA-seq on the Illumina HiSeq V4 2500.

treatment_protocol: Antibiotics were omitted from culture medium and cells were seeded 24 hours prior to transfection. A549 NSCLC cells were transfected with 25nM siRNA and 0.05% DharmaFECT1. A549 NSCLC cells were harvested after 72 hours.

value: lung

value: epithelial

tag: condition

value: Carcinoma


title: High altitude Day 14 (4,111m, Indian) Sample 14


title: A549 siSNRPD3_rep1


title: AS-109491-LR-16311


title: AS-109489-LR-16311


title: A549 siSF3B1_rep2

description:
A549 NSCLC cells treated with siRNA targeting SF3B1
SF3B1_DE.csv
siSF3B1_A3SS.MATS.JunctionCountOnly.txt
siSF3B1_A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt
siSF3B1_A5SS.MATS.JunctionCountOnly.txt
siSF3B1_A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt
siSF3B1_MXE.MATS.JunctionCountOnly.txt
siSF3B1_MXE.MATS.ReadsOnTargetAndJunctionCounts.txt
siSF3B1_RI.MATS.JunctionCountOnly.txt
siSF3B1_RI.MATS.ReadsOnTargetAndJunctionCounts.txt
siSF3B1_SE.MATS.JunctionCountOnly.txt
siSF3B1_SE.MATS.ReadsOnTargetAndJunctionCounts.txt


title: High altitude Day 14 (4,111m, Indian) Sample 13


title: High altitude Day 7 (4,111m, Kyrgyz) Sample 12


title: AS-109487-LR-16311


title: A549 siSF3B1_rep1


title: A549 siNT_rep2

description: A549 NSCLC cells treated with non-targeting siRNA


title: High altitude Day 7 (4,111m, Kyrgyz) Sample 11


title: A549 siNT_rep1


title: AS-109485-LR-16311


title: High altitude Day 7 (4,111m, Indian) Sample 10


title: AS-109483-LR-16311


title: HuD_KO_2

description: circRNAs


title: 10-2 114 h (2-5)

city: Guiyang

first: wu

last: liangtao

address: huaxi district

institute: Guizhou University

data_processing:
Torrent Suite software used for basecalling.
Mapping of single-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent of bases with qualities of <13. The clean reads were then aligned to duck genome (version:BGI_duck_1.0) using the MapSplice program (v2.2.0). In alignment, preliminary experiments were performed to optimize the alignment parameters (-s 22 -p 12 --ins 6 --del 6 --non-canonical) to provide the largest information on the AS events.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EB-Seq aligorithm from Leng et al., Bayes hierarchical model, 2013. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: BGI_duck_1.0
Supplementary_files_format_and_content: count and RPKM

organism: Anas platyrhynchos

source_name: Spleen

growth_protocol: 70 9-day old ducks , provided from duck breeds of Sansui County of Guizhou province,China, serological and etiological detection showed clinical health, were divided into 3 groups in the special biological safety cabinet. Feed full price of feed, three times a day.

extract_protocol:
Ion Total RNA-Seq Kit v2.0 (Life Technologies)
RNA libraries were prepared for sequencing using standard Ion Proton protocols

treatment_protocol: For 50-day old, the ducks of experimental groups were injected with different titers of DEV and control group was injected with normal saline by leg muscles, collected spleen for 66 hours, 90 hours and 114 hours, respectively.

tag: agent

value: 10-2 titer two different viral titers of DEV

value: spleen

value: post natal day 50

tag: time point


title: [Sample_6, Control]

description: circRNAs

source_name: nucleus accumbens

treatment_protocol: cocaine conditioned place preference (CPP)

value: control

value: male


title: [Sample_4, CPP]

description: circRNAs

value: cocaine conditioned


title: High altitude Day 7 (4,111m, Indian) Sample 9


title: [Sample_1, Control]

description: circRNAs


title: [Sample_3, CPP]

description: circRNAs


title: [Sample_5, Control]

description: circRNAs


title: 10-2 90 h (2-4)


title: AS-109481-LR-16311


title: 10-2 66 h (2-2)


title: High altitude Day 3 (4,111m, Kyrgyz) Sample 8


title: AS-109479-LR-16311


title: 100 114 h (1-5)

value: 100 titer (The TCID50 of DEV was 10-9/0.1mL)


title: High altitude Day 3 (4,111m, Kyrgyz) Sample 7


title: 22Rv1_DHT_siAR

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
We used Trimmomatic-033 to trim and crop of Illumina (fastq) data by removing the sequences of adapters.
To remove rRNA sequence, we used bowtie 2 version 2.2.6. Mapping to human genome (hg19) was performed using tophat 2.1.0.
Generate alignments in the SAM format from BAM given single-end reads. The reads were mapped to the human RefSeq mRNA database for RIP-seq data.
The expression levels of mapped transcripts were normalized into Reads Per Kilobase of exon per Million mapped reads (RPKM) to facilitate comparison among different samples.
Genome_build: hg19
Supplementary_files_format_and_content: Summary of RPKM for RefSeq genes

source_name: prostate cancer cells

growth_protocol: CRPC model 22Rv1 cells were cultured in RPMI 1640 medium supplemented with 10 % fetal bovine serum (FBS). For androgen treatment, cells were cultured in androgen-depleted medium (phenol red free RPMI 1640 medium supplemented with 2.5 % charcol stripped FBS) for 3 days.

extract_protocol:
Total RNA was extracted by ISOGEN (Nippon gene, Tokyo, Japan)
SureSelect RNAXT RNA Target Enrichment for Illumina Multiplexed Sequencing (Agilent) was used for library construction according to the manufacturer's protocol.

treatment_protocol: Then cells were treated with 10 nM DHT or vehicle for 24 h. To reduce the expression of AR, we treated cells with 10 nM siRNA targeting AR (siAR) fro 48 h. We treated other cells with sicontrol. We treated cell with ribavirin 10 µM for 48 h before androgen treatment.

value: 22Rv1 cells

value: DHT 10 nM treatment

tag: sirna

value: siAR


title: AS-109477-LR-16311

source_name: Granule precursor cells P7

tag: tissue

value: brain


title: 22Rv1_Et_siAR

value: ethanol (Vehicle) treatment


title: Basal (≤ 800m, Kyrgyz) Sample 4

value: Whole blood


title: AS-109475-LR-16311


title: 22Rv1_DHT_Ct

value: Control


title: 100 90 h (1-3)


title: 22Rv1_DHT_R

value: R


title: 100 66 h (1-2)


title: 22Rv1_Et_Ct


title: AS-109473-LR-16311


title: seronegative control(0-2)

value: seronegative control(0-2)


title: 22Rv1_Et_R


title: Basal (≤ 800m, Kyrgyz) Sample 3


title: C6 FSHD + 1uM pamapimod_112917_FTEV-008_LL5023_S8

status: Public on Jun 26 2020

city: Cambridge

first: Alejandro

last: Rojas

state: MA

address: 26 Landsdowne Street

institute: Fulcrum Therapeutics

data_processing:
Genome alignment and gene quantitation was performed using OmicSoft Array Studio
Cleaned reads were aligned to the Hg38 genome using the OmicSoft Aligner with a maximum of 2 allowed mismatches
Gene level counts were determined by the RNA-Seq by expectation maximization algorithm as implemented in OmicSoft Array Studio and using Ensembl.R89 gene models
FPKM normalization was applied to RNA-Seq counts
Genome_build: Hg38
Supplementary_files_format_and_content: excel file of FPKM values for each Sample

source_name: C6 FSHD + 1uM pamapimod

growth_protocol: Myotubes differentiated for 5 days grown in 6 well plates using the methods described in this reference

extract_protocol:
Qiagen RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated at the time of differentiation induction and collectd 5 days after

tag: source subject status

value: Facioscapulohumeral Muscular Dystrophy (FSHD)

value: Myotubes

value: Pamapimod 1 uM


title: WT + DMSO_112917_FTEV-003_LL5023_S3

source_name: WT + DMSO

value: WT/healthy

value: DMSO


title: C6 FSHD + 1uM pamapimod_112917_FTEV-007_LL5023_S7


title: WT + DMSO_112917_FTEV-002_LL5023_S2


title: C6 FSHD + 1uM losmapimod_112917_FTEV-018_LL5023_S12

source_name: C6 FSHD + 1uM losmapimod

value: Losmapimod 1 uM


title: C6 FSHD + 1uM losmapimod_112917_FTEV-016_LL5023_S10


title: C6 FSHD + DMSO_112917_FTEV-005_LL5023_S5

source_name: C6 FSHD + DMSO


title: C6 FSHD + 1uM losmapimod_112917_FTEV-017_LL5023_S11


title: C6 FSHD + 1uM pamapimod_112917_FTEV-009_LL5023_S9


title: C6 FSHD + DMSO_112917_FTEV-006_LL5023_S6


title: WT + DMSO_112917_FTEV-001_LL5023_S1


title: [Sample_2, CPP]

description: circRNAs

value: cocaine conditioned

value: male


title: MCF-7-Norm-p3

city: Indianapolis

first: Mircea

last: Ivan

state: IN

address: 980 W Walnut Street

institute: Indiana University School of Medicine

data_processing:
NextSeq read sequences were cleaned using Trimmomatic version 0.32 with the paramaters “2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17” to remove adapter sequences and perform quality trimming
FASTX-Toolkit was then used to reverse complement the reads.
The resulting reads were mapped against GRCh38.p5 using TopHat2 version 2.1.1 with parameters “--b2-very-sensitive --read-edit-dist 2 --max-multihits 100”
Read counts for each gene were created using HTSeq-Count from the HTSeq package version 0.6.1p1and Gencode v23 as the annotation
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: breast cancer cell line

growth_protocol: MCF-7 cells were tested mycoplasma-free and maintained at 37°C in 5% CO2 with DMEM/High glucose medium supplemented with 10% (v/v) FBS and antibiotics

extract_protocol:
For RNA extraction, cells were lysed using QIAzol Lysis Reagent (QIAGEN) and total RNA was isolated using the RNeasy kit (QIAGEN) following manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: One set of replicates were cultivated in hypoxia (1% O2) for 24 hours and the other set was grown in  normoxia (21% O2) for the same time period, before RNA isolation.

value: normoxia:21% O2


title: MCF-7-Hypo-p5

value: hypoxia:1% O2


title: MCF-7-Hypo-p3


title: MCF-7-Norm-p5


title: MCF-7-Norm-p2


title: T_a21_3

city: Cosenza

first: Cirino

last: Botta

address: Via Migliori

department: Hematology Unit

country: Italy

institute: "Annunziata" Hospital of Cosenza

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to HG19 by using, sequentially bcl2fastq2 v2.19.1.403; cutadapt v1.13-gcc-6.4.0-2dfskgp; star v2.5.3a-gcc-4.9.4-vojlnhd. Raw table containing gene counts was obtained by using quant3p
Genome_build: HG19
Supplementary_files_format_and_content: counts_Th17.txt

source_name: PBMCs

extract_protocol:
Purification of RNA from sorted cells using Dynabeads mRNA DIRECT Purification Kit
We barcoded RNA from each sample in a retrotranscription (RT) reaction with AffinityScript Multiple Temperature Reverse Transcriptase (Agilent, Santa Clara, CA) and different RT primers. After qPCR, cDNA with similar Ct values were pooled together. cDNA was purified with SPRIselect 1.2X (Beckman Coulter –BC-, Brea, CA) and amplified using the T7 promotor as template previously introduced in the RT reaction. T7 polimerase (NEB) was added for 16 hours at 37ºC. RNA molecules were fragmented with 2µL of 10X Zn2+ fragmentation buffer (Ambion™, ThermoFisher) for 1 min at 70ºC and purified with SPRIselect 2X. Afterwards, a ssRNA adaptor (Illumina, San Diego, CA) was ligated to the 3’-end of the RNA fragments in presence of DMSO, 100 mM ATP, 50% PEG and T4 RNA ligase I (NEB) for 2 hours at 22ºC. A second RT reaction was performed with AffinityScript Multiple Temperature Reverse Transcriptase and resulting cDNA was purified with SPRIselect 1.5X. Finally, cDNA was amplified with 12.5µL Kappa Hifi ready mix + 1µL 25 µM primer mix per sample and purified with SPRIselect 0.7X. Qubit, TapeStation and qPCR analysis were done as quality controls.

treatment_protocol: Synthetic miR-21 inhibitor (miR-21i) and anti-miR inhibitor scramble  (miR-SC) were purchased from Invitrogen™(ThermoScientific) and were used  to antagonize or not  mir-21 expression, at a final concentration of 100nM. 1x10e6 cells were transfected using Neon® Transfection System (Invitrogen™, Thermo Scientific) according to the manufacture protocols using the same conditions for each transfection experiment.

value: T cells

value: Synthetic miR-21 inhibitor (miR-21i)

tag: concentration


title: T_SC_3

value: control

value: 0 uM


title: T_a21_2


title: T_a21_1


title: T_SC_2


title: T_SC_1


title: C6 FSHD + DMSO_112917_FTEV-004_LL5023_S4


title: g2.S66

first: Xin

last: Jin

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S66_XJ4276-3_S18

data_processing:
Basecalling and sample demultiplexing were performed in Illumina NextSeq Control Software.
Potential mouse contaminating reads were removed by competitive mapping to the human/mouse hybrid genome using BBSplit (https://sourceforge.net/projects/bbmap/).
Reads that uniquely mapped to the human genome were then used as input for mapping and gene-level counting with RSEM (https://deweylab.github.io/RSEM/).
Barcode reads corresponding to cell line fractions were mapped to the barcode reference using Bowtie 2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml).
Genome_build: hg19, mm8
Supplementary_files_format_and_content: Tab-delimited text files that contain estimated count values and annotations for each sample.

source_name: in vitro

growth_protocol: Breast cancer cell lines were individually barcoded using lentiviral barcode vectors. Cell lines were pooled and injected into NSG mice through intracardiac route. Five weeks post injection, organs were harvested, and purified for GFP+ cancer cells.

extract_protocol:
Individual cell lines, cell line pools prior to injection, and cells isolated from metastases were subjected to RNA-Seq. RNA extraction was performed using Quick-RNA MicroPrep according to instructions (Zymo Research). RNA was quantified using RNA 6000 Pico Kit on a 2100 Bioanalyzer (Agilent). RNA samples from cell numbers lower than 500 were not measured but all were used as input for library preparation.
cDNA was synthesized using Clontech SmartSeq v4 reagents from up to 2 ng RNA input. Full length cDNA was fragmented to a mean size of 150bp with a Covaris M220 ultrasonicator and Illumina libraries were prepared from 2 ng of sheared cDNA using Rubicon Genomics Thruplex DNAseq reagents. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on Illumina NextSeq500 runs with paired-end 75bp reads.

tag: pool

value: group 2 (g2)

tag: tissue/cell type

tag: cancer cell line composition


title: g2.S63

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S63_XJ4276-3_S15

value: CAL851_BREAST:0; HCC1143_BREAST:0; HCC70_BREAST:0; HCC1395_BREAST:0; HCC1187_BREAST:0; HCC38_BREAST:0; HCC1569_BREAST:0; HCC1937_BREAST:0; BT20_BREAST:1; HCC1599_BREAST:0


title: g2.S64

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S64_XJ4276-3_S16


title: g2.S62

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S62_XJ4276-3_S14

value: CAL851_BREAST:0; HCC1143_BREAST:0; HCC70_BREAST:0; HCC1395_BREAST:0; HCC1187_BREAST:0; HCC38_BREAST:0; HCC1569_BREAST:0; HCC1937_BREAST:1; BT20_BREAST:0; HCC1599_BREAST:0


title: g2.S61

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S61_XJ4276-3_S13


title: g2.S60

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S60_XJ4276-3_S12


title: g2.S57

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S57_XJ4276-3_S9

value: CAL851_BREAST:0; HCC1143_BREAST:0; HCC70_BREAST:0; HCC1395_BREAST:0; HCC1187_BREAST:0; HCC38_BREAST:1; HCC1569_BREAST:0; HCC1937_BREAST:0; BT20_BREAST:0; HCC1599_BREAST:0


title: g2.S59

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S59_XJ4276-3_S11


title: g2.S58

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S58_XJ4276-3_S10


title: g2.S55

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S55_XJ4276-3_S7


title: g2.S44

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S44_XJ4276-3_S3

value: CAL851_BREAST:0; HCC1143_BREAST:0; HCC70_BREAST:1; HCC1395_BREAST:0; HCC1187_BREAST:0; HCC38_BREAST:0; HCC1569_BREAST:0; HCC1937_BREAST:0; BT20_BREAST:0; HCC1599_BREAST:0


title: g2.S54

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S54_XJ4276-3_S6


title: g2.S43

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S43_XJ4276-3_S2

value: CAL851_BREAST:0; HCC1143_BREAST:1; HCC70_BREAST:0; HCC1395_BREAST:0; HCC1187_BREAST:0; HCC38_BREAST:0; HCC1569_BREAST:0; HCC1937_BREAST:0; BT20_BREAST:0; HCC1599_BREAST:0


title: g2.S53

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S53_XJ4276-3_S5

value: CAL851_BREAST:0; HCC1143_BREAST:0; HCC70_BREAST:0; HCC1395_BREAST:1; HCC1187_BREAST:0; HCC38_BREAST:0; HCC1569_BREAST:0; HCC1937_BREAST:0; BT20_BREAST:0; HCC1599_BREAST:0


title: MCF-7-Hypo-p2

tag: cell line


title: g2.S56

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S56_XJ4276-3_S8

value: CAL851_BREAST:0; HCC1143_BREAST:0; HCC70_BREAST:0; HCC1395_BREAST:0; HCC1187_BREAST:1; HCC38_BREAST:0; HCC1569_BREAST:0; HCC1937_BREAST:0; BT20_BREAST:0; HCC1599_BREAST:0


title: g2.S41

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S41_XJ4276-2_S18

value: CAL851_BREAST:1; HCC1143_BREAST:0; HCC70_BREAST:0; HCC1395_BREAST:0; HCC1187_BREAST:0; HCC38_BREAST:0; HCC1569_BREAST:0; HCC1937_BREAST:0; BT20_BREAST:0; HCC1599_BREAST:0


title: g2.S38

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S38_XJ4276-2_S15


title: g2.S37

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S37_XJ4276-2_S14


title: g2.S42

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S42_XJ4276-3_S1


title: g2.S36

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S36_XJ4276-1_S18


title: g2.S35

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S35_XJ4276-1_S17

source_name: in vivo

value: lung


title: g2.S65

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S65_XJ4276-3_S17


title: g2.S34

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S34_XJ4276-1_S16

value: liver


title: g2.S30

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S30_XJ4276-1_S15


title: g2.S31

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S31_XJ4276-1_S12

value: bone


title: g2.S29

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S29_XJ4276-1_S14


title: g2.S25

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S25_XJ4276-2_S13


title: g2.S27

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S27_XJ4276-1_S11

value: brain


title: g2.S45

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S45_XJ4276-3_S4


title: g2.S23

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S23_XJ4276-1_S10

value: kidney


title: g2.S22

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S22_XJ4276-1_S9


title: g2.S24

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S24_XJ4276-2_S12


title: g2.S20

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S20_XJ4276-2_S10


title: g2.S21

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S21_XJ4276-2_S11


title: g2.S14

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S14_XJ4276-2_S6


title: g2.S12

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S12_XJ4276-1_S7


title: g2.S09

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S09_XJ4276-2_S3


title: g2.S07

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S07_XJ4276-1_S5


title: g2.S11

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S11_XJ4276-2_S5


title: g2.S08

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S08_XJ4276-1_S6


title: g2.S19

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S19_XJ4276-2_S9


title: g2.S06

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S06_XJ4276-1_S4


title: g2.S15

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S15_XJ4276-2_S7


title: g2.S39

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S39_XJ4276-2_S16


title: g2.S02

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S02_XJ4276-1_S2


title: g1.S64

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S64_XJ3969-3_S20

value: group 1 (g1)

value: BT549_BREAST:0; HDQP1_BREAST:0; JIMT1_BREAST:0; MDAMB157_BREAST:0; MDAMB436_BREAST:0; HCC1806_BREAST:0; HMC18_BREAST:0; MDAMB468_BREAST:0; DU4475_BREAST:1


title: g2.S03

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S03_XJ4276-2_S1


title: g1.S63

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S63_XJ3969-3_S19


title: g1.S61

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S61_XJ3969-3_S17


title: g1.S60

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S60_XJ3969-3_S16

value: BT549_BREAST:0; HDQP1_BREAST:0; JIMT1_BREAST:0; MDAMB157_BREAST:0; MDAMB436_BREAST:0; HCC1806_BREAST:0; HMC18_BREAST:1; MDAMB468_BREAST:0; DU4475_BREAST:0


title: g1.S57

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S57_XJ3969-3_S13

value: BT549_BREAST:0; HDQP1_BREAST:0; JIMT1_BREAST:0; MDAMB157_BREAST:0; MDAMB436_BREAST:0; HCC1806_BREAST:1; HMC18_BREAST:0; MDAMB468_BREAST:0; DU4475_BREAST:0


title: g1.S56

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S56_XJ3969-3_S12

value: BT549_BREAST:0; HDQP1_BREAST:0; JIMT1_BREAST:0; MDAMB157_BREAST:0; MDAMB436_BREAST:1; HCC1806_BREAST:0; HMC18_BREAST:0; MDAMB468_BREAST:0; DU4475_BREAST:0


title: g2.S04

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S04_XJ4276-2_S2

value: group 2 (g2)


title: g1.S55

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S55_XJ3969-3_S11


title: g1.S59

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S59_XJ3969-3_S15


title: g1.S52

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S52_XJ3969-3_S9

value: BT549_BREAST:0; HDQP1_BREAST:0; JIMT1_BREAST:1; MDAMB157_BREAST:0; MDAMB436_BREAST:0; HCC1806_BREAST:0; HMC18_BREAST:0; MDAMB468_BREAST:0; DU4475_BREAST:0


title: g1.S53

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S53_XJ3969-3_S10

value: BT549_BREAST:0; HDQP1_BREAST:0; JIMT1_BREAST:0; MDAMB157_BREAST:1; MDAMB436_BREAST:0; HCC1806_BREAST:0; HMC18_BREAST:0; MDAMB468_BREAST:0; DU4475_BREAST:0


title: g2.S10

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S10_XJ4276-2_S4


title: g1.S51

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S51_XJ3969-3_S8


title: g1.S50

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S50_XJ3969-3_S7

value: BT549_BREAST:0; HDQP1_BREAST:1; JIMT1_BREAST:0; MDAMB157_BREAST:0; MDAMB436_BREAST:0; HCC1806_BREAST:0; HMC18_BREAST:0; MDAMB468_BREAST:0; DU4475_BREAST:0


title: g1.S49

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S49_XJ3969-3_S6


title: g1.S48

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S48_XJ3969-3_S5

value: BT549_BREAST:1; HDQP1_BREAST:0; JIMT1_BREAST:0; MDAMB157_BREAST:0; MDAMB436_BREAST:0; HCC1806_BREAST:0; HMC18_BREAST:0; MDAMB468_BREAST:0; DU4475_BREAST:0


title: g2.S05

description:
The g2 pool contains CAL851_BREAST, HCC1143_BREAST, HCC70_BREAST, HCC1395_BREAST, HCC1187_BREAST, HCC38_BREAST, HCC1569_BREAST, HCC1937_BREAST, BT20_BREAST, HCC1599_BREAST.
20170602_S05_XJ4276-1_S3


title: g1.S46

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S46_XJ3969-3_S3


title: g1.S45

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S45_XJ3969-3_S2


title: g1.S42

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S42_XJ3969-2_S18


title: g1.S47

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S47_XJ3969-3_S4


title: g1.S43

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S43_XJ3969-2_S19


title: g1.S44

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170313_S44_XJ3969-3_S1


title: g1.S41

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S41_XJ3969-2_S17


title: g1.S40

description:
The g1 pool contains BT549_BREAST, HDQP1_BREAST, JIMT1_BREAST, MDAMB157_BREAST, MDAMB436_BREAST, HCC1806_BREAST, HMC18_BREAST, MDAMB468_BREAST, DU4475_BREAST.
20170311_S40_XJ3969-2_S16