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26 rows where experiment.library_selection = "size fractionation" and tissue_curation = "Skin"

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technology 2

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tissue_curation 1

  • Skin · 26 ✖

experiment.library_source 1

experiment.library_selection 1

  • size fractionation · 26 ✖

experiment.library_layout 1

devstage_curation_coarse 1

devstage_curation 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
39610 39610 SRR1873570 SRX915250 SRS870224 SRP056014 PRJNA277780 Identification of small non coding RNAs in zebrafish GSE66718 Transcriptome Analysis MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes namely developmental timing cell differentiation cell proliferation immune response and infection. For this reason their identification is essential to understand eukaryotic biology. Their small size low abundance and high instability complicated early identification; however cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages namely 24 hpf 72 hpf 96 hpf 5 dpf dpf 45 dpf young adult and from adult brain eyes gills heart skin and fins.   pubmed:26694924   skin GSM1630514   source name:adult skin 1 year old|strain/background:AB|genotype/variation:wild type|tissue:skin|developmental stage:adult|age:1 year skin Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12 the traditional blast output and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept and using the remaining alignments as guidelines the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation using miRDeep. To overcome the inherent lack of sensitivity of miRDeep novel transcripts encoding miRNAs… adult skin 1 year old   100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing. Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle. strain/background:AB|genotype/variation:wild type|tissue:skin|developmental stage:adult|age:1 year GSM1630514 GSM1630514: skin; Danio rerio; miRNA Seq GSM1630514   1 100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter "Nelson's linker" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime for 1 hour at 37°C followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides as detailed next. 24hpf ATC; 72hpf ACT; 96hpf CAG; 5dpf ATG; 45dpf CCG; entire adult GTA; brain CGG; Heart CTG; Eyes GCT; fins GTT; skin TAC; gills TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche following established protocols for DNA library sequencing. GEO Accession:GSM1630514 miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE LS454 454 GS FLX   SRP056014         79232.0 1527.0 GSM1630514 r1 0:4 1:47.89 A:20622;C:23508;G:19017;T:15967;N:118 4 47     20622 23508 19017 15967 118 SRX915250 SRS870224 SRA246117 GEO University of Aveiro 1 0.0   0.0   1.0       53   T   under 1.2% mapping rate legacy early 3prime size_fractionation unknown bulk other_seq 454   Portugal 2015-03-09 Adult Adult Skin Surface Structure
49015 49015 SRR7613129 SRX4477829 SRS3603028 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 100 ZF skin smallRNAseq GSM3309731   source name:skin|strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male NH FLI 100 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male GSM3309731 GSM3309731: NH FLI 100 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309731   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309731 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         1018240050.0 20364801.0 GSM3309731 r1 0:50 A:207814229;C:262063346;G:311334117;T:236957867;N:70491 50       207814229 262063346 311334117 236957867 70491 SRX4477829 SRS3603028 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.1074   0.00618   0.9906   0.54934   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49016 49016 SRR7613128 SRX4477828 SRS3603027 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 111 ZF skin smallRNAseq GSM3309730   source name:skin|strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male NH FLI 111 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male GSM3309730 GSM3309730: NH FLI 111 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309730   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309730 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         356381250.0 7127625.0 GSM3309730 r1 0:50 A:70456264;C:88928211;G:109830748;T:87141036;N:24991 50       70456264 88928211 109830748 87141036 24991 SRX4477828 SRS3603027 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.12249   0.00713   0.99299   0.51987   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49017 49017 SRR7613127 SRX4477827 SRS3603046 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 109 ZF skin smallRNAseq GSM3309729   source name:skin|strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male NH FLI 109 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male GSM3309729 GSM3309729: NH FLI 109 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309729   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309729 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         591923400.0 11838468.0 GSM3309729 r1 0:50 A:118873766;C:162031990;G:180619895;T:130356928;N:40821 50       118873766 162031990 180619895 130356928 40821 SRX4477827 SRS3603046 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.09696   0.00911   0.99133   0.52082   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49018 49018 SRR7613126 SRX4477826 SRS3603047 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 108 ZF skin smallRNAseq GSM3309728   source name:skin|strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male NH FLI 108 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male GSM3309728 GSM3309728: NH FLI 108 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309728   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309728 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         736154900.0 14723098.0 GSM3309728 r1 0:50 A:138956520;C:196877364;G:231633259;T:168650452;N:37305 50       138956520 196877364 231633259 168650452 37305 SRX4477826 SRS3603047 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01397   0.0029   0.99312   0.79541   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49019 49019 SRR7613125 SRX4477825 SRS3603026 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 107 ZF skin smallRNAseq GSM3309727   source name:skin|strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male NH FLI 107 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male GSM3309727 GSM3309727: NH FLI 107 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309727   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309727 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         749544400.0 14990888.0 GSM3309727 r1 0:50 A:141473710;C:216076836;G:236230720;T:155730665;N:32469 50       141473710 216076836 236230720 155730665 32469 SRX4477825 SRS3603026 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.03825   0.00867   0.99439   0.74015   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49020 49020 SRR7613124 SRX4477824 SRS3603024 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 106 ZF skin smallRNAseq GSM3309726   source name:skin|strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male NH FLI 106 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male GSM3309726 GSM3309726: NH FLI 106 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309726   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309726 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         611281450.0 12225629.0 GSM3309726 r1 0:50 A:111669012;C:149529261;G:189562873;T:160496848;N:23456 50       111669012 149529261 189562873 160496848 23456 SRX4477824 SRS3603024 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02484   0.00442   0.9936   0.64597   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49021 49021 SRR7613123 SRX4477823 SRS3603023 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 150 ZF skin smallRNAseq GSM3309725   source name:skin|strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male NH FLI 150 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male GSM3309725 GSM3309725: NH FLI 150 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309725   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309725 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         2447513950.0 48950279.0 GSM3309725 r1 0:50 A:468043633;C:693473223;G:731577603;T:554251791;N:167700 50       468043633 693473223 731577603 554251791 167700 SRX4477823 SRS3603023 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.07052   0.01139   0.99263   0.59059   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49022 49022 SRR7613122 SRX4477822 SRS3603025 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 149 ZF skin smallRNAseq GSM3309724   source name:skin|strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male NH FLI 149 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male GSM3309724 GSM3309724: NH FLI 149 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309724   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309724 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         1871316900.0 37426338.0 GSM3309724 r1 0:50 A:380496272;C:509217150;G:560916561;T:420592548;N:94369 50       380496272 509217150 560916561 420592548 94369 SRX4477822 SRS3603025 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.03136   0.00816   0.99488   0.79162   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49023 49023 SRR7613121 SRX4477821 SRS3603022 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 147 ZF skin smallRNAseq GSM3309723   source name:skin|strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male NH FLI 147 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male GSM3309723 GSM3309723: NH FLI 147 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309723   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309723 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         445551200.0 8911024.0 GSM3309723 r1 0:50 A:89205774;C:110497307;G:135908107;T:109919980;N:20032 50       89205774 110497307 135908107 109919980 20032 SRX4477821 SRS3603022 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01905   0.00266   0.99504   0.62127   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49024 49024 SRR7613120 SRX4477820 SRS3603021 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 146 ZF skin smallRNAseq GSM3309722   source name:skin|strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male NH FLI 146 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male GSM3309722 GSM3309722: NH FLI 146 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309722   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309722 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         982200100.0 19644002.0 GSM3309722 r1 0:50 A:192209302;C:247406918;G:306793998;T:235751163;N:38719 50       192209302 247406918 306793998 235751163 38719 SRX4477820 SRS3603021 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02155   0.00424   0.99368   0.62937   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49025 49025 SRR7613119 SRX4477819 SRS3603020 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 145 ZF skin smallRNAseq GSM3309721   source name:skin|strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male NH FLI 145 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male GSM3309721 GSM3309721: NH FLI 145 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309721   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309721 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         1336985700.0 26739714.0 GSM3309721 r1 0:50 A:257049527;C:368876598;G:422514962;T:288505412;N:39201 50       257049527 368876598 422514962 288505412 39201 SRX4477819 SRS3603020 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.04358   0.00841   0.99312   0.76026   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49026 49026 SRR7613118 SRX4477818 SRS3603019 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 137 ZF skin smallRNAseq GSM3309720   source name:skin|strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male NH FLI 137 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male GSM3309720 GSM3309720: NH FLI 137 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309720   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309720 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         1039359300.0 20787186.0 GSM3309720 r1 0:50 A:200252400;C:286646217;G:322574775;T:229813195;N:72713 50       200252400 286646217 322574775 229813195 72713 SRX4477818 SRS3603019 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.10832   0.00654   0.99113   0.52929   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49027 49027 SRR7613117 SRX4477817 SRS3603018 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 136 ZF skin smallRNAseq GSM3309719   source name:skin|strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male NH FLI 136 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male GSM3309719 GSM3309719: NH FLI 136 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309719   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309719 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         858942900.0 17178858.0 GSM3309719 r1 0:50 A:168340182;C:217323317;G:266544838;T:206688895;N:45668 50       168340182 217323317 266544838 206688895 45668 SRX4477817 SRS3603018 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.00791   0.00151   0.99439   0.71291   50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49028 49028 SRR7613116 SRX4477816 SRS3603017 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 135 ZF skin smallRNAseq GSM3309718   source name:skin|strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male NH FLI 135 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male GSM3309718 GSM3309718: NH FLI 135 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309718   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309718 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         1468015400.0 29360308.0 GSM3309718 r1 0:50 A:275374756;C:419939586;G:454098567;T:318538086;N:64405 50       275374756 419939586 454098567 318538086 64405 SRX4477816 SRS3603017 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01694   0.00341   0.99511   0.72261   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49029 49029 SRR7613115 SRX4477815 SRS3603016 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 134 ZF skin smallRNAseq GSM3309717   source name:skin|strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male NH FLI 134 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male GSM3309717 GSM3309717: NH FLI 134 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309717   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309717 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         678693700.0 13573874.0 GSM3309717 r1 0:50 A:137270784;C:164359833;G:207871154;T:169165189;N:26740 50       137270784 164359833 207871154 169165189 26740 SRX4477815 SRS3603016 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02269   0.00427   0.99295   0.61091   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49030 49030 SRR7613114 SRX4477814 SRS3603015 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 133 ZF skin smallRNAseq GSM3309716   source name:skin|strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male NH FLI 133 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:2 years|Sex:male GSM3309716 GSM3309716: NH FLI 133 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309716   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309716 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         847740400.0 16954808.0 GSM3309716 r1 0:50 A:168475291;C:220114466;G:260254419;T:198870005;N:26219 50       168475291 220114466 260254419 198870005 26219 SRX4477814 SRS3603015 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02431   0.00324   0.99226   0.63318   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49031 49031 SRR7613113 SRX4477813 SRS3603014 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 125 ZF skin smallRNAseq GSM3309715   source name:skin|strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male NH FLI 125 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male GSM3309715 GSM3309715: NH FLI 125 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309715   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309715 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         1020735000.0 20414700.0 GSM3309715 r1 0:50 A:205383345;C:253177983;G:308564152;T:253535814;N:73706 50       205383345 253177983 308564152 253535814 73706 SRX4477813 SRS3603014 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.10278   0.00523   0.99155   0.53907   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49032 49032 SRR7613112 SRX4477812 SRS3603012 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 122 ZF skin smallRNAseq GSM3309714   source name:skin|strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male NH FLI 122 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male GSM3309714 GSM3309714: NH FLI 122 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309714   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309714 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         647896400.0 12957928.0 GSM3309714 r1 0:50 A:130330780;C:160929346;G:200383433;T:156218597;N:34244 50       130330780 160929346 200383433 156218597 34244 SRX4477812 SRS3603012 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.00732   0.0014   0.99401   0.68357   50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49033 49033 SRR7613111 SRX4477811 SRS3603013 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 121 ZF skin smallRNAseq GSM3309713   source name:skin|strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male NH FLI 121 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male GSM3309713 GSM3309713: NH FLI 121 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309713   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309713 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         1387064850.0 27741297.0 GSM3309713 r1 0:50 A:262170854;C:395102028;G:446088168;T:283643764;N:60036 50       262170854 395102028 446088168 283643764 60036 SRX4477811 SRS3603013 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01646   0.00363   0.9922   0.73895   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49034 49034 SRR7613110 SRX4477810 SRS3603011 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 120 ZF skin smallRNAseq GSM3309712   source name:skin|strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male NH FLI 120 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male GSM3309712 GSM3309712: NH FLI 120 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309712   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309712 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         771712600.0 15434252.0 GSM3309712 r1 0:50 A:154765175;C:193689306;G:236383702;T:186844174;N:30243 50       154765175 193689306 236383702 186844174 30243 SRX4477810 SRS3603011 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02376   0.00465   0.99166   0.64918   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49035 49035 SRR7613109 SRX4477809 SRS3603010 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 119 ZF skin smallRNAseq GSM3309711   source name:skin|strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male NH FLI 119 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male GSM3309711 GSM3309711: NH FLI 119 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309711   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309711 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         582866200.0 11657324.0 GSM3309711 r1 0:50 A:113005827;C:152497718;G:181963234;T:135381588;N:17833 50       113005827 152497718 181963234 135381588 17833 SRX4477809 SRS3603010 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.02894   0.00364   0.99208   0.58438   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49036 49036 SRR7613108 SRX4477808 SRS3603008 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 98 ZF skin smallRNAseq GSM3309710   source name:skin|strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male NH FLI 98 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male GSM3309710 GSM3309710: NH FLI 98 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309710   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309710 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         663294800.0 13265896.0 GSM3309710 r1 0:50 A:137734100;C:161855118;G:201382193;T:162288125;N:35264 50       137734100 161855118 201382193 162288125 35264 SRX4477808 SRS3603008 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.00618   0.00111   0.99478   0.65659   50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49037 49037 SRR7613107 SRX4477807 SRS3603009 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 96 ZF skin smallRNAseq GSM3309709   source name:skin|strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male NH FLI 96 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male GSM3309709 GSM3309709: NH FLI 96 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309709   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309709 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         569130200.0 11382604.0 GSM3309709 r1 0:50 A:116615049;C:147340637;G:176081367;T:129067210;N:25937 50       116615049 147340637 176081367 129067210 25937 SRX4477807 SRS3603009 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.01763   0.00207   0.99389   0.63527   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49038 49038 SRR7613106 SRX4477806 SRS3603007 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 94 ZF skin smallRNAseq GSM3309708   source name:skin|strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male NH FLI 94 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male GSM3309708 GSM3309708: NH FLI 94 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309708   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309708 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         941640450.0 18832809.0 GSM3309708 r1 0:50 A:181731779;C:249059327;G:290464823;T:220348739;N:35782 50       181731779 249059327 290464823 220348739 35782 SRX4477806 SRS3603007 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.03203   0.00641   0.98993   0.72488   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure
49039 49039 SRR7613105 SRX4477805 SRS3603006 SRP155559 PRJNA483229 Sequencing of Danio rerio skin for 5 age groups GSE117820 Transcriptome Analysis Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6 12 24 36 month and 42 month. Jena Centre for Systems Biology of Ageing JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples 12 month 5 samples 24 month 5 samples 36 month 5 samples 42 month 5 samples.       NH FLI 85 ZF skin smallRNAseq GSM3309707   source name:skin|strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male NH FLI 85 ZF skin smallRNAseq Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter: n 0 o 0 e 0 l 8 k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample. skin   Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.   strain:AB JxT\xFC|tissue:skin|age:6 month|Sex:male GSM3309707 GSM3309707: NH FLI 85 ZF skin smallRNAseq; Danio rerio; ncRNA Seq GSM3309707   1 Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction. GEO Accession:GSM3309707 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP155559         974950550.0 19499011.0 GSM3309707 r1 0:50 A:188952378;C:263095911;G:305812761;T:217059876;N:29624 50       188952378 263095911 305812761 217059876 29624 SRX4477805 SRS3603006 SRA745967 GEO Leibniz Institute for Age Research - Fritz Lipmann Institute 1 0.03216   0.00571   0.99015   0.67028   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   Germany 2018-07-27 Adult Adult Skin Surface Structure

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;