A resource for genomic piRNA clusters in animal species

Statistics for the current piRNA cluster database release:
Species in piRNA cluster database 12
Total number of SRA datasets 112
Total number of proTRAC runs 128
Total number of piRNA clusters 33964


If you make use of the data deposited at piRNA cluster database please cite the following papers that refer to the proTRAC software and the piRNA cluster database paper:

Where applicable, please also make sure to cite the original papers that are linked to the according SRA datasets. Click here for a quick guide how to access the deposited data. Feedback or suggestions for improvement of the piRNA cluster database are most welcome! Let us know if you miss a certain SRA dataset in this collection. This database is subject to constant extension. Just send an email to David Rosenkranz.


Browse by species and SRA dataset


→ Homo sapiens → Macaca fascicularis → Macaca mulatta → Callithrix jacchus → Tupaia belangeri → Mus musculus → Rattus norvegicus → Bos taurus → Sus scrofa → Gallus gallus → Danio rerio → Drosophila melanogaster



Overview of available SRA datasets
Click on a category to sort the SRA datasets accordingly. Use the search function to search for SRA datasets, species, tissues etc. Click on the desired SRA accession to open the 'browse piRNA clusters' table which provides further links to the deposited data.


Species SRA
dataset
Sex Tissue or
Cell Type
Dev.
Stage
Genotype Selection Reads Mapped reads Clustered
reads
Clustered
reads [%]
piRNA
clusters
Callithrix jacchusSRR606715maletestisadultwtsize59494802636450125540.4830
Callithrix jacchusSRR1041905maletestisadultwtsize17073924141486301043053473.72485
Callithrix jacchusSRR1041906maletestisadultwtMarwi-IP77744129614627135306869486.34702
Callithrix jacchusSRR1041907maletestisadultwtMarwi-IP57663847451080043887799586.19697
Macaca mulattaSRR116839maletestisadultwtsize88173755054416349839169.21313
Macaca mulattaSRR116840maleepididymisadultwtsize787365060255593361765.58109
Macaca mulattaSRR116841maleprostateadultwtsize753070362468711016501.6377
Macaca mulattaSRR116842maleseminal vesicleadultwtsize898245075657211340001.7777
Macaca mulattaSRR116843malecortexadultwtsize75098246231565203500.3344
Macaca mulattaSRR116844maleprincipal and basal cellsadultwtsize48545621653479466332.824
Macaca mulattaSRR116845malepertibular tissueadultwtsize812107250620411404222.775
Macaca mulattaSRR553581maletestisadultwtsize2465442214658444849285857.94317
Macaca mulattaSRR605664maletestisadultwtsize173979623180.197
Macaca mulattaSRR606728maletestisadultwtsize78328841669191799934.79183
Macaca fascicularisSRR1755241femaleovaryadultwtsize62220684405103219473049.82286
Macaca fascicularisSRR1755242femaleovaryadultwtsize389546667789748774571.95166
Macaca fascicularisSRR1755243maletestisadultwtsize31040165214294841805099984.23540
Macaca fascicularisSRR1755244maletestisadultwtsize1119451362846103220215.12120
Mus musculusSRR014231maletestis16.5 dpcwtsize2526951169406355559532.8853
Mus musculusSRR014232maletestis16.5 dpcwtMili-IP2392686966881725717.5140
Mus musculusSRR014233maletestis16.5 dpcwtMiwi-IP1769365144902915951311.0182
Mus musculusSRR014234femaleovaryadultwtsize2692972050993124015.23336
Mus musculusSRR014235maletestis2 dppwtsize1270529100461739025638.85722
Mus musculusSRR772028maletestis10.5 dppwtsize137369929402852181865919.34512
Mus musculusSRR772029maletestis12.5 dppwtsize63888724593578021335253022.49857
Mus musculusSRR772030maletestis14.5 dppwtsize113472381969189571946376920.08827
Mus musculusSRR772031maletestis17.5 dppwtsize44351844044162322912779.85623
Mus musculusSRR772032maletestis20.5 dppwtsize80087647557291560888074.22675
Mus musculusSRR772033maletestis42.5 dppwtsize87575268245798644690378.18624
Mus musculusSRR772050maletestis10.5 dppwtsize71942638617572722073189433.57725
Mus musculusSRR772051maletestis12.5 dppwtsize42502080396198052165149654.651176
Mus musculusSRR772052maletestis14.5 dppwtsize95909901863819224158217548.141069
Mus musculusSRR772053maletestis17.5 dppwtsize65140936001647562871493.79842
Mus musculusSRR772054maletestis20.5 dppwtsize83539337898061745542994.4909
Mus musculusSRR772055maletestis42.5 dppwtsize91285738600832827018496.16826
Gallus gallusSRR772049maletestisadultwtsize4222673024660698297668312.0780
Gallus gallusSRR772069maletestisadultwtsize116234474815343512952629436.21166
Danio rerioSRR298567maletestisadultwtZili-IP18971042128625818933556.9578
Danio rerioSRR298568maletestisadultwtZiwi-IP784194535202252762387.8599
Danio rerioSRR363984femaleovaryadultHen1size919330577811356267058.0596
Danio rerioSRR363985femaleovaryadultwtsize79805596675287118513217.75178
Danio rerioSRR578904femaleovaryadultwtsize2197411518795018302438116.09147
Danio rerioSRR578905femaleovaryadultwtsize3776787246083845110318.33163
Danio rerioSRR578906femaleovaryadultwtsize6901444459779489556319.48195
Danio rerioSRR578907femaleovaryadultSJD-Tu hybridsize2635530923550521523907122.25188
Danio rerioSRR578908femaleovaryadultSJD-Tu hybridsize86883616677921160244524237
Danio rerioSRR578909femaleovaryadultSJD-Tu hybridsize88662764818918118930324.68239
Danio rerioSRR578910femaleovaryadultSJD-Tu hybridsize2408949721611260410774819.01192
Danio rerioSRR578911femaleovaryadultSJD-Tu hybridsize92631107788386179260523.02226
Danio rerioSRR578912femaleovaryadultSJD-Tu hybridsize77601916626040164861924.88247
Danio rerioSRR578913femaleovaryadultwtsize2343325820979747567140827.03246
Danio rerioSRR578914femaleovaryadultwtsize66128634967482106314821.4165
Danio rerioSRR578915femaleovaryadultwtsize5890450427636158022113.57173
Danio rerioSRR578916femaleovaryadultSJD-Tu hybridsize2626836623356864496672721.26201
Danio rerioSRR578917femaleovaryadultSJD-Tu hybridsize82867296767536153660122.71228
Danio rerioSRR578918femaleovaryadultSJD-Tu hybridsize73585786127308146679523.94248
Danio rerioSRR578919femaleovaryadultSJD-Tu hybridsize2611477023315645496537121.3202
Danio rerioSRR578920femaleovaryadultSJD-Tu hybridsize6033725537242590426616.83154
Danio rerioSRR578921femaleovaryadultSJD-Tu hybridsize90151666946457182646226.29238
Danio rerioSRR578922maletestisadultwtsize2419905122374438579328925.89211
Danio rerioSRR578923maletestisadultwtsize2359960319398459195381710.07103
Sus scrofaSRR066809femaleovaryadultwtsize1567692610895053154960.1455
Sus scrofaSRR066810maletestisadultwtsize1729052411782589314719726.71456
Sus scrofaSRR1274763femaleovaryadultwtsize1984503187267419710.1121
Sus scrofaSRR1274764maletestisadultwtsize45301904204507233104555.44501
Sus scrofaSRR1654828maletestisadultwtsize15401196135812371084911879.88598
Homo sapiensERR328151maletestisadultwtsize1431447013804722303864022.01369
Homo sapiensSRR835324maletestisadultwtsize1575915714606168518310835.49328
Homo sapiensSRR835325maletestisadultwtsize1656454915425588673085943.63358
Homo sapiensSRR950451maletestisadultwtsize3613257238792296104140.25355
Homo sapiensSRR1755247femaleovaryadultwtsize52046404120839642411.5635
Homo sapiensSRR1755248femaleovaryadultwtsize516943735231301020412.932
Homo sapiensSRR1755251femaleovary1st trimester embryowtsize26393502099070392931.8710
Homo sapiensSRR1755252femaleovary1st trimester embryowtsize2859936238672150.918
Homo sapiensSRR1755255femaleovary2nd trimester embryowtsize109996579593426413534943.11605
Homo sapiensSRR1755256femaleovary2nd trimester embryowtsize3095294114447329209225.52368
Drosophila melanogasterSRR618933femaleovaryadultwtsize2058041818216952200935311.0317
Drosophila melanogasterSRR797070femaleovaryadultwtsize1711539815994382322574420.1715
Drosophila melanogasterSRR797071femaleovaryadultwtsize1061811999888873139043.1420
Drosophila melanogasterSRR797172femaleovaryadultwtsize1507649913680446193469514.1422
Drosophila melanogasterSRR797179femaleovaryadultwtsize1026033696664443323693.4415
Drosophila melanogasterSRR797182femaleovaryadultwtsize93400188802566143437516.2914
Drosophila melanogasterSRR797187femaleovaryadultwtsize71235496452372130814420.2717
Drosophila melanogasterSRR797193femaleovaryadultwtsize1146277495871643710383.8720
Drosophila melanogasterSRR797195femaleovaryadultwtsize902300780367371844832.315
Drosophila melanogasterSRR797196femaleovaryadultwtsize1780805816750338556430.3317
Drosophila melanogasterSRR797197femaleovaryadultwtsize1655693315118892395310.2616
Drosophila melanogasterSRR797198femaleovaryadultwtsize1164153210431319146902914.0816
Drosophila melanogasterSRR797199femaleovaryadultwtsize53493345070471194300.3822
Drosophila melanogasterSRR797200femaleovaryadultwtsize28104851266312001168540.4417
Drosophila melanogasterSRR797203femaleovaryadultwtsize1549398013571173443250.339
Tupaia belangeriSRR1184429maletestisadultwtsize1924830613389207163926512.24139
Bos taurusSRR1755219femaleoocytesGVwtsize29548814261576122017905977.14260
Bos taurusSRR1755220femaleoocytesGVwtsize26258549233525211841073178.84288
Bos taurusSRR1755221femaleoocytesMIwtsize24781186201863971596867779.11303
Bos taurusSRR1755222femaleoocytesMIwtsize24339995216619811696273878.31304
Bos taurusSRR1755223femaleoocytesMIIwtsize25431045216990331589506973.25293
Bos taurusSRR1755224femaleoocytesMIIwtsize117386616681379511262576.52271
Bos taurusSRR1755225femaleoocytesMIIwtsize18139949147218021106693675.17203
Bos taurusSRR1755226femaleoocytesMIIwtsize26188806226877541535149367.66274
Bos taurusSRR1755227femaleovaryadultwtsize116689949045011303730.3442
Bos taurusSRR1755228femaleovaryadultwtsize100939206122784148760.2439
Bos taurusSRR1755229femaleovaryadultwtsize176467080214615537819.37116
Bos taurusSRR1755230femaleovaryadultwtsize276349517090967053.9271
Bos taurusSRR1755231maletestisadultwtsize30762310280084112510178289.62601
Bos taurusSRR1755232maletestisadultwtsize24720581224010901991384688.9588
Bos taurusSRR1755237mixembryo2-4 cellwtsize54914053678476275773374.97241
Bos taurusSRR1755238mixembryo2-4 cellwtsize68576314386826328185474.81227
Rattus norvegicusSRR035653malebrainadultwtsize1341554726004192313158.965
Rattus norvegicusSRR035657maletestisadultwtsize76231142582607225017787.13192
Rattus norvegicusSRR035659malebrainadultwtsize89617111971069112810.5748
Rattus norvegicusSRR035663maletestisadultwtsize84071812901429254154187.6231




FAQ
- What is the aim of this database? - Where does the small RNA sequence data come from? - How was the raw sequence data processed? - Do the small RNA sequences exclusively represent piRNAs? - How were piRNA clusters annotated? - Can I get the processed sequence data that was used for piRNA cluster prediction? - Which genome builds were used? - How can I get a complete list of piRNA cluster coordinates predicted with a specific SRA dataset? - How can I get a complete list of piRNA cluster coordinates for a species? - Why do piRNA cluster coordinates in the piBrowser differ from the original proTRAC outputs? - How where the generic datasets generated? - Where can I download all sequence reads that map to a specific piRNA cluster? - How can I compare sequence read coverage for one piRNA cluster across different SRA datasets? - What do the values in the FASTA header of the mapped sequence read file mean? - What does the Ping-Pong Z-score mean?

How to access the data
To see the SRA datasets that are available for a certain species click on the desired species name or icon. You will get some basic information on the SRA dataset by moving the mouse cursor over the SRA accession. Each accession is followed by a number of icons that will lead you to the deposited data.


By clicking on the proTRAC you can download the complete proTRAC output. Take a look at the proTRAC documentation for a detailed description of the different output files.


Clicking the statistics icon will open a new window that provides useful information about the SRA dataset as for example total number of sequence reads, mapped sequence reads, clustered sequence reads, number of predicted piRNA clusters. Additional figures and tables provide information on length distribution and positional nucleotide composition of mapped and clustered sequence reads.


Clicking this icon will open a karyomap that displays the location of piRNA clusters on chromosomes. The location of a piRNA cluster is indicated with a bar whose color refers to the number of mapped sequence reads (in relation to the other piRNA clusters). Moving the mouse cursor over a piRNA cluster will show you the sequence read coverage of the according locus as well as some additional information about the mapped sequence reads. By left click you can directly download a FASTA formatted file that comprises the mapped sequence reads for the piRNA cluster in question. Each FASTA header refers to chromosome, starting coordinate, sequence read counts, genomic hits for that sequence, sequence read counts allocated to this locus (using the reallocate tool), and strand. All FASTA files can be obtained by downloading the complete proTRAC output (see above).


Clicking this icon will open a detailed repeat annotation (based on RepeatMasker output) of the mapped sequence reads. In addition, you will find a repeat annotation for the whole genome of the species as well as a repeat annotation for the predicted piRNA clusters. Major classes of repeats (like LINEs, SINEs, DNA elements etc) are listed in the left panel. Each major class is splitted into repeat families (e.g L1, L2 etc. for LINEs) in the right panel. Moving the mouse cursor over a repeat family will show you the exact read counts for this repeat element seperated by sense and antisense reads.


Clicking this icon will open the results of testing for a ping-pong signature (10 nt 5' overlap of mapped sequence reads) using the pingpong tool provided as part of the NGS toolbox. A high amount of 18-22 nt 5' overlap may indicate the presence of Dicer products (miRNAs, siRNAs) in the SRA dataset.


This is a direct link to the metadata linked to the SRA dataset deposited at NCBI's Sequece Read Archive.


Moving the mouse cursor over this icon will show you download links for processed sequence datasets. For each SRA dataset we provide a cleaned up sequence set in FASTA format. In these sequence sets adapter sequences have been removed and the set was collapsed to non-identical sequences using the collapse tool from the NGS toolbox (FASTA headers refer to sequence read counts). In addition, low complexity reads have been removed using the duster tool from the NGS toolbox (default settings). These datasets have been used for mapping and subsequence piRNA cluster prediction with proTRAC.
Further sequence sets comprise miRNAs (perferct global hits to miRBase mature sequences) and putative miRNAs (perfect hits to miRBase hairpin sequences, but not to annotated mature miRNA sequences).


Clicking this icon will open a drop down table that comprises piRNA clusters for the given SRA dataset. Loading the table may take some seconds depending on the number of entries. You can sort and search the table as desired. Each piRNA cluster entry comprises download links for the piRNA cluster sequence, mapped sequence reads and the original proTRAC image output.


This download link provides BED files for the respective dataset. The zip-compressed folder comprises two BED files which list i) individual mapped piRNAs as well as ii) predicted piRNA clusters.


Clicking this icon will open a heatmap that displays the relative transcription rate (normalized, rpm) for genomic loci accross different SRA datasets. The highest value for each locus was set to 1 (color code: 0=blue, 1=red). The data is available as a tab delimited table that comprises rpm values via the download link. This map comprises all genomic loci that were annotated as a piRNA cluster using any SRA dataset. Adjacent loci with a distance less than 10kb were merged.


Use the pi-browser to explore all genomic loci in a species that were found to produce piRNAs under certain conditions. Loci are listed in a sortable table and can also be accessed by clicking on their location on a karyogram. Selecting a specific locus will show you read coverage for every SRA dataset of the species in question as well as annotation of genes, transposons, transcription factor binding sites. The mouse gene annotation includes piRNA precursor transcripts identified by Li and coworkers (Mol Cell. 2013 50(1):67-81. doi: 10.1016/j.molcel.2013.02.016).



Advanced users...
... may want to use our small fetching tool piFETCH to download data deposited at piRNA cluster database without using the web interface. The software including a detailed documentation is available here.




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