{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_strategy = \"OTHER\" and tissue_curation_coarse = \"Reproductive System\"", "rows": [[29746, "SRR27467679", "SRX23139227", "SRS20090270", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "ovary BS R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: ovary  BS  rep2", "EV02003", "EV02003", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV02003.R1.fastq.gz EV02003.R2.fastq.gz", "fastq fastq", 1031891720.0, 3416860.0, "EV02003.R1.fastq.gz", "0:151 1:151", "A:264464363;C:153440613;G:408557241;T:205367487;N:62016", 151, 151, null, null, 264464363, 153440613, 408557241, 205367487, 62016, "SRX23139227", "SRS20090270", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 2, 0.0, 0.00019, 0.0, 0.00015, 1.0, 0.99993, null, 1.0, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Adult", "Adult", "Gonad", "Reproductive System"], [29755, "SRR27467688", "SRX23139218", "SRS20090261", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "ovary DM R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: ovary  DM  rep2", "EV02002", "EV02002", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV02002.R1.fastq.gz EV02002.R2.fastq.gz", "fastq fastq", 861320308.0, 2852054.0, "EV02002.R1.fastq.gz", "0:151 1:151", "A:205625519;C:162178974;G:334206312;T:159256900;N:52603", 151, 151, null, null, 205625519, 162178974, 334206312, 159256900, 52603, "SRX23139218", "SRS20090261", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 2, 2e-05, 0.00049, 0.0, 0.00027, 1.0, 0.99947, null, 0.44444, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Adult", "Adult", "Gonad", "Reproductive System"], [29756, "SRR27467689", "SRX23139217", "SRS20090260", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "ovary mock R2", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: ovary  mock  rep2", "EV02001", "EV02001", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV02001.R1.fastq.gz EV02001.R2.fastq.gz", "fastq fastq", 520371066.0, 1723083.0, "EV02001.R1.fastq.gz", "0:151 1:151", "A:116107273;C:90896560;G:218652568;T:94682244;N:32421", 151, 151, null, null, 116107273, 90896560, 218652568, 94682244, 32421, "SRX23139217", "SRS20090260", "SRA1781872", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 2, 2e-05, 0.00086, 0.0, 0.00078, 0.99995, 0.99981, 0.0, 0.61538, 151, 151, "T", "T", "mates < 9% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-09", "Adult", "Adult", "Gonad", "Reproductive System"], [29765, "SRR27437485", "SRX23109812", "SRS20064566", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "ovary BS R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: ovary  BS  rep3", "EV04017", "EV04017", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV04017.R1.fastq.gz", "fastq", 576584540.0, 4118461.0, "EV04017.R1.fastq.gz", "0:140", "A:149516980;C:91163801;G:169046762;T:166831111;N:25886", 140, null, null, null, 149516980, 91163801, 169046762, 166831111, 25886, "SRX23109812", "SRS20064566", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Adult", "Adult", "Gonad", "Reproductive System"], [29776, "SRR27437496", "SRX23109801", "SRS20064555", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "ovary DM R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: ovary  DM  rep3", "EV04016", "EV04016", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV04016.R1.fastq.gz", "fastq", 635752880.0, 4541092.0, "EV04016.R1.fastq.gz", "0:140", "A:160072248;C:143996869;G:189137330;T:142516059;N:30374", 140, null, null, null, 160072248, 143996869, 189137330, 142516059, 30374, "SRX23109801", "SRS20064555", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 1e-05, null, 0.0, null, 0.99997, null, 1.0, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Adult", "Adult", "Gonad", "Reproductive System"], [29777, "SRR27437497", "SRX23109800", "SRS20064554", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "ovary mock R3", null, "strain:TLAB fish|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: ovary  mock  rep3", "EV04015", "EV04015", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV04015.R1.fastq.gz", "fastq", 489700680.0, 3497862.0, "EV04015.R1.fastq.gz", "0:140", "A:126641754;C:126582886;G:130564204;T:105889815;N:22021", 140, null, null, null, 126641754, 126582886, 130564204, 105889815, 22021, "SRX23109800", "SRS20064554", "SRA1780298", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 6e-05, null, 0.0, null, 0.99983, null, 0.55555, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-06", "Adult", "Adult", "Gonad", "Reproductive System"], [29786, "SRR27435871", "SRX23108225", "SRS20063062", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "ovary BS R4", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:BS|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: ovary  BS  rep4", "EV08003", "EV08003", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08003.R1.fastq.gz", "fastq", 571689580.0, 4083497.0, "EV08003.R1.fastq.gz", "0:140", "A:141414131;C:88722455;G:138790445;T:202723075;N:39474", 140, null, null, null, 141414131, 88722455, 138790445, 202723075, 39474, "SRX23108225", "SRS20063062", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 3e-05, null, 0.0, null, 0.99991, null, 0.75, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Adult", "Adult", "Gonad", "Reproductive System"], [29797, "SRR27435882", "SRX23108214", "SRS20063050", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "ovary DM R4", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:DM|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: ovary  DM  rep4", "EV08002", "EV08002", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08002.R1.fastq.gz", "fastq", 668593800.0, 4775670.0, "EV08002.R1.fastq.gz", "0:140", "A:164584224;C:175789134;G:175538168;T:152637106;N:45168", 140, null, null, null, 164584224, 175789134, 175538168, 152637106, 45168, "SRX23108214", "SRS20063050", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.00525, null, 2e-05, null, 0.99192, null, 0.63501, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Adult", "Adult", "Gonad", "Reproductive System"], [29798, "SRR27435883", "SRX23108213", "SRS20063051", "SRP482074", "PRJNA1061456", "tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development", "PRJNA1061456", "Other", null, null, null, null, null, "ovary mock R4", null, "strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:adult|collection date:2022|geo loc name:Austria|sex:female|tissue:ovary|treatment:mock|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "tRAM seq of zebrafish: ovary  mock  rep4", "EV08001", "EV08001", "RNA was extracted with Trizol  tRNA isolated by size selection on denaturing polyacrylamide gel  range 50 150 nt. The RNA was end repaired by alkaline deacylation and T4 PNK treatment  three prime adapter ligated with T4 RNA ligase 2  reverse transcribed with TGIRT. The cDNA was circularized with CircLigase and amplified with KAPA HiFi polymerase  using NEB Next indexed primers.", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP482074", null, null, "EV08001.R1.fastq.gz", "fastq", 753247460.0, 5380339.0, "EV08001.R1.fastq.gz", "0:140", "A:183862675;C:196453674;G:197604061;T:175275086;N:51964", 140, null, null, null, 183862675, 196453674, 197604061, 175275086, 51964, "SRX23108213", "SRS20063051", "SRA1780265", "Medical University of Vienna|Cell and Developmental Biology", "Medical University of Vienna", 1, 0.00754, null, 4e-05, null, 0.98957, null, 0.51048, null, 140, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Austria", "2024-01-05", "Adult", "Adult", "Gonad", "Reproductive System"], [36424, "SRR516545", "SRX156307", "SRS347187", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   unfertilized egg", "D. rerio unfertilized egg", "D. rerio unfertilized egg", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio unfertilized egg", "CAGE   D. rerio unfertilized egg run2", "D. rerio unfertilized egg", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, null, null, 115273233.0, 4269379.0, "CAGE   D. rerio unfertilized egg run1", "0:27", "A:29909511;C:24823784;G:32519899;T:28020039;N:0", 27, null, null, null, 29909511, 24823784, 32519899, 28020039, 0, "SRX156307", "SRS347187", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.49872, null, 0.07655, null, 0.81673, null, 0.80445, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [36425, "SRR516546", "SRX156307", "SRS347187", "SRP013950", "PRJNA169500", "Danio rerio embryonic promoterome", "PRJNA169500", "Transcriptome Analysis", "Goal of this study is to generate genome wide maps of transcription initiation throughout early embryonic development of zebrafish Danio rerio. Cap analysis of gene expression CAGE is used to detect transcription start sites at 1bp resolution. CAGE data is complemented by ChIPseq datasets for promoter associated histone modifications to study dynamic changes of promoter usage and chromatin configuration throughout early embryonic development.", null, "pubmed:24531765", "Zebrafish wild type AB strain   unfertilized egg", "D. rerio unfertilized egg", "D. rerio unfertilized egg", null, null, null, null, null, null, null, null, null, null, "CAGE   D. rerio unfertilized egg", "CAGE   D. rerio unfertilized egg run2", "D. rerio unfertilized egg", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "CAGE", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP013950", null, null, null, null, 112673943.0, 4173109.0, "CAGE   D. rerio unfertilized egg run2", "0:27", "A:28315221;C:24199098;G:32599482;T:27560142;N:0", 27, null, null, null, 28315221, 24199098, 32599482, 27560142, 0, "SRX156307", "SRS347187", "SRA055273", "University of Bergen", "ZEPROME consortium", 1, 0.46201, null, 0.06422, null, 0.82118, null, 0.82184, null, 27, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "cage", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2012-06-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [44644, "SRR6268204", "SRX3374372", "SRS2671596", "SRP124609", "PRJNA417597", "Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation", "GSE106677", "Other", "The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.", null, "pubmed:29225039", null, "oocyte A+ 7h", "GSM2845358", null, "source name:zebrafish oocyte|developmental stage:7h|tissue:oocyte", "oocyte A+ 7h", "Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5\u2019 terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels", "zebrafish oocyte", "Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.", "Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3\u2019UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3\u2019UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3\u2019UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors", "Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.", "developmental stage:7h|tissue:oocyte", "GSM2845358", "GSM2845358: oocyte A+ 7h; Danio rerio; OTHER", "GSM2845358", null, "1", "Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors", "GEO Accession:GSM2845358", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "SRP124609", null, null, "AR22-SL21.fastq.gz", "fastq", 463495840.0, 2896849.0, "GSM2845358 r1", "0:160 1:0", "A:145685088;C:104925443;G:89232572;T:123650704;N:2033", 160, 0, null, null, 145685088, 104925443, 89232572, 123650704, 2033, "SRX3374372", "SRS2671596", "SRA629220", "GEO", "Broad Institute", 1, 4e-05, null, 1e-05, null, 0.99991, null, 0.5, null, 160, null, "T", null, "under 1.2% mapping rate", "illumina", "miseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-11-08", "Gastrula", "Embryo", "Oocyte", "Reproductive System"], [44645, "SRR6268203", "SRX3374371", "SRS2671594", "SRP124609", "PRJNA417597", "Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation", "GSE106677", "Other", "The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.", null, "pubmed:29225039", null, "oocyte A+ 4h", "GSM2845357", null, "source name:zebrafish oocyte|developmental stage:4h|tissue:oocyte", "oocyte A+ 4h", "Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5\u2019 terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels", "zebrafish oocyte", "Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.", "Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3\u2019UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3\u2019UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3\u2019UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors", "Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.", "developmental stage:4h|tissue:oocyte", "GSM2845357", "GSM2845357: oocyte A+ 4h; Danio rerio; OTHER", "GSM2845357", null, "1", "Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors", "GEO Accession:GSM2845357", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "SRP124609", null, null, "AR21-SL41.fastq.gz", "fastq", 474802240.0, 2967514.0, "GSM2845357 r1", "0:160 1:0", "A:145810423;C:111330144;G:93000312;T:124660574;N:787", 160, 0, null, null, 145810423, 111330144, 93000312, 124660574, 787, "SRX3374371", "SRS2671594", "SRA629220", "GEO", "Broad Institute", 1, 2e-05, null, 0.0, null, 0.99997, null, 0.0, null, 160, null, "T", null, "under 1.2% mapping rate", "illumina", "miseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-11-08", "Blastula", "Embryo", "Oocyte", "Reproductive System"], [44646, "SRR6268202", "SRX3374370", "SRS2671595", "SRP124609", "PRJNA417597", "Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation", "GSE106677", "Other", "The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.", null, "pubmed:29225039", null, "oocyte A+ 1h", "GSM2845356", null, "source name:zebrafish oocyte|developmental stage:1h|tissue:oocyte", "oocyte A+ 1h", "Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5\u2019 terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels", "zebrafish oocyte", "Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.", "Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3\u2019UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3\u2019UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3\u2019UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors", "Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.", "developmental stage:1h|tissue:oocyte", "GSM2845356", "GSM2845356: oocyte A+ 1h; Danio rerio; OTHER", "GSM2845356", null, "1", "Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors", "GEO Accession:GSM2845356", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "SRP124609", null, null, "AR20.fastq.gz", "fastq", 647004960.0, 4043781.0, "GSM2845356 r1", "0:160 1:0", "A:196358573;C:155899107;G:129095192;T:165649225;N:2863", 160, 0, null, null, 196358573, 155899107, 129095192, 165649225, 2863, "SRX3374370", "SRS2671595", "SRA629220", "GEO", "Broad Institute", 1, 1e-05, null, 0.0, null, 0.99997, null, 0.0, null, 160, null, "T", null, "under 1.2% mapping rate", "illumina", "miseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-11-08", "Cleavage", "Embryo", "Oocyte", "Reproductive System"], [44647, "SRR6268201", "SRX3374369", "SRS2671601", "SRP124609", "PRJNA417597", "Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation", "GSE106677", "Other", "The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.", null, "pubmed:29225039", null, "oocyte A  7h", "GSM2845355", null, "source name:zebrafish oocyte|developmental stage:7h|tissue:oocyte", "oocyte A  7h", "Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5\u2019 terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels", "zebrafish oocyte", "Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.", "Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3\u2019UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3\u2019UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3\u2019UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors", "Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.", "developmental stage:7h|tissue:oocyte", "GSM2845355", "GSM2845355: oocyte A  7h; Danio rerio; OTHER", "GSM2845355", null, "1", "Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors", "GEO Accession:GSM2845355", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "SRP124609", null, null, "AR19-SL40.fastq.gz", "fastq", 437084640.0, 2731779.0, "GSM2845355 r1", "0:160 1:0", "A:138575507;C:98512376;G:80808399;T:119186452;N:1906", 160, 0, null, null, 138575507, 98512376, 80808399, 119186452, 1906, "SRX3374369", "SRS2671601", "SRA629220", "GEO", "Broad Institute", 1, 2e-05, null, 0.0, null, 0.99995, null, 1.0, null, 160, null, "T", null, "under 1.2% mapping rate", "illumina", "miseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-11-08", "Gastrula", "Embryo", "Oocyte", "Reproductive System"], [44648, "SRR6268200", "SRX3374368", "SRS2671593", "SRP124609", "PRJNA417597", "Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation", "GSE106677", "Other", "The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.", null, "pubmed:29225039", null, "oocyte A  4h", "GSM2845354", null, "source name:zebrafish oocyte|developmental stage:4h|tissue:oocyte", "oocyte A  4h", "Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5\u2019 terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels", "zebrafish oocyte", "Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.", "Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3\u2019UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3\u2019UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3\u2019UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors", "Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.", "developmental stage:4h|tissue:oocyte", "GSM2845354", "GSM2845354: oocyte A  4h; Danio rerio; OTHER", "GSM2845354", null, "1", "Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors", "GEO Accession:GSM2845354", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "SRP124609", null, null, "AR18-SL39.fastq.gz", "fastq", 533958880.0, 3337243.0, "GSM2845354 r1", "0:160 1:0", "A:163118236;C:125487590;G:106580813;T:138769793;N:2448", 160, 0, null, null, 163118236, 125487590, 106580813, 138769793, 2448, "SRX3374368", "SRS2671593", "SRA629220", "GEO", "Broad Institute", 1, 1e-05, null, 0.0, null, 0.99997, null, 0.0, null, 160, null, "T", null, "under 1.2% mapping rate", "illumina", "miseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-11-08", "Blastula", "Embryo", "Oocyte", "Reproductive System"], [44649, "SRR6268199", "SRX3374367", "SRS2671602", "SRP124609", "PRJNA417597", "Massively parallel reporter assay of three primeUTR sequences identifies in vivo rules for mRNA degradation", "GSE106677", "Other", "The stability of mRNAs is regulated by signals within their sequences  but a systematic and predictive understanding of the underlying sequence rules remains elusive. Here  we introduce UTR Seq  a combination of massively parallel reporter assays and regression models  to survey the dynamics of tens of thousands of three primeUTR sequences during early zebrafish embryogenesis. UTR Seq revealed two temporal degradation programs: a maternally encoded early onset program and a late onset program that accelerated degradation post zygotic genome activation. Three signals regulated early onset rates: stabilizing poly U and UUAG sequences  and destabilizing GC rich signals. Three signals explained late onset degradation: miR 430 seeds  AU rich sequences and Pumilio recognition sites. Sequence based regression models translated three primeUTRs into their unique decay patterns  and predicted the in vivo impact of sequence signals on mRNA stability. Their application led to the successful design of artificial three primeUTRs that conferred specific mRNA dynamics. UTR Seq provides a general strategy to uncover the rules of RNA cis regulation. Overall design: temporal expression profiles of reporter mRNAs from zebrafish embryos 7 replicates total or oocytes 2 replicates total. A total of five embryo replicates were collected using pre adenylated A+ reporters in three separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment  a single sample was collected every hour between 1h to 10h  and split into two post RNA extraction to produce two technical replicates techrep. In the third experiment  two separate samples were collected every two hours between 2h to 10h to produce two same day biological replicates biorep. A total of two replicates were collected using non adenylated A  reporters in two separate experiments. In the first experiment  a sample was collected every hour between 1h to 8h  and at 10h. In the second experiment rep  samples were collected at 1h  2h  3h  4h 3 samples  6h  8h and 10h.", null, "pubmed:29225039", null, "oocyte A  1h", "GSM2845353", null, "source name:zebrafish oocyte|developmental stage:1h|tissue:oocyte", "oocyte A  1h", "Library strategy: UTR Seq data 160nt reads was filtered to retain only sequences that contained both terminal adapter sequences with up to 10 mismatches and an insert of 90nt or longer. data 100nt reads was filtered to retain only sequences that contained the 5\u2019 terminal adapter sequence with up to 10 mismatches and an insert of 62nt or longer. Bowtie2 was used to align retained reads to a reference set of all 90 000 synthetic oligonucleotide sequences The number of UMIs that were mapped to each oligonucleotide sequence was recorded and adjusted to represent the expected number of mRNA molecules in the sample. A generalized binomial linear regression model was fitted to counts of five control mRNAs that were added to samples at known quantities in 2 fold increments highest 50fg  lowest 3.125fg  and the resulting linear transformation was used to normalize UMI counts. Genome build: The file sequences.txt is a FASTA file with the oligonucleotide sequences used for real alignment. This file is available on the series record. Supplementary files format and content: tab delimited files of normalized mRNA levels", "zebrafish oocyte", "Embryos/oocytes were removed from their chorion and injected with 50 80pg of reporter mRNAs at the one cell stage.", "Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known 3\u2019UTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant 3\u2019UTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant 3\u2019UTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors", "Fertilized zebrafish eggs or oocytes were collected at 28C  and kept in culture medium 5.03mM NaCl  0.17mM KCl  0.33mM CaCl2  0.33mM MgSo4  0.1% Methylene blue.  A total of 20 40 injected embryos/oocytes were randomly collected per sample post ensuring that all embryos were at the same expected developmental stage.", "developmental stage:1h|tissue:oocyte", "GSM2845353", "GSM2845353: oocyte A  1h; Danio rerio; OTHER", "GSM2845353", null, "1", "Total RNA was isolated using TRIzol Invitrogen  post adding 120fg of mRNA with 5 known three primeUTR control sequences into each RNA sample during the initial TRIzol lysis step. In the first step  total RNA was reverse transcribed with Maxima RT Thermo Fisher and a gene specific primer that matched the constant three primeUTR of mRNA reporters. RT primer also added a random 8nt UMI and a constant RT adaptor sequence. In the second step  resulting cDNA was amplified by 18 cycles of Phusion PCR with primers that matched the reporter's constant three primeUTR sequence and the RT adaptor. PCR primers also added the appropriate Illumina sample barcodes and sequencing. adaptors", "GEO Accession:GSM2845353", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina MiSeq", null, "SRP124609", null, null, "AR17-SL38.fastq.gz", "fastq", 532076160.0, 3325476.0, "GSM2845353 r1", "0:160 1:0", "A:162057480;C:125858627;G:108494717;T:135663057;N:2279", 160, 0, null, null, 162057480, 125858627, 108494717, 135663057, 2279, "SRX3374367", "SRS2671602", "SRA629220", "GEO", "Broad Institute", 1, 2e-05, null, 0.0, null, 0.99995, null, 1.0, null, 160, null, "T", null, "under 1.2% mapping rate", "illumina", "miseq", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "United States", "2017-11-08", "Cleavage", "Embryo", "Oocyte", "Reproductive System"], [59512, "SRR11924307", "SRX8469983", "SRS6770634", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "Unf egg 3", "GSM4591051", null, "source name:unfertilized egg|tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA", "Unf egg 3", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "unfertilized egg", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591051", "GSM4591051: Unf egg 3; Danio rerio; OTHER", "GSM4591051", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591051", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "GSE151797_Reference_sequence.fa Unf_egg_3.bam", "bam bam", 149835556.0, 5777340.0, "GSM4591051 r1", "0:25.94", "A:27873539;C:50837956;G:37710769;T:33413292;N:0", 25, null, null, null, 27873539, 50837956, 37710769, 33413292, 0, "SRX8469983", "SRS6770634", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.74561, null, 0.22616, null, 0.89441, null, 0.76897, null, 34, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [59513, "SRR11924305", "SRX8469982", "SRS6770633", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "Unf egg 2", "GSM4591050", null, "source name:unfertilized egg|tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA", "Unf egg 2", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "unfertilized egg", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591050", "GSM4591050: Unf egg 2; Danio rerio; OTHER", "GSM4591050", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591050", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "GSE151797_Reference_sequence.fa Unf_egg_2.bam", "bam bam", 235014832.0, 8915586.0, "GSM4591050 r1", "0:26.36", "A:43825969;C:79775479;G:60531219;T:50882165;N:0", 26, null, null, null, 43825969, 79775479, 60531219, 50882165, 0, "SRX8469982", "SRS6770633", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.78414, null, 0.23044, null, 0.90352, null, 0.76934, null, 40, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [59514, "SRR11924304", "SRX8469981", "SRS6770632", "SRP265951", "PRJNA637293", "The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites", "GSE151797", "Other", "A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.", null, "pubmed:32912962", null, "Unf egg 1", "GSM4591049", null, "source name:unfertilized egg|tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA", "Unf egg 1", "Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.", "unfertilized egg", null, "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", null, "tissue:unfertilized egg|rna fraction:size fractionated 20 40 nt whole cell RNA", "GSM4591049", "GSM4591049: Unf egg 1; Danio rerio; OTHER", "GSM4591049", null, "1", "Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description", "GEO Accession:GSM4591049", "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP265951", null, "intentional duplicate", "GSE151797_Reference_sequence.fa Unf_egg_1.bam", "bam bam", 245529952.0, 9182415.0, "GSM4591049 r1", "0:26.74", "A:46557080;C:80893860;G:66050448;T:52028564;N:0", 26, null, null, null, 46557080, 80893860, 66050448, 52028564, 0, "SRX8469981", "SRS6770632", "SRA1083099", "GEO", "RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen", 1, 0.87423, null, 0.27943, null, 0.91721, null, 0.76816, null, 37, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "5prime", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Denmark", "2020-06-04", "Zygote", "Embryo", "Oocyte", "Reproductive System"]], "truncated": false, "filtered_table_rows_count": 20, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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], 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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 from run_metadata where \"experiment.library_strategy\" = :p0 and \"tissue_curation_coarse\" = :p1 order by rowid limit 101", "params": {"p0": "OTHER", "p1": "Reproductive System"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_strategy=OTHER&tissue_curation_coarse=Reproductive+System", "results": [{"value": "OTHER", "label": "OTHER", "count": 20, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation_coarse=Reproductive+System", "selected": true}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": 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"toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_strategy=OTHER&tissue_curation_coarse=Reproductive+System&experiment.library_selection=size+fractionation", "selected": false}, {"value": "CAGE", "label": "CAGE", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_strategy=OTHER&tissue_curation_coarse=Reproductive+System&experiment.library_selection=CAGE", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_strategy=OTHER&tissue_curation_coarse=Reproductive+System", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 17, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_strategy=OTHER&tissue_curation_coarse=Reproductive+System&experiment.library_layout=SINGLE", "selected": false}, {"value": "PAIRED", "label": "PAIRED", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_strategy=OTHER&tissue_curation_coarse=Reproductive+System&experiment.library_layout=PAIRED", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_strategy=OTHER&tissue_curation_coarse=Reproductive+System", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 17, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_strategy=OTHER&tissue_curation_coarse=Reproductive+System&experiment.platform=ILLUMINA", "selected": false}, {"value": "ION_TORRENT", "label": "ION_TORRENT", "count": 3, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_strategy=OTHER&tissue_curation_coarse=Reproductive+System&experiment.platform=ION_TORRENT", 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