{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"other\" and tissue_curation = \"Oocyte\"", "rows": [[40701, "SRR3231363", "SRX1637111", "SRS1342926", "SRP071849", "PRJNA315400", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]", "GSE79161", "Transcriptome Analysis", "Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "Input 3", "GSM2087141", null, "tissue:Zebrafish Zygotes|fraction:Input", "Input 3", "Reads were mapped to Zv9 using tophat trapnell et al  2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al  2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.", "Zebrafish Zygotes", null, "mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.", "Zebrafish were maintained under standard conditions.", "fraction:Input", "GSM2087141", "GSM2087141: Input 3; Danio rerio; RIP Seq", "GSM2087141", null, "1", "mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.", "GEO Accession:GSM2087141", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP071849", null, null, "WT_Input_3.fastq.gz", "fastq", 1902296226.0, 37299926.0, "GSM2087141 r1", "0:51", "A:466290166;C:465344039;G:486942278;T:483240280;N:479463", 51, null, null, null, 466290166, 465344039, 486942278, 483240280, 479463, "SRX1637111", "SRS1342926", "SRA385813", "GEO", "Rene Ketting, RNA silencing, IMB", 1, 0.85793, null, 0.14814, null, 0.79941, null, 0.55214, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Germany", "2016-03-13", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [40702, "SRR3231362", "SRX1637110", "SRS1342927", "SRP071849", "PRJNA315400", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]", "GSE79161", "Transcriptome Analysis", "Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "Input 2", "GSM2087140", null, "tissue:Zebrafish Zygotes|fraction:Input", "Input 2", "Reads were mapped to Zv9 using tophat trapnell et al  2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al  2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.", "Zebrafish Zygotes", null, "mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.", "Zebrafish were maintained under standard conditions.", "fraction:Input", "GSM2087140", "GSM2087140: Input 2; Danio rerio; RIP Seq", "GSM2087140", null, "1", "mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.", "GEO Accession:GSM2087140", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP071849", null, null, "WT_Input_2.fastq.gz", "fastq", 1540737999.0, 30210549.0, "GSM2087140 r1", "0:51", "A:380481772;C:379741192;G:395453141;T:384675313;N:386581", 51, null, null, null, 380481772, 379741192, 395453141, 384675313, 386581, "SRX1637110", "SRS1342927", "SRA385813", "GEO", "Rene Ketting, RNA silencing, IMB", 1, 0.8787, null, 0.14935, null, 0.79202, null, 0.54381, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Germany", "2016-03-13", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [40703, "SRR3231361", "SRX1637109", "SRS1342928", "SRP071849", "PRJNA315400", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]", "GSE79161", "Transcriptome Analysis", "Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "Input 1", "GSM2087139", null, "tissue:Zebrafish Zygotes|fraction:Input", "Input 1", "Reads were mapped to Zv9 using tophat trapnell et al  2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al  2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.", "Zebrafish Zygotes", null, "mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.", "Zebrafish were maintained under standard conditions.", "fraction:Input", "GSM2087139", "GSM2087139: Input 1; Danio rerio; RIP Seq", "GSM2087139", null, "1", "mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.", "GEO Accession:GSM2087139", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP071849", null, null, "WT_Input_1.fastq.gz", "fastq", 1109818905.0, 21761155.0, "GSM2087139 r1", null, null, null, null, null, null, null, null, null, null, null, "SRX1637109", "SRS1342928", "SRA385813", "GEO", "Rene Ketting, RNA silencing, IMB", 1, 0.87467, null, 0.18794, null, 0.79411, null, 0.63378, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Germany", "2016-03-13", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [40704, "SRR3231360", "SRX1637108", "SRS1342929", "SRP071849", "PRJNA315400", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]", "GSE79161", "Transcriptome Analysis", "Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "Tdrd6a IP 3", "GSM2087138", null, "tissue:Zebrafish Zygotes|fraction:Tdrd6a IP", "Tdrd6a IP 3", "Reads were mapped to Zv9 using tophat trapnell et al  2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al  2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.", "Zebrafish Zygotes", null, "mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.", "Zebrafish were maintained under standard conditions.", "fraction:Tdrd6a IP", "GSM2087138", "GSM2087138: Tdrd6a IP 3; Danio rerio; RIP Seq", "GSM2087138", null, "1", "mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.", "GEO Accession:GSM2087138", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP071849", null, null, "WT_Tdrd6a_IP_3.fastq.gz", "fastq", 843641439.0, 16541989.0, "GSM2087138 r1", "0:51", "A:216465581;C:196892096;G:207722567;T:222361382;N:199813", 51, null, null, null, 216465581, 196892096, 207722567, 222361382, 199813, "SRX1637108", "SRS1342929", "SRA385813", "GEO", "Rene Ketting, RNA silencing, IMB", 1, 0.84615, null, 0.08957, null, 0.78768, null, 0.50612, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Germany", "2016-03-13", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [40705, "SRR3231359", "SRX1637107", "SRS1342930", "SRP071849", "PRJNA315400", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]", "GSE79161", "Transcriptome Analysis", "Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "Tdrd6a IP 2", "GSM2087137", null, "tissue:Zebrafish Zygotes|fraction:Tdrd6a IP", "Tdrd6a IP 2", "Reads were mapped to Zv9 using tophat trapnell et al  2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al  2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.", "Zebrafish Zygotes", null, "mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.", "Zebrafish were maintained under standard conditions.", "fraction:Tdrd6a IP", "GSM2087137", "GSM2087137: Tdrd6a IP 2; Danio rerio; RIP Seq", "GSM2087137", null, "1", "mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.", "GEO Accession:GSM2087137", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP071849", null, null, "WT_Tdrd6a_IP_2.fastq.gz", "fastq", 391198050.0, 7670550.0, "GSM2087137 r1", "0:51", "A:99015594;C:91525929;G:97155710;T:103371571;N:129246", 51, null, null, null, 99015594, 91525929, 97155710, 103371571, 129246, "SRX1637107", "SRS1342930", "SRA385813", "GEO", "Rene Ketting, RNA silencing, IMB", 1, 0.85778, null, 0.12015, null, 0.80515, null, 0.47541, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Germany", "2016-03-13", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [40706, "SRR3231358", "SRX1637106", "SRS1342931", "SRP071849", "PRJNA315400", "Tdrd6a recruits Ziwi bound piRNAs and coordinates deposition of germ plasm mRNAs into primordial germ cells [RIP Seq]", "GSE79161", "Transcriptome Analysis", "Germ plasm  the Balbiani body and nuage are evolutionary conserved structures essential for germ cell specification and maintenance. We describe Tdrd6a as a component of these structures with two distinct molecular functions. First  Tdrd6a facilitates the accumulation of the typical antisense bias of piRNAs  without xxx effects on piRNA biogenesis signatures. Second  we show that Tdrd6a is required for Balbiani body and germ plasm integrity  and associates with RNA binding proteins and germ plasm mRNAs. On the cell biological level  maternally contributed Tdrd6a strongly impacts germ cell formation  but is dispensable for fertility. Using single cell RNA sequencing we demonstrate that Tdrd6a promotes early germ cell development and regulates the stoichiometry of germ plasm mRNAs. We propose that Tdrd6a functions as a scaffold to recruit correct ratios of germ plasm transcripts and to accumulate antisense piRNA complexes in order to ensure both specification and maintenance of germ cells. Overall design: RNA was extracted from ovary tissue or from RIP experiments by Trizol extraction.", "parent bioproject:PRJNA315403", "pubmed:30086300", null, "Tdrd6a IP 1", "GSM2087136", null, "tissue:Zebrafish Zygotes|fraction:Tdrd6a IP", "Tdrd6a IP 1", "Reads were mapped to Zv9 using tophat trapnell et al  2009to the ENSEMBLE gene build and further processing of the read counts was performed using Deseq Anders et al  2009 Genome build: zv9 Supplementary files format and content: The mRNA counts.csv contains the DESeq normalized read counts per Ensemble gene as indicated. Headers indicate the sample name.", "Zebrafish Zygotes", null, "mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.", "Zebrafish were maintained under standard conditions.", "fraction:Tdrd6a IP", "GSM2087136", "GSM2087136: Tdrd6a IP 1; Danio rerio; RIP Seq", "GSM2087136", null, "1", "mRNA was extracted from zygotes or by RIP experiments followed by Trizol extraction The RNA was extracted using chloroform and precipitated with iso propanol. Ovation RNA seq System V2 NuGEN library preperation kit was used and the library was sequenced on an Illumina HISEQ using 50bp single end sequencing.", "GEO Accession:GSM2087136", "RIP-Seq", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP071849", null, null, "WT_Tdrd6a_IP_1.fastq.gz", "fastq", 1927415052.0, 37792452.0, "GSM2087136 r1", "0:51", "A:498125298;C:444860381;G:468826607;T:515142356;N:460410", 51, null, null, null, 498125298, 444860381, 468826607, 515142356, 460410, "SRX1637106", "SRS1342931", "SRA385813", "GEO", "Rene Ketting, RNA silencing, IMB", 1, 0.86194, null, 0.09753, null, 0.80146, null, 0.47808, null, 51, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "other", "unknown", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Germany", "2016-03-13", "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"], [66194, "SRR16096233", "SRX12382357", "SRS10353019", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep5", "GSM5599725", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep5", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599725", "GSM5599725: ZF zygote IP 1cell Rep5; Danio rerio; RIP Seq", "GSM5599725", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599725", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep5_R1.fastq.gz ZF_zygote_IP_1cell_Rep5_R2.fastq.gz", "fastq fastq", 3660517860.0, 35887430.0, "GSM5599725 r1", "0:51 1:51", "A:858138600;C:924733544;G:1002150083;T:875349961;N:145672", 51, 51, null, null, 858138600, 924733544, 1002150083, 875349961, 145672, "SRX12382357", "SRS10353019", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.83384, 0.82667, 0.09687, 0.11892, 0.79076, 0.79326, 0.63739, 0.60941, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66195, "SRR16096232", "SRX12382356", "SRS10353018", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep4", "GSM5599724", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep4", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599724", "GSM5599724: ZF zygote IP 1cell Rep4; Danio rerio; RIP Seq", "GSM5599724", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599724", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep4_R1.fastq.gz ZF_zygote_IP_1cell_Rep4_R2.fastq.gz", "fastq fastq", 3660205842.0, 35884371.0, "GSM5599724 r1", "0:51 1:51", "A:895738659;C:880838836;G:971118499;T:912364119;N:145729", 51, 51, null, null, 895738659, 880838836, 971118499, 912364119, 145729, "SRX12382356", "SRS10353018", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.87258, 0.86932, 0.06573, 0.07958, 0.78044, 0.78374, 0.55531, 0.5462, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66196, "SRR16096231", "SRX12382355", "SRS10353016", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep3", "GSM5599723", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep3", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599723", "GSM5599723: ZF zygote IP 1cell Rep3; Danio rerio; RIP Seq", "GSM5599723", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599723", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep3_R1.fastq.gz ZF_zygote_IP_1cell_Rep3_R2.fastq.gz", "fastq fastq", 2732409048.0, 26788324.0, "GSM5599723 r1", "0:51 1:51", "A:669345195;C:656715671;G:724415204;T:681825149;N:107829", 51, 51, null, null, 669345195, 656715671, 724415204, 681825149, 107829, "SRX12382355", "SRS10353016", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.85204, 0.83607, 0.06526, 0.08046, 0.78535, 0.78748, 0.60467, 0.50165, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66197, "SRR16096230", "SRX12382354", "SRS10353017", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep2", "GSM5599722", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599722", "GSM5599722: ZF zygote IP 1cell Rep2; Danio rerio; RIP Seq", "GSM5599722", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599722", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep2_R1.fastq.gz ZF_zygote_IP_1cell_Rep2_R2.fastq.gz", "fastq fastq", 2235668028.0, 21918314.0, "GSM5599722 r1", "0:51 1:51", "A:552522700;C:535947981;G:588168855;T:558939713;N:88779", 51, 51, null, null, 552522700, 535947981, 588168855, 558939713, 88779, "SRX12382354", "SRS10353017", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.85597, 0.85298, 0.06663, 0.07927, 0.79058, 0.79237, 0.57626, 0.56525, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66198, "SRR16096229", "SRX12382353", "SRS10353015", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 1cell Rep1", "GSM5599721", null, "tissue:ZF zygote IP 1cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 1cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 1cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599721", "GSM5599721: ZF zygote IP 1cell Rep1; Danio rerio; RIP Seq", "GSM5599721", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599721", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_1cell_Rep1_R1.fastq.gz ZF_zygote_IP_1cell_Rep1_R2.fastq.gz", "fastq fastq", 1785761736.0, 17507468.0, "GSM5599721 r1", "0:51 1:51", "A:429081683;C:435813601;G:481376346;T:439419714;N:70392", 51, 51, null, null, 429081683, 435813601, 481376346, 439419714, 70392, "SRX12382353", "SRS10353015", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.75314, 0.75693, 0.0543, 0.06639, 0.79482, 0.79594, 0.57979, 0.56522, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66199, "SRR16096228", "SRX12382352", "SRS10353014", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 5cell Rep3", "GSM5599720", null, "tissue:ZF zygote IP 5cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 5cell Rep3", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 5cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599720", "GSM5599720: ZF zygote IP 5cell Rep3; Danio rerio; RIP Seq", "GSM5599720", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599720", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_5cell_Rep3_R1.fastq.gz ZF_zygote_IP_5cell_Rep3_R2.fastq.gz", "fastq fastq", 2179659420.0, 21369210.0, "GSM5599720 r1", "0:51 1:51", "A:539092949;C:513857324;G:569620218;T:556940661;N:148268", 51, 51, null, null, 539092949, 513857324, 569620218, 556940661, 148268, "SRX12382352", "SRS10353014", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.92028, 0.90706, 0.03967, 0.05572, 0.78431, 0.78886, 0.49727, 0.48541, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66200, "SRR16096227", "SRX12382351", "SRS10353012", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 5cell Rep2", "GSM5599719", null, "tissue:ZF zygote IP 5cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 5cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 5cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599719", "GSM5599719: ZF zygote IP 5cell Rep2; Danio rerio; RIP Seq", "GSM5599719", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599719", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_5cell_Rep2_R1.fastq.gz ZF_zygote_IP_5cell_Rep2_R2.fastq.gz", "fastq fastq", 2527184538.0, 24776319.0, "GSM5599719 r1", "0:51 1:51", "A:628307375;C:594702688;G:657847712;T:646151885;N:174878", 51, 51, null, null, 628307375, 594702688, 657847712, 646151885, 174878, "SRX12382351", "SRS10353012", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91811, 0.90487, 0.03919, 0.05376, 0.78315, 0.78729, 0.49414, 0.48564, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66201, "SRR16096226", "SRX12382350", "SRS10353011", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 5cell Rep1", "GSM5599718", null, "tissue:ZF zygote IP 5cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 5cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 5cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599718", "GSM5599718: ZF zygote IP 5cell Rep1; Danio rerio; RIP Seq", "GSM5599718", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599718", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_5cell_Rep1_R1.fastq.gz ZF_zygote_IP_5cell_Rep1_R2.fastq.gz", "fastq fastq", 3481342518.0, 34130809.0, "GSM5599718 r1", "0:51 1:51", "A:865680250;C:823420389;G:907146965;T:884854199;N:240715", 51, 51, null, null, 865680250, 823420389, 907146965, 884854199, 240715, "SRX12382350", "SRS10353011", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91893, 0.90939, 0.04544, 0.06005, 0.78025, 0.78348, 0.50569, 0.49155, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66202, "SRR16096225", "SRX12382349", "SRS10353013", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 10cell Rep3", "GSM5599717", null, "tissue:ZF zygote IP 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 10cell Rep3", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599717", "GSM5599717: ZF zygote IP 10cell Rep3; Danio rerio; RIP Seq", "GSM5599717", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599717", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_10cell_Rep3_R1.fastq.gz ZF_zygote_IP_10cell_Rep3_R2.fastq.gz", "fastq fastq", 2172362850.0, 21297675.0, "GSM5599717 r1", "0:51 1:51", "A:536043605;C:513512883;G:568368414;T:554284996;N:152952", 51, 51, null, null, 536043605, 513512883, 568368414, 554284996, 152952, "SRX12382349", "SRS10353013", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91859, 0.90522, 0.03736, 0.05214, 0.78715, 0.79129, 0.49736, 0.48681, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66203, "SRR16096224", "SRX12382348", "SRS10353010", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 10cell Rep2", "GSM5599716", null, "tissue:ZF zygote IP 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 10cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599716", "GSM5599716: ZF zygote IP 10cell Rep2; Danio rerio; RIP Seq", "GSM5599716", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599716", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_10cell_Rep2_R1.fastq.gz ZF_zygote_IP_10cell_Rep2_R2.fastq.gz", "fastq fastq", 1840839492.0, 18047446.0, "GSM5599716 r1", "0:51 1:51", "A:454385290;C:437082102;G:482351138;T:466893642;N:127320", 51, 51, null, null, 454385290, 437082102, 482351138, 466893642, 127320, "SRX12382348", "SRS10353010", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.92217, 0.90956, 0.04012, 0.05483, 0.78819, 0.79318, 0.49756, 0.48256, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66204, "SRR16096223", "SRX12382347", "SRS10353009", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote IP 10cell Rep1", "GSM5599715", null, "tissue:ZF zygote IP 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote IP 10cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote IP 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599715", "GSM5599715: ZF zygote IP 10cell Rep1; Danio rerio; RIP Seq", "GSM5599715", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599715", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_IP_10cell_Rep1_R1.fastq.gz ZF_zygote_IP_10cell_Rep1_R2.fastq.gz", "fastq fastq", 2400553680.0, 23534840.0, "GSM5599715 r1", "0:51 1:51", "A:594878203;C:567573525;G:625488388;T:612448386;N:165178", 51, 51, null, null, 594878203, 567573525, 625488388, 612448386, 165178, "SRX12382347", "SRS10353009", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91641, 0.908, 0.03979, 0.05394, 0.78455, 0.7892, 0.48862, 0.47478, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66205, "SRR16096222", "SRX12382346", "SRS10353008", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote Input 10cell Rep2", "GSM5599714", null, "tissue:ZF zygote Input 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote Input 10cell Rep2", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote Input 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599714", "GSM5599714: ZF zygote Input 10cell Rep2; Danio rerio; RIP Seq", "GSM5599714", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599714", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_Input_10cell_Rep2_R1.fastq.gz ZF_zygote_Input_10cell_Rep2_R2.fastq.gz", "fastq fastq", 3842772582.0, 37674241.0, "GSM5599714 r1", "0:51 1:51", "A:843564828;C:1054412690;G:1130769812;T:813758353;N:266899", 51, 51, null, null, 843564828, 1054412690, 1130769812, 813758353, 266899, "SRX12382346", "SRS10353008", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91511, 0.90868, 0.32791, 0.38048, 0.89457, 0.89441, 0.81532, 0.75274, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"], [66206, "SRR16096221", "SRX12382345", "SRS10353007", "SRP339082", "PRJNA766854", "RNA m6A methylome from zebrafish zygotes  mouse liver polyA selected RNAs  mouse embryonic stem cells  spike in RNA controls  and single mouse oocytes and embryos", "GSE184893", "Other", "N6 methyladenosine m6A is a prevalent RNA modification that has key roles in distinct biological processes  including meiosis and early embryo development. Despite advances in methodology for m6A mapping  the applicability of current methods is limited by the need for large amounts of input material. We develop a sensitive picogram scale m6A RNA immunoprecipitation and sequencing picoMeRIP seq method  also suitable for single cell scMeRIP seq. We validate the down scaling of the method by profiling m6A from picogram amounts of mouse liver polyA selected RNA  mouse embryonic stem cells  and zebrafish zygotes. We provide proof of principle of m6A profiling in single mouse oocytes and preimplantation embryos. Our work opens a new avenue for studying m6A in single cells and scarce cell types in a transcriptome wide manner. Overall design: Transcriptome wide m6A maps were generated from zebrafish and mouse samples as below. 11 zebrafish zygote samples: 3 biological replicates for 10 zygotes  3 biological replicates for 5 zygotes  and 5 biological replicates for single zygote. 6 mouse liver polyA selected RNA samples: 10 ng  1 ng  and 100 pg; 2 biological replicates for each amount. 9 mouse embryonic stem cell R1 cell line  from ATCC  SCRC 1011 samples: 1000 cells  100 cells  and 10 cells; 3 biological replicates for each amount. 3 spike in RNA control add 0.001 fmol Gaussia luciferase/GLuc with m6A modification and 0.001 fmol Cypridina luciferase/CLuc without xxx modification into the 12 ng polyA selected RNAs related samples: 12 ng polyA selected RNA from mouse liver; 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from wild type/WT mouse embryonic stem cells from Geula  S.  et al. Science 2015; and 6 ng polyA selected RNA from mouse liver and 6 ng polyA selected RNA from Mettl3 knock out/KO mouse embryonic stem cells from Geula  S.  et al. Science 2015. 12 single mouse oocyte and embryo samples: oocytes at germinal vesicle GV and metaphase II MII stages  and embryos at zygote  2 cell  8 cell and blastocyst stages; 2 biological replicates per developmental stage. The pooled Input samples for GV oocyte GSM5746922  zygote GSM5746930  2 cell GSM5746911 and 8 cell GSM5746914 stages can be found in GSE192440.", null, "pubmed:37349523", null, "ZF zygote Input 10cell Rep1", "GSM5599713", null, "tissue:ZF zygote Input 10cell|developmental stage:Zygote|molecule subtype:rRNA free RNA", "ZF zygote Input 10cell Rep1", "Quality of raw reads was assessed using FastQC v0.11.8 and sequencing adapters were trimmed using Cutadapt v1.8.1 if clear adapter signal was detected at the three primeend of the reads. There is no adapter removal for zebrafish zygote samples GSM5599713  GSM5599714  GSM5599715  GSM5599716  GSM5599717  GSM5599718  GSM5599719  GSM5599720  GSM5599721  GSM5599722  GSM5599723  GSM5599724  GSM5599725  mouse polyA selected RNA samples GSM5599726  GSM5599727  GSM5599728  GSM5599729  GSM5599730  GSM5599731  GSM5599732  GSM5599733  and mouse MII oocyte Input sample GSM5599734. Trimmed reads were aligned to the reference genome mm10 for mouse  danRer11 for zebrafish using HISAT2 v2.1.0 with the parameter \u201c 5 8   no mixed   no discordant\u201d. Multiply aligned reads were discarded as indicated by HISAT2. PCR duplicates were removed using Samtools v1.9. The read pairs that overlapped with ribosomal RNAs were removed using BEDTools v2.28.0. Genome coverage bigWig files bin size = 10 bp  normalized by RPKM were generated by deepTools v3.2.0 bamCoverage with the parameter \u201c bs 10   normalizeUsing RPKM\u201d. Genome build: mm10 for mouse  danRer11 for zebrafish Supplementary files format and content: The bigWig files are generated by deepTools v3.2.0 bamCoverage with the bin size=10bp and normalized by RPKM.", "ZF zygote Input 10cell", "For mouse GV oocyte collection  8 wpf C57BL6/N females were injected with 5 units U of pregnant mare serum gonadotropin PMSG. post 48 hours  ovaries were dissected and oocytes were isolated by puncturing the follicles. The procedure was carried out in M2 medium Sigma supplemented with 0.2 mM of the cyclic nucleotide phosphodiesterase inhibitor 3 Isobutyl 1 methylxanthine IBMX  Sigma to prevent the oocytes from further progress to germinal vesicle breakdown GVBD. The cumulus cells were gently removed by pipetting  and the oocytes were briefly exposed to acidic Tyrode's solution Sigma to remove the zona pellucida  followed by three washes in M2 medium. For mouse MII oocyte collection  4 wpf 5 wpf C57BL6/N females were injected with 5 U of PMSG followed by 5 U of human chorionic gonadotropin hCG 45 hours later. The oviducts were dissected 20 22 hours later and transferred to a clean dish containing M2 medium. The oviduct ampulla was identified under a stereomicroscope to isolate MII oocytes containing the cumulus mass. The oocytes were treated with 0.3 mg/ml hyaluronidase dissolved in M2 medium to remove the cumulus cells  and then exposed to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium. For mouse early embryo collection  8 wpf C57BL/6N females were superovulated by hormone injection 5 U PMSG followed by 5 U hCG 45 hours later and transferred to cages with 8 wpf C57BL/6N males for mating. At 27 28\u2009hours zygote  39 43\u2009hours 2 cell  68 70\u2009hours 8 cell  and 92 94\u2009hours blastocyst post hCG administration  the female mice were euthanized by cervical dislocation. Embryos were flushed from the reproductive tract into HEPES buffered CZB medium  then transferred to acidic Tyrode's solution for a few seconds to remove the zona pellucida  followed by three washes in M2 medium.", "For zebrafish bulk zygote samples  total RNA was extracted from 100 zebrafish zygotes using TRIzol\u2122 Reagent and eluated in 100 \u03bcl of RNase free water. Then  10 \u03bcl and 5 \u03bcl samples were taken for 10 zygote and 5 zygote samples  respectively  and volumes were adjusted to 12 \u03bcl with nuclease free water. For zebrafish single zygote samples  single zygote was manually picked and distributed into 12 \u03bcl of 1X Lysis buffer Takara. For the polyA selected RNA samples of mouse liver and embryonic stem cell WT and Mettl3 KO  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For mouse embryonic stem cell samples  the cells were sorted into 12 \u03bcl 1X Lysis buffer using BD FACSMelody\u2122 Cell Sorter BD Biosciences. For mouse oocyte and embryo samples  post three washes in M2 medium  oocytes and embryos were manually picked and put into 12 \u03bcl 1X Lysis buffer. For picoMeRIP seq experiment  NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sheared by sonication  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", null, "developmental stage:Zygote|molecule subtype:rRNA free RNA", "GSM5599713", "GSM5599713: ZF zygote Input 10cell Rep1; Danio rerio; RIP Seq", "GSM5599713", null, "1", "For mouse liver  total RNA was extracted using TRIzol\u2122 Reagent Thermo Fisher Scientific and PolyA+ RNA was selected twice by Dynabeads\u2122 mRNA Purification Kit Thermo Fisher Scientific. For zebrafish zygote  mouse MII oocyte and mouse blastocyst samples  the single cells were manually picked and sorted into 12 \u03bcl 1X lysis buffer Takara; NEBNext\u00ae rRNA Depletion Kit NEB was used to delete DNA and rRNA; RNA samples were sonicated for 2\u2009\u00d7\u200930\u2009seconds  incubated with the anti m6A antibody from Millipore ABE572  and precipitated using ethanol. SMART Seq\u00ae Stranded Kit Takara  Cat. # 634442 was used to prepare RNA sequencing library. Libraries were quantified with KAPA Library Quantification Kits Roche and the size distribution was checked using TapeStation D1000 ScreenTape Agilent Technologies.", "GEO Accession:GSM5599713", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP339082", null, "loader:fastq load.py", "ZF_zygote_Input_10cell_Rep1_R1.fastq.gz ZF_zygote_Input_10cell_Rep1_R2.fastq.gz", "fastq fastq", 4029368016.0, 39503608.0, "GSM5599713 r1", "0:51 1:51", "A:893562237;C:1096986475;G:1180690796;T:857849967;N:278541", 51, 51, null, null, 893562237, 1096986475, 1180690796, 857849967, 278541, "SRX12382345", "SRS10353007", "SRA1301707", "GEO", "Room 2035, Palmer Commons, Department of Computational Medicine and Bioinformatics, University of Michigan", 2, 0.91491, 0.90807, 0.32799, 0.37836, 0.89292, 0.89282, 0.81006, 0.73354, 51, 51, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "3prime", "poly_a", "nebnext", "bulk", "bulk", "bulk", null, "United States", "2021-09-28", "Zygote", "Embryo", "Oocyte", "Reproductive System"]], "truncated": false, "filtered_table_rows_count": 28, "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], [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 from run_metadata where \"experiment.library_selection\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "other", "p1": "Oocyte"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte", "results": [{"value": "RIP-Seq", "label": "RIP-Seq", "count": 19, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte&experiment.library_strategy=RIP-Seq", "selected": false}, {"value": "OTHER", "label": "OTHER", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte&experiment.library_strategy=OTHER", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte", "results": [{"value": "other", "label": "other", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation=Oocyte", "selected": true}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 15, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte&experiment.library_layout=SINGLE", "selected": false}, {"value": "PAIRED", "label": "PAIRED", "count": 13, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte&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_selection=other&tissue_curation=Oocyte", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 25, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte&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_selection=other&tissue_curation=Oocyte&experiment.platform=ION_TORRENT", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte", "results": [{"value": "Embryo", "label": "Embryo", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte", "results": [{"value": "Zygote", "label": "Zygote", "count": 22, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte&devstage_curation=Zygote", "selected": false}, {"value": "Blastula", "label": "Blastula", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte&devstage_curation=Blastula", "selected": false}, {"value": "Cleavage", "label": "Cleavage", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte&devstage_curation=Cleavage", "selected": false}, {"value": "Gastrula", "label": "Gastrula", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte&devstage_curation=Gastrula", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte", "results": [{"value": "Reproductive System", "label": "Reproductive System", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte&tissue_curation_coarse=Reproductive+System", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte", "results": [{"value": "Oocyte", "label": "Oocyte", "count": 28, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte", "results": [{"value": "bulk", "label": "bulk", "count": 13, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte&technology=bulk", "selected": false}, {"value": "unknown", "label": "unknown", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte&technology=unknown", "selected": false}, {"value": "generic-scrnaseq-only", "label": "generic-scrnaseq-only", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_selection=other&tissue_curation=Oocyte&technology=generic-scrnaseq-only", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 74.37403700168943}