Project description:We used PacBio data to identify more reliable transcripts from hESC, based on which we can estimate gene/transcript abundance better from Illumina data. PacBio long reads and Illumina short reads were generated from the same hESC cell line H1. PacBio reads were error-corrected by Illumina reads to identify transcripts. rSeq is used to estimate gene/transcript abundance of the identified transcriptome.
Project description:PacBio SMRTseq long reads and Illumina short reads of pig testis, epididymis, vesicular gland, prostate gland, and bulbourethral gland
Project description:Since short reads from Illumina RNA-seq data are challenging to map to repetitive elements , we wanted to confirm the bulk RNA-seq findings using an orthogonal method, namely, using the long read technology of Pacific Biosciences (PacBio) full-length transcriptome sequencing. This dataset provided around 1.1 (WT) and 1.3 (RBM4 KO) million sequence reads of 2.6 kb average length mapping to the human genome.
2020-10-20 | GSE147896 | GEO
Project description:Genome of Hygrophila difformis
Project description:We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. melanogaster with respect to synteny blocks and dosage compensation as a chromosome-wide gene-regulatory mechanism.
Project description:Pioneering studies (PXD014844) have identified many interesting molecules by LC-MS/MS proteomics, but the protein databases used to assign mass spectra were based on short Illumina reads of the Amblyomma americanum transcriptome and may not have captured the diversity and complexity of longer transcripts. Here we apply long-read Pacific Bioscience technologies to complement the previously reported short-read Illumina transcriptome-based proteome in an effort to increase spectrum assignments. Our dataset reveals a small increase in assignable spectra to supplement previously released short-read transcriptome-based proteome.
Project description:Pioneering studies (PXD014844) have identified many interesting molecules in tick saliva by LC-MS/MS proteomics, but the protein databases used to assign mass spectra were based on short Illumina reads of the Amblyomma americanum transcriptome and may not have captured the diversity and complexity of longer transcripts. Here we apply long-read Pacific Bioscience technologies to complement the previously reported short-read Illumina transcriptome-based proteome in an effort to increase spectrum assignments. Our dataset reveals a small increase in assignable spectra to supplement the previously released short-read transcriptome-based proteome.
Project description:We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. melanogaster with respect to synteny blocks and dosage compensation as a chromosome-wide gene-regulatory mechanism.
Project description:The Yeonsan Ogye (Ogye) is the rare black chicken breed domesticated in Korean peninsula, which has been noted for entire black color upon its appearances including feather, skin, comb, eyes, shank, claws and internal organs. In this study, whole genome, transcriptome and epigenome sequencings of Ogye were performed using high-throughput NGS sequencing platforms. We have produced Illumina short-reads (Paired-End, Mate-Pair and FOSMID) and PacBio long-reads for whole genome sequencing (WGS), 1.4 billion reads for RNA-seq, and 123 million reads for RRBS (reduced representation bisulfite sequencing) data. Using WGS data, Ogye genome has been assembled, and coding/non-coding transcriptome maps were constructed on Ogye genome given largescale sequencing data. We have predicted 17,472 (3,550 newly annotated and 13,922 known) protein-coding transcripts, and 9,443 (6,689 novel and 2,754 known) long non-coding RNAs (lncRNAs).
Project description:The Yeonsan Ogye (Ogye) is the rare black chicken breed domesticated in Korean peninsula, which has been noted for entire black color upon its appearances including feather, skin, comb, eyes, shank, claws and internal organs. In this study, whole genome, transcriptome and epigenome sequencings of Ogye were performed using high-throughput NGS sequencing platforms. We have produced Illumina short-reads (Paired-End, Mate-Pair and FOSMID) and PacBio long-reads for whole genome sequencing (WGS), 1.4 billion reads for RNA-seq, and 123 million reads for RRBS (reduced representation bisulfite sequencing) data. Using WGS data, Ogye genome has been assembled, and coding/non-coding transcriptome maps were constructed on Ogye genome given largescale sequencing data. We have predicted 17,472 (3,550 newly annotated and 13,922 known) protein-coding transcripts, and 9,443 (6,689 novel and 2,754 known) long non-coding RNAs (lncRNAs).