|
| Status |
Public on Oct 31, 2017 |
| Title |
3'-seq in Embryo 12-24h [Virilis_12_24hr_embryos] |
| Sample type |
SRA |
| |
|
| Source name |
Embryo 12-24h
|
| Organism |
Drosophila virilis |
| Characteristics |
tissue: Embryo 12-24h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
3'-seq libraries were prepared and sequenced as described (Sanfilippo P, Miura P, Lai EC: Genome-wide profiling of the 3' ends of polyadenylated RNAs. Methods 2017, 75:in press.), using 2 μg of total RNA as starting material. Total RNA-seq libraries were prepared starting with 1 μg of total RNA in water.
The 3p-seq libraries were sequenced using a hiseq-1000 with SE-50 mode at the genomics core facility at MSKCC. Total RNA-seq libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Kit (cat. No. RS-122-2201). The protocol was followed exactly as per manufacturer's instructions. The libraries were sequenced on a hiseq-1000 sequencer at the genomics core facility at MSKCC.
3p-seq hiseq-1000 with SE-50; Total RNA-seq paired-end PE75
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
| |
|
| Description |
3'-seq
|
| Data processing |
3' adapter sequences were trimmmed using Trimmomatic-0.36
Total RNA-seq paired-end reads from four datasets to UCSC Drosophila melanogaster (dm6) genome assembly using HISAT2
Supplementary_files_format_and_content: The mapping alignments in bam format and counts of genes and 3'UTR extension were generated
dm6flybase_3seq_genePlus3ext_counts.tab: 3'-seq raw counts on gene and 3'UTR extension
dm6flybase_RNAseq_genePlus3ext_counts.tab: RNA-seq raw counts on gene and 3'UTR extension
dyak3_3seq_genePlus3ext_counts.tab: 3'-seq raw counts on gene and 3'UTR extension
dyak3_RNAseq_genePlus3ext_counts.tab: RNA-seq raw counts on gene and 3'UTR extension
dvir3_3seq_genePlus3ext_counts.tab: 3'-seq raw counts on gene and 3'UTR extension
dvir3_RNAseq_genePlus3ext_counts.tab: RNA-seq raw counts on gene and 3'UTR extension
|
| |
|
| Submission date |
Jul 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jiayu Wen |
| Organization name |
John Curtin School of Medical Research, The Australian National University
|
| Department |
Department of Genome Science
|
| Lab |
The Wen Lab
|
| Street address |
133 Garran Rd
|
| City |
CANBERRA |
| State/province |
ACT |
| ZIP/Postal code |
2601 |
| Country |
Australia |
| |
|
| Platform ID |
GPL23800 |
| Series (1) |
| GSE101603 |
Landscape and evolution of tissue-specific alternative polyadenylation across Drosophila species |
|
| Relations |
| BioSample |
SAMN07367997 |
| SRA |
SRX3015353 |
