|
| Status |
Public on Oct 13, 2018 |
| Title |
03h_4 |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo_03h
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Oregon_R
tissue: whole embryo
developmental stage: 03h
|
| Growth protocol |
Population cages of wild-type Oregon R flies containing only fertilized females were maintained at 25°C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Embryos were dechorionated using 7.5% hypochlorite for 2 min and rinsed with water. At this point, approximately 30% of the embryos (20 µl embryo pellets) were transferred to PBS buffer. Total RNA was extracted from approximately 20 µl embryo pellets with the RNeasy Mini Kit (Qiagen) and RNA integrity checked by Bioanalyzer.
NGS library prep was performed with Illumina’s TruSeq stranded mRNA LT Sample Prep Kit following Illumina’s standard protocol (Part #15031047 Rev. E). Libraries were prepared with a starting amount of 500 ng and amplified in 11 PCR cycles. All 68 embryo samples were pooled in equimolar ratio and sequenced on 8 HiSeq 2500 lanes, SR for 1x 51 cycles plus 7 cycles for the index read.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were demultiplexed and fastq files were generated with Illumina bcl2fastq-1.8.4
Fastq files were mapped with STAR_2.4.0h to the BDGP6 reference genome
Secondary alignments were filtered with samtools 1.2
Counts for every gene were calculated with HTSeq-0.6.1p1 using the gene model provided with Ensembl version 79 for BDGP6
Genome_build: dm6
Supplementary_files_format_and_content: tab separated file containing counts per gene
|
| |
|
| Submission date |
Oct 12, 2018 |
| Last update date |
Oct 13, 2018 |
| Contact name |
Sergi Sayols |
| Organization name |
Institute of Molecular Biology, Mainz
|
| Street address |
Ackermannweg 4
|
| City |
Mainz |
| ZIP/Postal code |
55128 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17275 |
| Series (2) |
| GSE121160 |
Quantifying post-transcriptional regulation in the development of Drosophila melanogaster [devel] |
| GSE121167 |
Quantifying post-transcriptional regulation in the development of Drosophila melanogaster |
|
| Relations |
| BioSample |
SAMN10234676 |
| SRA |
SRX4870794 |
