|
| Status |
Public on Aug 04, 2017 |
| Title |
simXmel_cyc14C_rep2_sl20 |
| Sample type |
SRA |
| |
|
| Source name |
simXmel_cyc14C_rep2
|
| Organism |
Drosophila melanogaster x Drosophila simulans |
| Characteristics |
strain(s): w501, DGRP-340
hybrid: (Drosophila simulans F) x (Drosophila melanogaster M) F1 Hybrid
developmental stage: embryonic blastoderm cycle 14C
|
| Treatment protocol |
Methanol fixation of embryos
|
| Growth protocol |
25C incubator. 2 hour lay, age to appropriate stage in incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol Extraction with 1ug of glycogen
SMART-seq2 with minor modifications (see Combs & Eisen, 2015)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava 1.8.2 software used for basecalling.
Reads were mapped to the melanogaster genome with interspecific polymorphisms masked with Ns using STAR v.2.4.2a, with arguments --clip5pNbases 6 --outSAMattributes MD NH
Absolute expression was called using cufflinks v.2.2.1 with arguments --multi-read-correct --frag-bias-correct, and using the --mask-file argument to exclude a set of ribosomal, tRNA, microRNA, and histone features.
Allele-specific expression was called using ASEr commit cfe619c69a (https://github.com/TheFraserLab/ASEr/commit/cfe619c69a31f4600670859a82aae4378381b648)
Genome_build: FlyBase r5.57
Supplementary_files_format_and_content: Tab-delimited text files containing absolute expression (.fpkms) and allele-specific (.ase) expression data for each sample.
ase_summary.tsv (Tab-separated file with complete matrix of allele-specific expression values)
expr_summary.tsv (Tab-separated file with complete matrix of absolute expression values)
|
| |
|
| Submission date |
Aug 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Acuña Combs |
| E-mail(s) |
[email protected]
|
| Organization name |
Stanford University
|
| Department |
Biology
|
| Lab |
Hunter Fraser
|
| Street address |
Gilbert Rm 309, 371 Serra Mall
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL23864 |
| Series (1) |
| GSE102233 |
Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic |
|
| Relations |
| BioSample |
SAMN07447645 |
| SRA |
SRX3059486 |
