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| Status |
Public on Aug 04, 2017 |
| Title |
simXsim_cyc14C_sl10 |
| Sample type |
SRA |
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| Source name |
simXsim_cyc14C
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| Organism |
Drosophila simulans |
| Characteristics |
strain(s): w501
developmental stage: embryonic blastoderm cycle 14C
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| Treatment protocol |
Methanol fixation of embryos
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| Growth protocol |
25C incubator. 2 hour lay, age to appropriate stage in incubator.
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| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol Extraction with 1ug of glycogen
SMART-seq2 with minor modifications (see Combs & Eisen, 2015)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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)
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| Submission date |
Aug 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Acuña Combs |
| E-mail(s) |
pcombs@stanford.edu
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| Organization name |
Stanford University
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| Department |
Biology
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| Lab |
Hunter Fraser
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| Street address |
Gilbert Rm 309, 371 Serra Mall
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL23865 |
| Series (1) |
| GSE102233 |
Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic |
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| Relations |
| BioSample |
SAMN07447628 |
| SRA |
SRX3059503 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2731177_simXsim_cyc14C_sl10.ase.txt.gz |
563.7 Kb |
(ftp)(http) |
TXT |
| GSM2731177_simXsim_cyc14C_sl10.fpkm.txt.gz |
366.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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