|
| Status |
Public on Feb 19, 2019 |
| Title |
III^M #1 male head replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Head
|
| Organism |
Musca domestica |
| Characteristics |
strain: III^M (CS)
genomic background: isogenic except for III^M across males
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Individual flies were dissected for abdomen and head tissues, frozen at -80˚C, and RNA was extracted from the individual tissues with TRIzol Reagent and the Zymo Direct-zol kit following the manufacturer’s protocol including DNA digestion steps.
The Illumina TruSeq Stranded mRNA Sample Preparation Kit was used with 4 ug of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
YM_IIM_head_pub.tsv
CS_male_head_1
|
| Data processing |
Illumina Casava v 1.8 was used for basecalling.
Sequenced reads were mapped to house fly genome assembly v2.0.2 using hisat2 in HISAT2 v0.12.2
The aligned reads were assigned to all annotated genes with htseq-count in HTSeq v0.9.1
The HTSeq output was used as input into DESeq2 v1.16.1 to identify differentially expressed genes with pair-wise comparisons between males of each strain and pair-wise comparisons of males from each strain against females.
Genome_build: house fly genome assembly v2.0.2 and annotation release 102
Supplementary_files_format_and_content: tab-delimited text files include pair-wise comparison, log2FoldChange, and FDR-corrected P value
|
| |
|
| Submission date |
Feb 18, 2019 |
| Last update date |
Feb 19, 2019 |
| Contact name |
Richard Meisel |
| Organization name |
University of Houston
|
| Department |
Biology and Biochemistry
|
| Street address |
3455 Cullen Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77204-5001 |
| Country |
USA |
| |
|
| Platform ID |
GPL22576 |
| Series (1) |
| GSE126685 |
Effects of naturally ocurring proto-Y chromosomes on house fly gene expression |
|
| Relations |
| BioSample |
SAMN10962298 |
| SRA |
SRX5387787 |
