|
| Status |
Public on Nov 01, 2022 |
| Title |
attp2_1wk_3 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Heart
|
| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Heart
age: 1 week
strain: attp2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hearts were exposed and removed, put in Quizol reagent before flash freezing and storing at -80. Subsequently RNA was harvested using Qiagen miRNeasy extraction kit. TruSeq Stranded mRNA Library Prep Kit High Throughput was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
attp2 1 wk and 5 wk and 1 wk Lamin C KD_normalizedCounts
C1d
|
| Data processing |
Data was analyzed by ROSALIND® (https://rosalind.onramp.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Reads were trimmed using cutadapt
Quality scores were assessed using FastQC2. Reads were aligned to the Drosophila melanogaster genome build dm6 using STAR
Individual sample reads were quantified using HTseq4Â and normalized via Relative Log Expression (RLE) using DESeq2 R library
Genome_build: dm6
Supplementary_files_format_and_content: text files with Relative Log Expression (RLE) values for each sample
|
| |
|
| Submission date |
Oct 15, 2021 |
| Last update date |
Nov 01, 2022 |
| Contact name |
Adam Jeffrey Engler |
| E-mail(s) |
[email protected]
|
| Phone |
858-246-0678
|
| Organization name |
UC San Diego
|
| Department |
Bioengineering
|
| Street address |
9500 Gilman Drive, MC 0412
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL25244 |
| Series (2) |
| GSE185967 |
Age-dependent Lamin remodeling induces cardiac dysfunction via dysregulation of cardiac transcriptional programs [RNA-Seq] |
| GSE185968 |
Age-dependent Lamin remodeling induces cardiac dysfunction via dysregulation of cardiac transcriptional programs |
|
| Relations |
| BioSample |
SAMN22321276 |
| SRA |
SRX12630408 |
