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Sample GSM5953390

Query DataSets for GSM5953390

Status

Public on Mar 19, 2022

Title

11_r4_TFAM_IR7,Li15947

Sample type

SRA

Source name

Larval fat bodies

Organism

Drosophila melanogaster

Characteristics

tissue: 96 hr AEL larval fat body
genotype: r4-Gal4>TFAM RNAi

Extracted molecule

total RNA

Extraction protocol

Drosophila larval fat bodies were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using the Ultra II Directional RNA library kit (New England BioLabs) according the manufacturer's instructions

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Data processing

1.Using Fast QC for reads quality control. The reads number per sample is around 20 million, and average reads length is 51 bp. All samples passed reads quality control.
2. Map the reads to Drosophila_melanogaster reference version: GCF_000001215.4_Release_6_plus_ISO1_MT_rna
3. QC for reads mapping quality: at least 90% of reads pseudo aligned to reference.
4. PCA plot for experiments QC, didn’t see obvious experimental problem, for example, uneven rRNA depletion.
5. Apply Wald-test from software sleuth do differential expression analysis, both on transcript level and gene level.

Submission date

Mar 14, 2022

Last update date

Mar 19, 2022

Contact name

Savraj Grewal

E-mail(s)

[email protected]

Organization name

University of Calgary

Street address

3330 Hospital Drive