GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM8188830

Query DataSets for GSM8188830

Status

Public on Jul 31, 2024

Title

Hindgut F1 hybrid SU26xZI197 Biological replicate 2

Sample type

SRA

Source name

hindgut

Organism

Drosophila melanogaster

Characteristics

tissue: hindgut
strain: SU26xZI197
age: 6 days
Sex: female

Growth protocol

Flies were reared on cornmeal-molasses medium under standard lab conditions (21°C, 14 hour light: 10 hour dark cycle). Reciprocal F1 hybrids were generated in both directions (i.e. parental genotypes were switched) by crossing 2–3 virgin females of one line with 4–5 males of the other line. Crosses were carried out in 8–13 replicate vials and parental strains were similarly reared (2–3 females and 3–5 males per vial with 8–12 replicate vials) in order to control for rearing density among genotypes.

Extracted molecule

total RNA

Extraction protocol

Midguts (from below the cardia to the midgut/hindgut junction, 20 per biological replicate) and hindguts (from the midgut/hindgut junction to the anus, 60 per biological replicate) were dissected from 6-day-old females in cold 1X PBS and stored in RNA/DNA shield (Zymo Research Europe; Freiburg, Germany) at -80°C until RNA extraction. For F1 hybrids, half of the tissues were dissected from each of two reciprocal crosses in order to avoid potential parent-of-origin effects. RNA was extracted from three biological replicates per genotype and tissue type with the RNeasy Mini kit (Qiagen; Hilden, Germany) as directed by the manufacturer.
Poly-A selection, fragmentation, reverse transcription, library construction, and high- throughput sequencing was performed by Novogene (Hong Kong).

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

HG_SU26xZI197_2
HG_gcounts_allgenotypes_allreads.tsv

Data processing

Reads were mapped to the reference transcriptomes using NextGenMap in paired-end mode. Read pairs matching more than one transcript of a gene were randomly assigned to one of the transcripts of that gene. For downstream analyses, we analyzed the sum of read counts across all of a gene’s transcripts (across all annotated exons), i.e. on the individual gene-level. To identify genes with poor mapping quality, for each parental transcriptome, we simulated RNA-seq data with 200 reads per transcript and 150 bp reads, then mapped the reads back to the corresponding transcriptome. Genes for which more than 5% of reads mapped incorrectly were removed from the analysis.
Assembly: FlyBase annotation version 6.29; Reference genomes for each parental strain were constructed using published genome sequence assemblies of SU26, SU58, ZI197, and ZI418 strains. If a nucleotide sequence difference on the major chromosome arms (X, 2R, 2L, 3R, 3L) occurred between a parental strain and the reference genome, the parental nucleotide variant was included in the new reference transcriptome. If the parental sequence contained an uncalled base (“N”), the reference sequence was used.
Supplementary files format and content: Tab separated file containing gene identifiers (FBgn and CG numbers), length, chromosome, and gene counts for all reads per sample (without subsampling) in the hindgut.
Supplementary files format and content: Tab separated file containing gene identifiers (FBgn and CG numbers), length, chromosome, and gene counts for all readsper sample (without subsampling) in the midgut.

Submission date

Apr 04, 2024

Last update date

Jul 31, 2024

Contact name

Amanda Glaser-Schmitt

E-mail(s)

glaser@bio.lmu.de

Organization name

LMU München

Department

Biology