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Sample GSM2285894 Query DataSets for GSM2285894
Status Public on Dec 31, 2016
Title kr-h1 mutant larvae replicate 1
Sample type SRA
Source name kr-h1 mutant larvae
Organism Drosophila melanogaster
Characteristics Stage: 100 hr after egg laying
genotype/variation: kr-h1 mutant
tissue: whole larvae
Growth protocol Flies were maintained at 25°C, 40% relative humidity and 12-hour light/dark. Adults were reared on agar-based diet with 0.8% cornmeal, 10% sugar, and 2.5% yeast
Extracted molecule total RNA
Extraction protocol Message RNAs were extracted using Poly-A mRNA isolation kit (Promega) from wildtype and kr-h1[7] homozygous 3rd instar larvae at 100 hr AEL. After fragmentation, message RNAs were reverse transcribed to cDNA following be double-stranded DNA synthesis.
Libraries made using PrepX library prep kits with double-stranded cDNA (sheared to 320 bp insert using Covaris shearing) and ligated to Illumina adapter and indices (see below) using the WaferGen Apollo 324 robot (end repair, a-tailing, adapter/index ligation, and size-selection using Ampure XP beads) and PCR enrichment and cleanup of the final library.
NextGen sequencing was performed using Illumina MiSeq paired-end sequencing, and MiSeq v2 300-cycle kit.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
Description kr-h1 mutant-1
Data processing MiSeq Imaging and Base Calling Script
Galaxy-FastQ trimmer. Offset from 5' end:9 bp. Offset from 3' end: 5 bp.
Galaxy-Tophat2: Mapping the reads against a reference genome
Galaxy-Cufflinks: Reconstructing Transcripts
Galaxy-Cuffmerge: Merge together several Cufflinks assemblies
Genome_build: Galaxy-Cuffdiff: Find significant changes in transcript expression
Supplementary_files_format_and_content: List of differential expressed gene
Submission date Aug 19, 2016
Last update date May 15, 2019
Contact name Hua Bai
Organization name Brown University
Department EEB
Lab Marc Tatar Lab
Street address 34 Olive St, BMC502
City Providence
State/province RI
ZIP/Postal code 02912
Country USA
Platform ID GPL16479
Series (1)
GSE85863 Transcriptome analysis of Drosophila Kr-h1 mutants
Reanalyzed by GSM3281791
BioSample SAMN05597735
SRA SRX2036003

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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