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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
E-mail(s) hua_bai@brown.edu
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
Relations
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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