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General Information
Name
RAMPAGE-Seq_GSE36212_WPP_4d
Species
D. melanogaster
Assay type
FlyBase ID
FBlc0001069
Project
Data Provider
Title
RAMPAGE-Seq of capped transcript 5' ends from D. melanogaster, iso-1 strain, puap (4d APF).
Accessions
Biosample Source
Overview
Sex
Tissue isolated
Other tissues studied
Cell component
Cell line
Key genes
Methods
Sample preparation

Two-hour embryo collections were transferred to cornmeal medium bottles and allowed to develop. The positions of new white prepupae on the bottle walls were marked and allowed for four days before being washed and snap frozen in liquid nitrogen.

Biosamples used (1)
Biosample
Type
Title
D. melanogaster, iso-1 strain, pupa (4d APF), source for RNA.
Assay Details
Key genes
Protocol

Total RNA was isolated using the RNAdvance Tissue kit (Agencourt) and treated with DNase I. RNA quality was checked on a Bioanalyzer (Agilent). 5'-monophosphate RNA species, mainly ribosomal RNA, were depleted by TEX digest (Epicentre). Reverse transcriptase was done under conditions that promote "template switching" to preferentially add linkers to the 5' ends of 5'-complete cDNAs for second strand synthesis. 5'-capped RNA molecules were then biotinylated and pulled down to serve as templates for second strand cDNA synthesis. cDNA was PCR amplified and DNA quality was confirmed on a DNA HS Bioanalyzer chip.

Three multiplexed libraries were prepared: one for embryos (24 samples), one for larvae and pupae (10 samples) and one for adults (two samples).

Mode of Assay

Read length (bases): 101

Samples were processed as multiplexed libraries: one that pooled all 24 embryonic samples, one that pooled all 10 larval and pupal samples, and one that pooled both adult fly samples.

Read length (bases): 76

Total reads: 296,251,429

Uniquely mapped reads: 228,277,829

Comments
Associated Data
Size
16,810,584 reads
Files
Additional Information
Synonyms and Secondary IDs (2)
Reported As
Symbol Synonym
RAMPAGE-Seq_GSE36212_WPP_4d
Name Synonyms
RAMPAGE-Seq of capped transcript 5' ends from D. melanogaster, iso-1 strain, puap (4d APF).
Secondary FlyBase IDs
    References (2)