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Sample GSM981224 Query DataSets for GSM981224
Status Public on Aug 17, 2012
Title S2-dsMbl-mem
Sample type SRA
 
Source name Drosophila S-2R+ cell, Mbnl depleted, membrane fraction
Organism Drosophila melanogaster
Characteristics cell line: S-2R+
subcellular fraction: membrane
Extracted molecule total RNA
Extraction protocol S-2R+ cells were fractionated using hypotonic lysis and ultracentrifugation to obtain cytosolic, membrane, and insoluble fractions. RNA was isolated by Trizol.
RNA-seq libraries were prepared using paired end Illumina adapters.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Mbl_mem
RNA-Seq, paired end
Membrane RNA
Processed data file: fly_fractionation_RPKM.txt
Data processing Reads were aligned to the dm3 Drosophila genome and splice junctions using Bowtie.
RPKM values were computed by counting the number of reads mapping to constitutive exons.
Genome_build: dm3
Supplementary_files_format_and_content: tissue_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: myoblast_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: myoblast_fractionation_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: fly_fractionation_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: myoblast_ribo_RPKM.txt: RPKM values in tab-delimited matrix format. This file is linked to the Series record as a supplementary file.
Supplementary_files_format_and_content: B6Brain_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: 129Brain_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: B6Heart_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: B6Muscle_clusters.bed: Bed file of CLIPseq clusters.
Supplementary_files_format_and_content: C2C12_clusters.bed: Bed file of CLIPseq clusters.
 
Submission date Aug 06, 2012
Last update date May 15, 2019
Contact name Eric T Wang
Organization name University of Florida
Street address 2033 Mowry Rd
City Gainesville
State/province FL
ZIP/Postal code 32610
Country USA
 
Platform ID GPL13304
Series (1)
GSE39911 Transcriptome-wide Regulation of Splicing and mRNA Localization by Muscleblind Proteins
Relations
Reanalyzed by GSM3278957
SRA SRX174059
BioSample SAMN01103336

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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