|
| Status |
Public on Aug 17, 2012 |
| Title |
S2-dsMbl-cyto |
| Sample type |
SRA |
| |
|
| Source name |
Drosophila S-2R+ cell, Mbnl depleted, cytosolic fraction
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S-2R+
subcellular fraction: cytosolic
|
| 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_cyto
RNA-Seq, paired end
Cytosolic 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 |
GSM3278956 |
| SRA |
SRX174058 |
| BioSample |
SAMN01103335 |
