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| Status |
Public on Aug 17, 2012 |
| Title |
C2C12-shMbnl12-mem |
| Sample type |
SRA |
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| Source name |
C2C12 mouse myoblast, Mbnl1 and Mbnl2 depleted, membrane fraction
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| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
shRNA: Mbnl1, Mbnl2
subcellular fraction: membrane
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| Extracted molecule |
total RNA |
| Extraction protocol |
C2C12 mouse myoblasts were grown in DMEM with 20% FBS, and infected with lentiviral shRNAs against Mbnl1 and Mbnl2. Cytosolic, membrane, and insoluble fractions were isolated using 0.015% digitonin, 0.5% Triton X-100, and 1 M NaCl, respectively. RNA was isolated by guanidium isothiocyanate, followed by ethanol precipitation and RNeasy cleanup.
Ribosomal RNA was depleted by Ribozero (Epicentre) and libraries were prepared using paired end Illumina adapters.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Mbnl-mem
RNA-Seq, paired end
Membrane RNA
Processed data file: myoblast_fractionation_RPKM.txt
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| Data processing |
Reads were aligned to the mm9 mouse genome and splice junctions using Bowtie.
RPKM values were computed by counting the number of reads mapping to constitutive exons.
For CLIP-seq data, adapters were trimmed prior to mapping.
CLIP clusters were defined as previously described (Yeo et al., NSMB 2009 (PMID 19136955)).
For ribosome footprinting data, polyA tails were trimmed prior to mapping.
Genome_build: mm9
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.
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| Submission date |
Aug 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Eric T Wang |
| Organization name |
University of Florida
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| Street address |
2033 Mowry Rd
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| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32610 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE39911 |
Transcriptome-wide Regulation of Splicing and mRNA Localization by Muscleblind Proteins |
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| Relations |
| SRA |
SRX174053 |
| BioSample |
SAMN01103330 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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