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| Status |
Public on Aug 17, 2012 |
| Title |
brainWT3 |
| Sample type |
SRA |
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| Source name |
whole brain, WT
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| Organism |
Mus musculus |
| Characteristics |
strain/background: 129/SvJ
genotype: wildtype
age: 16 weeks
tissue: whole brain
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| Extracted molecule |
total RNA |
| Extraction protocol |
Five 16-week-old 129/SvJ Mbnl1∆E3/∆E3 mice and littermate WT mice were sacrificed for isolation of whole brain, heart, and skeletal muscle (vastus lateralis). Total RNA was prepared by lysis in guanidium isothiocyanate, followed by phenol/chloroform extraction.
Poly(A)+ RNA was selected by oligo-dT magnetic beads, and prepared for single-end RNA sequencing using Illumina single end sequencing primers.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| Description |
RNA-Seq, single end
PolyA RNA
Processed data file: tissue_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 |
GPL9250 |
| Series (1) |
| GSE39911 |
Transcriptome-wide Regulation of Splicing and mRNA Localization by Muscleblind Proteins |
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| Relations |
| SRA |
SRX174022 |
| BioSample |
SAMN01103299 |
| 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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