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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 23, 2013 |
| Title |
Mouse Caecum |
| Sample type |
SRA |
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| Source name |
Caecum
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| Organism |
Mus musculus |
| Characteristics |
strain: Bl6/C57
tissue: Caecum
age: E13.5
genotype: wild type
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| Treatment protocol |
Polyadenylated RNA was prepared using TruSeq RNA Sample Preparation (Illumina).
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| Extracted molecule |
total RNA |
| Extraction protocol |
For transcriptome profiling along the mouse gut (E13.5), in addition to stomach, caecum and colon samples, the small intestine was separated into three isometric portions considered as the presumptive duodenum, jejunum and ileum. Tissues were stored in RNAlater reagent (QIAGEN) until further processing. After disruption of single samples with PT1200E Polytron (Kinematica), RNA was isolated using either the RNeasy micro- or minikit (QIAGEN).
Libraries and clusters were prepared and sequenced with Illumina Genome Analyzer IIx and paired-end sequencing of 100 bp.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Reads were mapped to the mm9 (NCBI m37, July 2007) Mouse genome assembly with bowtie version 0.12.7 (Langmead et al, 2009) with parameters -n 2 --best -strata -m 5. Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads (times 10^-7).
Reads Per Kilobase per Million reads (RPKM) for each gene were calculated from the number of reads for all the exons and normalized by the total length of the exons and by then total number of reads mapped.
Differential expression analysis was done using the R package DEseq (Anders et al. 2010)
Both the mapping and the differential expression analysis were done through HTSstation (http://htsstation.epfl.ch/).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include raw counts, RPKM values, fold change and p-values.
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| Submission date |
Feb 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Marion LELEU |
| Organization name |
EPFL
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| Department |
School of Life Sciences
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| Lab |
Laboratory of developmental genomics
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| Street address |
EPFL-SV-ISREC-UPDUB- Station 19
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| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platform ID |
GPL13112 |
| Series (2) |
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| Relations |
| SRA |
SRX238155 |
| BioSample |
SAMN01921749 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1083972_Mu_ca_rep_merged.bw |
212.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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