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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 31, 2013 |
| Title |
Condylura_TG2 |
| Sample type |
SRA |
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| Source name |
trigeminal ganglia
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| Organism |
Condylura cristata |
| Characteristics |
tissue: trigeminal ganglia
age: adult
Sex: male
strain: wild
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were removed and homogenized in Trizol (Invitrogen) as per the manufacturer’s instructions.
Illumina TruSeq RNA Sample Prep Kit was used with about 1 ug of total RNA for the construction of sequencing libraries. After poly-A mRNA selection, the first Condylura trigeminal and dorsal root ganglia samples (Condylura_TG1 and Condylura_DRG1) were retrotranscribed and the Illumina Genomic Sample Prep Kit was used to generate libraries. These were sequenced on a Genome Analyzer II (76 bp). The remaining Condylura and Mus samples were processed using the Illumina TruSeq kit, and libraries were sequenced on a HighSeq 2000 (36 bp or 50bp). WHICH ONES ON WHICH The Condylura samples are single reads, the Mus samples are paired-end.
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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 |
readcounts_cc.txt
TG_Cc.txt
TG_overlap.txt
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| Data processing |
Alignments were performed with Stampy v1.0.11 (substitution rate = 0.03). For Condylura sequences, the total read count was the sum of all reads aligning to the homologs of that gene in Homo sapiens, Canis familiaris, or Mus musculus (Entrez Gene database, ncbi.nlm.nih.gov, Jan 2011). Homology was based on the HomoloGene database (build 64) and manual annotation. For Mus sequences, only the Mus musculus transcriptome database was used.
Differential expression was assessed using the DESeq package for R, with a padj < 0.05
Genome_build: Homo sapiens transcriptome downloaded Nov 25th 2010 (genome.ucsc.edu). Canis lupus familiaris and Mus musculus transcriptomes downloaded Nov28th 2010, (ncbi.nlm.nih.gov)
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values and variance for each sample based on the analysis performed using DESeq
Supplementary_files_format_and_content: readcounts_cc.txt: Read counts for genes in Condylura cristata trigeminal and dorsal root ganglia
Supplementary_files_format_and_content: readcounts_mm.txt: Read counts for genes in Mus musculus trigeminal and dorsal root ganglia
Supplementary_files_format_and_content: TG_Cc.txt: Genes overexpressed in Condylura cristata trigeminal versus dorsal root ganglia
Supplementary_files_format_and_content: DRG_Cc.txt: Genes overexpressed in Condylura cristata dorsal root versus trigeminal ganglia
Supplementary_files_format_and_content: TG_overlap.txt: Set of genes overxpressed in both mouse and mole trigeminal versus dorsal root ganglia
Supplementary_files_format_and_content: DRG_overlap.txt: Set of genes overxpressed in both mouse and mole dorsal root versus trigeminal ganglia
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| Submission date |
May 29, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Maurizio Pellegrino |
| E-mail(s) |
mpellegri@berkeley.edu
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| Organization name |
University of California - Berkeley
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| Street address |
355 LSA
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platform ID |
GPL17216 |
| Series (1) |
| GSE47480 |
The star-nosed mole reveals clues to the molecular basis of mammalian touch. |
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| Relations |
| BioSample |
SAMN02183194 |
| SRA |
SRX287490 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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