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| Status |
Public on Sep 26, 2018 |
| Title |
SKIN_REP1 |
| Sample type |
SRA |
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| Source name |
Dorsal and ventral skin
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| Organism |
Bolitoglossa ramosi |
| Characteristics |
days post amputation: Not apply
developmental stage: Adult
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from tissues were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of mRNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
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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 |
Sequenced reads were assembly using Trinity V 2.0.6 software pipeline, and default Trimmomatic parameters to remove sequence adapters and low quality reads (Phred score < 5), The reference transcriptome was assembled from all RNA samples and all contigs with length ≥ 200 nucleotides.
Sequence reads generated from limb tissue samples were aligned to the reference transcriptome using Bowtie2 (Langmead & Salzberg 2012) and RSEM (RNA-Seq by Expectation Maximization) was used to obtain estimates of transcript abundance for all transcripts (Li & Dewey 2011). Expression levels were calculated as transcripts per million (TPM) and Fragments Per Kilobase Million (FPKM)
transcript with the highest expression estimate was evaluated statistically using EBseq. Transcripts were considered differently expressed between control and post-amputation samples with FDR < 0.05, the fold change were calculate as condition 1 /condition 2, log2 of FC is provided
Supplementary_files_format_and_content: tab-delimited text files include TPM and FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include transcripts DEG calculated by Ebseq, the file include the normalized mean count value for each transcript at each condition and the log2 of the fold change of each time point over control
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| Submission date |
Oct 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jean Paul Delgado |
| E-mail(s) |
jean.delgado@udea.edu.co
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| Organization name |
University of Atioquia
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| Department |
Biology
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| Lab |
Genética, Regeneración y Cáncer
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| Street address |
Calle 62 # 52-59
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| City |
medellin |
| State/province |
antioquia |
| ZIP/Postal code |
00000 |
| Country |
Colombia |
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| Platform ID |
GPL24157 |
| Series (1) |
| GSE105232 |
Bolitoglossa ramosi differential expressed genes during limb regeneration |
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| Relations |
| BioSample |
SAMN07814226 |
| SRA |
SRX3302628 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2825100_SKIN_REP1_genes_RSEM.txt.gz |
5.1 Mb |
(ftp)(http) |
TXT |
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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