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| Status |
Public on May 04, 2012 |
| Title |
Clutch1_Stage11-12_Set1 |
| Sample type |
SRA |
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| Source name |
embryo_stage 11-12
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| Organism |
Xenopus tropicalis |
| Characteristics |
strain: Outbred
clutch: 1
developmental stage: stage 11-12
tissue: embryo
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| Extracted molecule |
total RNA |
| Extraction protocol |
The general Illumina mRNA-Seq library preparation workflow was followed with some modifications. First, polyA-containing RNAs were selected. The RNAs were then fragmented in 5X First-Strand Buffer (Invitrogen) at 85oC for 7-8 minutes. Random hexamers and SuperScript III (Invitrogen) were used to synthesize the first strand cDNA. Second strand cDNA synthesis was performed with dUTP in place of dTTP to mark the second strand. After end repair and addition of adenosine to the 3'ends, standard Illumina adapters were ligated. DNA fragments in the size range of 300 to 600bp were gel extracted and treated with UDG before each library was amplified using Phusion (Finnzymes).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
polyA-selected RNA
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| Data processing |
Bowtie was used for alignment.
TopHat and SpliceMap were used for splice junction detection.
Cufflinks and Rseq were used to generate abundance measurements.
Genome_build: XenTro3
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| Submission date |
Apr 20, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Kin Fai Au |
| E-mail(s) |
kinfai@stanford.edu
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| Organization name |
Stanford
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| Department |
Statistics
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| Street address |
James H. Clark Center, 1st Floor East, 318 Campus Drive,
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| City |
Stanford |
| ZIP/Postal code |
CA 94305 |
| Country |
USA |
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| Platform ID |
GPL15472 |
| Series (1) |
| GSE37452 |
RNA sequencing reveals diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development. |
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| Relations |
| SRA |
SRX143518 |
| BioSample |
SAMN00861985 |
| 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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