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Status |
Public on Nov 04, 2020 |
Title |
DMZ.11.5_rep2 |
Sample type |
SRA |
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Source name |
DMZ
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Organism |
Xenopus laevis |
Characteristics |
replicate: 2 Stage: 11.5 tissue: Dorsal Marginal Zone
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Treatment protocol |
50 DMZ explants were isolated from stage 10.5 embryos using forceps, hair loop, and hair knife, then cultured in 1x Steinberg’s solution
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Growth protocol |
Fertilized eggs were incubated in 1/3 MMR at 16°C until stage 10.5
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Extracted molecule |
total RNA |
Extraction protocol |
When sibling embryos became stage 11, 11.5, 12, 12.5, 13, 14, 15, 16, 17, and 18, five or six DMZs were collected and dissolved in TRIzol Reagent for each time point. The time interval between the stages was approximately 30 minutes to an hour at room temperature. 20 animal caps and five VMZs were excised from stage 8 and 10.5, respectively. Animal caps and VMZs were dissolved in TRIzol when sibling embryos were at stage 11. Standard illumina RNA-Seq library preparation at a core facility
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Data processing |
Trimming adaptors: Trim Galore! psuedoalignment: kallisto quant log2 normalized counts: DeSeq2::rlog Genome_build: X.laevis transcriptome v9.2: Supplementary_files_format_and_content: counts.csv: CSV file containing raw count output from kallisto for each sample Supplementary_files_format_and_content: SupplementTable(090920).csv: CSV file containing DESeq2 rlog normalized counts for each sample including analysis metadata
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Submission date |
Nov 03, 2020 |
Last update date |
Nov 04, 2020 |
Contact name |
Anneke Dixie Kakebeen |
E-mail(s) |
akakebee@uw.edu
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Organization name |
University of Washington
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Department |
Biochemistry
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Lab |
Andrea Wills
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Street address |
5611 9th Ave NW
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City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98107 |
Country |
USA |
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Platform ID |
GPL21248 |
Series (1) |
GSE160777 |
A temporally resolved transcriptome for developing “Keller” explants of the Xenopus laevis dorsal marginal zone |
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Relations |
BioSample |
SAMN16655532 |
SRA |
SRX9427739 |
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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