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Sample GSM4879086

Query DataSets for GSM4879086

Status

Public on Nov 04, 2020

Title

VMZ.11_rep1

Sample type

SRA

Source name

VMZ

Organism

Xenopus laevis

Characteristics

replicate: 1
Stage: 11
tissue: Ventral Marginal Zone

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

Growth protocol

Fertilized eggs were incubated in 1/3 MMR at 16°C until stage 10.5

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

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

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

Submission date

Nov 03, 2020

Last update date

Nov 04, 2020

Contact name

Anneke Dixie Kakebeen

E-mail(s)

akakebee@uw.edu

Organization name

University of Washington

Department

Biochemistry