RNAseq Branchiostoma floridae whole larvae Cdx mutant 34h - SRA

SRX7351856: RNAseq Branchiostoma floridae whole larvae Cdx mutant 34h
1 BGISEQ (BGISEQ-500) run: 67.9M spots, 6.8G bases, 3.9Gb downloads

Design: Embryos and larvae from heterozygote crosses were sorted by visual phenotype. Samples for RNA-seq library construction were pools of ~100 (Pdx) or ~300 (Cdx) larvae. RNA sequencing was performed by BGI (Shenzhen, China) on the BGISEQ platform, >60 million 100 nt paired end reads per sample, using mRNA enrichment, random priming reverse transcription and low PCR cycle number. Methods text from BGI 1)mRNA enrichment and purification: rRNA depletion or Oligo dT Selection to enrich the mRNA 2)RNA fragment and reverse transcription 3)End repair, add A and adaptor ligation 4)RCR amplification 5)Single strand separation and cyclization 6)DNA nanoball synthesis 7)Sequencing on BGISEQ platform. For each sample, one library was constructed and run on 4 lanes; the fastq files for the 4 lanes were concatenated to generate the fastq files uploaded.

Submitted by: University of Oxford

Study: RNA-seq of Branchiostoma floridae Pdx and Cdx mutants

PRJNA594548 • SRP237289 • All experiments • All runs

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Pdx and Cdx genes are part of the ParaHox gene cluster, hypothesized to pattern the gut and anus. The goal was to examine the downstream molecular effects of mutation to Pdx and Cdx homeobox genes in amphioxus, Branchiostoma floridae. Frameshift mutations were made in Pdx and Cdx using TALENs and stable heterozygous lines generated. Heterozygous animals for each mutation were crossed (separately for Pdx and Cdx) , and larvae reared until phenotypes were evident: 5 gill slits for Pdx -/- and 2-3 gill slits (34h or 42h) for Cdx -/-. Approximately 100 to 300 larvae were collected for each sample: 3 samples each of Pdx -/- mutants, Pdx wild type (mix of +/+ and +/-), Cdx -/- mutants, Cdx wild type (mix of +/+ and +/-). These data were used to uncover downstream genetic pathways affected by each gene and also demonstrated a predominant effect of gut-associated genes.

Sample:

SAMN13521182 • SRS5811333 • All experiments • All runs

Organism: Branchiostoma floridae

Library:

Name: Cdx-mutant-larvae-34h

Instrument: BGISEQ-500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Runs: 1 run, 67.9M spots, 6.8G bases, 3.9Gb

Run	# of Spots	# of Bases	Size	Published
SRR10674591	67,862,074	6.8G	3.9Gb	2020-05-05

ID:: 9634710

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