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Sample GSM8579717 Query DataSets for GSM8579717
Status Public on Oct 27, 2024
Title Zebrafish, RNAseq, Sibling-4cell-1
Sample type SRA
 
Source name whole embryo
Organism Danio rerio
Characteristics tissue: whole embryo
Stage: 4-cell stage
cell type: embryonic cell
genotype: wild type
Growth protocol Zebrafish embryos were maintained in 1/3x Ringer's at 28.5C
Extracted molecule polyA RNA
Extraction protocol Total RNAs were extracted from WT and Mrbm24a embryos at 4-cell sphere 24-hpf stage, using TRIzol reagent (Invitrogen), and were precipitated by cold isopropanol (50%, v/v) in the presence of carrier glycogen (20 µg/each sample).
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Each library was amplified by a 11-cycle PCR, and 150 bp paired-end sequencing was subjected to Illumina HiSeq 2000 to obtain the raw data.
Assembly: GRCz10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample
 
Submission date Oct 17, 2024
Last update date Oct 27, 2024
Contact name yizhuang zhang
E-mail(s) zhangyizhuang@mail.sdu.edu.cn
Organization name Shandong university
Street address binhai road
City qingdao
ZIP/Postal code 26600
Country China
 
Platform ID GPL14875
Series (1)
GSE279756 Rbm24 dictates mRNA recruitment for germ plasm assembly
Relations
BioSample SAMN44337415
SRA SRX26418794

Supplementary file Size Download File type/resource
GSM8579717_Sibling_4cell_1.tsv.gz 166.2 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA

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