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Sample GSM7989692 Query DataSets for GSM7989692
Status Public on Apr 05, 2024
Title Peripheral blood cells, EPO, 4.0 hour, biol rep 3
Sample type SRA
 
Source name Blood
Organism Xenopus tropicalis
Characteristics tissue: Blood
cell line: Total peripheral blood cells
cell type: Blood cells
genotype: Wild type
treatment: Culture with EPO
Treatment protocol 5,000,000 cells were suspended in 7/9 x IMDM-10% FCS and reacted with 1 ng/mL Xenopus tropicalis EPO expressed in E.coli for 1.5 or 4.0 hours.
Growth protocol Blood cells were corrected from the heart and mixed with anti-coagulator EDTA-2Na. Cells were washed three times with 7/9 x phosphate buffered serine containing 2 mM EDTA-2Na and 2% fetal calf serum.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by the acid guanidine phenol-chloroform method. 50 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-Seq were prepared by Lasy-Seq v1.1 (https://sites.google.com/view/lasy-seq/)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description 115
Data processing Read 1 reads were processed with fastp (version 0.21.0) 1 using the following parameters: --trim_poly_x -w 20 --adapter_sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --adapter_sequence_r2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -l 31.
The trimmed reads were then mapped to the reference transcriptome sequences of X. tropicalis was prepared from the Xenbase v10.0 (https://www.xenbase.org/xenbase/), using BWA mem (version 0.7.17-r1188) 2 with the default parameters.
The read count for each gene was calculated with salmon using -l IU, which specifies the library type (version v0.12.0) 3.
Then, using R (version 4.3.2) 4, the sums of read counts per gene were calculated.
Assembly: UCB_Xtro_10.0
Supplementary files format and content: csv data file includes raw counts for each sample.
 
Submission date Dec 22, 2023
Last update date Apr 05, 2024
Contact name Kazuki Omata
E-mail(s) oma_drum.k@moegi.waseda.jp
Organization name Waseda University
Department Graduate school of advanced science and engineering
Street address Wakamatsucho, 2-2
City Shinjuku
State/province Tokyo
ZIP/Postal code 332-0031
Country Japan
 
Platform ID GPL30213
Series (1)
GSE251901 Effect of erythropoietin on the gene expression of Xenopus tropicalis peripheral blood cells.
Relations
BioSample SAMN39083344
SRA SRX23007709

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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