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Sample GSM7670817 Query DataSets for GSM7670817
Status Public on Aug 01, 2023
Title ICSI-TE-RNAseq-rep1
Sample type SRA
 
Source name trophoblast
Organism Macaca fascicularis
Characteristics tissue: trophoblast
cell line: trophoblast
cell type: embryo trophoblast cells
genotype: wild type
treatment: ICSI
Extracted molecule total RNA
Extraction protocol The RNA was extracted by following the instructions of NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® NEB #E6420S
1. RNA Extraction
2. Reverse Transcription and Adapter Ligation
3. cDNA Amplification
4. cDNA Fragmentation
5. cDNA Adapter Ligation
6. cDNA PCR Enrichment
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing The raw sequencing reads were trimmed by using trim_galore with parameters of "-q 25 --phred33 --length 36 -e 0.1 --stringency 4" to remove low-quality bases and adapters in paired-end reads.
The remaining reads were mapped to the Macaca fascicularis genome (macFas5) using hisat2 with default parameters "--dta --no-mixed --no-discordant --no-softclip -p 12".
The sam files were converted to bam files using samtools, then the bam file were sorted and the index files were created.
Raw read counts were calculated by featureCounts.
Assembly: macFas5
Supplementary files format and content: a tab-delimited text file include count values for each Sample
 
Submission date Aug 01, 2023
Last update date Aug 01, 2023
Contact name Liao Zhaodi
E-mail(s) zhaodiliao@ion.ac.cn
Phone 17521632708
Organization name Chinese Academy of Sciences
Department Institute of Neuroscience
Street address 500, Qiangye Road
City Shanghai
ZIP/Postal code 2016000
Country China
 
Platform ID GPL28212
Series (2)
GSE239741 A somatic cell cloned rhesus monkey obtained by trophoblast replacement [RNA-seq]
GSE239746 A somatic cell cloned rhesus monkey obtained by trophoblast replacement
Relations
BioSample SAMN36780474
SRA SRX21206055

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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