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Sample GSM7708705 Query DataSets for GSM7708705
Status Public on Jan 16, 2024
Title ctrl1
Sample type SRA
 
Source name human MSCs
Organism Homo sapiens
Characteristics cell type: Human umbilical cord MSCs
agent: ctrl
Treatment protocol MSCs were treated with rhIL-10 or not for 8 h.
Growth protocol Human umbilical cord mesenchymal stem cells (MSC) were culture in MEM-α medium, 10% fetal bovine serum, human FGF (20 ng/mL) and human EGF (20 ng/mL).
Extracted molecule total RNA
Extraction protocol RNA from MSCs were treated with rhIL-10 or not were extracted using TRIZOL (Life Technologies) followed by purification using an RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Illumina Casava 2.19 software used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample
 
Submission date Aug 14, 2023
Last update date Jan 16, 2024
Contact name Jiajia Wang
E-mail(s) wangjiajia3301@zju.edu.cn
Organization name Zhejiang University
Lab GLP_lab
Street address 866 Yuhangtang Road
City Hangzhou
ZIP/Postal code 310058
Country China
 
Platform ID GPL11154
Series (1)
GSE240755 The initiating IL-10 production dominates the therapy of mesenchymal stem cell scaffold in spinal cord injury
Relations
BioSample SAMN36978202
SRA SRX21356272

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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