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Sample GSM5603730 Query DataSets for GSM5603730
Status Public on Feb 04, 2022
Title hiPSC (mRNA)-#1
Sample type SRA
 
Source name human induced pluripotent stem cells
Organism Homo sapiens
Characteristics cell type: induced pluripotent stem cells
treatment: induced pluripotent stem cells derived from adipose derived fibroblasts using mRNA reprogramming strategy
Growth protocol hADFs were cultured in Mesenchymal Stem Cell Growth Medium 2 (Promo Cell, C-28009) with supplement mix (Promo Cell, C-39809). Pluripotent stem cell lines were cultured in mTeSR1 (Stem Cell, Cat# 85850) on 1: 40 diluted Matrigel-coated (BD BioSciences, Cat# 356231) 6-well plate (Corning, Cat# 353046).
Extracted molecule total RNA
Extraction protocol Cells were harvested and resuspended in PBS with 0.04% BSA at 1×10^6 cells per milliliter. Cells were lysed and the released RNA for the construction of sequencing libraries.
Sequencing libraries were prepared using Illumina protocols
Bulk RNA sequencing
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Quality control was performed by using FastQC v0.11.8.
The adapter of raw RNA sequencing fastq reads were trimmed using TrimGalore v0.6.6.
The cleaned RNA sequencing fastq reads were aligned to hg19 UCSC human reference genome using STAR v2.7.3 with default parameters.
Output bam files were then sorted by samtools v1.9.
The number of alignments mapped to each gene were counted using htseq-count v0.11.3 with parameters '-f bam -r name -s reverse -a 10 -t exon -i gene_id -m union '.
The count matrix was made by merging htseq-count outputs of every sample.
Genome_build: hg19
Supplementary_files_format_and_content: .csv file containing raw count values of all genes for every sample.
 
Submission date Sep 29, 2021
Last update date Feb 04, 2022
Contact name Yaqi Wang
E-mail(s) yaqi_wang@pku.edu.cn
Organization name Peking University
Street address No.5 Yiheyuan Road Haidian District
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
 
Platform ID GPL20795
Series (2)
GSE185035 Human Pluripotent Stem Cell-derived Islets Ameliorate Diabetes in Nonhuman Primates [human_bulk]
GSE185038 Human Pluripotent Stem Cell-derived Islets Ameliorate Diabetes in Nonhuman Primates
Relations
BioSample SAMN21903807
SRA SRX12405074

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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