|
| Status |
Public on Feb 04, 2022 |
| Title |
hCiPSC-#3 |
| 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 pure chemical 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 |
SAMN21903814 |
| SRA |
SRX12405081 |
