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| Status |
Public on Aug 11, 2020 |
| Title |
APG+ niPSCs rep1 |
| Sample type |
SRA |
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| Source name |
pluripotent stem cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: APG secondary niPSCs
passages: 23-26
genotype/variation: Wild type
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| Growth protocol |
For cell culture, hiF-T were cultured in DMEM (Gibco) supplemented with 10% FBS (Gibco) and 2mM GlutaMAX (Millipore). Primed ESCs/iPSCs (pESCs/piPSCs) were cultured in hESM containing DMEM/F12 (Gibco) with 20% KnockOut SR (Gibco), 1% nonessential amino acids (Millipore), 2mM GlutaMAX (Millipore), Penicillin Streptomycin(Millipore),8 ng/ml bFGF (Peprotech). Naïve ESCs/iPSCs (nESCs/niPSCs) were cultured in 5iLAF medium containing DMEM/F12: Neurobasal (1:1) (Gibco), 1% N2 supplement (Gibco), 2% B27 supplement (Gibco), 0.5% KnockOut SR (Gibco), 1% nonessential amino acids (Millipore), 2mM GlutaMAX (Millipore), Penicillin Streptomycin(Millipore), 20ng/ml human LIF (Milipore), 8 ng/ml bFGF (Peprotech), 50 μg/ml BSA (Sigma) and the following cytokines and small molecules: PD0325901 (Selleck, 1 μM), SB590885 (Selleck, 0.5 μM), WH-4-023 (Selleck, 1 μM), Y-27632 (Selleck, 10 μM), and Activin A (Peprotech, 20 ng/ml) and passaged by Accutase (Sigma) every 4-5 days as previously reported. All hESCs were routinely cultured at 37 °C in 5% CO2, 5% O2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For mRNA-seq, total RNAs were isolated from cells using TRizol (Invitrogen). To generate RNA sequencing libraries, KAPA Stranded mRNA-Seq Kit (KAPA) was used following the manufacturer’s instructions. For single cell RNAseq, cell clones were mechanically picked and washed with PBS supplemented with 0.5% BSA. Following the Covaris DNA shearing protocol for Smart-seq sequence library generation as previously described. Briefly, cells were lysed, RNAs with a polyadenylated tail were captured, reverse transcripted and preamplified.
RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
PolyA RNA
APG 2° niPSCs
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| Data processing |
All sequenced reads were checked for quality control by using FastQC (v0.11.7) with default parameters.
Sequenced reads was removed adapters and low-quality sequence by using trim_galore (v0.4.2 ) with the default parameters.
The processed RNA-Seq reads were mapped to hg19 genome using STAR (v0.6.0). RefSeq genes were quantified to FPKM using Stringtie.
The processed RIP-Seq reads were mapped to hg19 genome using TopHat (v2.1.1) with default parameters.
FPKM for each sample and log2 fold change were calculated by using cuffdiff (v2.1.1).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *fpkm: Tab-delimited text files include FPKM values.
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| Submission date |
Aug 11, 2020 |
| Last update date |
Aug 12, 2020 |
| Contact name |
Bi Yan |
| E-mail(s) |
[email protected]
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| Phone |
18916058932
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| Organization name |
Tongji university
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| Street address |
Siping Road 1239
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| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE133097 |
Identification of ALPPL2 as a novel specific and functional surface marker for naïve pluripotency |
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| Relations |
| BioSample |
SAMN15792602 |
| SRA |
SRX8926475 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4721290_APGnips.1.fpkm.txt.gz |
206.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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