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| Status |
Public on Nov 21, 2015 |
| Title |
P5-N |
| Sample type |
SRA |
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| Source name |
monkey neuroepithelial stem cells (NESCs)
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| Organism |
Macaca mulatta |
| Characteristics |
neural tube morphology: Neural tube formation at high cell density
culture media: NESC culture meida containg bFGF, LIF, CHIR99021 and SB431542
single cell passage and self-ograinzation into neural tubes: moderate
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| Growth protocol |
For NESCs, monkey embryonic stem cell-derived NESCs were cultured in NESCs culture media composed of Neurobasal media including 1xB27,1x N2, 1xNEAA, 1% Glutmax, 3 μM CHIR99021, 5μM SB431542, 10ng/ml bFGF, and 1000U/ml hLIF. 0.025% trypsin was used to digest NESCs when passaging to encourage cell propagation. NESCs were routinely passaged to 1:8 to 1:16 ratios every 3-4 days. For NT formation, NESCs were continually cultured 8-10 days before passaging. For RPGCs, NESCs were cultured in NESCs culture media without 3 μM CHIR99021 for 7 days. For differentiated neurons, NESCs were cultured on laminin (5μg/ml) and gelatin (0.05%) coated plates in differentiation media (SDM) [Neurobasal supplemented with N2, B27, NEAA and Glutmax] for 13 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
500 ng mRNA of each sample was used to produce its respective sequence library.
mRNA was fragmented using the fragmentation Buffer (Ambion) and double-stranded cDNA was then synthesized using SuperScript II (Invitrogen) RT and random primers. Libraries were prepared according to Illumina's instructions. Sequencing was then performed in a HiSeq 2500 apparatus (Illumina) according to the TruSeq RNA Sample Preparation Guide (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
the 5th passage NESCs
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| Data processing |
Fastx (version:0.0.13) software was used to get clean reads. The following describe the detailed information:
Remove the poor reads with poor quality, in which the percentage of Q>20 is less than 50%. Q=-10logerror_ratio
Remove the reads with Q <10 in 3'-terminal. Or, the error_ratio of base is < 0.1.
Remove the all linker sequences in the reads.
Remove the N base in the reads
Remove the reads with the length of less than 20.
Genome_build: Genome mapping was performed by spliced mapping algorithm of Tophat (version:2.0.9) software for clean reads. The reference of genome is Ensembl Macaca_mulatta.MMUL_1.72; the link address is the following:
Genome_build: ftp://ftp.ensembl.org/pub/release-72/fasta/macaca_mulatta/dna/Macaca_mulatta.MMUL_1.72.dna.toplevel.fa.gz.
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| Submission date |
Oct 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Tianqing Li |
| E-mail(s) |
litq@lpbr.cn
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| Organization name |
Primate Translational Medicine Research Center, Kunming University of Science and Technology
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| Street address |
No. Boda Road, Yuhua Area, Chenggong New Town
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| City |
Kunming |
| ZIP/Postal code |
650500 |
| Country |
China |
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| Platform ID |
GPL19129 |
| Series (1) |
| GSE73892 |
A robust single primate neuroepithelial cell clonal expansion system for neural tube development and disease studies |
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| Relations |
| BioSample |
SAMN04158533 |
| SRA |
SRX1322872 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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