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Sample GSM1905076 Query DataSets for GSM1905076
Status Public on Nov 21, 2015
Title P24-N
Sample type SRA
 
Source name monkey neuroepithelial stem cells (NESCs)
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: strong
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.
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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description the 24th passage NESCs
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.
 
Submission date Oct 09, 2015
Last update date May 15, 2019
Contact name Tianqing Li
E-mail(s) litq@lpbr.cn
Organization name Primate Translational Medicine Research Center, Kunming University of Science and Technology
Street address No. Boda Road, Yuhua Area, Chenggong New Town
City Kunming
ZIP/Postal code 650500
Country China
 
Platform ID GPL19129
Series (1)
GSE73892 A robust single primate neuroepithelial cell clonal expansion system for neural tube development and disease studies
Relations
BioSample SAMN04158534
SRA SRX1322873

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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