|
| Status |
Public on Mar 22, 2018 |
| Title |
squirrel 4c 1h rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
iPSC induced neurons
|
| Organism |
Ictidomys tridecemlineatus |
| Characteristics |
cell type: neuron
treatment: cold
|
| Treatment protocol |
On the day of experiment, neural differentiation medium was removed from the cultures, fresh hibernate-medium was added, and the cultures were placed
|
| Growth protocol |
Human iPSC lines and iPSC-derived neural precursor cells were established and deposited at the Stem Cell Unit of the National Institutes of Health (B. Mallon; barbara.mallon@nih.gov). Human neurons were cultured as described at https://stemcells.nih.gov/research/nihresearch/scunit/protocols.htm. GS iPSC-derived neuron cultures mainly followed the human protocol except that additional 5% knock-out serum replacement was included in the neural precursor medium, and 5% knock-out serum replacement and 20 ng/ml ACTIVIN A were included in the first 2 days of neuronal differentiation medium. The human and GS NPCs were first expanded in NPC medium described above for 3 days, and then switched to neural differentiation medium (Neural basal A/B-27 or N21-Max/L-Glutamine /antibiotics/BDNF/GDNF) for at least 7 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected and lysed in TRIzol (Thermo Fisher)
total RNA were purified with RNeasy kit (Qiagen), and further processed for RNA-sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
GS3-4c-1h
|
| Data processing |
bcl2fastq was used for base calling.
Trimmed reads were aligned to Ictidomys tridecemlineatus genome reference (Ensembl spetri2) with Tophat v2.0.11. The parameter options applied in alignment were -g 20, -p 8, --no-coverage-search, --library-type fr-firststrand and -G corresponding GTF file.
only the reads aligned to exons uniquely were counted using the Rsubread package
Genome_build: spetri2, hg19
Supplementary_files_format_and_content: tab-delimited text files include raw count values of genes for each Sample ...
|
| |
|
| Submission date |
Jan 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Yizhao Luan |
| E-mail(s) |
luanyz_leo@163.com
|
| Organization name |
Sun Yat-sen university
|
| Department |
Zhongshan Ophthalmic Center
|
| Street address |
Xianlie South Rd. 54, Yuexiu Dist
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510060 |
| Country |
China |
| |
|
| Platform ID |
GPL22974 |
| Series (1) |
| GSE93935 |
Studying iPSCs from a hibernating mammal reveals molecular mechanisms of cold resistance in neural tissues |
|
| Relations |
| BioSample |
SAMN06250289 |
| SRA |
SRX2510858 |
