|
| Status |
Public on Mar 24, 2016 |
| Title |
H9-derived neuroectoderm rep3 |
| Sample type |
SRA |
| |
|
| Source name |
H9 hESC
|
| Organism |
Homo sapiens |
| Characteristics |
days after differentiation: Day 5
cell line: H9 hESC
|
| Growth protocol |
H9 cells were maintained on Matrigel (BD Biosciences) in mTeSR1 medium (Stem Cell Technologies). Neuroectoderm was derived with NOGGIN (200 nM) and SB431542 (10 μM). Mesendoderm was derived with mTeSR1 containing hBMP4 (5 ng/ml).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using mirVana miRNA isolation kit.
Total RNA was subjected to DNase treatment using the Turbo DNA-free kit (Life Technologies #AM1907) followed by ribosomal RNA depletion with the RiboMinus Eukaryote Kit v2 (Life Technologies #A15020). Remaining RNA was used for library preparation according to the Ion Total RNA-Seq Kit v2 protocol (Life Technologies #4475936).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
F
|
| Data processing |
ion torrent proton, Torrent Suite 4.42 software used for basecalling.
Sequenced reads were aligned to human genome by using tophat TopHat v2.0.13, known transcripts of refSeq download from UCSC genome browser were provided tp tophat.
unmapped reads from Tophat were realigned by using bowtie2 --local --very-sensitive-local,version 2.1.0
alignments were conbined, reads for each refseq transcript were counted by using RPKM_count.py from RSeQC v2.6.1,stranded,exon only
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values of refSeq for each Sample ...
|
| |
|
| Submission date |
Jun 18, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kenneth S. Kosik |
| Organization name |
UCSB
|
| Department |
NRI
|
| Lab |
Kosik
|
| Street address |
UC Santa Barbara
|
| City |
Santa Barbara |
| State/province |
California |
| ZIP/Postal code |
93106 |
| Country |
USA |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE69982 |
Primary cilium-autophagy-Nrf2 (PAN) axis links the cell cycle to neuroectoderm fate in human embryonic stem cells |
|
| Relations |
| BioSample |
SAMN03781973 |
| SRA |
SRX1064704 |
