NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1715069 Query DataSets for GSM1715069
Status Public on Mar 24, 2016
Title H9 hESC rep3
Sample type SRA
 
Source name H9 hESC
Organism Homo sapiens
Characteristics days after differentiation: Day 0
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 C
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 SAMN03781970
SRA SRX1064701

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap