|
| Status |
Public on Nov 06, 2017 |
| Title |
Long_28 |
| Sample type |
SRA |
| |
|
| Source name |
human embryonic stem cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: WA26
|
| Growth protocol |
Human embryonic stem cell (WA26) were routinely maintained in undifferentiated state in E8 medium (A1517001, Life technologies) on Matrigel (356230, BD Bioscience) coated tissue culture plates with medium change daily and passaged every 3 days using 0.5 mM EDTA in PBS at 1:20 ratio added with Rocki (sc-281642A, Santa Cruz).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Separation of gDNA and mRNA was performed as described previously. Briefly, samples were incubated at 72 °C for 3 min, the Biotin-oligo-dT primer was hybridized to poly (A)+ tail mRNA. Dynabeads in 4 μL (65001, Life technologies) were added to capture poly (A)+ tail mRNA, collected by a magnet, and the gDNA supernatant transferred to a fresh PCR tube. Single-cell cDNA was synthesized in the tubes containing mRNA according to Smart-seq2 protocol.
The libraries were prepared by using TruePrep DNA Library Prep Kit V2 for Illumina® (TD503-02, Vazyme Biotech) according to the instruction manual.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
single hESC 28
|
| Data processing |
Clean reads were aligning to hg19 with TopHat2 (Kim et al., 2013). Gene expression levels (TPM) were estimated by RSEM. Genome DNA sequence and gene annotation were download from iGenome (ftp://igenome:[email protected]/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz).
Genome_build: hg19
Supplementary_files_format_and_content: TPM data
|
| |
|
| Submission date |
May 08, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kunshan Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Tongji Hospital, Tongji University
|
| Department |
Stem cell Translational Research center
|
| Street address |
389 Xincun Road
|
| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE98644 |
Telomere heterogeneity linked to metabolism and pluripotency state revealed by simultaneous measurement of telomere length and RNA-seq in the same human ES cell |
|
| Relations |
| BioSample |
SAMN06915081 |
| SRA |
SRX2789009 |
