|
| Status |
Public on Feb 04, 2016 |
| Title |
5iLAF UCLA20n RNA-seq technical replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
5iLAF SSEA4- subpopulation UCLA20n hESCs
|
| Organism |
Homo sapiens |
| Characteristics |
library type: Ovation RNASeq System V2
passage number: Passage 20
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA for RNA-seq was extracted using the RNeasy Micro Kit (Qiagen) and quantified using a Nanodrop ND-1000 (Nanodrop)
RNA sequencing libraries were prepared using the Nugen RNA-seq System V2 with 5-100ng starting material.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Bisulfite Sequencing: Reads were aligned to the hg19 genome using BSMAP (Xi and Li, 2009) by allowing up to 2 mismatches and only retaining reads mapped to one location. Methylation ratio are calculated by #C/(#C+#T) at CG sites.
RNASeq: Reads were first aligned to hg19 gene annotation using Tophat (Trapnell et al., 2009) by allowing up to two mismatches and only keeping reads that mapped to one location. When reads did not mapped to the annotated genes, the reads were mapped to hg19 genome. Number of reads mapping to genes were calculated by HTseq (Anders et al., 2015) with default parameters. Expression levels were determined by RPKM (reads per kilobase of exons per million aligned reads).
Genome_build: hg19
Supplementary_files_format_and_content: Bisulfite seq: Methylation over mapped CGs. Column 1: chromosome; column 2: base; column 3: strand; column 4: C count; column 5: C+T count
Supplementary_files_format_and_content: RNAseq: Readcount by gene
|
| |
|
| Submission date |
Jan 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
William Abraham Pastor |
| E-mail(s) |
william.pastor@mcgill.ca
|
| Phone |
514-618-3348
|
| Organization name |
McGill University
|
| Department |
Biochemistry
|
| Lab |
Pastor
|
| Street address |
3655 Promenade Sir William Osler
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H3G 1Y6 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE76970 |
Reversion to naïve human pluripotency creates a new methylation landscape devoid of blastocyst or germline memory |
|
| Relations |
| BioSample |
SAMN04421923 |
| SRA |
SRX1534805 |
