|
| Status |
Public on Jun 27, 2019 |
| Title |
SMARTer_experiment_100cells_1 |
| Sample type |
SRA |
| |
|
| Source name |
ES cell line
|
| Organism |
Mus musculus |
| Characteristics |
strain: J1 (129SV)
genotype: Zbtb24 knockout (1lox/1lox)
number of cells: 100
tissue: mouse embryonic stem cells (mESCs)
|
| Growth protocol |
Mouse ES cells were cultured in serum-containing ES cell medium on gelatin-coated plates without feeder cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The cells were used directly without isolating total RNA in accordance with manufacturer recommendations.
mESCs were lysed in the reaction buffer included in the SMARTer Ultra Low RNA Kit v3 (TaKaRa, Japan). cDNA was then synthesized using the SMARTer Ultra Low RNA Kit followed by library construction using the Nextera DNA Sample Preparation Kit (Illumina, San Diego, CA), according to the manufacturers’ protocols. We performed 10 cycles of PCR for 1000 cells (~10 ng RNA) (SMARTer 1000), and 18 cycles of PCR for 100 cells (~ 1 ng RNA) (SMARTer 100).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
Reads were mapped to rRNA sequences (GI numbers: 262231778, 120444901, 120444900, 328447215, 38176281 and Ensembl IDs: ENSMUST00000082388, ENSMUST00000082390, ENSMUST00000083988, ENSMUST00000157970) using Bowtie2 (version 2.1.0).
Reads that were not mapped to rRNAs were then mapped to the mouse genome (mm10) using TopHat (version 2.0.10).
The number of fragments in each known gene from GENCODE Release M4 was enumerated using the htseq-count script within the HTSeq package (version 0.6.1) with options -m union and -s no.
Genome_build: mm10
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are the raw numer of fragments in each gene.
|
| |
|
| Submission date |
May 17, 2019 |
| Last update date |
Jun 27, 2019 |
| Contact name |
Yue Lu |
| E-mail(s) |
ylu4@mdanderson.org
|
| Phone |
7135637960
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Epigenetics & Molecular Carcinogenesis
|
| Street address |
1881 East Road
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77054 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE131396 |
Systematic evaluation of RNA-Seq preparation protocol performance (RNASeq: SMARTer) |
| GSE131398 |
Systematic evaluation of RNA-Seq preparation protocol performance |
|
| Relations |
| BioSample |
SAMN11668766 |
| SRA |
SRX5855563 |
