|
| Status |
Public on Jan 01, 2016 |
| Title |
0_M |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cells (E14)_normal
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
developmental stage: E14
cell type: normal E14 cell
lif(leukemia inhibitory factor) status: cultured with LIF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from E14 was extracted with Qiazol (QIAGEN). The mRNA in total RNA converted into a library of template molecules suitable for subsequent cluster generation using the reagents provided in the Illumina ® TruSeq™ RNA Sample Preparation Kit v2.
The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide (KAPA Library Quantificatoin kits for Illumina Sequecing platforms) and qualified using a Caliper Labchip GX (Caliper Life Sciences,USA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads for each sample were aligned to the mouse genome (NCBI build 37/mm9) using TopHat v2.0.7 with default settings.
Cufflinks v2.0.2 was used to quantify FPKM (Fragments Per Kilobase of exon per Megabase of library size) values of genes defined from RefSeq transcripts.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Jan 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hyunsoo Kim |
| E-mail(s) |
khsoo82@snu.ac.kr
|
| Organization name |
Seoul National University
|
| Street address |
103 Daehakro, Jongro-gu
|
| City |
Seoul |
| ZIP/Postal code |
110-799 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE65246 |
Expression profiling of E14 cells overexpressing Hk2/Pkm2 |
|
| Relations |
| BioSample |
SAMN03292486 |
| SRA |
SRX851966 |
