|
| Status |
Public on Apr 08, 2021 |
| Title |
RNA_ESC_shKap1_1 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: blastocyst-derived ES cells
genotype: Kap1 shRNA expressed
|
| Growth protocol |
Cells were cultured in ES cell medium (DMEM, 15% FBS, 1×Nucleosides, 1 mM L-Glutamine, 1×Non Essential Amino Acids, 0.1 mM 2-Mercaptoethanol, 1000 U/ml LIF) supplemented with 3 mM CHIR-99021 and 1 mM PD0325901.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ES cells were disrupted in TRIzol Reagent and total RNAs were isolated by chloroform extraction coupled with isopropanol precipitation.
1 μg RNA per reaction was subjected to rRNA elimination and library generation using VAHTS Total RNA-seq (H/M/R) Library Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Successfully infected ES cells were screened by FACS.
|
| Data processing |
Primary fastq data were generated with the Illumina Casava (v 1.8.2) pipeline.
Sequencing reads were trimmed by Trim Galore (v 0.6.4) with parameters: --phred33, --illumina, --clip_R1 9, --clip_R2 9, --paired to remove adapter sequences.
Trimmed reads were aligned to mm9 reference genome using Tophat2 (v2.1.1) with default parameters.
Expression levels of individual were quantified by FPKM using Cufflinks (v 2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files containing FPKM values for each transcript.
|
| |
|
| Submission date |
Sep 01, 2020 |
| Last update date |
Apr 08, 2021 |
| Contact name |
Chuan Chen |
| E-mail(s) |
chenchuan@tongji.edu.cn
|
| Organization name |
Tongji University
|
| Street address |
1239 Siping Road
|
| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE157262 |
Nuclear m6A reader YTHDC1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos [ES cell RNA-seq] |
| GSE157268 |
Nuclear m6A reader Ythdc1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos. |
|
| Relations |
| BioSample |
SAMN15957347 |
| SRA |
SRX9052288 |
