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| Status |
Public on Nov 07, 2019 |
| Title |
RNA_KO_Zcchc8_2 |
| Sample type |
SRA |
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| Source name |
RNA_KO_Zcchc8
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| Organism |
Mus musculus |
| Characteristics |
strain: BDF1
cell type: derived ESC
genotype/variation: Zcchc8 KO and Zcchc9 overexpression
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| Growth protocol |
ESC derived from blastocysts (BDF1 strain) were cultured in ESC medium: DMEM (Gibco),15% fetal bovine serum (Hyclone), nucleosides (100×),1 mM l-glutamine,1% nonessential amino acid stock, 0.1 mM mercaptoethanol, 1,000 U/ml LIF (Merk Millipore), 3 m CHIR99021 (S2924; Selleck) and 1 M PD0325901 (S1036; Selleck).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was obtained from at least 5×10^5 ESCs via RNeasy Mini Kit extraction(Qiagen).
For total RNA (rRNA erased), 1μg total RNA were used for RNA-seq with the KAPA RiboErase Kit (Roche) following the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
RNA_KO_Zcchc8_2_H3JCGCCXY_L8
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| Data processing |
Illumina Casava1.8 software used for basecalling.
For RNA seq, sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v2.1.1 with default parameters.
Gene expression for each sample was quantified to FPKM using Cufflinks(v 2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each transcript.
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| Submission date |
Mar 04, 2019 |
| Last update date |
Nov 08, 2019 |
| Contact name |
You Wu |
| E-mail(s) |
wuyou@tongji.edu.cn
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| Organization name |
tongji university
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| Department |
school of life science and technology
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| Street address |
1239 siping road
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| City |
shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE127790 |
Nuclear exosome targeting complex core factor Zcchc8 regulates the degradation of LINE1 RNA in early embryos and embryonic stem cells |
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| Relations |
| BioSample |
SAMN11050352 |
| SRA |
SRX5460529 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3638753_RNA_KO_Zcchc8_2.fpkm_tracking.gz |
864.7 Kb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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