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| Status |
Public on May 25, 2022 |
| Title |
P1 ciTotiSC RNA-seq rep2 |
| Sample type |
SRA |
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| Source name |
ciTotiSC induced from OG2 mESC
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| Organism |
Mus musculus |
| Characteristics |
cell line: OG2
cell type: ciTotiSC
passage: P1
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| Growth protocol |
ciTotiSCs were cultured in KSR basal medium composed of KO DMEM, 5% KSR (Gibco, 10828010), CDL (CD lipid concentrate, 500X, Gibco, 11905-031), 1% N2 (ThermoFisher, A1370701), 1X L-glutaMAX, 1X penicillin-streptomycin, 1X non-essential amino acids (NEAA), 1X sodium pyruvate, 55 μM 2-mercaptoethanol and 1000 U/mL mouse leukemia inhibitory factor (mLIF), 50 ng/ml Sodium L-ascorbyl-2-phosphate (Selleck, S5115) supplemented with 2.5 μM 1-Azakenpaullone (Selleck, S7193), 0.5 μM WS6 (Selleck, S7442) and 0.2 μM TTNPB (Selleck, S4627). Cells were passaged every 2-3 days using 0.05% Trypsin-EDTA at a ratio of 1:3-1:5 on inactivated MEF feeder layers.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using TRIzol reagent.
mRNA-seq libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) according to the manufacturer’s protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
ciTotiSC_P1_total-2
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| Data processing |
TrimGalore software (with Cutadapt v1.18) was used to trim adaptor and first 10-bp of both reads
TopHat2 (v2.1.1) was used for the alignment to the mm10 reference genome with default parameters
The gene expression count matrix and FPKM value were analyzed by Cufflinks (v2.2.1) default pipline
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated-value table with FPKM values for every gene and every sample
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| Submission date |
Sep 29, 2021 |
| Last update date |
Aug 08, 2022 |
| Contact name |
Pengcheng Tan |
| E-mail(s) |
tpchengbjhd@126.com
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| Organization name |
Tsinghua University
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| Street address |
30 Shuangqing Rd
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| City |
Haidian |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE185000 |
Induction of mouse totipotent stem cells by a defined chemical cocktail [bulk RNA-seq] |
| GSE185005 |
Induction of mouse totipotent stem cells by a defined chemical cocktail |
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| Relations |
| BioSample |
SAMN21898846 |
| SRA |
SRX12403358 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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