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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 13, 2014 |
| Title |
01_ESC_KY |
| Sample type |
SRA |
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| Source name |
ES cells
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| Organism |
Mus musculus |
| Characteristics |
genotype: wild-type
days after differentiation: 0
cell line: KY1.1
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| Treatment protocol |
In vitro differentiation of ESCs was performed as described recently (Umemura et al. 2013). Briefly, after ESCs were trypsinized and feeder cells were removed, embryoid bodies (EBs) were generated by harvesting 2,000 cells and seeding them onto low-attachment 96-well plates (Lipidure Coat, NOF, Tokyo, Japan) in a differentiating medium without LIF supplementation (EFM), which was comprised of a high-glucose DMEM (Nacalai Tesque) containing 10% FBS, 1 mM sodium pyruvate (Nacalai Tesque), 0.1 mM nonessential amino acids, GlutaMaxTM-I (Invitrogen), 100 µM β-mercaptoethanol and 100 units/mL penicillin-streptomycin. Two day later, EBs were plated onto gelatin-coated tissue culture 24-well plates and grown for several additional weeks. EFM was changed every 1–2 day.
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| Growth protocol |
ES cell lines were cultured on a feeder layer of mitomycin C-treated primary MEFs in an ES medium containing Glasgow Minimum Essential Medium (G-MEM, Wako, Osaka, Japan) supplemented with 15% fetal bovine serum (FBS, Hyclone, South Logan, UT), 0.1 mM MEM nonessential amino acids (Nacalai Tesque, Kyoto, Japan), 0.1 mM 2-mercaptoethanol (Sigma, St. Louis, U.S.A.), 1,000 units/mL of leukemia inhibitory factor (LIF) and 100 units/mL of penicillin–streptomycin (Nacalai Tesque).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with miRNeasy Mini Kit (QIAGEN), according to the manufacturer’s instructions.
0.5 µg of total RNA was depleted of ribosomal RNAs using Ribo-Zero Gold (Illumina). Sequencing libraries were constructed using TruSeq Stranded Total RNA LT Sample Prep Kit according to the manufacturer’s instruction (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
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| Description |
rRNA depleted total RNA
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| Data processing |
Illumina Casava1.8.2 software was used for basecalling.
Sequence reads were mapped to the mouse genome (GRCm38/mm10) with Tophat v2.0.9 41 using the following parameters: -r 90 --solexa-quals --library-type fr-firststrand. To obtain reliable alignments, the reads with mapping quality less than 10 were removed by SAMtools.
The paired end reads were treated as separate single-end runs. The bigWig files were normalized to display uniquely mapped reads per 50 million uniquely mapped reads with duplicates. There are separate bigWig files for + and - genomic strands.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig
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| Submission date |
Sep 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Kazuhiro Yagita |
| E-mail(s) |
kyagita@koto.kpu-m.ac.jp
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| Organization name |
Kyoto Prefectural University of Medicine
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| Street address |
Kawaramachi-Hirokoji, Kamigyo-ku
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| City |
Kyoto |
| ZIP/Postal code |
602-8566 |
| Country |
Japan |
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| Platform ID |
GPL16173 |
| Series (1) |
| GSE61184 |
Transcriptional Program of Kpna2 (Importin-alpha2) Regulates Cellular Differentiation-Coupled Circadian Clock Development in Mammalian Cells |
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| Relations |
| BioSample |
SAMN03022886 |
| SRA |
SRX695151 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1498988_01_ESC_KY.neg.bw |
84.8 Mb |
(ftp)(http) |
BW |
| GSM1498988_01_ESC_KY.pos.bw |
87.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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