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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 25, 2022 |
| Title |
N33 RNA-seq rep1 |
| Sample type |
SRA |
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| Source name |
ES Cell
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| Organism |
Mus musculus |
| Characteristics |
cell type: ESC
genotype: wildtype
strain: C57BL/6
chip antibody: none
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| Growth protocol |
The embryonic stem cells were cultured on feeder in medium consisted of knock-out DMEM (Invitrogen) containing 20% FBS (HyClone), 1,000 U/ml mouse leukemia inhibitory factor (LIF; ESG1107, Millipore), 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, 1 mM L-glutamine, penicillin (100 U/ml) and streptomycin (100 μg/ml). For the culture of ESCs, the medium was changed daily, and cells were routinely passaged every two days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq, total RNA was purified using an RNA mini kit (Qiagen) and treated with DNase I (Qiagen).
For RNA-seq, total RNA were poly(A) enriched with oligo(T) beads and RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Raw RNA-seq reads were firstly aligned to the mouse genome (version: UCSC mm10) using STAR (version 2.5.1). To study the expression of repeat elements, for read with multiple hits, only one hit was randomly picked as final alignment by setting STAR parameter as “—outSAMprimaryFlag AllBestScore –outSAMmultNmax 1”. The CUFFDIFF (v2.2.1) was used to identify differential gene expression.
genome build: mm10
processed data files format and content: bedgraph file generated using Bedtools
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| Submission date |
Jun 19, 2017 |
| Last update date |
Dec 25, 2022 |
| Contact name |
Xinyi Lu |
| E-mail(s) |
rnagenomics@foxmail.com
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| Organization name |
Nankai University
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| Street address |
94 Weijin Road
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| City |
Tianjin |
| ZIP/Postal code |
300071 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE100168 |
Telomeres suppress the activity of retrotransposons in pluripotent stem cells [exp1] |
| GSE118027 |
Telomeres suppress the activity of retrotransposons in pluripotent stem cells |
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| Relations |
| BioSample |
SAMN07252385 |
| SRA |
SRX2931280 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2673306_WT_rep1_R1.bedgraph.gz |
185.9 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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