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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 15, 2015 |
| Title |
RNA_TELP_d7_N9_ss |
| Sample type |
SRA |
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| Source name |
C3H10T1/2 cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C3H
cell type: mesenchymal stem cell
cell line: C3H10T1/2
chip-antibody: NA
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| Growth protocol |
Growth medium: DMEM (high glucose), 10% Fetalclone III serum, PenStrep; Induction medium (d0-d2): DMEM (high glucose), 10% Fetalclone III serum, PenStrep, 5uM DEX, 0.5mM IBMX, 0.12ug/ml Insulin, 1uM Rosi, 1nM T3; Differentiation medium (d2-d7): DMEM (high glucose), 10% Fetalclone III serum, PenStrep, 0.12ug/ml Insulin, 1uM Rosi, 1nM T3. Before differentiation cells were seeded at 70% confluency and growth medium was supplemented with 8.3nM human recombinant BMP7 for 3 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent following the manufactorer's instructions and treated with DnaseI
RNA-seq libraries were generated following the procedue described in "TELP, a sensitive and versatile library construction method for next-generation sequencing" by Peng X, Wu J, Brunmeir R, Kim SY, Zhang Q, Ding C, Han W, Xie W, Xu F., published in Nucleic Acids Res. 2015 Mar 31;43(6):e35. doi: 10.1093/nar/gku818. Epub 2014 Sep 15.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
ChIP-seq reads were aligned to the mm9 genome using bowtie 2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
RNA-seq data sets were aligned to the mouse genome mm9 using TopHat.
The mapped reads were further quantified as fragments per kilobase of transcript per million mapped reads (FPKM) based on the RefSeq database using the Cufflinks program
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited wig files counted by the number of reads falling into 100bp bin in the genome for each ChIP-seq sample
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each RNA-seq Sample
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| Submission date |
Dec 14, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Wei Xie |
| E-mail(s) |
xiewei121@tsinghua.edu.cn
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| Organization name |
Tsinghua University
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| Street address |
zhongguancun beidajie
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| City |
Beijing |
| ZIP/Postal code |
100086 |
| Country |
China |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE75966 |
TELP, a sensitive and versatile library construction method for next-generation sequencing |
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| Relations |
| BioSample |
SAMN04334975 |
| SRA |
SRX1480017 |
| 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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