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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 11, 2018 |
| Title |
Control 1 |
| Sample type |
SRA |
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| Source name |
Control, BMMSCs
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Bone marrow mesenchymal stem cells (BMMSCs)
passage: p2
treatment: Control
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| Treatment protocol |
0.2×10^6 BMMSCs were seeded on a 6-well culture plate. Tet1 and Tet2 siRNAs (Santa Cruz Biotechnology) were used to treat the BMMSCs according to the manufacturer’s instructions. Non-targeting control siRNAs (Santa Cruz Biotechnology) were used as negative controls.
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| Growth protocol |
Bone marrow cells were flushed out from femurs and tibias with 2% heat-inactivated fetal bovine serum (FBS; Equitech-Bio, Kerrville, NY, USA) in PBS. All nuclear cells (ANC) were seeded (15 × 10^6 cells per dish) in 100 mm culture dishes (Corning, Tewsburg, MA, USA) and incubated at 37°C under 5% CO2 conditions. Non-adherent cells were removed after 48 h and adherent cells were cultured for an additional 14 days in alpha minimum essential medium (α-MEM, Invitrogen, Grand Island, NY, USA) supplemented with 20% FBS, 2 mM L-glutamine (Invitrogen), 55 μM 2-mercaptoethanol (Invitrogen), 100 U/ml penicillin, and 100 μg/ml streptomycin (Invitrogen).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from BMMSCs were extracted using Qiagen RNeasy mini kit.
The NEBNext Ultra RNA library Pre Kit was used to prepare a sequencing library from 1μg of total RNA, and 2×100 paired-end sequencing in fat run mode was performed using the HiSeq 2500 and Illumina TruSeq SBS-Kit v2 (200 Cycles).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
c1
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| Data processing |
The resulting base calling (.bcl) files were converted to FASTQ files using Illunina’s bcl cl2fastq v1.8.4 software (Illumina,San Diego, CA).
Mapping RNA-seq reads on the mouse genome after trimming the adaptors, transcript assembly, and abundance estimation were performed using DNASTAR Lasergene v15.0 (DNASTAR, Madison, WI)
For each sample (Control1: C1; Control2: C2; Control3:C3; si(Tet1/Tet2) 1: s1; si(Tet1/Tet2) 2: s2; si(Tet1/Tet2) 3: s3), the individual gene expression was reported using linear total RPKMs. The difference of each gene bewteen control and si(Tet1/Tet2) 2 was analyzed by two tailed Student’s t-tests and showed as P value.
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: RPKMs
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| Submission date |
Jan 08, 2018 |
| Last update date |
Apr 11, 2018 |
| Contact name |
Ruili Yang |
| E-mail(s) |
ruiliyangabc@163.com
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| Organization name |
Peking University
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| Street address |
22# South Zhongguancun Ave
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| City |
Beijing |
| ZIP/Postal code |
10081 |
| Country |
China |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE108872 |
Tet1 and Tet2 Maintain Mesenchymal Stem Cell Homeostasis via demethylation of P2rX7 promoter |
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| Relations |
| BioSample |
SAMN08326887 |
| SRA |
SRX3541045 |
| 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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