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| Status |
Public on Mar 07, 2018 |
| Title |
shNcor2 OSKM day9 replicate 2 |
| Sample type |
SRA |
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| Source name |
Mouse MEFs, OSKM day 9
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| Organism |
Mus musculus |
| Characteristics |
day: 9
shRNA transfection: shRNA Ncor2
transfection: OSKM lentiviral transfection
presumed cell type: Intermediate pluripotent reprogramed cells
strain: C57BL/6J-OG2
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| Treatment protocol |
15,000 MEFs were transducted once in 12-well plates using virus-containing supernatants generated by PlatE or HEK293T cells. After infection the medium was changed to mouse ESC serum-based medium (DMEM-High glucose supplemented with 15% FBS, non-essential amino acids, GlutaMAX, sodium-pyruvate, penicillin/streptomycin, 0.1 mM β-mercaptoethanol and 100 units/ml LIF or mouse ESC KSR medium (DMEM-High glucose supplemented with 15% Knockout Serum Replacement (Gibco), non-essential amino acids, GlutaMAX, sodium-pyruvate, penicillin/streptomycin, 0.1 mM β-mercaptoethanol, N2, 5 ng/ml basic fibroblast growth factor (bFGF) (Peprotech) and 100 units/ml LIF, and renewed daily.
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| Growth protocol |
Maintenance of mouse ESCs and fully reprogramed iPSCs was conducted in chemically defined N2B27-based medium: DMEM/F12 (HyClone) and Neurobasal (Gibco) mixed 1:1, supplemented with N2 (Invitrogene), B27 (Invitrogene), non-essential amino acids, GlutaMAX, sodium-pyruvate (Gibco), penicillin/streptomycin (HyClone), 0.1 mM β-mercaptoethanol (Sigma), 100 units/ml leukemia inhibitory factor (LIF) (Millipore), small-molecule inhibitors CHIR99021 (3 μM, Selleck), and PD0325901 (1 μM, Selleck)
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| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol
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 |
Illumina HiSeq 2000 |
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| Data processing |
rsem v1.2.17/bowtie2 v2.2.0 was used to align to the ensembl transcriptome (mm10, v76)
transcripts with more than 25 sequence tags in 2 or more timepoints were kept for further analysis
mapping tag counts were GC normalised using EDASeq v2.0.0
Genome_build: mm10
Supplementary_files_format_and_content: tab delimeted text file containing ensembl gene accession number, gene name and normalised abundance estimates for each transcript
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| Submission date |
Jul 10, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrew P Hutchins |
| E-mail(s) |
andrewh@sustech.edu.cn
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| Organization name |
Southern University of Science and Technology
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| Department |
Bioinformatics
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| Lab |
Bioinformatics and Genomics
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| Street address |
1088 Xueyuan Rd
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| City |
Shenzhen |
| ZIP/Postal code |
518055 |
| Country |
China |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE70738 |
NCoR/SMRT co-repressors cooperate with c-MYC to create an epigenetic barrier to somatic cell reprogramming [RNA-seq] |
| GSE70740 |
NCoR/SMRT co-repressors cooperate with c-MYC to create an epigenetic barrier to somatic cell reprogramming |
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| Relations |
| BioSample |
SAMN03854044 |
| SRA |
SRX1091773 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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