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Status |
Public on Mar 07, 2018 |
Title |
shNcor2 OSKM day9 replicate 1 |
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 |
SAMN03854043 |
SRA |
SRX1091772 |
Supplementary data files not provided |
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Processed data are available on Series record |
Raw data are available in SRA |
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