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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 24, 2014 |
| Title |
iCdx2_ES_TC_plastic |
| Sample type |
SRA |
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| Source name |
Embryonic Stem Cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Embryonic Stem Cells
cell line: 5ECER4G20
condition: 5 days of reprogramming in TS conditions on MEFs, and then replated for a further 3 days on gelatinised TC plastic (without MEFs)
treatment protocol: During the experimental time course of trans-differentiation, cells were plated on MEFs in TS cell conditions, as specified, with 4HT at a seeding denisty of approximately 1x10E4 cells/25cm2. Media was changed every 2 days. After 5 days, cells were trypsinised and replated with and without MEFs for a further 3 days culture. At the end of the trans-differentiation time-course, cells were FACS-purified to remove MEFs.
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| Growth protocol |
ES cells, iCdx2 and iCdx2/iRaf ES cells (prior to the start of the reprogramming protocol), were maintained in serum+LIF conditions on a layer of irradiated mouse embryonic fibroblasts (MEFs). TS cells were maintained in 70% MEF-conditioned media, 30% TS media 25ng/ml bFGF and 1µg/ml Heparin on uncoated tissue culture plastic, as standard.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using TRI reagent (Sigma) followed by DNase treatment using the TURBO-DNA-free kit (Life Technologies), according to manufacturers' instructions.
mRNA was isolated from total DNA-free RNA (150-240 ng) using the Dynabeads mRNA purification kit (Life Technologies 61006) and prepared into an indexed, strand-specific library using the ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre SSV21106) according to manufacturers‘ instructions. Libraries were quantified/assessed using both the KAPA Library Quantification Kit (KAPA Biosystems KK4824) and Bioanalyzer 2100 system (Agilent). Indexed libraries were pooled and sequenced with a 100bp single-end protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1000 |
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| Data processing |
Raw FastQ data were trimmed with Trim Galore (v0.3.7, default parameters) and mapped to the mouse NCBIM37 genome assembly using TopHat v2.0.12, guided by gene models from Ensembl v61. Data were quantitated at mRNA level using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk)
Genome_build: NCBIM37
Supplementary_files_format_and_content: Quantitated RNA-Seq data files are delimited and contain the following 7 columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Description (Ensembl); (7-14) log2 Expression Value
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| Submission date |
Oct 07, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Felix Krueger |
| E-mail(s) |
fkrueger@altoslabs.com
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| Organization name |
Altos Labs
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| Department |
Bioinformatics
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| Street address |
Granta Park
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| City |
Cambridge |
| ZIP/Postal code |
CB21 6GP |
| Country |
United Kingdom |
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| Platform ID |
GPL15103 |
| Series (2) |
| GSE62149 |
Epigenetic memory of the first cell fate decision prevents complete ES cell reprogramming into trophoblast [RNA-Seq] |
| GSE62150 |
Epigenetic memory of the first cell fate decision prevents complete ES cell reprogramming into trophoblast |
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| Relations |
| BioSample |
SAMN03098181 |
| SRA |
SRX727182 |
| 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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