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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 29, 2016 |
| Title |
G2+dox_rep3 |
| Sample type |
SRA |
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| Source name |
embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: EKOiE-Ccna-Gfp
strain: 129/Ola
cell-cycle phase: G2
treatment: DOX
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| Growth protocol |
ES cells were cultured on plastic coated with 0.1% gelatine (SIGMA, cat. G1890-100G). The cells were passaged every 2-3 days using trypsin and replated at a 1:10 ratio. Cells were cultured either in conventional ES cell media consisting of DMEM +GlutaMax-I (Gibco, cat. 31966-021) supplemented with 10% FCS (Gibco 10270-098), 0.1% 2-mercaptoethanol (Gibco, cat. 31350-010), 1x MEM non-essential amino acids (Gibco, cat. 1140- 035), and 100 ng/ml recombinant LIF (MILTENYI BIOTEC, cat. 130-099-895).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Illumina TruSeq Stranded mRNA sample preparation kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
exonic_counts
intronic_counts
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| Data processing |
basecalls performed using CASAVA 1.8
reads were aligned with Bowtie
ChIP-Seq: peaks were identified with MACS, filtered with DESEQ2 (FDR<0,2), quantitated with SeqMonk
RNA-Seq: counts were calculated using the iRNAseq pipeline as previously described (PMID:25564527)
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited files
Supplementary_files_format_and_content: Esrrb_peaks - annotated peak coordinates with RPKM values in all replicates
Supplementary_files_format_and_content: exonic_counts - exonic raw counts in all replicates
Supplementary_files_format_and_content: intronic_counts - intronic raw counts in all replicates
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| Submission date |
Nov 16, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Pablo Navarro |
| E-mail(s) |
[email protected]
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| Phone |
+33145688285
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| Organization name |
Institut Pasteur
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| Street address |
25 rue du Docteur Roux
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| City |
paris |
| ZIP/Postal code |
75015 |
| Country |
France |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE75066 |
Genome-wide analysis of mitosis, early G1, late G1 and G2 in mouse pluripotent cells |
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| Relations |
| BioSample |
SAMN04271966 |
| SRA |
SRX1434663 |
| 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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