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| Status |
Public on Mar 01, 2012 |
| Title |
ES_XX_Solexa_i_IDT |
| Sample type |
SRA |
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| Source name |
ES PGK female cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: PGK
cell type: embryonic stem cells
technology: Solexa
barcode/index: index
comment: Illumina 3' adapter
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| Growth protocol |
Female PGK and male E14 embryonic stem (ES) cell lines (from the Dr. E. Heard laboratory) were cultured in Dulbecco’s Modified Eagle Media (DMEM) (Invitrogen) containing 15% FCS (Bio West), 1000 U/ml LIF (Chemicon), 0.1 mM beta-mercaptoethanol (Invitrogen), 0.05 mg/ml of streptomycin (Invitrogen) and 50 U/ml of penicillin (Invitrogen) on a gelatin-coated support in the absence of feeder cells. The culture medium was changed daily. All cells were grown at 37°C in 8% CO2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA samples (5-10 μg), prepared using Trizol reagent (MRC Molecular Research Center), were processed into sequencing libraries using: 1) a homemade protocol (Pfeffer, 2007) for the 454 technology and sequenced at Genoscope (Evry, France), 2) adapted Illumina protocols for Solexa technology and sequenced by Fasteris ((http://www.fasteris.com, Switzerland), and 3) the Small RNA Expression Kit (SREK, Life Technology, version C) and the SOLiD Total RNA kit (STaR-Seq, Life Technology) for the SOLiD technology and sequenced at Institut Curie (Paris, France) or Life Technology (USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Small RNA-Seq
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| Data processing |
The remaining part of the adapter sequences were removed from the reads. The trimmed reads were mapped on the mm9 genome using Bowtie. Respectively, two mismatches in nucleotide space or colour space were allowed for the mapping of the 454 and the SOLiD data, while for Solexa the sum of qualities of mismatching bases was required to not exceed 50. Only the best alignments are reported for each reads. The reads with up to 5,000 repeated alignments on the genome were used for the repeats analysis.
Mature miRNAs profiling: The genomic positions of mature miRNAs and miR* were obtained from the database miRBase (release 16). Aligned reads of length 19-26nt were considered to correspond to a mature miRNA (or miR*) only if: 1) the aligned position did not differ from the annotated position of the mature miRNA by more than 2 bp and 2) the reads had at most as many genomic match positions as the number of genomic copies of the respective mature miRNA. The miRNA profiling data are in the supplementary *miRNA.bed files.
Repeats profiling: The repeats profiles contain the coverage of raw reads mapped on the genome (without pre-miRNAs) and intersected with the RepeatMasker annotation. Strands are separated. These profiles are not normalized. The repeats profiling data are in the supplementary *rmsk.bed files.
Genome Build:
ES_XX_Solexa_i_IDT_minus_rmsk.bed: mm9
ES_XX_Solexa_i_IDT_plus_rmsk.bed: mm9
ES_XX_Solexa_i_IDT_miRNA.bed: mm9
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| Submission date |
Jan 26, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicolas Servant |
| E-mail(s) |
[email protected]
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| Organization name |
Institut Curie
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| Street address |
26 rue d'ulm
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| City |
Paris Cedex 05 |
| ZIP/Postal code |
75248 |
| Country |
France |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE35368 |
Deep-sequencing influences the results obtained in small-RNA sequencing |
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| Relations |
| SRA |
SRX117949 |
| BioSample |
SAMN00779257 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM866988_ES_XX_Solexa_i_IDT_miRNA.bed.gz |
7.8 Kb |
(ftp)(http) |
BED |
| GSM866988_ES_XX_Solexa_i_IDT_minus_rmsk.bed.gz |
35.0 Mb |
(ftp)(http) |
BED |
| GSM866988_ES_XX_Solexa_i_IDT_plus_rmsk.bed.gz |
35.0 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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