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Sample GSM866983 Query DataSets for GSM866983
Status Public on Mar 01, 2012
Title ES_XY_Solexa_i_IDT
Sample type SRA
Source name ES E14 male cells
Organism Mus musculus
Characteristics cell line: E14
cell type: embryonic stem cells
technology: Solexa
barcode/index: index
comment: IDT 3' adapter
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.
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 ((, 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).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Small RNA-Seq
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_XY_Solexa_i_IDT_minus_rmsk.bed: mm9
ES_XY_Solexa_i_IDT_plus_rmsk.bed: mm9
ES_XY_Solexa_i_IDT_miRNA.bed: mm9
Submission date Jan 26, 2012
Last update date May 15, 2019
Contact name Nicolas Servant
Organization name Institut Curie
Street address 26 rue d'ulm
City Paris Cedex 05
ZIP/Postal code 75248
Country France
Platform ID GPL13112
Series (1)
GSE35368 Deep-sequencing influences the results obtained in small-RNA sequencing
SRA SRX117944
BioSample SAMN00779252

Supplementary file Size Download File type/resource
GSM866983_ES_XY_Solexa_i_IDT_miRNA.bed.gz 7.7 Kb (ftp)(http) BED
GSM866983_ES_XY_Solexa_i_IDT_minus_rmsk.bed.gz 33.9 Mb (ftp)(http) BED
GSM866983_ES_XY_Solexa_i_IDT_plus_rmsk.bed.gz 34.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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