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Sample GSM1096579 Query DataSets for GSM1096579
Status Public on Mar 27, 2013
Title Wild Type 10.5 dpp CAGE
Sample type SRA
Source name testes
Organism Mus musculus
Characteristics tissue: testes
developmental stage: 10.5 dpp
strain: C57BL/6J
genotype: wild-type
Growth protocol Mice were maintained and used according to the guidelines of the Institutional Animal Care and Use Committee of the University of Massachusetts Medical School.
Extracted molecule total RNA
Extraction protocol CAGE (cap analysis of gene expression) was as described (Yang et al., 2011)
Library strategy RNA-Seq
Library source transcriptomic
Library selection CAGE
Instrument model Illumina HiSeq 2000
Data processing CAGE libraries were analyzed as follows: After removing adaptor sequences and checking read quality using Flexbar 2.2 with the parameters of “-at 3 -ao 10 --min-readlength 20 --max-uncalled 70 --phred-pre-trim 10”, we retained only reads beginning with NG or GG (the last two nucleotides on the 5′ adaptor). We then removed the first two nucleotides and mapped the sequences to the mouse genome using TopHat 2.0.4. All unique 5′ ends of the mapped positions were considered as CAGE-tag starting sites and grouped into tag clusters using a distance-based method in which the maximal distance between two neighboring tags was required to be <20 bp. The peak position of a tag cluster was then reported as the transcription start site.
Genome_build: mm9
Supplementary_files_format_and_content: BED
Submission date Mar 12, 2013
Last update date May 15, 2019
Contact name Christian Roy
Organization name Umass Med
Street address 364 Plantation St
City Worcester
State/province Massachusetts
ZIP/Postal code 01605
Country USA
Platform ID GPL13112
Series (2)
GSE44690 An Ancient Transcription Factor Initiates the Burst of piRNA Production During Early Meiosis in Mouse Testes
GSE45048 An Ancient Transcription Factor An Ancient Transcription Factor During Early Meiosis in Mouse Testes (PAS-Seq and CAGE)
SRA SRX247985
BioSample SAMN01943339

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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