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Sample GSM1096581 Query DataSets for GSM1096581
Status Public on Mar 27, 2013
Title Wild Type Adult PAS
Sample type SRA
Source name testes
Organism Mus musculus
Characteristics tissue: testes
developmental stage: Adult
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 PAS-seq libraries (Table S1) were prepared essentially as described (Shepard et al., 2011) and sequenced using a HiSeq 2000 (100 nt read length).
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
Description library strategy: PAS-Seq
Data processing PAS library was analyzed as follows: We first removed adaptors and performed quality control using Flexbar 2.2 ( with the parameters “-at 3 -ao 10 --min-readlength 30 --max-uncalled 70 --phred-pre-trim 10.” For reads beginning with GGG including (NGG, NNG or GNG) and ending with three or more adenosines, we removed the first three nucleotides and mapped the remaining sequence with and without the tailing adenosines to the mouse genome using TopHat 2.0.4. We retained only those reads that could be mapped to the genome without the trailing adenosine residues. Genome-mapping reads containing trailing adenosines were regarded as potentially originating from internal priming and thus discarded. The 3′ end of the mapped, retained read was reported as the site of cleavage and polyadenylation.
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 SRX247987
BioSample SAMN01943341

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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