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Sample GSM539873 Query DataSets for GSM539873
Status Public on Jun 07, 2010
Title mouse pancreatic tissue [09-002]
Sample type SRA
 
Source name Mouse Pancreas
Organism Mus musculus
Characteristics strain: C57BL/6J
gender: male
tissue: pancreas
Extracted molecule total RNA
Extraction protocol RNA isolation method: Trizol. Small RNA library preparation: Illumina protocol "Preparing Samples for Analysis of Small RNA" (Part # 11251913 Rev. A)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer II
 
Data processing Image analysis, base calling, quality filtering: Standard settings of GAPipeline 1.0-1.4 using PhiX control; Fastq files contain full length reads (26 or 36 nts) that passed the chastity filter. Qualities are in phred64 format for all files. Alignments were done with a custom software that used bowtie 0.9.9.3 to find the longest, mismatch-free alignable prefix of each read, trimmed any remaining adapter sequence, and then stored the unique sequence reads and their frequency. This data is given in the data table, which therefore gives frequencies only for alignable reads. For further analysis, the alignments were matched up with annotation to determine where the small RNA reads originated from and to profile miRNA expression in different tissues. These tab-delimited files (supplied as supplementary files below) have a header line and give the expression level of each miRNA (previously described and putatively new) in tags per million miRNA tags. No expression level cutoff was applied, so all miRNAs are included if there were any reads detected.
 
Submission date May 03, 2010
Last update date May 15, 2019
Contact name Seolkyoung Jung
Organization name NIH
Department NIAMS
Lab biodata mining and discovery section
Street address 10 Center Dr
City bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL9250
Series (1)
GSE21630 Regulation of microRNA Expression and Abundance during Lymphopoiesis
Relations
SRA SRX020075
BioSample SAMN00012398

Data table header descriptions
SEQUENCE sequence of longest alignable and adapter-sequence free read prefix
COUNT count

Data table
SEQUENCE COUNT
CGGGACGCGGTAGAATGGCG 1
TGGAGACGCGGCCCTGTTGG 5
CTTTCAGTCGGATGTTTACAG 795
AACATTCATTGCTGTCGGT 580
AGTGGTTAGGATTCGGCGCT 71
AACATTCAACGCTGTCGGT 1767
AGCAGCATTGTACAGGGCTATGAA 702
TGACCTATGAATTGACAGC 48
TGAGGTAGTAGATTGTATA 72507
TGAGGTAGTAGGTTGTATAG 4358
GGGGGGTGGTGTGGTGGTG 1
CAGCCTGGGCTACACATTTTTA 1
GTAGTCGTGGCCGAGTGGT 263
TGAGAACTGAATTCCATGGGTTATA 2
TGAGAACTGAATTCCATAG 34
TGAGGTAGTAGGTTGTATGGT 52120
AAAAAAAAAAAAAAAAATGTTTGC 1
TGAGGTAGGAGGTTGTATAGTT 28351
CATTGCACTTGTCTCGGTCTGA 6080
GGGGGATTAGCTCAAATGGTA 21

Total number of rows: 92774

Table truncated, full table size 2540 Kbytes.




Supplementary file Size Download File type/resource
GSM539873.txt.gz 20.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data included within Sample table
Processed data provided as supplementary file
Raw data are available in SRA

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