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Sample GSM539841 Query DataSets for GSM539841
Status Public on Jun 07, 2010
Title mouse B cells activated in vitro with LPS/IL4 replicate 2 [09-002]
Sample type SRA
 
Source name Mouse Mature B cells, Spleen, in vitro LPS/IL-4 activated
Organism Mus musculus
Characteristics strain: C57BL/6J
gender: male
source: spleen
isolation: CD43 negative magnetic beads selection
Growth protocol Culture of CD43 depleted splenocytes with LPS (50 mcg/ml) and IL-4 (2.5 ng/ml) for 72 hrs
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 SRX020043
BioSample SAMN00012366

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

Data table
SEQUENCE COUNT
TTTGTTGGTTTATGGACATACT 1
AAGAACCAGAACTTCCCAGGCCCTACT 1
AAAGTCGGAGGTTCGAAGA 443
TGGAGACGCGGCCCTGTTGG 2
CTTTCAGTCGGATGTTTACAG 3304
AACATTCATTGCTGTCGGT 460
AGTGGTTAGGATTCGGCGCT 500
AACATTCAACGCTGTCGGT 1020
AGCAGCATTGTACAGGGCTATGAA 1659
ATATGCACTGTACATTCCACGAGCATTG 1
TGTGGGTGTTGTGGAACCAGGC 1
TGACCTATGAATTGACAGC 49
AACTGGACTTGGTGGCGCATGCTT 1
TGAGGTAGTAGATTGTATA 60784
TGAGGTAGTAGGTTGTATAG 5231
CAGCCTGGGCTACACATTTTTA 31
GTAGTCGTGGCCGAGTGGT 59
TCAAATCCCGGACGAGCCCCCAA 1
CCCTGTATTAGACTCCGTTT 1
CATCTTAAGAACTCCATGG 1

Total number of rows: 337557

Table truncated, full table size 8300 Kbytes.




Supplementary file Size Download File type/resource
GSM539841.txt.gz 20.9 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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