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Sample GSM569190 Query DataSets for GSM569190
Status Public on Jul 24, 2010
Title Human memory B cell [09-001]
Sample type SRA
 
Source name Human Memory B cells, Tonsil, FACS
Organism Homo sapiens
Characteristics cell type: memory B cell
source tissue: tonsil
gender: female
age: 5 years
isolation: fluorescence activated cell sorting
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
 
Description Cell surface markers used for cell sorting: CD19+CD27+D38-/low
Data processing Image analysis, base calling, quality filtering: Standard settings of GAPipeline 1.0-1.4 using PhiX control; Fastq files contain 30 nt length reads 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.
 
Submission date Jul 22, 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 GPL9115
Series (1)
GSE23090 microRNA expression in human tonsillar B cell populations
Relations
SRA SRX023951
BioSample SAMN00017492

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

Data table
SEQUENCE COUNT
GCCAGCGGGCTGAGGGTAGGAAGTA 2
AATGTCTGAACCTGTCTGAAG 1
AACTCTGGAAAAACAAGTCAG 1
CAGCAAGACGAGAAGACCCTATG 1
GTGGTTGGGCCCTGGGAGGGTGTGGG 1
TTCTGGATAACATGCTGAAGCT 2
TGAGGTAGTAGGTTGTATAGTT 315573
GAAGCTGTCGACCTTGCACGG 1
CCAGGAGGTGGAGGGTGCAT 1
AAGATGGCGGACGAGAAGGA 1
CAGTGCGGCCAGGCAGGTCTGGGCTCTG 1
ACGCCGTCTGGGTAGATGGGTCCTT 1
AACGGAATCCCAAAAGCAGCTG 1385
AGAGACGCACAGTAGAGCA 1
GTGAGTAGCGGGCTGCTGGG 1
CACGGAGATGGTGGCTGAG 1
CTCACGGCGATCCTGGACTGA 1
AAGCTACTGTAGTGAGGACGTCTA 1
TATTGCACTTGTCCCGGCCTG 597
AGCTACATCTGGCTACTGGGTC 833

Total number of rows: 263871

Table truncated, full table size 5851 Kbytes.




Supplementary file Size Download File type/resource
GSM569190_09-001_HuMemoryB.mirna.tsv.gz 7.3 Kb (ftp)(http) TSV
GSM569190_09-001_HuMemoryB.summary.txt.gz 1.7 Mb (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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