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Sample GSM971331 Query DataSets for GSM971331
Status Public on Mar 25, 2013
Title B cell polyA RNA-Seq
Sample type SRA
Source name Blood
Organism Homo sapiens
Characteristics tissue: blood
developmental stage: Adult
genotype/variation: wild type
cell type: in vivo differentiated B cell
Growth protocol N/A
Extracted molecule polyA RNA
Extraction protocol As in Chepelev et al, Nucleic Acids Research, 2009.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
Description Purified from whole blood using human Naive B cell isolation kit II kits (Miltenvi #130-091-150).
Data processing Illumina Casava1.7 software used for basecalling.
Reads were aligned using TopHat 1.3.1 on top of Bowtie 0.12.7 to the hg18 genome with default parameters
accepted_hits file was converted to BED using SAMtools. For graph-making and RPKM calculations, and all subsequent analyses, chromosome Y reads were discarded as some sources in study were female.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Hu et al 2011. Briefly reads in RefSeq gene exons were counted and normalized by total genic exon size and library size.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample with columns: RefSeq ID, RPKM, exon base pair count, read count, unique ID, num genes w/ ID
Supplementary_files_format_and_content: BED file of TopHat mapped reads
Submission date Jul 20, 2012
Last update date May 15, 2019
Contact name Brian J Abraham
Organization name St. Jude Children's Research Hospital
Department Computational Biology
Street address 262 Danny Thomas Blvd
City Memphis
State/province TN
ZIP/Postal code 38112
Country USA
Platform ID GPL9115
Series (2)
GSE39229 Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis
GSE39537 Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis [RNA-Seq]
SRA SRX170344
BioSample SAMN01091969

Supplementary file Size Download File type/resource
GSM971331_Naive_B_cells_RNA-Seq.rpkm.gz 585.7 Kb (ftp)(http) RPKM
GSM971331_Naive_B_cells_RNA-Seq_tophat_accepted_hits.bed.gz 373.3 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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