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Sample GSM7112307 Query DataSets for GSM7112307
Status Public on Jul 11, 2023
Title donor6_biorepl2_spikein_10pRNA_M
Sample type SRA
 
Source name peripheral blood monocytes / pro-B cells
Organisms Homo sapiens; Mus musculus
Characteristics cell type: peripheral blood monocytes / pro-B cells
genotype: WT
strain: donor no. 6 / 129S1/SvImJ x Cast/EiJ F1
Extracted molecule polyA RNA
Extraction protocol Qiagen Mini / Agilent Mini
SMART-Seq v4 PLUS kit (Takara)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description donor no. 6 peripheral blood monocytes / v-Abl pro-B clonal cell line Abl.1
Donor no. 6 peripheral blood monocytes, biological replicate 2, with 10 % Abl. 1 cell line (129S1xCAST F1) RNA spike-in
STARA_E3.Human_Mouse.counts.tsv
Data processing Sequence reads were aligned on two alellic pseudogenomes using STAR v2.7.9a (with parameters –outSAMattributes vA vG).
Uniquely aligned reads were assigned towards one of the alleles according to their SNP calls and alignment quality (see https://github.com/gimelbrantlab/fastq2allelictabs).
Allelic gene counts were calculated using featurecounts v2.0.2.
Supplementary files format and content: Tab-delimited text files include allelic gene count values for each sample.
 
Submission date Mar 22, 2023
Last update date Jul 11, 2023
Contact name Asia Mendelevich
Organization name Altius
Street address 2211 Elliott Ave
City Seattle
State/province WA
ZIP/Postal code 98121
Country USA
 
Platform ID GPL25526
Series (2)
GSE228004 Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale [III]
GSE228009 Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale
Relations
BioSample SAMN33874444
SRA SRX19751499

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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