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Sample GSM2255638 Query DataSets for GSM2255638
Status Public on Dec 16, 2016
Title 8571Tx_WT
Sample type SRA
 
Source name LSK progenitor cell
Organism Mus musculus
Characteristics niche genotype: WT
strain: 129Ly5.1
library protocol: Smart-seq2
Extracted molecule total RNA
Extraction protocol cDNA was synthesized and pre-amplified according to Picelli et al 2013. 500 pg of cDNA was used for library preparation using the Nextera XT Kit (Illumina)
Lineage-negative, Sca-1+, Kit+ (LSK) and niche cells were FACS sorted according to Istvanffy et al. 2011. Cells were sorted into lysis buffer composed of 0.2 % Triton-X100 and 0.5 U/µl RNAse Inhibitor
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description Smartseq_LSK_count_table.txt
Data processing For Smart-seq2 libraries: Sequencing reads were demultiplexed from the Nextera (i5 and i7) indices using deML (Renaud 2014, Bioinformatics) Demultiplexed reads were aligned to the mouse genome mm10 and ERCC reference using NextGenMap (Sedlazeck et al., 2013) Count data was generated from mapped reads using featureCounts (Liao et al., 2014) on ENSEMBL gene models (GRCm38.74)
For UMI-seq libraries: Reads were tagged with UMI and sample barcode using the Drop-seq pipeline (Macosko et al., 2015). Reads were aligned to the mouse genome mm10 using STAR (Dobin et al., 2013). Unique gene-wise counts were generated using the Drop-seq pipeline. Sample-barcode annotation can be found in additional file "UMIseq_niche_cells_barcode_annotation.txt". For data deposition, samples were demultiplexed using bamtools filter command.
Genome_build: mm10
Supplementary_files_format_and_content: sample- and gene-wise expression tables
 
Submission date Jul 29, 2016
Last update date May 15, 2019
Contact name Christoph Ziegenhain
E-mail(s) ziegenhain@bio.lmu.de
Organization name Ludwig-Maximilians University Munich
Department Department Biology II
Lab Anthropology & Human genomics
Street address Großhaderner Str. 2
City Martinsried
State/province Bavaria
ZIP/Postal code 82152
Country Germany
 
Platform ID GPL18480
Series (1)
GSE84993 Niche WNT5A regulates expression of the actin regulatory pathway in regenerating repopulating hematopoietic stem cells
Relations
BioSample SAMN05464454
SRA SRX1989251

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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