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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 16, 2016 |
| Title |
MSC_Wnt5a_4 |
| Sample type |
SRA |
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| Source name |
MSC niche cell
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| Organism |
Mus musculus |
| Characteristics |
niche genotype: Wnt5a
strain: 129Ly5.1
library protocol: UMI-seq
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| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA was synthesized, barcoded, pooled and pre-amplified according to Soumillon et al. 2014. 800 pg of the cDNA pool 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
UMIseq_niche_cells_UMItable.txt
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| 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
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| Submission date |
Jul 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Christoph Ziegenhain |
| E-mail(s) |
ziegenhain@bio.lmu.de
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| Organization name |
Ludwig-Maximilians University Munich
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| Department |
Department Biology II
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| Lab |
Anthropology & Human genomics
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| Street address |
Großhaderner Str. 2
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| City |
Martinsried |
| State/province |
Bavaria |
| ZIP/Postal code |
82152 |
| Country |
Germany |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE84993 |
Niche WNT5A regulates expression of the actin regulatory pathway in regenerating repopulating hematopoietic stem cells |
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| Relations |
| BioSample |
SAMN05464438 |
| SRA |
SRX1989267 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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