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| Status |
Public on Jan 18, 2017 |
| Title |
WT21.1 |
| Sample type |
SRA |
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| Source name |
hematopoetic stem cell
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
Sex: F
developmental stage: fetus
tissue: liver
age: 13/14 dpc
genotype: WT
cell markers: CD45.2+ Lin- Mac+/low Sca1+ cKit+ (LSK)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Liver single cell suspensions by homogenization of fetal liver tissue with a 1ml Eppendorf pipette and Hank ́s buffered salt solution (HBSS) with 3% foetal calf serum (FCS) were prepared. Cells were then stained with anti-CD45.2-FITC (BD Pharmingen), biotinylated lineage antibodies (anti-B220, -CD3,Gr-1, and -Ter-119; all BD), anti-Mac1/CD11b-eFluor 450 (eBioscience), anti-CD117/c-kit-Alexa Fluor®780 (eBioscience) and anti-Sca-1-PeCy7 (eBioscience). Biotinylated monoclonal antibodies were labeled by incubation with Streptavidin-PerCP/PerCP-Cy5.5 (eBioscience) and LSK cells sorted directly into lysis buffer (0.2%TritonX supplemented with RNAse Inhibitor (Promega))
RNA was cleaned-up from the crude lysate with Agencourt RNAclean XP SPRI beads (Beckman-Coulter). cDNA was synthesized and pre-amplified from 5 μ l of lysate as described in Picelli et al 2014 (Smart-seq2). 0.7 ng of pre-amplified cDNA was used as input for tagmentation by the Nextera XT Sample Preparation Kit (Illumina), where a second amplification round was performed for 12 cycles. For each sample, 5 ng of final library was pooled.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
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)
Genome_build: mm10
Supplementary_files_format_and_content: gene-wise count data in tab delimited text file
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| Submission date |
Jul 21, 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) |
| GSE84703 |
Chromatin remodelling factor SMARCD2 (BAF60B) regulates transcriptional networks controlling early and late differentiation of neutrophil granulocytes |
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| Relations |
| BioSample |
SAMN05427755 |
| SRA |
SRX1969269 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2247840_WT21.1.count.txt.gz |
140.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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