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| Status |
Public on Apr 02, 2022 |
| Title |
Wildtype_1_2 |
| Sample type |
SRA |
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| Source name |
TV251_12_vav_cre
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| Organism |
Mus musculus |
| Characteristics |
cell type: Hematopoietic stem cells (LSKs) sorted from Mouse Bone marrow
gender: Female
genotype: vavCre
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| Extracted molecule |
total RNA |
| Extraction protocol |
LSKs were sorted into lysis buffer from the bone marrow of wiltype and mutCALR homozygous mice
For the generation of full-length cDNA, the Smart-seq2 protocol (Picelli, S. et al, Nat Protoc. 2014 Jan;9(1):171-81. doi:10.1038/nprot.2014.006) was used.
The subsequent library preparation from the amplified cDNA was performed using the Nextera XT DNA library prep kit (Illumina).
For sequencing, libraries were pooled, diluted and sequenced on Illumina HiSeq 3000/4000 using 50 bp single-read chemistry.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
Wildtype_HSCs
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| Data processing |
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/DanieleBarreca/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e100 (April 2020) with STAR 2.7.1a and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.9 package DESeq2 1.24.0, running under R 3.6.0.
Genome_build: UCSC mm10 based on GRCm38
Supplementary_files_format_and_content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format
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| Submission date |
Apr 06, 2021 |
| Last update date |
Apr 02, 2022 |
| Contact name |
Christoph Bock |
| E-mail(s) |
cbock@cemm.oeaw.ac.at
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| Organization name |
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
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| Street address |
Lazarettgasse 14
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| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE171563 |
Gene expression profile of hematopoietic stem cells from mutCALR transgenice mice |
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| Relations |
| BioSample |
SAMN18632364 |
| SRA |
SRX10521167 |
| 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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