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| Status |
Public on Mar 11, 2024 |
| Title |
RNAseq_ESC_bptf_ko_C_2 |
| Sample type |
SRA |
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| Source name |
embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: embryonic stem cells
cell line: 129S6/SvEvTac
cell type: embryonic stem cells
genotype: bptf knock-out
treatment: none
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with Qiagen Rneasy Mini Kit following manufacture's instruction.. Potential contaminating genomic DNA was removed using Invitrogen DNA-free removal kit, following manufacture's instructions.
Sequencing libraries were prepared from 100ng of purified total RNA using TruSeq stranded mRNA Library Prep (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina RTA 2.4.1 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing. RNA-seq reads were mapped to mm10 using QuasR in spliced alignment mode (splicedAlignment = TRUE) with the option (aligner="Rhisat2"), which internally uses hisat2 (Kim, Paggi, Park et al, Nature Biotech 2019)
Alignments overlapping the opposite strand of any exon of a known gene (gene annotation from the Bioconductor package TxDb.Mmusculus.UCSC.mm10.knownGene, version 3.10.0) were counted using the qCount function from the QuasR Bioconductor package (Gaidatzis et al, Bioinformatics, 2015) with default parameters.
Assembly: mm10
Supplementary files format and content: csv, count table
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| Submission date |
Jun 06, 2023 |
| Last update date |
Mar 11, 2024 |
| Contact name |
Dirk Schuebeler |
| Organization name |
Friedrich Miescher Institute for Biomedical Research
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| Street address |
Maulbeerstrasse 66
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| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE234248 |
Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [RNA-seq] |
| GSE234295 |
Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF |
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| Relations |
| BioSample |
SAMN35642053 |
| SRA |
SRX20601780 |
| 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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