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Status |
Public on Apr 28, 2023 |
Title |
RNA-seq of Del(CBS1) stembryos at 96h, rep1 |
Sample type |
SRA |
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Source name |
stembryo
|
Organism |
Mus musculus |
Characteristics |
tissue: stembryo cell type: mES cells genotype: Del(CBS1) stage (in_hours_after_aggregation): 96
|
Extracted molecule |
total RNA |
Extraction protocol |
Stembryos for each condition were collected and pooled in a 2 ml Eppendorf tube. After centrifugation and medium removal, pelleted stembryos were stored at -80°C until RNA extraction. RNeasy Plus Micro kit (Qiagen) with on-column DNase digestion was used for RNA extraction following the manufacturer’s instructions. RNA-seq library preparation with Poly-A selection was performed with 1 µg of purified RNA using the TruSeq Stranded mRNA kit from Illumina and following the manufacturer’s protocol. Library quality was assessed with Fragment analyzer.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Data processing |
All scripts are available on https://github.com/lldelisle/scriptsForRekaikEtAl2022 Adapter sequences were trimmed from reads using cutadapt (Martin et al 2011) version 1.16 (-a 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC' -A 'GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT'). Trimmed reads were aligned on mm10 with STAR version 2.7.7a (Dobin et al. 2013) with ENCODE options using a custom gtf based on Ensembl version 102 (https://doi.org/10.5281/zenodo.4596490). Only uniquely mapped reads (tag NH:i:1) were kept using bamFilter version 2.4.1 (Barnett et al. 2011). FPKM values were computed using cufflinks version 2.2.1 (Trapnell et al. 2010; Roberts et al. 2011) with default parameters. Assembly: mm10 Supplementary files format and content: *_FPKM.txt.gz: output of cufflinks with FPKM values per gene Supplementary files format and content: all_FPKM.txt.gz: all FPKM values combined into a single table, one raw per gene_id and one column per sample
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Submission date |
Jun 09, 2022 |
Last update date |
Apr 28, 2023 |
Contact name |
Lucille Lopez-Delisle |
E-mail(s) |
lucille.delisle@epfl.ch
|
Organization name |
EPFL
|
Street address |
Station 19
|
City |
Lausanne |
ZIP/Postal code |
1015 |
Country |
Switzerland |
|
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Platform ID |
GPL19057 |
Series (2) |
GSE205781 |
Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos [RNA-seq] |
GSE205783 |
Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos |
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Relations |
BioSample |
SAMN28944740 |
SRA |
SRX15651645 |