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Sample GSM6226338 Query DataSets for GSM6226338
Status Public on Apr 28, 2023
Title RNA-seq of Del(CBS1) stembryos at 120h, rep1
Sample type SRA
Source name stembryo
Organism Mus musculus
Characteristics tissue: stembryo
cell type: mES cells
genotype: Del(CBS1)
stage (in_hours_after_aggregation): 120
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.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing All scripts are available on
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 (
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
Submission date Jun 09, 2022
Last update date Apr 28, 2023
Contact name Lucille Lopez-Delisle
Organization name EPFL
Street address Station 19
City Lausanne
ZIP/Postal code 1015
Country Switzerland
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
BioSample SAMN28944738
SRA SRX15651647

Supplementary file Size Download File type/resource
GSM6226338_Del_CBS1_120h_RNAseq_rep1_FPKM.txt.gz 1.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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