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Sample GSM2948471 Query DataSets for GSM2948471
Status Public on Apr 25, 2019
Title mESC - Rb TKO (D1.10)
Sample type SRA
 
Source name mESC - Rb TKO
Organism Mus musculus
Characteristics cell type: ESC
genotype: Rb TKO
Growth protocol mESC lines were maintained feeder-free on 0.2% gelatin-coated (Sigma G9382) plates in Dulbecco’s modified Eagle’s medium (Gibco SH30243.01) containing 15% fetal bovine serum (Hyclone SH30071.03; VWR Seradigm 97068-085), MEM non-essential amino acids (Gibco 11140-050), penicillin-streptomycin-glutamine (Gibco 10378-016), and 0.1 mM beta-mercaptoethanol (Gibco 21985-023), and supplemented with LIF. Cells were passaged enzymatically using 0.05% Trypsin-EDTA (Gibco 15400-054). Single-cell suspensions of 1000 mESCs/mL were cultured in low density assays.
Extracted molecule total RNA
Extraction protocol Cells were grown at low density for four days. RNA extraction was performed using the RNeasy micro kit (Qiagen 74004).
Libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina RS-122-2101).
Four wild-type and four E2F4KO mESC lines were sequenced on a HiSeq4000, generating on average 42 million paired-end (2x76) reads per sample. Two of the wild-type lines (J3.3 and J3.14) were expanded from clones that had retained E2F4 protein expression following transfection with a gRNA against E2F4, and the other two wild-type lines (C1 and C2) were obtained following transfection of an empty pX330 vector. Similarly, four TKO and four QKO lines were sequenced on a separate run of a HiSeq4000, also generating on average 45 million paired-end (2x76) reads per sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description D1.10
Data processing Reads were mapped to mouse reference genome mm10 with STAR2.5.1b using default settings. Genes that have at least ten reads in two out of four samples of either the control group or the E2F4KO group were further used for analysis. Differentially expressed genes were obtained using DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: File including counts and FPM, log2 Foldchanges and p-values obtained with DEseq2
 
Submission date Jan 25, 2018
Last update date Apr 25, 2019
Contact name Julia Arand
E-mail(s) juliaarand@googlemail.com
Organization name Medical University of Vienna
Street address Schwarzspanierstr. 16
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platform ID GPL21103
Series (1)
GSE109684 E2F4 regulates transcriptional activation in mouse embryonic stem cells independently of the RB family
Relations
BioSample SAMN08397774
SRA SRX3601335

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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