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| Status |
Public on Apr 01, 2021 |
| Title |
RNAseq_Tex191ESC_KO3 |
| Sample type |
SRA |
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| Source name |
RNAseq_Tex191ESC_KO
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| Organism |
Mus musculus |
| Characteristics |
strain background: 129/Ola
cell type: Embryonic stem cells
passages: 12-18
genotype/variation: Tex19.1-/-
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| Growth protocol |
Mouse embryonic stem cells derived from the parental E14Tg2a line were cultured in gelatinised flasks in Glasgow Modified Eagle’s Media (GMEM), 10% foetal calf serum, 1% non-essential amino acid, 1% sodium pyruvate, 1% penicillin-streptomycin, 1% L-glutamine, 0.001% β-mercaptoethanol, and 0.2% leukaemia inhibitory factor-conditioned media at 37°C in 5% CO2 and passaged using 0.05% trypsin, 0.02% EDTA in PBS.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed with TRIzol reagent, and RNA used to construct Illumina TruSeq Stranded mRNA library.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep kit and sequenced using an Illumina HiSeq 4000 150PE sequencing system.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Adapter sequenced removed with TrimGalore! v0.4.1 with the following settings: --stringency 5 --length 30 --paired.
Sequences aligned to the mouse mm10 reference genome with TopHat2 v2.1.0 using using an Ensembl known transcriptome model and settings: -g 1 --mate-inner-dist 77 --mate-std-dev 64 --no-coverage-search --no-novel-juncs --no-novel-indels --b2-sensitive.
Counts were calculated using HTSeq v0.11.2 to count reads in GENCODE Basic VM18 gene predictions.
Read counts were normalised to the number of mapped reads (CPM, counts per million mapped reads) by EdgeR and low coverage genes (CPM<5 is more than half the samples) were removed. Differential enrichment analysis of read counts was performed using EdgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files generated by EdgeR that include logCPMs for all samples, and logFCs, P values and FDR-adjusted P values for the Tex19.1-/- vs Tex19.1+/- comparison.
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| Submission date |
Apr 01, 2019 |
| Last update date |
Apr 01, 2021 |
| Contact name |
Ian Adams |
| Organization name |
MRC Human Genetics Unit
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| Department |
Genome Regulation
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| Street address |
Crewe Road
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| City |
Edinburgh |
| ZIP/Postal code |
EH42XU |
| Country |
United Kingdom |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE129101 |
RNA Sequencing of Tex19.1-/- Mouse Embryonic Stem Cells [RNA-seq] |
| GSE129102 |
H3K9me3 ChIP-Seq and RNA-seq of Tex19.1-/- Mouse Embryonic Stem Cells |
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| Relations |
| BioSample |
SAMN11296816 |
| SRA |
SRX5611051 |
| 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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