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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 30, 2023 |
| Title |
Q128_Kdm2b_EXP2_rep1 |
| Sample type |
SRA |
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| Source name |
mouse embryo
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| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic stem cell
strain: 129/Ola
phenotype: adherent
genotype: Rex1GFP-d2 cells expressing N-terminal of human huntingtin gene, with 128 CAG repeats and with CAG-Kdm2b
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| Growth protocol |
ES cell lines (Rex1GFP-d2) were cultured in feeder free conditions (plastic coated with 0.2% gelatine [Sigma, cat. G1890]) and replated every 3–4 days at a split ratio of 1:10 following dissociation with Accutase (GE Healthcare, cat. L11-007) or 0.25% Trypsin (Life Technologies). Cells were cultured in serum-containing KSR medium (GMEM [Sigma, cat. G5154] supplemented with 10% KSR [Life Technologies], 2%FBS [Sigma, cat. F7524], 100mM 2-mercaptoethanol [Sigma, cat. M7522], 1× MEM non- essential amino acids [Invitrogen, cat. 1140-036], 2mM L-glutamine, 1mM sodium pyruvate [both from Invitrogen]), supplemented with two small-molecule inhibitors (2i) PD (1μM, PD0325901), CH (3mM, CHIR99021) from Axon (cat. 1386 and 1408) and LIF (100 units/ml purchased from Qkine - Cambridge UK).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Total RNA Purification kit (Norgen Biotek), according to manufactorer's protocol.
3'DGE mRNA-seq (research*/clinical**/diagnostic***) grade sequencing service (Next Generation Diagnostics srl)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts
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| Submission date |
Mar 21, 2023 |
| Last update date |
May 30, 2023 |
| Contact name |
Graziano Martello |
| E-mail(s) |
graziano.martello@unipd.it
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| Organization name |
University of Padua
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| Department |
Department of Molecular Medicine
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| Street address |
viale Colombo 3
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| City |
Padua |
| ZIP/Postal code |
35121 |
| Country |
Italy |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE166567 |
A genome-wide screening in pluripotent cells identifies Mtf1 as a suppressor of mutant huntingtin toxicity |
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| Relations |
| BioSample |
SAMN33845401 |
| SRA |
SRX19742073 |
| 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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