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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 11, 2023 |
| Title |
MEF, KO, ctrl, rep1 |
| Sample type |
SRA |
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| Source name |
mouse embryonic fibroblast
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| Organism |
Mus musculus |
| Characteristics |
cell type: mouse embryonic fibroblast
genotype: LKB1 knockout
treatment: control
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
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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 |
Reads were trimmed with TrimGalore v0.6.0.
Using STAR v2.7.8a, trimmed reads were aligned to mm10 GENCODE vM24 to obtain read counts per gene.
Assembly: mm10
Supplementary files format and content: tab-delimited file containing read counts per gene.
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| Submission date |
Oct 04, 2022 |
| Last update date |
May 11, 2023 |
| Contact name |
Russell Jones |
| E-mail(s) |
russell.jones@vai.org
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| Phone |
6166001610
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| Organization name |
Van Andel Institute
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| Street address |
333 Bostwick Ave. NE
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| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE214823 |
RNA-seq profiling of WT, LKB1 KO, and LKB1/CRTC2 KO mouse embryonic fibroblasts |
| GSE214824 |
WT, LKB1 KO, and LKB1/CRTC2 KO mouse embryonic fibroblasts |
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| Relations |
| BioSample |
SAMN31155893 |
| SRA |
SRX17797895 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6616333_SC3.ReadsPerGene.out.tab.gz |
343.7 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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