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GEO help: Mouse over screen elements for information. |
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Status |
Public on May 11, 2023 |
Title |
MEF, DKO_A1, ctrl, rep2 |
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/CRTC2 knockout clone A1 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 |
SAMN31155883 |
SRA |
SRX17797905 |
Supplementary file |
Size |
Download |
File type/resource |
GSM6616343_SC13.ReadsPerGene.out.tab.gz |
342.7 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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