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Sample GSM8171481 Query DataSets for GSM8171481
Status Public on Mar 30, 2024
Title Kmt2d +/+ line 3, D7, exp2
Sample type SRA
 
Source name ATDC5
Organism Mus musculus
Characteristics cell line: ATDC5
cell type: chondrocyte
genotype: Kmt2d +/+
line: line 3
time: D7
group: exp2
Treatment protocol Cells were differentiated for either 7 or 14 days.
Growth protocol CRISPR-Cas9 edited ATDC5 cells were maintained at 37°C, 5% CO2, with ATDC5 Complete Media (DMEM/F-12 supplemented with 5% heat-inactivated fetal bovine serum, 2 mM L-glutamine, 100 U/mL penicillin and 100 μg/mL streptomycin). To differentiate cells towards chondrocytes, media was exchanged for ATDC5 Complete Media supplemented with 0.05 mg/mL L-ascorbic acid, 10 mM β-glycerophosphoric acid, and 1x Insulin-Transferrin-Selenium (ITS-G). Cells were differrentiated for up to 7 or 14 days at 37°C, 5% CO2, with supplemented media changes every 48-72 hours.
Extracted molecule polyA RNA
Extraction protocol Cells were homogenized with TRIzol reagent, followed by phenol-chloroform separation. Total RNA was purified from the aqueous phase using the Zymo RNA Clean and Concentrator-5 kit with DNase I treatment.
Library preparation was performed with the NEBNext Ultra II RNA Library Prep kit in conjunction with NEBNext Poly(A) mRNA Magnetic Isolation Module.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Reads were pseudoaligned to the GRCm38 transcriptome (Ensembl release 102) using Salmon 1.9.0 for paired-end reads, with selective alignment and GC bias correction enabled.
Raw transcript-level counts were imported and summarized to genes with tximeta 1.12.4.
Assembly: GRCm38.p6
Supplementary files format and content: Output from Salmon containing transcript-level quantification, in .sf format
 
Submission date Mar 26, 2024
Last update date Mar 30, 2024
Contact name Christine W Gao
E-mail(s) cgao13@jhmi.edu
Organization name Johns Hopkins University School of Medicine
Street address 733 N. Broadway, Rm 406
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platform ID GPL24247
Series (1)
GSE262539 Growth retardation in a mouse model of Kabuki syndrome 2 bears mechanistic similarities to Kabuki syndrome 1.
Relations
BioSample SAMN40622338
SRA SRX24068104

Supplementary file Size Download File type/resource
GSM8171481_Con_10-8_D7_S12_L001_quant.sf.gz 1.6 Mb (ftp)(http) SF
GSM8171481_Con_10-8_D7_S12_L002_quant.sf.gz 1.6 Mb (ftp)(http) SF
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Raw data are available in SRA

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