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Status |
Public on Mar 30, 2024 |
Title |
Kmt2d +/+ line 3, D7, exp2 |
Sample type |
SRA |
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Source name |
ATDC5
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Organism |
Mus musculus |
Characteristics |
cell line: ATDC5 cell type: chondrocyte genotype: Kmt2d +/+ line: line 3 time: D7 group: exp2
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Treatment protocol |
Cells were differentiated for either 7 or 14 days.
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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.
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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.
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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 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
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Submission date |
Mar 26, 2024 |
Last update date |
Mar 30, 2024 |
Contact name |
Christine W Gao |
E-mail(s) |
cgao13@jhmi.edu
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Organization name |
Johns Hopkins University School of Medicine
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Street address |
733 N. Broadway, Rm 406
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City |
Baltimore |
State/province |
MD |
ZIP/Postal code |
21205 |
Country |
USA |
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Platform ID |
GPL24247 |
Series (1) |
GSE262539 |
Growth retardation in a mouse model of Kabuki syndrome 2 bears mechanistic similarities to Kabuki syndrome 1. |
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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 |
SRA Run Selector |
Raw data are available in SRA |
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