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| Status |
Public on Jan 14, 2024 |
| Title |
E14_ESC_+dtag_4hrs_Rep3 |
| Sample type |
SRA |
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| Source name |
E14
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| Organism |
Mus musculus |
| Characteristics |
cell line: E14
cell type: mESC
genotype: KDM3A: WT/WT KDM3B: WT/WT
treatment: +dTAG-13 4 hours
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| Growth protocol |
ESCs were grown on 0.1% gelatin coated plates and maintained in ESC media (knock-out DMEM, 15% FBS, 1x non-essential amino acids, 1x glutamax, 1x penicillin/streptomycin, 2-Mercaptoethanol (4 μl/525ml), and leukemia inhibitory factor).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with TRIzol and chloroform, cleaned using the Qiagen Rneasy Mini kit, and Dnase treated (Qiagen 79254) for 30 min.
1 ug of RNA was used for library construction. TruSeq RNA Sample Preparation kit V2 (RS-122-2002) was used to construct cDNA libraries
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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 |
Libraries were sequenced to a depth of ~50 million reads/sample were sequenced PE150 by Novogene on an Illumina Novaseq 6000 platform.
Sequencing quality was assessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequenced reads were processed using Trimmomatic (Bolger et al., 2014) with the following parameters: LEADING:3 TRAILING:3 CROP:135 HEADCROP:15 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned to the mm9 genome using RSEM-1.2.4 (Li and Dewey, 2011) with a mismatch per seed set to 2 and seed length set to 28 (- bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 --paired-end). RSEM-1.2.4 alignment yielded transcripts per million (TPM) for each gene
Differentially expressed (DE) genes were called with EBSeq (Leng et al., 2013). Differentially expressed genes were filtered to have a posterior probability DE greater than 0.95 and a 2 or 0.5 greater posterior fold change (PostFC). Expression changes reported are PostFC values determined by EBSeq unless otherwise noted to be TPM
Assembly: mm9
Supplementary files format and content: Output from RSEM is .results text file containing genes, transcript ID, length, counts, transcripts per million (TPM), and FPKM.
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| Submission date |
Apr 22, 2023 |
| Last update date |
Jan 14, 2024 |
| Contact name |
Rupa Sridharan |
| E-mail(s) |
rsridharan2@wisc.edu
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| Organization name |
University of Wisconsin
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| Department |
Wisconsin Institute for Discovery
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| Lab |
Sridharan
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| Street address |
330 N. Orchard Street
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53715 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE230341 |
KDM3A and KDM3B maintain naïve pluripotency through regulation of alternative splicing |
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| Relations |
| BioSample |
SAMN34313629 |
| SRA |
SRX20062656 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7220189_E14Rep3.rsem.genes.results.gz |
393.0 Kb |
(ftp)(http) |
RESULTS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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