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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 01, 2022 |
| Title |
RNAseq in Zfp131KO ES grown in -2i+LIF replicate 3 |
| Sample type |
SRA |
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| Source name |
Embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
strain: Ainv15(iZfp131-HA Zfp131KO)
treatment: No treatment
cell type: Embryonic stem cells
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| Treatment protocol |
Wildtype, iZbtb10-HA Zbtb10KO, iZbtb11-HA Zbtb11KO and iZfp131-HA Zfp131KO cells were grown in the absence of doxycycline in +2i+LIF or -2i +LIF media for 3 days.
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| Growth protocol |
ESCs were cultured on 0.1% gelatin (Milipore) coated dishes at 37 °C, 8% CO2 in ESC medium (Advanced DMEM/F12: Neurobasal (1:1) Medium (Gibco), supplemented with 2.5% mESC-grade fetal bovine serum (Corning), 1x N2 (Gibco), 1x B27 (Gibco), 2 mM L-glutamine (Gibco), 0.1 mM ß-mercaptoethanol (Gibco)) supplemented with LIF (leukemia inhibitory factor, 1,000 U ml–1 (Millipore)) and 2-inhibitor cocktail (3 mM CHIR (BioVision) and 1 mM PD0325901 (Sigma)) unless stated otherwise.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-seq: 500K cells were collected and RNA was extracted by resuspending in Trizol reagent (Invitrogen, 15596026) followed by purification using Qiagen RNeasy mini kit (Qiagen, 74106).
TruSeq Stranded mRNA Library Preparation kit (Illumina, 20020594) was used to prepare RNA-seq libraries. High Sensitivity DNA ScreenTape (Agilent, 5067-5584) was used to verify library sizes. A KAPA library amplification kit was used on Roche Lightcycler 480 to quantify the library prior to sequencing.
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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 |
RNA-seq fastq files were aligned to the mouse genome (version mm10) using Hisat2 (version 2.1.0)(D. Kim, Langmead, and Salzberg 2015)
FeatureCounts R package was used to assign reads to genomic features (Liao, Smyth, and Shi 2014).
The DESeq2 package was used for differential gene expression analysis and for data visualization (volcano plots, heatmaps, PCA plots)(Love, Huber, and Anders 2014). A q-value cutoff of < 0.01 was used for significantly misregulated genes.
PANTHER (version 14) (http://geneontology.org) was used to perform Gene Ontology term enrichment analysis (Mi et al. 2019).
Genome_build: mm10
Supplementary_files_format_and_content: TXT: tab-delimited text files containing output of featurecounts or DEseq2 for Refseq genes.
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| Submission date |
Jan 31, 2022 |
| Last update date |
Feb 01, 2022 |
| Contact name |
Shaun Mahony |
| E-mail(s) |
mahony@psu.edu
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| Phone |
814-865-3008
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| Organization name |
Penn State University
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| Department |
Biochemistry & Molecular Biology
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| Lab |
Shaun Mahony
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| Street address |
404 South Frear Bldg
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| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE160960 |
The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes [RNA-Seq] |
| GSE160966 |
The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by pausing POL II at pro-differentiation genes |
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| Relations |
| BioSample |
SAMN25519957 |
| SRA |
SRX13999582 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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