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Sample GSM5851442 Query DataSets for GSM5851442
Status Public on Feb 01, 2022
Title RNAseq in Zbtb11KO ES grown in -2i+LIF replicate 3
Sample type SRA
 
Source name Embryonic stem cells
Organism Mus musculus
Characteristics strain: Ainv15(iZbtb11-HA Zbtb11KO)
treatment: No treatment
cell type: Embryonic stem cells
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.
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.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
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.
 
Submission date Jan 31, 2022
Last update date Feb 01, 2022
Contact name Shaun Mahony
E-mail(s) mahony@psu.edu
Phone 814-865-3008
Organization name Penn State University
Department Biochemistry & Molecular Biology
Lab Shaun Mahony
Street address 404 South Frear Bldg
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
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
Relations
BioSample SAMN25519955
SRA SRX13999580

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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