Transcriptome Analysis of Eomes-null Hematopoietic Cells

RNA isolated from Flk-1^hi/PdgfRa^- single cell suspensions (1.5x10^{5 (link)} cells) from three independent hematopoietic differentiations of WT (CCE) and Eomes-null (clone 6A6, CCE) cells using the RNeasy Micro Kit (QIAGEN, Cat#74004) was normalized to 800ng per sample, depleted of cytoplasmic and mitochondrial ribosomal RNA sequences (Ribo-Zero Gold rRNA Removal Kit (H/M/R), Cat: #MRZG12324) and library preparation performed using the Illumina TruSeq Stranded Total RNA Library Prep (H/M/R) (Cat: #20020597), followed by sequencing (75-cycle paired end) on the Illumina HiSeq4000 platform.

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Harland L.T., Simon C.S., Senft A.D., Costello I., Greder L., Imaz-Rosshandler I., Gottgens B., Marioni J.C., Bikoff E.K., Porcher C., de Bruijn M, & Robertson E.J. (2021). The T-box Transcription Factor Eomesodermin Governs Hemogenic Competence of Yolk-Sac Mesodermal Progenitors. Nature cell biology, 23(1), 61-74.

Publication 2021

RNeasy Micro Kit Ribo-Zero Gold rRNA Removal Kit (H/M/R), TruSeq Stranded Total RNA Library Prep (H/M/R) HiSeq4000 platform

Cells Clone Cytoplasmic Gold Hematopoietic Library Mitochondrial ribosomal Rna sequences Rrna

Corresponding Organization :

Other organizations : University of Oxford, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Wellcome/MRC Cambridge Stem Cell Institute, University of Cambridge, European Bioinformatics Institute

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Variable analysis

independent variables

Genotype (WT (CCE) vs. Eomes-null (clone 6A6, CCE))

dependent variables

Gene expression profiles of Flk-1^hi/PdgfRa^- single cell suspensions (1.5x10^5 cells) from three independent hematopoietic differentiations

control variables

RNA isolation method (RNeasy Micro Kit (QIAGEN, Cat#74004))
RRNA depletion method (Ribo-Zero Gold rRNA Removal Kit (H/M/R), Cat: #MRZG12324)
Library preparation method (Illumina TruSeq Stranded Total RNA Library Prep (H/M/R) (Cat: #20020597))
Sequencing platform (Illumina HiSeq4000, 75-cycle paired end)

controls

Positive control: Not specified
Negative control: Not specified

Annotations

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