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Series GSE139049 Query DataSets for GSE139049
Status Public on Apr 23, 2020
Title TET1 and 5-hydroxymethylation preserve the stem cell state of mouse trophoblast
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Summary Analysis of 5mC and 5hmC and associated transcription in trophoblast stem cells cultured and differentiated at 20% and 5% oxygen, integrated with previously published datasets
Overall design meDIP and hmeDIP was carried out to determine 5mC and 5hmC genomic distribution in tcontrol rophoblast stem cells and those lacking Tet1. hmeDIP and RNA-seq was also carried out in trophoblast stem cells cultured in 5% Oxygen to determine the effect of hypoxia on 5hmC and associated transcription
Contributor(s) Senner CE, Chrysanthou S, Burge S, Lin H, Branco M, Hemberger M
Citation(s) 32442533
Submission date Oct 17, 2019
Last update date Dec 22, 2020
Contact name Felix Krueger
Organization name The Babraham Institute
Department Bioinformatics
Street address Babraham Hall
City Cambridge
ZIP/Postal code CB22 3AT
Country United Kingdom
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (25)
GSM4128026 Control_1_TS_hmeDIP
GSM4128027 Control_1_TS_meDIP
GSM4128028 Control_2_TS_hmeDIP
BioProject PRJNA578148
SRA SRP226100

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE139049_Control_and_Tet1KO_meDIP_and_hmeDIP_quantification.txt.gz 29.9 Mb (ftp)(http) TXT
GSE139049_RAW.tar 15.6 Mb (http)(custom) TAR (of TXT)
GSE139049_RNAseq_quantification.txt.gz 1.2 Mb (ftp)(http) TXT
GSE139049_TS_and_TS_DIFF_5percent_and_20percent_RNAseq_quantification.txt.gz 559.0 Kb (ftp)(http) TXT
GSE139049_TS_and_TS_DIFF_5percent_and_20percent_hmeDIP_quantification.txt.gz 23.9 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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