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Series GSE153005 Query DataSets for GSE153005
Status Public on Jun 05, 2021
Title Dynamic landscape of chromatin accessibility and transcriptomic changes during differentiation of human embryonic stem cells into dopaminergic neurons
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary We profiled chromatin accessibility and gene expression changes along the differentiation of human pluripotent stem cells to dopaminergic neurons. We integrated the epigenomic and transcriptomic profiles to infer the activity of transcription factors (TFs) and DNA regulatory regions such as enhancers and long non-coding RNAs.
Overall design Time series gene expression profiles and chromatin accessibility genome-wide maps were obtained through ATAC-sequencing and RNA-sequencing of samples obtained during dopaminergic neural induction of human pluripotent stem cells. We used 3 induction time points: day 0, day 14, and day 28. H9 cells expressing GFP (WA09-GFP) were used as pluripotent stem cells. For RNA-seq we obtained 3, 4, and 2 replicates from induction time points D0, D14, and D28 respectively. For ATAC-seq we used one replicate for each time point.
Contributor(s) Melendez-Ramirez C, Duran RC, Barrios-Garcia T, Giacoman M, Lopez-Ornelas A, Herrera-Gamboa J, Velasco I, Treviño V
Citation(s) 34417498
Submission date Jun 22, 2020
Last update date Sep 04, 2021
Contact name Raquel Cuevas Diaz Duran
Organization name Tecnologico de Monterrey
Department Escuela de Medicina y Ciencias de la Salud
Street address Av Morones Prieto No. 3000, Colonia Los Doctores
City Monterrey
ZIP/Postal code 64710
Country Mexico
Platforms (2)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (13)
GSM4632925 D0_r1_RNAseq
GSM4632926 D0_r2_RNAseq
GSM4632927 D0_r3_RNAseq
BioProject PRJNA641151
SRA SRP268344

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Supplementary file Size Download File type/resource
GSE153005_FPKM_mat.txt.gz 1.1 Mb (ftp)(http) TXT
GSE153005_RAW.tar 363.7 Mb (http)(custom) TAR (of BW)
GSE153005_count_mat.txt.gz 617.7 Kb (ftp)(http) TXT
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Processed data are available on Series record
Raw data are available in SRA
Processed data provided as supplementary file

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