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Series GSE111929 Query DataSets for GSE111929
Status Public on Aug 19, 2019
Title Long noncoding RNA CCDC144NL-AS1 knockdown induces naïve-like state conversion of human pluripotent stem cells
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Human naïve pluripotency state cells can be derived from direct isolation of inner cell mass or primed-to-naïve resetting of human embryonic stem cells (hESCs) through different combinations of transcription factors, small molecular inhibitors and growth factors. Long noncoding RNAs (lncRNAs) have been identified to be crucial in diverse biological processes, including pluripotency regulatory circuit of mouse pluripotent stem cells (PSCs), but few are involved in human PSCs’ regulation of pluripotency and naïve pluripotency derivation. This study initially planned to discover more lncRNAs possibly playing significant roles in the regulation of human PSCs’ pluripotency, but accidently identified a lncRNA whose knockdown in human PSCs induced naïve-like pluripotency conversion. The results indicated that knockdown of CCDC144NL-AS1 induces naïve-like state conversion of human PSCs in the absence of additional transcription factors or small molecular inhibitors. CCDC144NL-AS1-KD human PSCs reveal naïve-like pluripotency features, such as elevated expression of naïve pluripotency associated genes, increased developmental capacity, analogous transcriptional profiles to human naïve PSCs, and global reduction of repressive chromatin modification marks. Furthermore, CCDC144NL-AS1-KD human PSCs display inhibition of MAPK (ERK), accumulation of active β-catenin, and upregulation of some LIF/STAT3 target genes, and all of these are concordant with previous reported traits of human naïve PSCs.
Overall design The transcriptional profiles of CCDC144NL-AS1-KD-H9, NC-H9, CCDC144NL-AS1-KD-H14, NC-H14, CCDC144NL-AS1-KD-HDF-iPS, NC-HDF-iPS cells were generated by deep sequencing, the epigenetic landscape of CCDC144NL-AS1-KD-H9 cells and NC-H9 cells were analysed by chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) of H3k4me3 and H3K27me3, using the Illumina platform.
Contributor(s) Wang Y, Luo Y, Li S
Citation(s) 31358062
Submission date Mar 16, 2018
Last update date Aug 19, 2019
Contact name Kunshan Zhang
Organization name Tongji Hospital, Tongji University
Department Stem cell Translational Research center
Street address 389 Xincun Road
City Shanghai
ZIP/Postal code 200092
Country China
Platforms (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (28)
GSM3045183 H9_CCDC144NL_AS1_KD_1
GSM3045184 H9_CCDC144NL_AS1_KD_2
GSM3045185 H9_CCDC144NL_AS1_KD_3
BioProject PRJNA438591
SRA SRP135858

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Supplementary file Size Download File type/resource
GSE111929_RAW.tar 1.6 Mb (http)(custom) TAR (of BED)
GSE111929_data_count.csv.gz 642.9 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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