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Series GSE181756 Query DataSets for GSE181756
Status Public on Nov 10, 2021
Title Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis
Organism Gallus gallus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Ovarian follicle development is a complex and well-orchestrated biological process. Granulosa cells (GCs) are the most important somatic cells in the ovary, which play important roles in the growth of follicles. Three-dimensional (3D) chromatin architecture has emerged as an important regulator of transcription in eukaryote, but how these changes in granulosa cells during folliculogenesis of chicken are largely unexplored. Here, we performed an integrative analysis of transcriptomic and chromatin structural characterization for chicken follicular granulosa cells of 10 and 3 growth stages respectively.
 
Overall design In this study, focusing on the special folliculogenesis process in chicken, we conducted bulk RNA-seq of GCs at ten follicle growth stages (SWF, LWF, SYF, LYF, F5, F4, F3, F2, F1, and POF) and single cell RNA-seq (scRNA-seq) of GCs at three representative stages (SWF, F1, and POF) to depict the transcriptome landscapes during the stepwise folliculogenesis. We also performed in situ high-throughput chromatin conformation capture (Hi-C) sequencing, ATAC-seq, and ChIP-seq analyses for GCs at the three representative stages to further investigate the chromatin architecture dynamics and their close associations with the temporal gene expression profiling during the development.
 
Contributor(s) Ning C, Zhang J, Li D, Li M
Citation(s) 35013308
BioProject PRJNA742199
Submission date Aug 10, 2021
Last update date Jan 28, 2022
Contact name hua kui
E-mail(s) 2020102003@stu.sicau.edu.cn
Organization name Sichuan Agricultural University
Street address No 211 Huimin Road
City chengdu
ZIP/Postal code 611130
Country China
 
Platforms (2)
GPL26853 Illumina NovaSeq 6000 (Gallus gallus)
GPL30495 DNBSEQ-T7 (Gallus gallus)
Samples (78)
GSM5510405 follicular_granulosa_cell_layers-SWF_RNA-seq_replicate_1
GSM5510406 follicular_granulosa_cell_layers-SWF_RNA-seq_replicate_2
GSM5510407 follicular_granulosa_cell_layers-SWF_RNA-seq_replicate_3

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE181756_ATAC-F1_peaks.txt.gz 813.0 Kb (ftp)(http) TXT
GSE181756_ATAC-POF_peaks.txt.gz 1.1 Mb (ftp)(http) TXT
GSE181756_ATAC-SWF_peaks.txt.gz 603.6 Kb (ftp)(http) TXT
GSE181756_F1.POF.silico.bulk.DEG.result.by.DEseq2.txt.gz 459.1 Kb (ftp)(http) TXT
GSE181756_F1.filtered_feature_bc_matrix.h5 25.2 Mb (ftp)(http) H5
GSE181756_IP-F1_AllEnhancers.table.txt.gz 503.0 Kb (ftp)(http) TXT
GSE181756_IP-POF_AllEnhancers.table.txt.gz 385.0 Kb (ftp)(http) TXT
GSE181756_IP-SWF_AllEnhancers.table.txt.gz 650.8 Kb (ftp)(http) TXT
GSE181756_POF.filtered_feature_bc_matrix.h5 33.7 Mb (ftp)(http) H5
GSE181756_SWF.F1.silico.bulk.DEG.result.by.DEseq2.txt.gz 449.5 Kb (ftp)(http) TXT
GSE181756_SWF.POF.silico.bulk.DEG.result.by.DEseq2.txt.gz 466.5 Kb (ftp)(http) TXT
GSE181756_SWF.filtered_feature_bc_matrix.h5 40.8 Mb (ftp)(http) H5
GSE181756_TPM-submission.xlsx 11.6 Mb (ftp)(http) XLSX
GSE181756_bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx 11.7 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record
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