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Status |
Public on Nov 10, 2021 |
Title |
follicular_granulosa_cell_layers-SWF_RNA-seq_replicate_2 |
Sample type |
SRA |
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Source name |
granulosa cells
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Organism |
Gallus gallus |
Characteristics |
cell type: granulosa cells breed: Luhua hens developmental stage: prehierarchical follicles age: 31 weeks follicle growth stage: SWF
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Extracted molecule |
total RNA |
Extraction protocol |
total RNA was extracted from each sample using RNAiso Plus reagent (TaKaRa, Otsu, Shiga, Japan) following the manufacturer’s instructions. Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5min at 95 °C before PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. We estimated the integrity and quality of total RNA using a Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA, USA) with an RNA 6000 Nano kit. Subsequently, 30 strand-specific libraries (total of 10 stages with three biological replicates in each stage) were generated after depleting rRNA by the Ribo-Zero™ Gold Kit (Illumina, San Diego, CA, USA) and then sequenced on the Illumina HiSeq X Ten platform (Illumina Inc., San Diego, CA, USA) with a paired-end sequencing length of 150 bp (PE150) at Novogene Corporation (Beijing, China).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
DNBSEQ-T7 |
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Description |
bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx TPM-submission.xlsx SWF-2
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Data processing |
TPM-submission.xlsx: bulk-RNAseq reads were aligned to the galGal6 using kallisto version 0.44.0 ,then tpm and counts matrixs were generated using R version 3.6.1. bulk.RNAseq.all_counts.filt.0.5tpm.more.than.3num.xlsx: bulk-RNAseq reads were aligned to the galGal6 using kallisto version 0.44.0 ,then tpm and counts matrixs were generated using R version 3.6.1. SWF.filtered_feature_bc_matrix.h5: single cell reads were aligned to the galGal6 using cellranger version 6.0.1 F1.filtered_feature_bc_matrix.h5: single cell reads were aligned to the galGal6 using cellranger version 6.0.1 POF.filtered_feature_bc_matrix.h5: single cell reads were aligned to the galGal6 using cellranger version 6.0.1 ATAC-SWF_peaks.xls: ATAC-seq reads were algned to the galGal6 using bowtie2 version 2.2.6, mitochondrial alignments and PCR duplicates were filtered using removeChrom and Picard version 1.126 and peaks were called using macs2 version 2.1.1. ATAC-F1_peaks.xls: ATAC-seq reads were algned to the galGal6 using bowtie2 version 2.2.6, mitochondrial alignments and PCR duplicates were filtered using removeChrom and Picard version 1.126 and peaks were called using macs2 version 2.1.1. ATAC-POF_peaks.xls: ATAC-seq reads were algned to the galGal6 using bowtie2 version 2.2.6, mitochondrial alignments and PCR duplicates were filtered using removeChrom and Picard version 1.126 and peaks were called using macs2 version 2.1.1. IP-SWF_AllEnhancers.table.txt: chip-seq reads were aligned to the galGal6 using BWA version 0.7.15, data were filtered using samtools version 1.3.1 and super-enhancers were defined using ROSE algorithms. IP-F1_AllEnhancers.table.txt: chip-seq reads were aligned to the galGal6 using BWA version 0.7.15, data were filtered using samtools version 1.3.1 and super-enhancers were defined using ROSE algorithms. IP-POF_AllEnhancers.table.txt: chip-seq reads were aligned to the galGal6 using BWA version 0.7.15, data were filtered using samtools version 1.3.1 and super-enhancers were defined using ROSE algorithms. F1.POF.silico.bulk.DEG.result.by.DEseq2.txt: single cell reads were aligned to the galGal6 using cellranger version 6.0.1, silico bulk-RNAseq counts matrixs were extracted using Python 2.7 and DEGs were generated using DEseq2 algorithms. SWF.F1.silico.bulk.DEG.result.by.DEseq2.txt: single cell reads were aligned to the galGal6 using cellranger version 6.0.1, silico bulk-RNAseq counts matrixs were extracted using Python 2.7 and DEGs were generated using DEseq2 algorithms. SWF.POF.silico.bulk.DEG.result.by.DEseq2.txt: single cell reads were aligned to the galGal6 using cellranger version 6.0.1, silico bulk-RNAseq counts matrixs were extracted using Python 2.7 and DEGs were generated using DEseq2 algorithms. Genome_build: galGal6 Supplementary_files_format_and_content: bulk-RNAseq (xlsx files) Supplementary_files_format_and_content: single cell RNAseq (matrix.h5 files) Supplementary_files_format_and_content: ATAC-seq (peaks.xls files) Supplementary_files_format_and_content: chip-seq (AllEnhancers.table.txt files) Supplementary_files_format_and_content: single cell RNAseq (silico.bulk.DEG.result.by.DEseq2.txt files)
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Submission date |
Aug 10, 2021 |
Last update date |
Nov 10, 2021 |
Contact name |
hua kui |
E-mail(s) |
2020102003@stu.sicau.edu.cn
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Organization name |
Sichuan Agricultural University
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Street address |
No 211 Huimin Road
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City |
chengdu |
ZIP/Postal code |
611130 |
Country |
China |
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Platform ID |
GPL30495 |
Series (1) |
GSE181756 |
Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis |
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Relations |
BioSample |
SAMN19931134 |
SRA |
SRX11378130 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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