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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 09, 2020 |
| Title |
Sample 3_1969_control |
| Sample type |
SRA |
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| Source name |
WT mouse decidual
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype: Alk5F/F
age: embryonic day 6.5 (E6.5)
tissue: Mouse Decidual
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| Extracted molecule |
total RNA |
| Extraction protocol |
Decidual tissues from E6.5 were prepared by clearing away maternal myometrial and embryonic materials under a dissecting microscope. Samples were stored at -80 °C for subsequent RNA and/or protein isolation. Total RNA was isolated from mouse decidual tissues using RNeasy Mini Kit (Qiagen) based on manufacturer’s protocol. Briefly, mouse decidual tissues were collected and homogenized in lysis buffer (Qiagen) that contains β-mercaptoethanol prior to RNA extraction. Total RNA was eluted with nuclease-free water and concentration measured using a NanoDrop Spectrophotometer.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
03-1969-1_S3
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| Data processing |
After generating a list of read counts, the data reads were filtered by removing the genes that the sums of reads of entire row were less than three
Data were normalized using the effective library sizes and a trimmed mean-M correction factor based on standard edgeR model (PMID: 20196867). The common dispersion and tagwise dispersions were estimated as recommended in the edgeR manual
Pairwise comparison was performed in egdeR to determine differential gene expression.
Genome_build: GRCm38.94_mouse
Supplementary_files_format_and_content: logFC, logCPM, Pvalue, and FDR values for each gene
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Jul 15, 2020 |
| Last update date |
Dec 09, 2020 |
| Contact name |
Qinglei Li |
| Organization name |
Texas A&M University
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| Department |
Department of Veterinary Integrative Biosciences
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| Street address |
4458 TAMU
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| City |
COLLEGE STATION |
| State/province |
TX |
| ZIP/Postal code |
77840 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE154516 |
Transforming growth factor beta signaling and decidual development in mice |
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| Relations |
| BioSample |
SAMN15545089 |
| SRA |
SRX8740243 |
| 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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