 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 08, 2022 |
| Title |
WT-1 |
| Sample type |
SRA |
| |
|
| Source name |
Mammary gland
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Mammary gland
age: Post natal day 45
genotype: WT
treatment: untreated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mammary gland were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates.
The GO (Gene Ontology, http://geneontology.org/) enrichment of DEGs was implemented by the hypergeometric test, in which p-value is calculated and adjusted as q-value, and data background is genes in the whole genome.
KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) is a database resource containing a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Jun 28, 2022 |
| Last update date |
Oct 09, 2022 |
| Contact name |
Tingting Zhang |
| Organization name |
Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College
|
| Street address |
1 Xian Nong Tan Street
|
| City |
Beijing |
| ZIP/Postal code |
100050 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE207137 |
Next Generation Sequencing Facilitates Quantitative Analysis of WT and WT+CXCL14 mouse endothelial cells' Transcriptomes in mammary gland |
|
| Relations |
| BioSample |
SAMN29404906 |
| SRA |
SRX15931737 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6280134_WT-1.txt.gz |
170.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
