 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 18, 2018 |
| Title |
RNA-seq-WT2-L1 |
| Sample type |
SRA |
| |
|
| Source name |
Mammary gland
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: wild-type
Stage: Lactation day 1
tissue: Mammary gland
|
| Growth protocol |
Mouse mammary tissues were harvested at day one and ten of lactation (L1 and L10).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen mammary tissue from wild type mice at day one and ten of lactation and purified with RNeasy Plus Mini Kit (Qiagen, 74134). Ribosomal RNA was removed from 1ug of total RNAs and cDNA was synthesized using SuperScript III (Invitrogen).
Libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301) and paired-end sequencing was done with a HiSeq 2500 instrument (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome mm10 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). Rsubread (Liao et al., Nucleic Acids Research, 2013) was applied to calculate raw read counts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include raw read counts from RNA-seq samples.
|
| |
|
| Submission date |
Jun 05, 2018 |
| Last update date |
Sep 21, 2018 |
| Contact name |
Michaela Willi |
| Organization name |
NIH
|
| Department |
NIDDK
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| ZIP/Postal code |
20814 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE115369 |
Progressing enhancer landscape during mammary differentiation controls gene regulation [RNA-seq] |
| GSE115370 |
Progressing super-enhancer landscape during mammary differentiation controls tissue-specific gene regulation |
|
| Relations |
| BioSample |
SAMN09371563 |
| SRA |
SRX4169616 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3176756_RNA-seq-WT2-L1.txt.gz |
100.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
