|
| Status |
Public on Mar 09, 2018 |
| Title |
JNK_KO_3D_3 |
| Sample type |
SRA |
| |
|
| Source name |
JNK-/-_3 days_mammary gland
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
time of involution: 3 days
genotype/variation: JNK-/-
tissue: mammary gland
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pieces of mammary glands were flash frozen in liquid nitrogen and RNA was extracted using the RNEasy kit from Qiagen (#74106).
Illumina Neoprep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Bowtie2 (v 2-2.1.0) and Tophat2 (v 2.0.14) were used for alignment
Cufflinks(v2.2.1) was used to determine fpkms and cuffmerge and cuffdiff were used to identify differentially expressed genes
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: tab-delimited txt file includes FPKM values for all samples
|
| |
|
| Submission date |
Nov 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Dr Yvonne Edwards, PhD |
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Molecular Medicine
|
| Lab |
Bioinformatics Core
|
| Street address |
373 Plantation Street
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE89495 |
Efficient Mammary Gland Involution Requires c-Jun N-terminal kinase |
|
| Relations |
| BioSample |
SAMN05977057 |
| SRA |
SRX2324001 |
