 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 11, 2019 |
| Title |
WT_Basal_1 |
| Sample type |
SRA |
| |
|
| Source name |
mammary gland
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: ACI
genotype: Cdkn1b+/+
age: 9 weeks
tissue: mammary gland
cell type: basal/myoepithelial (Cd24+ Cd29HIGH)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen). The total RNA was measured by Aligent 2100 Bioanalyzer.
RNA-seq libraries were prepared using Clontech Low Input mRNA Library (Clontech SMARTer) v4 kit from less than 10ng of purified total RNA according to the manufacturer’s protocol. The concentrations of finished dsDNA library were measured by Qubit Fluorometer, the size of library fragment was measured by Agilent TapeStation 2200, and RT-qPCR for adapted library molar concentration measurement according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with Single-End 75bp (SE75) reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA-seq of basal/myoepithelial fraction of mammary gland of wild type ACI rats
|
| Data processing |
Quality check of the called bases of the reads were performed using the FastQC tool (Babraham Bioinformatics).
Datasets were aligned to the rat reference rn6 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b). Two-pass mapping was performed using the following modified parameters: --outSAMstrandField intronMotif, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outFilterType BySJout, --outFilterScoreMinOverLread 0.33, --outFilterMatchNminOverLread 0.33, --limitSjdbInsertNsj 1200000, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --twopassMode Basic.
he read counts for individual genes were generated using the htseq-count script of the HTSeq framework (version 0.6.1p1) using modified parameters (--stranded no) and the rn6 refGene annotation file available at the UCSC Genome Browser.
genome_build: rn6
Supplementary_files_format_and_content: Tab-separated file of the raw read counts for each gene.
|
| |
|
| Submission date |
Jul 09, 2018 |
| Last update date |
Feb 13, 2019 |
| Contact name |
Kornelia Polyak |
| E-mail(s) |
kornelia_polyak@dfci.harvard.edu
|
| Phone |
617-632-2106
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Polyak
|
| Street address |
450 Brookline Ave
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (1) |
| GSE116831 |
Deletion of Cdkn1b in ACI rats perturbs mammary progenitor cell proliferation and differentiation through non-cell-autonomous mechanisms |
|
| Relations |
| BioSample |
SAMN09634213 |
| SRA |
SRX4370810 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3262395_WT_Basal_1.counts.tsv.gz |
72.6 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
