|
| Status |
Public on Jan 14, 2019 |
| Title |
LIN28OE_litter number2_library number30 |
| Sample type |
SRA |
| |
|
| Source name |
whole kidney
|
| Organism |
Mus musculus |
| Characteristics |
age: P3
genotype/variation: LIN28OE
strain: C57BL/6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from each kidney was isolated using Trizol and treated with DNase.
Sequencing libraries were generated using a SMARTer Ultra Low RNA kit (V3) and sequenced on the HiSeq 2500 machine (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads were extracted and adaptors were removed using cutadapt tool(-n 1 -e 0.05 -O 20).
Then trimmed reads were mapped to mouse genome using tophat2(tophat-2.0.9, bowtie-2.0.6, samtools_0.1.19, --library-type=fr-unstranded --GTF= /Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf --min-intron-length=10 --coverage-search --microexon-search --min-isoform-fraction=0).
From the aligned bamfiles, we counted how many reads were mapped to each gene using the htseq-count tool.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph, bw = read density information for visualization on genome browsers
Supplementary_files_format_and_content: txt = tab-delimited text files include count values for each gene in each sample.
|
| |
|
| Submission date |
Jul 23, 2018 |
| Last update date |
Jan 14, 2019 |
| Contact name |
Areum Han |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston Children's Hospital
|
| Lab |
Daley lab
|
| Street address |
Karp Family Building, 7th Floor. 300 Longwood Ave.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE117510 |
Lin28/let-7 axis regulates the timig of cession of nephrogenesis |
|
| Relations |
| BioSample |
SAMN09703718 |
| SRA |
SRX4417622 |
