|
| Status |
Public on Jul 23, 2021 |
| Title |
Lung_7_DKO_1 |
| Sample type |
SRA |
| |
|
| Source name |
whole lung
|
| Organism |
Mus musculus |
| Characteristics |
cell type: whole lung
strain: C57BL/6J/mixed background
tissue: whole lung
genotype: Lin28a and Lin28b KO
|
| Treatment protocol |
Lin28a and b double knockout was acheived in the lung using tamoxifen to induce recombination of exon 2 flanked with loxP sites.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was collected using Trizol (Invitrogen) according to the manufacturer's instructions.
RNA-seq libraries were constructed following the standard protocol (The SMARTer® Ultra™ Low Input RNA Kit by Clontech).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
From the raw reads, we removed adaptor sequences using a Cutadapt tool, allowing some mismatches (The specific parameters we used were -n 2 -e 0.02).
Then, the cleaned reads were aligned to the mouse genome/transcriptome (mm10 and corresponding UCSC gene model) using a TopHat2 software with the following parameters (library-type=fr-unstranded, min-intron-length=10, microexon-search, min-isoform-fraction=0).
To estimate expression levels for each gene, we counted aligned reads per gene using a htseq-count tool with the following parameters (--stranded=no --idattr=gene_id -t exon -i transcript_id).
Genome_build: mm10
Supplementary_files_format_and_content: Text files generated from the htseq-count and edgeR tools. The text files have gene expression estimates, RPKM values.
|
| |
|
| Submission date |
Jan 12, 2017 |
| Last update date |
Jul 23, 2021 |
| Contact name |
Areum Han |
| E-mail(s) |
areum.han@childrens.harvard.edu
|
| 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) |
| GSE93571 |
Lin28a and Lin28b are required for lung branching morphogenesis and epithelial cell differentiation via coordination of signaling pathway feedback loops in a let7-independent manner |
|
| Relations |
| BioSample |
SAMN06226417 |
| SRA |
SRX2487385 |
