|
| Status |
Public on Sep 22, 2019 |
| Title |
E16.5-T1 (Vasa) |
| Sample type |
SRA |
| |
|
| Source name |
E16.5 embryonic lung
|
| Organism |
Mus musculus |
| Characteristics |
lin28a expression: Global expression
embryonic day: E16.5
|
| Treatment protocol |
Doxcycyclin was added to the driniking water at a concentration of 1g/L from E0.5
|
| Growth protocol |
Mice were hold in a SPF units. Crossing were preformed as described above. The day of finding plug was designated as E0.5. Pregant females were sacrified by CO2 at different time points as described and the lungs were harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryonic lungs were harvested from the embryos and were subjected to RNA extraction using regular Trizol protocol
Inhouse poly A based RNA seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
fastq files were generated by the usage bcl2fastq-v2.17.1.14 (basecalling)
Reads were trimmed using cutadapt
Sequenced reads were mapped to the Mus Musculus genome version GRCm38 using STAR (v2.4.2a) (using alignEndsType EndToEnd option).
Counting reads on genes annotated in ensembl release 92, was done with HTSeq-count (version 0.6.1p1)
Normalization of read counts and differential analysis were computed using Deseq2 (version 1.10.1)
Genome_build: GRC38
Supplementary_files_format_and_content: Excel file includes the raw counts, genereted by HTSeq-count
Supplementary_files_format_and_content: Excel file includes the normalized counts (DESeq2 normalization)
|
| |
|
| Submission date |
Nov 26, 2018 |
| Last update date |
Sep 22, 2019 |
| Contact name |
Achia Urbach |
| E-mail(s) |
[email protected]
|
| Phone |
972-3-7384281
|
| Organization name |
Bar Ilan University
|
| Department |
Faculty of Life Sciences
|
| Street address |
Ramat Gan
|
| City |
Ramat Gan |
| ZIP/Postal code |
5290002 |
| Country |
Israel |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE122919 |
Lin28 expression affect embryonic lung development |
|
| Relations |
| BioSample |
SAMN10476616 |
| SRA |
SRX5060301 |
