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| Status |
Public on Jan 06, 2019 |
| Title |
P1-2 |
| Sample type |
SRA |
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| Source name |
Whole lung
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype: WT
age: PND1
tissue: lung
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| Treatment protocol |
Whole lungs were surgically dissected at embryonic (E) days 16.5, 18.5 and postnatal days (PND) 1, 3, 7, 14, and 28
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| Growth protocol |
Embryos and mice for this study were collected from timed pregnant mice.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using the QIAamp Circulating Nucleic Acid Kit (QIAGEN). RNA was quality checked, transcribed into complementary DNA using the Verso complementary DNA synthesis kit (AB-1453; LifeTechnologies, Carlsbad, CA), sheared, amplified, adaptor ligated and sequenced for pair-end RNA-Seq reads (Illumina Inc. San Diego, CA, USA)
Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation Kit (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Mouse Whole Lung Time Course Expression (Reads and TPM).xlsx
Mouse_whole_lung_PND1_2
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| Data processing |
Embryos and mice for this study were collected from timed pregnant mice. Whole lungs were surgically dissected at embryonic (E) days 16.5, 18.5 and postnatal days (PND) 1, 3, 7, 14, and 28
Total RNA was extracted from cells using the QIAamp Circulating Nucleic Acid Kit (QIAGEN). RNA was quality checked, transcribed into complementary DNA using the Verso complementary DNA synthesis kit (AB-1453; LifeTechnologies, Carlsbad, CA), sheared, amplified, adaptor ligated and sequenced for pair-end RNA-Seq reads (Illumina Inc. San Diego, CA, USA).
Next-generation sequencing of equimolar pools of cDNA libraries was performed using a single read 75 rapid flow cell on a HiSeq 2500 sequencing platform (Illumina), generating greater than 30 million raw reads per sample.
The raw sequenced reads were aligned from FASTQ files to the human genome build GRCm38/mm10 and the UCSC reference transcriptome (http://ccb.jhu.edu/software/tophat/index.shtml) using Tophat 2.0.9.
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet including Reads and TPM expression
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| Submission date |
Nov 08, 2018 |
| Last update date |
Jan 06, 2019 |
| Contact name |
Yan Xu |
| E-mail(s) |
yan.xu@cchmc.org
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| Phone |
513-6368921
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| Organization name |
Cincinnati Children's Hospital Medical Center
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| Street address |
3333 Burnet Ave
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| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE122331 |
Preparing for the first breath at single cell level [whole lung time course] |
| GSE122332 |
Preparing for the first breath at single cell level |
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| Relations |
| BioSample |
SAMN10396506 |
| SRA |
SRX4996524 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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