|
| Status |
Public on Jan 26, 2023 |
| Title |
S2_S2_IgG, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
cell type: EGFP+ cell population
genotype: PdgfraEGFP/+
treatment: IgG
|
| Treatment protocol |
Timed pregnant PdgfraEGFP/+ dams were treated at E18.5 with either anti-HH antibody 5E1 or control IgG by intraperitoneal injection.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lungs were harvested genotyped PdgraEGFP/+ pups at P8, single cell suspensions were generated and live EGFP+ expressing cells were sorted by FACS for RNA library prep
RNA libraries for RNA-seq were prepared using the Illumina TruSeq Stranded mRNA Library Prep following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
P8 IgG
|
| Data processing |
Reads were mapped to the reference genome (mm10) using the STAR aligner (v2.5.0c) and aligned guided by a Gene Transfer Format (GTF) file.
Mean read insert sizes and corresponding standard deviations were calculated using Picard tools (v.1.126) (http://broadinstitute.github.io/picard).
The Read Per Million (RPM) normalized BigWig files were created using BEDTools (v2.17.0) and bedGraphToBigWig tool (v4)
Read count tables wre generated in HTSeq (v0.6.0)
The DESeq2 package (v.1.10.0) was used in R (v.3.5.1; http://www.R-project.org/) to normalize samples based on their library size factors and to carry out differential expression analysis among the different sample groups
Assembly: mm10
Supplementary files format and content: bw, tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jun 27, 2022 |
| Last update date |
Jan 26, 2023 |
| Contact name |
Matthias C Kugler |
| Organization name |
NYU School of Medicine
|
| Department |
Medicine
|
| Street address |
550 First Avenue, Medical Science Building, MSB-594
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE207051 |
Hedgehog signaling affects platelet-derived growth factor signaling mediated alveolar septum formation during postnatal lung development [bulk RNA-seq] |
| GSE207062 |
Hedgehog and PDGF signaling intersect during postnatal lung development |
|
| Relations |
| BioSample |
SAMN29379801 |
| SRA |
SRX15913945 |
