|
| Status |
Public on Jul 05, 2022 |
| Title |
RNA-seq AMs in vitro - 8W 0h rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Alveolar macrophages
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
condition: 0h, in vitro culture
age: 8 weeks
|
| Treatment protocol |
Alveolar macrophages were sorted from neonatal (postnatal day 4) and adult (8 to 10 weeks of age) mice and plated in 96-well plates at 60,000 to 100,000 cells/well. Culture media consisted of RPMI-1640 supplemented with 10% FBS, 100 U/mL penicillin/streptomycin, and 4 ng/mL recombinant murine M-CSF (R&D, 416-ML010). Cells were harvested at 0 h and 20 h of tissue culture.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA of alveolar macrophages were harvested using trizol reagent. TruSeq Stranded mRNA Sample Prep Kit with TruSeq Unique Dual Indexes (Illumina, San Diego, CA) was used with 60 ng of total RNA for generating sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols on the Illumina HiSeq 4000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
all_genes_results_invitro.txt
|
| Data processing |
RNAseq reads were trimmed using Trimmomatic 0.36 using the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:27
Trimmed reads were aligned using STAR v2.5.3a using default parameters
Reads were quantified using RSEM v1.3.0 using default parameters
ATAC samples were mapped to the mm10 genome using Bowtie2
IDR peak files were generated for each condition with IDR 2.0
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts matrices for each ENSEMBL gene and sample. .idr peaks files
|
| |
|
| Submission date |
Feb 16, 2022 |
| Last update date |
Jul 11, 2022 |
| Contact name |
Lawrence Stephen Prince |
| E-mail(s) |
lsprince@stanford.edu
|
| Phone |
6192269798
|
| Organization name |
Stanford University
|
| Department |
Pediatrics
|
| Lab |
Prince Lab
|
| Street address |
1701 Page Mill Rd
|
| City |
Palo Alto |
| State/province |
CA |
| ZIP/Postal code |
94304 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE196926 |
The Lung Microenvironment Instructs Gene Transcription in Neonatal and Adult Alveolar Macrophages |
|
| Relations |
| BioSample |
SAMN26000244 |
| SRA |
SRX14206536 |
