|
| Status |
Public on Aug 25, 2021 |
| Title |
V15_HJ7M2BBXX |
| Sample type |
SRA |
| |
|
| Source name |
Cortex
|
| Organism |
Mus musculus |
| Characteristics |
Sex: M
tissue: Cortex
treatment: Exposed
age (days): 3 to 5
strain: C57BL/6J
rin: 9.4
lane: 2
|
| Treatment protocol |
Prenatal transcriptome changes of air pollution were examined by exposing pregnant C57BL/6 dams to 300 mg/m3 nano-sized particulate matter (nPM) for 5 hr/day, 3 days/weeks beginning at gestational day 2 until birth.
A random number of 3 pups per sex of each group were euthanized at day 5 age for collection of blood and cerebral cortex
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were homogenized and disrupted with pestles, 22-gauge needles, pipetting and QIA shredders (Qiagen #79654). DNA was extracted using QIAzol (Qiagen #79306) from the organic layer for genotyping. RNA was extracted following the QIAGEN RNeasy plus universal protocol (Qiagen #73404). Extracted RNA was used to determine sex of mouse pups by qPCR for the Y-chromosome Sry gene.
RNA (600ng) was made into RNA-seq libraries using the Illumina RiboZero Gold library preparation kit and sequenced on an Illumina HiSeq 3000 sequencer at the Lieber Institute for Brain Development
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
gene counts.csv
gene map.csv
|
| Data processing |
Raw sequencing reads were quality checked with FastQC
adapter sequences were trimmed from the reads using Trimmomatic
Reads were aligned to the mm10 genome using the HISAT2 splice-aware aligner
alignments overlapping genes were counted using featureCounts version 1.5.0-p3 relative to Gencode version M11
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: csv files count values for each gene
|
| |
|
| Submission date |
Dec 20, 2019 |
| Last update date |
Aug 25, 2021 |
| Contact name |
Amin Haghani |
| E-mail(s) |
ahaghani@altoslabs.com
|
| Organization name |
Altos labs
|
| Lab |
Hovath lab
|
| Street address |
5510 Morehouse Dr
|
| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92121 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE142453 |
Cerebral cortex and blood transcriptome changes in mouse neonates prenatally exposed to air pollution particulate matter |
|
| Relations |
| BioSample |
SAMN13657012 |
| SRA |
SRX7423693 |
