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| Status |
Public on Dec 21, 2021 |
| Title |
RNA-seq Saline Cond rep1 |
| Sample type |
SRA |
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| Source name |
Anterior hypothalamus
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| Organism |
Gallus gallus |
| Characteristics |
cell type: microglia
treatment: Conditioned, saline injected
age: day 11 posthatch
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| Treatment protocol |
Chicks were heat‐conditioned on day 3 posthatch at 39°C for 24 h. One week later (day 10), LPS or saline was injected into the third ventricle. Chicks were sacrificed on day 11 and their AH dissected. Microglial cell population from hypothalamic cell pools of 10–12 chicks each was collected by FACS. Total RNA was isolated from each sample and subjected to RNA-Seq. DNA was extracted from microglia of 10-day-old heat-conditioned and non-conditioned chicks before LPS-challenge and subjected to RRBS.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with the RNA/DNA Purification Micro Kit (Norgen Biotek, Thorold, ON, Canada)
15 ng of purified RNA was used for library preparation with the bulk MARS-seq method (Jaitin et al. 2014 Science.343:776-9).100bp single reads were sequenced on a Novaseq 6000 sequencing system. The output was ~25 million reads per sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Poly-A/T stretches and Illumina adapters were trimmed from the reads using Cutadapt. Resulting reads shorter than 30bp were discarded. Remaining reads were mapped onto 3’ UTR regions (1000 bases) of the Gallus genome (galGal5.0, UCSD) according to Refseq annotations, using STAR.Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI. Read counts per gene were calculated using HTSeq-count, with the following parameters: 'htseq-count -s no --mode=union’. Normalization and differential expression analysis were performed using the DESeq2. Differentially expressed genes (DEG) were defined as genes that had a significant adjusted p value (padj) of less than 0.05 and at least 2-fold change. To elucidate gene alterations across all analyzed groups, the expression of all DEG was assessed. Respective heat maps were generated by custom R scripts and the Complexheatmap R package.
Genome_build: galGal5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
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| Submission date |
Nov 25, 2021 |
| Last update date |
Dec 21, 2021 |
| Contact name |
Tatiana Kisliouk |
| E-mail(s) |
tanya.kisliouk@gmail.com
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| Organization name |
ARO
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| Department |
Animal Sciences
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| Street address |
68 HaMaccabim Road
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| City |
Rishon LeZion |
| ZIP/Postal code |
7505101 |
| Country |
Israel |
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| Platform ID |
GPL26853 |
| Series (2) |
| GSE189566 |
Early-life thermal stress mediates long-term alterations in hypothalamic microglia [RNA-Seq] |
| GSE189567 |
Early-life thermal stress mediates long-term alterations in hypothalamic microglia |
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| Relations |
| BioSample |
SAMN23440562 |
| SRA |
SRX13228057 |
| 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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