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| Status |
Public on Nov 30, 2024 |
| Title |
WT4CD9POSATM |
| Sample type |
SRA |
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| Source name |
epiWAT
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| Organism |
Mus musculus |
| Characteristics |
tissue: epiWAT
cell type: Macrophage
genotype: Commd10fl/fl
treatment: HFD 12 weeks
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Animal experiments were performed with male adult mice (C57BL/6J background). Animals were maintained in specific pathogen-free animal facility, and experiments were performed according to protocols approved by the Animal Care Use Committee of the Sourasky Medical Center. Mice were housed with 12-h light cycles and a constant temperature of 22°C.
HFD for 12 weeks
ATM sorting was performed using the BD FACSAriaTM FUSION cell sorter (BD Bioscience) from SVF fraction directly to lysis buffer.
Bulk MARS-Seq protocol. In breif, mRNA was purified from ~100,000 cells of each sample using Dynabeads mRNA Direct purification kit (ThermoFisher), barcoded during reverse transcription and pooled. Following Agencourct Ampure XP beads cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR. Libraries were quantified by Qubit and TapeStation as well as by qPCR for mouse ActB gene. Sequencing was done on a Nextseq 75 cycles high output kit (Illumina).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
RNA-Seq (3') UMI appears in Read2
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome
Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI
Assembly: Counting proceeded over genes (1000 bases of the 3’ UTR) using htseq-count
Supplementary files format and content: Normalization and differential expression was performed using DESeq2
Supplementary files format and content: mm10
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| Submission date |
Nov 08, 2023 |
| Last update date |
Nov 30, 2024 |
| Contact name |
Nathan Gluck |
| E-mail(s) |
[email protected]
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| Organization name |
Tel Aviv University
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| Department |
Faculty of Medicine, Internal Medicine
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| Lab |
Prof. Nathan Gluck's Research Group
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| Street address |
35 Klatzkin
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| City |
Tel Aviv |
| ZIP/Postal code |
6997801 |
| Country |
Israel |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE247350 |
COMMD10-deficiency in adipose tissue macrophages attenuates obesity and insulin resistance by boosting mitochondrial and antioxidant functions |
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| Relations |
| BioSample |
SAMN38165811 |
| SRA |
SRX22428595 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7887607_WT4CD9POSATM_counts_htseq.tsv.gz |
93.7 Kb |
(ftp)(http) |
TSV |
| GSM7887607_WT4CD9POSATM_counts_htseq.umi_corrected.tsv.gz |
90.9 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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