 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 01, 2024 |
| Title |
DNMT3A-HET differentiated macrophages, IL6 treated, replicate 1, Day 8 |
| Sample type |
SRA |
| |
|
| Source name |
Macrophage
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Macrophage
genotype: DNMT3A-HET
Sex: Male
treatment: IL-6 treated
|
| Treatment protocol |
On Day 6, half of Het or WT samples were treated with IL-6 at a concentration of 10 ng/mL for 2 days.
|
| Growth protocol |
Bone marrow was collected from 3 male mice per genotype at 13 weeks of age (Day 0). Whole bone marrow was plated at 4 x10^5 cells per 10 cm dish in macrophage differentiation medium (DMEM, 10% FBS, 1x GlutaMAX, 1x non-essential amino acids, 1x sodium pyruvate, 1x penicillin/streptomycin, 1 uM beta-mercaptoethanol, and 50 ng/mL M-CSF) until Day 6.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
On Day 8, macrophages were collected for RNA isolation using the RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA library prep kit according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
MACRO_HET1_IL6
|
| Data processing |
Fastq quality control and filtering was performed using fastp (0.12.4) set to default parameters.
Filtered fastqs were aligned to the mouse genome (mm10, m22 Gencode annotation file) using STAR (2.7.9a). Sorting and indexing were performed using samtools (1.9).
Mapped reads were counted using featureCounts (v1.6.2) with parameters "-t exon -g gene_name" to the m22 Gencode annotation file.
Assembly: mm10
Supplementary files format and content: counts_table.txt: Tab-delimited text file of featureCounts output (read counts) including all samples as columns, genes as rows.
|
| |
|
| Submission date |
Jul 12, 2022 |
| Last update date |
Jan 01, 2024 |
| Contact name |
Margaret Goodell |
| Organization name |
Baylor College of Medicine
|
| Street address |
One Baylor Plaza, N1030
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL30172 |
| Series (1) |
| GSE208075 |
Hematologic DNMT3A Reduction and High Fat Diet Synergize to Promote Weight Gain and Tissue Inflammation |
|
| Relations |
| BioSample |
SAMN29670177 |
| SRA |
SRX16145873 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
