|
| Status |
Public on May 05, 2023 |
| Title |
monocyte derived macrophages from mouse ascites, ovarian tumour-bearing, bio rep1 [AeMM-1] |
| Sample type |
SRA |
| |
|
| Source name |
ascites
|
| Organism |
Mus musculus |
| Characteristics |
tissue: ascites
cell type: monocyte derived macrophages
genotype: Ms4a3TdT
strain background: C57BL/6
treatment: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using cell lysis buffer, followed by reverse transcription.The cDNA obtained by reverse transcription was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Smart-seq2 method.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
AeMM1 in matrix of processed data
|
| Data processing |
STAR(2.7.2a)
Data quality control was conducted by Fastp.
Trimmed sequence reads were mapped to mm10 using STAR(2.7.2a) (parameter: --quantMode GeneCounts \--twopassMode Basic \ --outSAMtype BAM SortedByCoordinate \ --outReadsUnmapped None \ --chimSegmentMin 12 \ --chimJunctionOverhangMin 12 \--alignSJDBoverhangMin 10 \--alignMatesGapMax 100000 \--alignIntronMax 100000 \--chimSegmentReadGapMax 3 \--alignSJstitchMismatchNmax 5 -1 5 5 \ --outSAMstrandField intronMotif \ --chimOutJunctionFormat 1)
Read count extraction and normalization were performed using subread featureCounts.
Assembly: mm10
Supplementary files format and content: comma-delimited csv. files include batch-removed tpm values for each Sample
|
| |
|
| Submission date |
Jan 18, 2023 |
| Last update date |
May 05, 2023 |
| Contact name |
Xipeng Wang |
| E-mail(s) |
wangxipeng@xinhuamed.com.cn
|
| Phone |
13817806602
|
| Organization name |
Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine
|
| Street address |
No. 1665, Kongjiang Road, Yangpu District, Shanghai
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE223121 |
Different biological roles of embryonic- and monocyte-derived macrophages in ovarian cancer ascites ecosystem. |
|
| Relations |
| BioSample |
SAMN32778845 |
| SRA |
SRX19058388 |
