|
| Status |
Public on Sep 05, 2022 |
| Title |
hMDMs-M.tb-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
hMDMs primary cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: hMDMs primary cells
cell type: macrophage
genotype: WT
treatment: H37Rv infection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNAiso Plus (Takara, Catalog code: 9109) according to manufacturer’s protocol.
Sequencing libraries were prepared using the VAHTS Stranded mRNA-Seq Library Prep Kit (Vazyme, Catalog code: NR602-02) according to manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Description |
GEO_merged_HMDM_counts.txt
|
| Data processing |
Trimmomatic (version: 0.33) was used to filter out the low quality bases and adapter sequences. Clean reads longer than 36 bp at both ends were kept for further processing.
TopHat (version: v2.1.1) with bowtie2 (version: 2.3.5.1) was used to align the paired end RNA-Seq reads to human reference genome (hg19).
HTSeq (version: 0.11.2) was used to count the mapped reads on the transcripts corresponding to each gene.
DESeq2 was used for normalization and differential expression analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw reads counts for each Sample
|
| |
|
| Submission date |
Jul 12, 2022 |
| Last update date |
Nov 16, 2022 |
| Contact name |
Da Lin |
| E-mail(s) |
a50044758@googlemail.com
|
| Phone |
+86-18771951925
|
| Organization name |
Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
|
| Street address |
No. 650 Songjiang Road
|
| City |
ShangHai |
| ZIP/Postal code |
201620 |
| Country |
China |
| |
|
| Platform ID |
GPL29480 |
| Series (2) |
| GSE208042 |
Gene expression levels of macrophage cells during differentiation and Immune activation |
| GSE208046 |
Decoding the Spatial Chromatin Organization and Dynamic Epigenetic Landscapes of Macrophage Cells During Differentiation and Immune Activation |
|
| Relations |
| BioSample |
SAMN29664731 |
| SRA |
SRX16137796 |
