|
| Status |
Public on Jul 13, 2022 |
| Title |
3-1-KO1 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor infiltrated macrophage from MC38 orthotopic tumors implanted in C57BL/6J mice.
|
| Organism |
Mus musculus |
| Characteristics |
genotype: TAM from APC-KO MC38 tumor 1
sample type: TAM from APC-KO MC38 tumor 1 replicate 1
|
| Treatment protocol |
After RBC lysis, cells were blocked with CD16/CD32 blocking antibody (BD Biosciences Cat# 553142, RRID:AB_394657) for 30 min and stained with antibodies: CD45 APC 30-F11 (BioLegend Cat# 103111, RRID:AB_312976), CD11b eFluor 605 M1/70 (Thermo Fisher Scientific Cat# 69-0112-82, RRID:AB_2637406), F4/80 PerCp-Cy5.5 BM8 (BioLegend Cat# 123127, RRID:AB_893496), and SYTOX green (ThermoFisher Cat# R37168).
|
| Growth protocol |
APC-WT and APC-KO MC38 orthotopic tumors implanted in C57BL/6J mice were digested with Liberase DL (Roche #5401160001) and Liberase TL (Roche #05401020001).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Stained cells were sorted as CD45+, CD11b+, and F4/80+.
Total RNA was isolated from sorted cells and were sequenced by Ultra low Input RAN sequencing (Illumina NexteraXT) with six replicates of each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The NextSeq RTA (version 2.4.11.0) was used for base calling and bcl2fastq (version 2.20.0) was used to convert the .bcl files into .fastq files.
Fastq files were aligned to the mouse reference genome (mm9) using HISAT2 software and assembled using StringTie.
Comparisons between groups were hampered by low input of total RNA isolated from tumor macrophages manifesting as inconsistent raw/normalized read counts for housekeeping genes in the different groups.
To enable comparisons between APC-WT and APC-KO tumors, we re-normalized the read counts of multiple M2 macrophage markers with housekeeping gene read counts (GAPDH and ACTB)
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Apr 15, 2022 |
| Last update date |
Aug 03, 2022 |
| Contact name |
Chang-Jiun Wu |
| Organization name |
University of Texas, MD Anderson Cancer Center
|
| Department |
Genomic Medicine
|
| Lab |
DePinho Lab
|
| Street address |
1515 Holcombe Blvd
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE200909 |
Synthetic Essentiality of Tryptophan 2,3-dioxygenase 2 in APC-Mutated Colorectal Cancer II |
| GSE200910 |
Synthetic Essentiality of Tryptophan 2,3-dioxygenase 2 in APC-Mutated Colorectal Cancer |
|
| Relations |
| BioSample |
SAMN27603920 |
| SRA |
SRX14870958 |
