|
| Status |
Public on Sep 29, 2021 |
| Title |
RNA-seq of Stroma IL6KO 1 |
| Sample type |
SRA |
| |
|
| Source name |
RNA-seq of Stroma IL6KO
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6J
genotype: IL6 KO
tissue: Bone marrow
cell type: Bone-marrow derived mCh- host stromal cells
|
| Growth protocol |
500,000 BCR-ABL+ B-ALL cells were injected into the tail vein of wild-type or IL6KO C57BL/6J mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extracted RNA as directed using Qiagen RNeasy Kit (Qiagen cat. # 74134)
Prepared library as directed using NEB Ultra II Directional RNA with rRNA Depletion Kit (NEB cat. # E7400)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNA-seq of host stroma isolated from the bone marrow of IL6KO C57BL/6J mouse
processed data file:
Stroma_Normalized_Counts.txt
Stroma_DESeq_Results.txt
|
| Data processing |
Fastq files were aligned to mm10 genome using salmon (version 1.3.0). The salmon quant command was executed with the following flags: --validateMappings --gcBias --seqBias
Salmon quant files were normalized and differentially expressed genes were identified using the DESeq2 R package (version 1.28.1). The DESeq command was executed with default options.
Table of read counts normalized by DESeq2 was output to a tab-delimited txt file.
Results of DESeq analysis of WT ~ IL6KO was output to a tab-delimited txt file.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized read counts and DESeq2 analysis output to tab delimited txt
|
| |
|
| Submission date |
Sep 14, 2021 |
| Last update date |
Sep 29, 2021 |
| Contact name |
Daniel Robert Goulet |
| E-mail(s) |
dgoulet@mit.edu
|
| Phone |
8604831381
|
| Organization name |
Massachusetts Institute of Technology
|
| Department |
Koch Institute
|
| Lab |
Michael T. Hemann
|
| Street address |
500 Main St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE184107 |
Microenvironmental IL-6 Inhibits Anti-Cancer Immune Responses Generated by Cytotoxic Chemotherapy |
|
| Relations |
| BioSample |
SAMN21431319 |
| SRA |
SRX12184144 |
