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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Nov 02, 2023 |
| Title |
COHP_44950_480_TET_OFF_B_10wks |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Mus musculus |
| Characteristics |
mouse id: 480
sample weeks: 10
batch: 2021_E
tissue: PBMC
strain: C57BL/6
Sex: M
genotype: tTA+/-, BCR-ABL+/-
treatment: TET_OFF_B
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| Treatment protocol |
Six to eight weeks old male and female SCLtTA/BCR-ABL mice were randomly divided into 4 groups: control (Tet on, n=3 mice), CML (Tet off, n=6 mice), Tet Off-On (TOTO; Tet off 6 weeks then Tet on for 12 weeks, n=4 mice), TKI [Tet off 6 weeks then TKI (Nilotinib, 50mg/kg, oral gavage, daily) treatment 4 weeks, n=7 mice]. Blood was collected from these mice weekly, i.e., before BCR-ABL induction (t = 0) and weekly after induction up to 18 weeks (t = 1 to 18) or when the mouse developed leukemia and became moribund, whichever event occurred first.
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| Growth protocol |
Inducible transgenic SCLtTA/BCR-ABL mice of B6 background were maintained on tetracycline (tet) water at 0.5 g/L. Tet withdrawal (tet-off) results in expression of BCR-ABL and generation of a CML-like disease in these mice with a median survival of approximately 10 weeks after induction of BCR-ABL, which recapitulates human CP CML.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from whole blood using the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany); quality and quantity were estimated using a BioAnalyser (Agilent, Santa Clara, CA). Samples with a RIN > 4.0 were included.
Sequencing libraries were constructed using the KapaHyper with RiboErase (Kapa Biosystems, Wilmington, MA) and are reverse stranded.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
cml_mrna_processed_1tpm_in_5_samples.tsv.gz
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| Data processing |
nf-core RNASeq pipeline version 3.7
Trimmed reads were mapped using STAR to the GRCm39 reference (Genbank accession GCA_000001635.9) amended with the human BCR-ABL1 fusion gene sequence (Genbank accession EF158045.1) using GENCODE annotation Release m28
Each library was subjected to extensive quality control, including estimation of library complexity, gene body coverage, and duplication rates, among other metrics detailed in the pipeline repository
Transcript abundance was estimated across genomic features using Salmon and merged into a matrix of pseudocounts per million transcripts (TPM) per gene for each sample. BCR-ABL1 transcript abundance was measured by counting reads that spanned the fusion boundary
Assembly: GCA_000001635.9
Supplementary files format and content: tab delimited file includes Salmon pseudocounts for each sample (TPM)
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| Submission date |
Oct 10, 2023 |
| Last update date |
Nov 02, 2023 |
| Contact name |
Denis OMeally |
| Phone |
6262188434
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| Organization name |
City of Hope
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| Department |
Arthur Riggs Diabetes & Metabolism Research Institute
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| Lab |
Diabetes & Cancer Discovery Science
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| Street address |
1500 E Duarte Rd
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| City |
Duarte |
| State/province |
California |
| ZIP/Postal code |
91024 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE244990 |
State-transition Modeling of Blood Transcriptome Predicts Disease Evolution and Treatment Response in Chronic Myeloid Leukemia (CML) |
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| Relations |
| BioSample |
SAMN37753943 |
| SRA |
SRX22048043 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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