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| Status |
Public on Aug 16, 2021 |
| Title |
GTGT5 |
| Sample type |
SRA |
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| Source name |
YUMM1.7 tumors
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| Organism |
Mus musculus |
| Characteristics |
genotype: IKKbFF
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| Treatment protocol |
No treatment has been applied apart from YUMM1.7 cell engraftment into female IkbkbF/F and IkbkbΔXcr1 mice
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| Growth protocol |
YUMM1.7 tumors in female IkbkbF/F and IkbkbΔXcr1, grown to a volume reaching 200-350mm3.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tumors were minced and digested in RPMI 1640, 1 mg/ml Collagenase II (Sigma-Aldrich), 50 µg/ml DNaseI (Roche), and 0.1% (wt/vol) BSA for 30 min at 37°C with 750 rpm agitation. Cell suspensions were subsequently passed through a 70-µm cell strainer (BD Biosciences) and collected by centrifugation. Purification of total RNA from sorted cells was performed by using the RNeasy Plus Micro Kit (Qiagen) and concentration was determined using the Quant-IT RiboGreen RNA assay kit (Thermo Fisher Scientific).
Full length cDNA were generated from 1000 pg of total RNA using Clontech SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio Europe, Saint Germain en Laye, France) according to manufacturer's instructions with 12 cycles of PCR for cDNA amplification by Seq-Amp polymerase. Six hundreds pg of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT DNA Library Preparation Kit (96 samples) (Illumina, San Diego, CA) followed by 12 cycles of library amplification. Following purification with Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France), the size and concentration of libraries were assessed by capillary electrophoreris.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads were preprocessed in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10.
Reads were mapped onto the mm10 assembly of Mus musculus genome using STAR version 2.5.3a.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1, with annotations from Ensembl version 95 and “union” mode.
Genome_build: mm10
Supplementary_files_format_and_content: a tab separated file (csv) containing genes (ENSembl IDs) and associated raw counts
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| Submission date |
May 07, 2021 |
| Last update date |
Aug 16, 2021 |
| Contact name |
Thien-Phong Vu Manh |
| Organization name |
CIML
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| Street address |
163 avenue de Luminy
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| City |
marseille |
| ZIP/Postal code |
13288 |
| Country |
France |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE174089 |
An NF-κB/IRF1 axis programs cDC1 to drive antitumor immunity II |
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| Relations |
| BioSample |
SAMN19070431 |
| SRA |
SRX10817204 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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