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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 20, 2016 |
| Title |
Nb, TN, Replicate 2 |
| Sample type |
SRA |
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| Source name |
Dendritic cells (DC)
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
Sex: male
tissue: Auricular lymph nodes
cell type: Dendritic cells (DC)
number of mice/sample: 15
ercc mix: Mix2
cell population: CD11c int, MHCII hi, CD103 neg, CD326 neg, CD11b lo (TN)
treatment: Nb
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| Treatment protocol |
N/A
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| Growth protocol |
N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from frozen purified cell pellets using QIAzol Lysis Reagent and RNeasy Micro Kit.
Ribosomal RNA was removed using RiboZero before RNA libraries were prepared for sequencing using the Illumina TruSeq kits.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Exp_TN.Nb.2_1257.2
Nb-treated Triple Negative cells
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| Data processing |
Paired-end raw read FASTq files ere pre-processed using Trimmomatic (v0.32) and quality checked using qrqc R package (v1.20.0)
Reads were mapped to mouse and ERCC reference transcripts using TopHat2 (v2.0.10)
Read hits to annotated genes were counted using HtSeq-count (HT-Seq, v0.6.0)
Technical replicates (across multiple flow cell lanes) were combined,see processed data file ('JEMsampleFiltered_collapsed_counts_JEM_2016-May-05.csv')
Data were split into the two experiments (Nb, DBP+FITC), then analysed separately with DESeq2 (v1.6.3) with sex as an additional model covariate for the Nb experiment
A variance-stabilised transformation was generated from the count data using DESeq2 (v1.6.3), and normalised based on the sum of gene exon lengths
Genome_build: C57BL/6 mouse reference genome (GRCm38.p3)
Supplementary_files_format_and_content: JEMsampleFiltered_collapsed_counts_JEM_2016-May-05.csv -- Gene Count Data as determined by HTSeq-count
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| Submission date |
Oct 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Franca Ronchese |
| E-mail(s) |
fronchese@malaghan.org.nz
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| Phone |
+64 4 499 6914
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| Organization name |
Malaghan Instititute of Medical Research
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| Department |
Immune Cell Biology
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| Street address |
Kelburn Parade
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| City |
Wellington |
| ZIP/Postal code |
6012 |
| Country |
New Zealand |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE88998 |
Th2 responses are primed by skin dendritic cells with distinct transcriptional profiles |
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| Relations |
| BioSample |
SAMN05930793 |
| SRA |
SRX2255232 |
| 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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