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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 24, 2019 |
| Title |
RNA_CCR6_Pos_1 |
| Sample type |
SRA |
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| Source name |
CCR6+ LTi progenitor
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: CCR6+ LTi progenitor
tissue: isolated from bone marrow
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cell suspension were obtained from the bone marrow of C57BL/6 mice. For sorting CLP and rChILP, the lineage negative cells were enriched with the "Lineage Cell Depletion Kit, mouse" from Miltenyi Biotec according to the manual. Enriched Lineage negative bone marrow cells were stained with relative antibodies followed by sorting on a cell sorter FACS Aria III (BD Biosciences) for "live Lineage-CD127+Flt-3+Integrin α4β7-Sca1+c-Kit+" CLP and "live Lineage-CD127+Flt-3-Integrin α4β7+T1/ST2-c-Κit+" rChILP. For sorting PD-1+ non-LTi ILC progenitors and CCR6+ LTi progenitors, the Fc receptor-blocked bone marrow single-cell suspension was stained with PE-conjugated anti-integrin α4β7 antibody, followed by washing and incubation with anti-PE microbeads. The samples were then applied to the Miltenyi LS columns in magnetic field and washed three times by PBS with 3% FBS according to the manufacturer’s instruction. The integrin α4β7+ cells on the column were finally flushed into a collection tube for further surface molecule staining. Non-LTi ILC progenitors (live Lineage-CD127+Flt-3-Integrin α4β7+T1/ST2-c-Κit+PD-1+CCR6-) and LTi progenitors (live Lineage-CD127+Flt-3-Integrin α4β7+T1/ST2-c-Κit+PD-1-CCR6+) were then sorted via FACS Aria III (BD Biosciences). CLPs, total rChILPs, PD-1+ or CCR6+ progenitors described above were sorted directly into 700 μL of QIAzol Lysis Reagent in the miRNAeasy Micro Kit (QIAGEN, Cat#217084). Total RNA was extracted and RNA-Seq libraries were prepared through the Smart-seq2 method (PMID: 24385147) as previously described (PMID: 29466755). Multiplex sequencing reads of 50 bp were generated by the NHLBI DNA Sequencing and Computational Biology Core.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
Basecalls performed using CASAVA 1.8.4
Sequence reads were mapped to the mouse (mm9) genomes with bowtie2 (2.2.2) with default settings. We kept one hit if multiple reads were mapped to the same position for each RNA-Seq libraries.
For each RNA-Seq sample, gene expression was quantified by RPKM with in-house script and RefSeq gene annotation.
Genome_build: mm9
Supplementary_files_format_and_content: rpkm: plan text file. Columns from left to right denote RefSeq ID, RPKM, gene transcript size, number of read mapped to exons, a combination of RefSeq ID, gene symbol, etc, and reserved column for future development.
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| Submission date |
Jan 19, 2017 |
| Last update date |
Dec 24, 2019 |
| Contact name |
Gangqing Hu |
| E-mail(s) |
michael.hu@hsc.wvu.edu
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| Organization name |
West Virginia University
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| Department |
MicroBiology, Immunology, and Cell Biology
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| Lab |
2072A, HSC North, Floor 2
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| Street address |
64 Medical Center Drive
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| City |
Morgantown |
| State/province |
West Virginia |
| ZIP/Postal code |
26506-9177 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE93863 |
Differential Expression of the Transcription Factor GATA3 Specifies Lineage and Functions of Innate Lymphoid Cells |
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| Relations |
| BioSample |
SAMN06242759 |
| SRA |
SRX2505753 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2464260_GA9336-GCCAAT-RNA-seq-mouse-CCR6p_1_0_0.rpkm.gz |
473.7 Kb |
(ftp)(http) |
RPKM |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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