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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 05, 2019 |
| Title |
Foxp3WT_Th1_r2 |
| Sample type |
SRA |
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| Source name |
Rag2 OT-II (WT) Th1 cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen and lymph nodes
culture condition: in vitro culture for 72 hours with anti CD3/28 and Th1-promoting cytokines/antibodies
chip antibody: N/A
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| Extracted molecule |
total RNA |
| Extraction protocol |
For in vitro polarized cells, total RNA was prepared from approximately 500,000 cells using an Ambion mirVana miRNA isolation kit following the manufacturer’s protocol (ThermoFisher AM1560). For in vivo IL-9 producing cells and other subsets, total RNA was prepared from approximately 2,000-10,000 cells using a Trizol-based extraction technique following the manufacturer’s protocol (ThermoFisher 15596026).
Total RNA was subsequently processed to mRNA-seq library using NEBNext Poly(A) mRNA Magnetic Isolation followed by either Ultra II Directional RNA Library Prep kit for Illumina (NEB E7490, E7760, E7335); or Mondrian Ovation Ultralow according to the vendor’s manual for the Illumina platform (Cat#0344; NuGEN).
The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2500 following the manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
160330_160420_combined_d_s05
RNA-Seq_R23-R70_rpkm.xlsx
R67
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| Data processing |
base calling was carried out using CASAVA1.8.2/bcl2fastq1.8.4
ATAC-seq, alignment: PE reads were mapped to the mouse genome (mm9 assembly) using Bowtie 1.1.1.
ATAC-seq, peak calling: Redundant reads were removed using Fastquniq. Uniquely mapped reads from fragments less than 175 bp were used to call peaks with MACS1.4.2 using a p-value threshold of 1 x 10-5
RNA-seq, alignment: SE reads were mapped to the mouse genome mm9 using TopHat 2.1.0
RNA-seq, RPKM calculation RNA-seq: RPKMs were calculated using Partek6.6
ChIP-seq, alignment: SE reads were aligned to the mouse genome build mm9 with Bowtie 1.1.1
ChIP-seq, peak calling: Non-redundant and Uniquely mapped reads were used to call peaks with MACS1.4.2 using a p-value threshold of 1 x 10-5
Genome_build: mm9
Supplementary_files_format_and_content: peak bed files for ATAC-seq & ChIP-seq generated by MACS1.4.2; RPKM files for RNA-seq generated by Partek 6.6
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| Submission date |
Dec 07, 2018 |
| Last update date |
Feb 05, 2019 |
| Contact name |
Hong-wei Sun |
| Organization name |
NIAMS
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| Department |
Office of Science & Technology
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| Lab |
Biodata Mining & Discovery Section
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| Street address |
9000 Rockville Pile
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE123501 |
Retinoic acid receptor alpha represses a Th9 transcriptional and epigenomic program to reduce allergic pathology |
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| Relations |
| BioSample |
SAMN10534107 |
| SRA |
SRX5122585 |
| 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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