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Status |
Public on Sep 26, 2019 |
Title |
Sample 15_TFH2 |
Sample type |
SRA |
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Source name |
TFH2
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Organism |
Mus musculus |
Characteristics |
strain background: C57BL/6 genotype/variation: OTII Tg IL-4BacTg x OTII Tg age: 8 weeks tissue: spleen cell type: CD4+CD45.2+CXCR5int PD1+
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Extracted molecule |
total RNA |
Extraction protocol |
Spleen were removed, stained TH cells were sorted using flow cytometer, and RNA was harvested using Trizol reagent. NEB Next Ultra RNA Library Prep Kit (Cat#E7530) for Sample1-8 or Lexogen 3'mRNA-seq library prep kit (Cat#015) for Sample9-30 was used with 10 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard NEB Ultra protocols or Lexogen 3'QuantSeq protocols Sample1-Sample8, RNA-Seq; Sample9-Sample30, 3'QuantSeq
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 1500 |
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Description |
S16140
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Data processing |
Illumina Casava1.7 software used for basecalling. Sample1-8; Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole mouse genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata Sample9-30; Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole mouse genome using STAR 2.7.0c (command --runThreadN 60 --outSAMtype BAM SortedByCoordinate) Genome: mm10 GRCm38.p6 ENSEMBL GTF: GRCm38.97 ENSEMBL Sample1-8; featurecounts v1.6.0 (command: -M -O -t exon -g gene_id -a) GTF: mm9 ENSEMBL release 67 Sample9-30; featurecounts v1.6.0 (command: -M -O -t exon -g gene_id -a) GTF: GRCm38.97 ENSEMBL Genome_build: mm9 and mm10 Supplementary_files_format_and_content: tab-delimited text files include read counts for genes
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Submission date |
Sep 25, 2019 |
Last update date |
Sep 26, 2019 |
Contact name |
Kosuke Miyauchi |
E-mail(s) |
kosuke.miyauchi@riken.jp
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Organization name |
RIKEN Center for Integrative Medical Sciences
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Street address |
1-7-22 Suehiro-sho
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City |
Yokohama |
State/province |
Kanagawa |
ZIP/Postal code |
230-0045 |
Country |
Japan |
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Platform ID |
GPL18480 |
Series (1) |
GSE137970 |
Next Generation Sequencing Facilitates Quantitative Analysis of TFH2 cell Transcriptomes |
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Relations |
BioSample |
SAMN12838984 |
SRA |
SRX6902625 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4095377_S16140.txt.gz |
244.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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