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| Status |
Public on Sep 26, 2019 |
| Title |
Sample 29_Bcl6KO |
| Sample type |
SRA |
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| Source name |
Bcl6KO
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Bcl6f/fCd4cre x OTII Tg
age: 8 weeks
tissue: spleen
cell type: CD4+hCD2+
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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 |
S16159
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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 |
SAMN12838989 |
| SRA |
SRX6902639 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4095391_S16159.txt.gz |
236.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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