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| Status |
Public on Jun 13, 2024 |
| Title |
Liver, all samples, Rep1-5 each |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Nothobranchius furzeri |
| Characteristics |
tissue: Liver
treatment: mixed multiplex samples
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue samples were lysed in TRIzol reagent (Thermo Fisher Science) and extract RNA by using RNA Clean & Concentrator kit (Zymo Research).
Libraries were prepared by BRB-Seq(Alpern D, et al.) method. Individual samples were reverse transcribed using dT primer with unique cell barcodes. Same tissue samples were mixed and amplified by PCR. 10nt of UMI followedby 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Liver
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| Data processing |
Liver and Muscle samples were demultiplexed by deML(v1.1.3), and for liver (female) and muscle samples, 1M reads were randomly sampled from each fastq file obtained by using seqtk Version: 1.3.
Read1(10bp of UMI + 9bp of barcode) was assigned to Read2(insert read) by following command "umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC".
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver.0.6.7).
Reads were mapped to the N. furzeri GRZ reference genome [GRZ Assembly (05/2015); https://nfingb.leibniz-fli.de/] using HISAT2 (ver.2.2.1).
Gene count was obtaind by featureCounts(ver.2.0.1) and UMI duplication was ramoved by using UMI tools (ver.1.1.1).
Assembly: GRZ Assembly (05/2015); https://nfingb.leibniz-fli.de/
Supplementary files format and content: compressed tab separated files(.tsv.gz, .txt.gz)
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| Submission date |
Jan 15, 2024 |
| Last update date |
Jun 13, 2024 |
| Contact name |
Kota Abe |
| E-mail(s) |
jo7gik@gmai.com
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| Phone |
09026005203
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| Organization name |
RIMD, Osaka univ
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| Street address |
3-1 Yamadaoka, Suita
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| City |
Osaka |
| ZIP/Postal code |
5620032 |
| Country |
Japan |
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| Platform ID |
GPL32658 |
| Series (1) |
| GSE253241 |
Gene expression profiles of the liver and skeletal muscle in germ-cell-removed animals |
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| Relations |
| BioSample |
SAMN39443303 |
| SRA |
SRX23218650 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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