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| Status |
Public on Feb 24, 2020 |
| Title |
Venom gland organoids |
| Sample type |
SRA |
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| Source name |
Venom gland organoids
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| Organism |
Naja nivea |
| Characteristics |
genotype: Wildtype
tissue: Venom gland
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| Treatment protocol |
Live cells were sorted in 384-well hard shell plates (Biorad) with 5 μl of vapor-lock (QIAGEN) containing 100 nl of RT primers (consisting of a 24 bp polyT stretch, a 4bp random molecular barcode (UMI), a cell-specific barcode, the 5′ Illumina TruSeq small RNA kit adaptor and a T7 promoter), dNTPs and mRNA ERCC Spike-Ins (Agilent) and immediately frozen to −80°C. Before starting with SORT-seq, cells were first lysed 5 min at 65°C.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was processed using the previously described SORT-seq tecnique, which is an implemented version of the CEL-seq2 technique. Libraries were sequenced on an Illumina NextSeq500 using 60bp and 26bp paired end sequencing.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Bulk rRNA sequencing from differentiated venom gland organoids.
NajaNivea_bulk.csv
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| Data processing |
The code used for data processing is deposited on GitHub: https://github.com/BuysDB/reptillianOrganoids
In brief, data were demultiplexed, mapped using STAR, deduplicated for UMI-scaffold pairs, counted using fractional counting and scaffolds pooled by BLAST annotation
Genome_build: De novo Aspidelaps lubricus transcriptome assembly.
Supplementary_files_format_and_content: The data are in csv format. The table contains UMI deduplicated counts, pooled by BLAST annotation. De novo transcriptome assembly using Trinity (transcriptome-assembly_min500bp (1).fna)
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| Submission date |
Nov 22, 2019 |
| Last update date |
Feb 24, 2020 |
| Contact name |
Joep Beumer |
| E-mail(s) |
joepbeumer@gmail.com
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| Organization name |
Hubrecht Institute
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| Street address |
Uppsalaan 8
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| City |
Utrecht |
| ZIP/Postal code |
3584CT |
| Country |
Netherlands |
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| Platform ID |
GPL27798 |
| Series (1) |
| GSE129581 |
RNA sequencing of venom glands and venom gland organoids |
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| Relations |
| BioSample |
SAMN13354309 |
| SRA |
SRX7202846 |
| 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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