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| Status |
Public on May 28, 2023 |
| Title |
mab-10 rep3 |
| Sample type |
SRA |
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| Source name |
Whole animal
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: MT19733
age: young adult
tissue: whole animal
genotype: mab-10 mutant
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| Growth protocol |
Age-synchronized young adult hermaphrodites (200 in total, picked manually) from wild-type, lin-29(n836), mab-10(tm2497), and ddx-23(n5705)
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA from three biological replicates for each genotype were prepared using a BeadBug microtube homogenizer (Sigma) and 0.5 mm zirconium beads (Sigma). RNA was extracted using the RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (using the NeoPrep system).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
D17-3250
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| Data processing |
Quality control:QC was carried out by MIT BMC/BCC in house pipeline including sequencing error rate estimation, sequencing reads complexity estimation, fastqc report, and sample contamination estimation. Hierarchical clustering and heatmap creation were carried out by TIBCO Spotfire 7.11.1.0.12 basing on log2(fpkm+1) values of the expressed coding genes to observe sample relationship and to detect outliers.
RNA-Seq mapping: against ws258 reference for Caenorhabditis elegans sequences using STAR/2.5.3a
Gene expression was quantified using RSEM v. 1.3.0
Genome_build: ws258
Supplementary_files_format_and_content: Text format matrix of normalized gene expression abundance, as measured by log2(fpkm+1). Each gene is a row, and each sample is a column.
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| Submission date |
May 28, 2020 |
| Last update date |
May 28, 2023 |
| Contact name |
Dunaduan Ma |
| E-mail(s) |
maduanduan8@gmail.com
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| Organization name |
MIT
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| Department |
Koch Institute
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| Lab |
Bioinformatics Core
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| Street address |
77 Massachusetts Ave
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| City |
Cambridge |
| State/province |
Ma |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platform ID |
GPL19757 |
| Series (1) |
| GSE151399 |
A DEAD-box helicase drives the partitioning of a pro-differentiation NAB protein into nuclear foci |
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| Relations |
| BioSample |
SAMN15048855 |
| SRA |
SRX8419220 |
| 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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