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| Status |
Public on Mar 10, 2022 |
| Title |
Gut, Clean, gfphis, rep3 |
| Sample type |
SRA |
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| Source name |
Gut
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| Organism |
Ixodes scapularis |
| Characteristics |
tissue: gut
condition: clean
treatment: Recombinant GFP
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tick gut was dissected, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Adip--gfp-all-genes.txt
tpm-values-all-samples.txt
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| Data processing |
Tick transcript data was downloaded from the VectorBase (https://vectorbase.org/vectorbase/app/) and indexed using the kallisto-index.
The reads from the sequencer were pseudo-aligned with the index reference transcriptome using kallisto.
The counts generated were processed by DESeq2 in RStudio (https://rstudio.com).
Assembly: IscaW1
Supplementary files format and content: tab-delimited text files include baseMean, log2Foldchange, TPMs, etc. for each gene
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| Submission date |
Mar 10, 2022 |
| Last update date |
Mar 11, 2022 |
| Contact name |
Xiaotian Tang |
| E-mail(s) |
xiaotian.tang@yale.edu
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| Organization name |
Yale School of Medicine
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| Department |
Internal Medicine
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| Street address |
300 Cedar Street
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06519 |
| Country |
USA |
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| Platform ID |
GPL29893 |
| Series (1) |
| GSE169293 |
Tick Adiponectin Receptor-Mediated Phospholipid Metabolism Contributes to Borrelia burgdorferi Colonization |
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| Relations |
| BioSample |
SAMN26566320 |
| SRA |
SRX14433877 |
| 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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