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| Status |
Public on Jan 03, 2024 |
| Title |
JSB075-Pero-1Week-M |
| Sample type |
SRA |
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| Source name |
Ear Punch
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| Organism |
Peromyscus leucopus |
| Characteristics |
tissue: Ear Punch
agent: B. burgdorferi strain B31
Sex: Male
time point: 1 Week Post Infection
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Skin placed in RNA-later, Frozen, Beadbeat in QIAzol, extracted with miRNeasy mini kit w/ additional RWT wash, digested with Turbo Dnase, repurified with Rneasy MinElute
Ear punches were placed directly in RNA-later reagent overnight. Samples were frozen at -80C before beadbeating in QIAzol and RNA isolation with the miRNeasy kit by Qiagen with an additional RWT wash. TURBO Dnase was used to degrade DNA following isolation and samples were cleaned with RNeasy MinElute Cleanup Kit by Qiagen. Purified RNA was sent to Azenta/Genewiz for library preparation and sequencing (Illumina HiSeq 2x150bp)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
TPM_JSB075.Pero.1Week.M
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| Data processing |
Genome built using RSEM and Bowtie, Genome GCF_004664715.2
Mapping completed using RSEM and STAR
Transcripts per Million for each gene saved as part of file pero_tpm_values_082923.csv
Assembly: GCF_004664715.2
Supplementary files format and content: data table containing the gene_id, transcript id(s), transcript length, effective length, expected_count (aka raw count), TPM (transcripts per million), and FPKM (fragments per kilobase of transcript per million mapped reads)
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| Submission date |
Sep 26, 2023 |
| Last update date |
Jan 03, 2024 |
| Contact name |
Jeffrey Bourgeois |
| E-mail(s) |
Jeffrey.Bourgeois@tufts.edu
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| Organization name |
Tufts University
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| Street address |
136 Harrison Ave
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| City |
Boston |
| ZIP/Postal code |
02111 |
| Country |
USA |
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| Platform ID |
GPL33254 |
| Series (1) |
| GSE244071 |
Borrelia burgdorferi fitness is constrained during Peromyscus leucopus infection |
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| Relations |
| BioSample |
SAMN37553751 |
| SRA |
SRX21898879 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7806170_JSB075-Pero-1Week-M.genes.results.gz |
624.5 Kb |
(ftp)(http) |
RESULTS |
SRA Run Selector |
| Raw data are available in SRA |
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