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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 06, 2023 |
| Title |
ISO S TN5 |
| Sample type |
SRA |
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| Source name |
TN
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| Organism |
Taeniopygia guttata |
| Characteristics |
tissue: TN
social treatment: ISO
injection treatment: S
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated from the aqueous layer produced after chloroform precipitation, using the RNA Clean & Concentrator Kit-5 (Zymo Research, item # R1013) following manufacturer’s instructions and including the DNase I in-column treatment step.
RNA libraries were prepared for sequencing using NEBNext® UltraTM RNA Library Prep Kit, following standard protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
TN5
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| Data processing |
Data filtering: reads containing adapters, reads containing N > 10% and low quality reads were filtered out
Mapping was done using HISAT2
HTSeq (v0.6.1) was used to count numbers of mapped reads.
Assembly: taeGut3.2.4, release 96, downloaded from Ensembl
Supplementary files format and content: tab-delimited text file includes raw (not normalized) readcount values for each sample
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| Submission date |
May 21, 2022 |
| Last update date |
Mar 06, 2023 |
| Contact name |
Patricia C Lopes |
| E-mail(s) |
lopes@chapman.edu
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| Organization name |
Chapman University
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| Department |
Biological Sciences
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| Street address |
450 N Center St
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| City |
Orange |
| State/province |
CA |
| ZIP/Postal code |
92866 |
| Country |
USA |
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| Platform ID |
GPL27119 |
| Series (1) |
| GSE203528 |
Neural transcriptomic responses to endotoxin challenge across social treatments |
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| Relations |
| BioSample |
SAMN28577856 |
| SRA |
SRX15406620 |
| 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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