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| Status |
Public on Sep 01, 2024 |
| Title |
KO_18271_8519 |
| Sample type |
SRA |
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| Source name |
Zip4 KO fed 40 ppm amino-complexed zinc
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| Organism |
Mus musculus |
| Characteristics |
tissue: whole small intestine
strain: C57BL/6
genotype: Zip4 KO
diet: 40 ppm amino-complexed zinc
age: 228 days
Sex: Female
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| Extracted molecule |
total RNA |
| Extraction protocol |
Gut was removed immediately upon sacrifice and flash frozen, and RNA extracted using a Qiagen RNEasy kit, RNA was stored at -80° C until use.
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 2000 |
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| Data processing |
Partek Flow platform used for data processing
Low quality sequence trimmed; 5.7-9.2% of sequences had an average of 2 bp trimmed.
Tophat 2 was used to align reads to the mm10 genome build
Reads were quantified to mm10 using the Partek E/M annotation model
Reads were normalized to counts per million (CPM) with 0.0001 added to the result.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file including CPM for each sample (in columns) and gene (in rows)
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| Submission date |
Jul 26, 2020 |
| Last update date |
Sep 01, 2024 |
| Contact name |
James West |
| E-mail(s) |
j.west@vanderbilt.edu
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| Organization name |
Vanderbilt University
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| Department |
Medicine
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| Lab |
Pulmonary
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| Street address |
4200 E 9TH Ave, Box B133
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| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37201 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE155125 |
Effect of hydroxy vs amino complex in zinc uptake, in WT and Zip4-/- mice |
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| Relations |
| BioSample |
SAMN15646719 |
| SRA |
SRX8827378 |
| 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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