|
| Status |
Public on May 31, 2023 |
| Title |
FA8mg_ND.2 |
| Sample type |
SRA |
| |
|
| Source name |
non-neoplastic, 8mg folic acid, rep2
|
| Organism |
Mus musculus |
| Characteristics |
cell type: laser microdissected non-neoplasitc colon epitheila cells
strain: Swiss Webster
treatment: 8 mg folic acid
|
| Treatment protocol |
AOM was injected at 7 weeks of age and DSS treatment was initiated at 9 weeks of age for 4 cycles (each cycle = 7 days of 2% DSS in drinking water plus 14 days of untreated water). At 11 weeks of age, mice were randomly assigned to receive folic acid at 0 or 8 mg/kg chow for 16 weeks. Mice were euthanized at 27 weeks of age. Colons were fixed in 10% formalin and processed for embedding.
|
| Growth protocol |
Mice were fed a diet containing folic acid 2 mg/kg chow, followed by carcinogen azoxymethane injection. Colitis was induced in all mice using 4 cycles of DSS. Immediately after the first DSS treatment, mice were randomized to receive folic acid 0 or 8 mg/kg chow for 16 weeks. At the end of study, mice were euthanized and colons were collected and process for gene expression analyses
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were microdissected from paraffin-embedded tissues usig Leica LMD6500 system. RNA was isolated using the RecoverAllTM total Nucleic Acid Isolation for FFPE kit. RNA concentration and quality were determined on an Agilent 2100 Bioanalyzer using RNA 6000 Pico chips.
Libraries were generated using SMARTerÒ Stranded RNA-Seq Kit V2- Pico Input Mammalian with 40 ng total RNA. Libraries were quantified using a Qubit ds DNA HS kit and size distribution validated on the Agilent 2100. Bioanalyzer using the Agilent High Sensitivity DNA kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
non-neoplastic colon epithelium form colitic mice treated with 8 mg folic acid
|
| Data processing |
Raw reads were aligned to mm10 genome using bowtie
Raw counts in each known gene from the Ensembl database were enumerated using htseq-count from the HTSeq package
Genome_build: mm10
Supplementary_files_format_and_content: raw count in tab-delimited format
|
| |
|
| Submission date |
Mar 09, 2021 |
| Last update date |
May 31, 2023 |
| Contact name |
Margie Clapper |
| E-mail(s) |
margie.clapper@fccc.edu
|
| Organization name |
Fox Chase Cancer Center
|
| Street address |
333 Cottman Ave
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19111 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE168525 |
Effects of dietary folic acid levles on colitis-associated tumorigenesis. |
|
| Relations |
| BioSample |
SAMN18221310 |
| SRA |
SRX10291251 |
