|
| Status |
Public on Sep 21, 2024 |
| Title |
7 day KN tumor, replicate methyl-seq 1 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
genotype: KrasFSF-G12D/+; Rosa26FSF-CreERT2/Sun1; Nkx2-1F/F
treatment: tamoxifen
|
| Treatment protocol |
Organoid cultures treated with 4-OH tamoxifen or ethanol for 48hr to delete Foxa1/2 conditional alleles. Cell pellets were collected two weeks post-deletion for DNA extraction. Mice were treated with tamoxifen (Sigma) dissolved in corn oil at a dose of 120mg/kg. Mice received 4 injections over the course of 5 days. One day following injections, mice were given pellets supplemented with 500mg/kg (Envigo) tamoxifen for 7 days. Tumors were harvested 8 weeks post tamoxifen treatment and cells were sorted for GFP+ DAPI- population.
|
| Growth protocol |
Organoid cultures grown in 50% L-WRN conditioned media (Miyoshi and Stappenbeck, 2013).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using the Dneasy Blood and Tissue (Qiagen).
DNA libraries were prepped using the NEBNext® Enzymatic Methyl-seq Kit with at least 10 ng of genomic DNA
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Fastq reads were aligned to the mouse genome (build mm10) with Novocraft novoalign (version 4.03.01) in bisulfite mode (-b 4) with the following options: set penalty for unconverted CHG or CHH cytosines (option -u) to 12, hard clip 3’ bases to quality 20 (option -H), adapter trimming (option -a), and performance tuning set to ‘NOVOSEQ’.
Extreme coverage regions were identified using depth-normalized (Reads Per Million) mean coverage of replicates and MACS2 bdgpeakcall with an absolute depth cutoff of 2 RPM (mean depth was < 0.1), length 200 bp, and gap 500 bp. Alignments overlapping extreme regions were excluded from further analysis. Duplicate alignments were removed using samtools (version 1.16) fixmate and markdup (mode -s).
Alignments were processed with USeq NovoalignBisulfiteParser (version 9.3.0) to collect converted and non-converted C counts with minimum mapping quality score (-q) of 13 and minimum base quality score (options -b and -c) of 20. Measured lambda phage DNA conversion efficiency was typically > 99.7%.
BisMark compatible coverage files were generated from the Converted and NonConverted .useq files using the useq2bismark_methylation_extractor application (https://github.com/tjparnell/HCI-Scripts/blob/master/Methylation/useq2bismark_methylation_extractor.pl).
Assembly: build mm10
Supplementary files format and content: Bismark compatible coverage files containing counts of coverted and non-coverted CpGs for each sample. BigWig CpG fraction methylation files for each sample.
|
| |
|
| Submission date |
Sep 19, 2024 |
| Last update date |
Sep 21, 2024 |
| Contact name |
Katherine Gillis |
| E-mail(s) |
katy.gillis@hci.utah.edu
|
| Phone |
3013955164
|
| Organization name |
Snyder Lab at Huntsman Cancer Institute
|
| Street address |
2000 CIRCLE OF HOPE DR
|
| City |
Salt Lake City |
| State/province |
UT |
| ZIP/Postal code |
84112-5550 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE247853 |
FoxA1/2-dependent epigenomic reprogramming drives lineage switching in lung adenocarcinoma [Bisulfite-Seq] |
| GSE247855 |
FoxA1/2-dependent epigenomic reprogramming drives lineage switching in lung adenocarcinoma |
|
| Relations |
| BioSample |
SAMN43827980 |
| SRA |
SRX26127166 |
