|
| Status |
Public on Apr 19, 2024 |
| Title |
7-wk mutant AT2 cell NKX2-1 ChIP-seq rep1 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
cell type: AT2
genotype: CebpaCKO/CKO; SftpcCreER/+;Sun1GFP/+
age: 7-wk
treatment: 3mg Tamoxifen started at 5-wk every other day
chip antibody: NKX2-1(ab133737, Abcam)
|
| Treatment protocol |
GFP labeling of AT2 cells was carried out by 250ug of Tamoxifen at P0 and 3mg of Tamoxifen 3 days before harvesting adults . CEBPA mutant were induced with Tamoxifen at the indicated timepoints
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Whole lung ChIP-seq were performed as described in the associated paper and cell type specific ChIp-seqs were performed on chromatin from sorted nulcei based on a SunGFP reporter induced by recombination undercontrol of cell type specific Cre or CreERs.
ChIP DNA quantity was measured using the Qubit dsDNA HS Assay Kit (Invitrogen, Q32851). 2-5ng of sample DNA was used to generate sequencing libraries using the NEB Next Ultra II DNA Library Prep Kit for Illumina (NEB, E7645). Step 3.1 in the NEB protocol was skipped to improve sample retention per manufacturer’s recommendation. Samples were PCR amplified for 12 cycles and barcoded using indexing primers (New England BioLabs, E7335s or E7500S) followed by a final (.65 x -1 x bead volume) size selection and purification step using a SPRIselect reagent (Beckman Coulter, B23318). Samples were then verified for library size by gel electrophoresis and concentration measured using the Qubit HS dsDNA assay. Samples were then sequenced on the Illumina NextSeq500.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Fastqc was run on the raw Fastq files to determine initial quality of reads.
Trimmomatic was performed to remove barcodes and poor quality bases.
Fastqc was run for quality control.
Bowtie alignment to the mm10 genomic with -m1 -k1 -v1 parameters and filtered for unmapped reads with sam file output
After alignment, sam files were converted to bam files and filtered for unmapped reads, chimeric alignments, low quality alignments, and PCR duplicates using Picard59 MarkDuplicates and samtools60 settings: -b -h -F 4 -F 1024 -F 2048 -q 30.
Assembly: mm10
Supplementary files format and content: .bw files can be opened with igv
|
| |
|
| Submission date |
Nov 08, 2023 |
| Last update date |
Apr 19, 2024 |
| Contact name |
Dalia Hassan |
| E-mail(s) |
dhassan@mdanderson.org
|
| Phone |
3467146254
|
| Organization name |
MD Anderson Cancer Center
|
| Department |
Pulmonary Medicine
|
| Lab |
Jichao Chen
|
| Street address |
6565 MD Anderson Blvd, Z9.4040, Z9.4040
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE247271 |
CEBPA restricts alveolar type 2 cell plasticity during development and injury-repair [ChIP-seq] |
| GSE247272 |
CEBPA restricts alveolar type 2 cell plasticity during development and injury-repair |
|
| Relations |
| BioSample |
SAMN38156445 |
| SRA |
SRX22416665 |
