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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 05, 2025 |
| Title |
CDX2P-CreERT2Apcfl/fl Hmga1-/- mouse #263 |
| Sample type |
SRA |
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| Source name |
colon crypt cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: colon crypt cells
genotype: CDX2P-CreERT2Apcfl/fl Hmga1-/-
treatment: tamoxifen induction at 12 weeks
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Enriched mouse colon crypt cells were washed once in 1x PBS, resuspended in ice-cold ATACseq lysis buffer (100 μl; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 and protease inhibitor) and centrifuged for 500 rpm, 10 minutes at 4 °C. After centrifugation, pellets were washed briefly in 1x PBS before incubating in the transposase reaction mix (12.5 μl 2 × TD buffer, 2 μl transposase; Illumina) and nuclease-free water (10.5 μl) for 30 minutes at 37° C. Genomic DNAs were eluted using MinElute kit; QIAGEN.
After DNA purification (MinElute kit; QIAGEN), eluted DNA (1 μl) was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles. Purified fragmented DNA was amplified by PCR.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
High thoughput sequencing was performed by Azenta HiSeq 2x150bp.
Trimmomatic 0.38 was used to trim the reads with default settings.
Sequencing reads were mapped back to mouse reference genome mm10 using Bowtie2.
Potential PCR duplicates were removed with samtools 1.9 to keep alignments that (1) have a minimum mapping quality of 30, (2) are aligned concordantly, and (3) are the primary called alignments. PCR or optical duplicates are marked using Picard 2.18.26 and removed.Prior to peak calling, reads mapping to mitochondria (mt) are called and filtered, and reads mapping to unplaced contigs are removed.. Peak calling was performed using Genrich (https://github.com/jsh58/Genrich) (0.6.1), followed by DiffBind (http://bioconductor.org/packages/release/ bioc/html/DiffBind.html) (3.4.11) to identify differentially accessible regions of chromatin
MACS2 2.1.2 was used for peak calling to identify open chromatin regions. If a blacklist If a ‘blacklist’ of artefactual regions (areas with extremely high- or low-mappability) is available for the provided reference genome, called peaks are filtered for blacklisted regions to mitigate errors due to mappability. Valid peaks froms each group or condition are merged and peaks called in at least 66% of samples are kept for downstream analyses.
For each pair-wise comparison, peaks from condition A and condition B are merged and peaks found in either condition are kept for downstream analyses. Reads falling beneath peaks were counted in all samples, and these counts were used for differential peak analyses using the R package Diffbind.
Assembly: mm10
Supplementary files format and content: KO263.filtered.bam.tdf
Supplementary files format and content: KO266.filtered.bam.tdf
Supplementary files format and content: KO284.filtered.bam.tdf
Supplementary files format and content: WT260.filtered.bam.tdf
Supplementary files format and content: WT269.filtered.bam.tdf
Supplementary files format and content: WT279.filtered.bam.tdf
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| Submission date |
Oct 05, 2024 |
| Last update date |
Feb 05, 2025 |
| Contact name |
LI LUO |
| E-mail(s) |
li.luo@jhmi.edu
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| Phone |
4106140723
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| Organization name |
Johns Hopskins University
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| Department |
Hematology
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| Lab |
Linda Resar
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| Street address |
720 Rutland Ave, Ross Build
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE278871 |
HMGA1 acts as an epigenetic gatekeeper of ASCL2 and Wnt signaling during colon tumorigenesis |
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| Relations |
| BioSample |
SAMN44072180 |
| SRA |
SRX26296676 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8556342_KO263.filtered.bam.tdf |
326.3 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
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