 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 25, 2021 |
| Title |
Ly6c+ c-kit+ cells_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
FACS-sorted Ly6c+c‑kit+ precursor cells
|
| Organism |
Mus musculus |
| Characteristics |
surface markers: CD11cNEGLy6c+c‑kit+
tissue: Tumor draining lymph node
strain: C57BL/6J
|
| Growth protocol |
B16F10 tumors were implanted bilaterally in the upper anterior thigh of C57BL/6 mice (Jackson).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were isolated by rapid mechanical disaggregation of TDLNs from established (day 14) untreated B16F10 tumors. LNs were pooled and stained for CD11c, Ly6c and c-kit (CD117), then the CD11cNEGLy6c+c-kit+ precursor population was sorted and used for ATAC-seq.
For each sample, 50,000 nuclei prepared from FACS-sorted Ly6c+c‑kit+ precursor cells were incubated with 2.5 mL Nextera Tn5 transposase (Illumina) in 50mL 1X transposition reaction mixture in a thermocycler at 37 °C for 1hr. The transposition reaction mixtures were purified with a DNA Clean and Concentrator kit (Zymo Research), and amplified for 11-13 cycles using NEBNext High-Fidelity 2X Master Mix (New England Biolabs) and Nextera Index primers (Illumina). The amplified libraries were size-selected by two rounds of AMPure beads purification (0.5X and 1.2X).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The ATACseq analysis was performed on Galaxy server. Adaptor and quality trimming were performed using Trim Glore! Modules (Galaxy v0.4.3.1). Trimmed reads were mapped to mouse genome mm10 using Bowtie2 (Galaxy v2.3.4.3) using default settings. Reads mapped to the mitochondria genome were removed using Filter SAM or BAM function under the samtools module (Galaxy v1.8), and PCR duplicates were removed using MarkDuplicates from Picard tool v2.20.2. The mapped reads overlapping with ENCODE blacklist regions (version 2) were filtered before calling peaks.
ATAC-seq peak calling was performed on Galaxy server using MACS2 v2.1.2 with following command “-q 0.05 --nomodel --shift --100 --extsize 200 -B --SPMR --keep-dup all --call -summits”.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated by bedGraphtoBigwig and visualized in Integrated genome viewer (IGV) v2.8.3.
|
| |
|
| Submission date |
Jul 13, 2021 |
| Last update date |
Aug 25, 2021 |
| Contact name |
Huidong Shi |
| E-mail(s) |
hshi@augusta.edu
|
| Phone |
706-721-6000
|
| Organization name |
Augusta University
|
| Department |
Georgia Cancer Center
|
| Lab |
2125 K
|
| Street address |
1120 15th Street, CN2138
|
| City |
Augusta |
| State/province |
GA |
| ZIP/Postal code |
30912 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE180026 |
Bruton’s tyrosine kinase (BTK) and indoleamine 2,3-dioxygenase (IDO) block differentiation of inflammatory dendritic cells in tumors [ATAC-seq] |
| GSE180039 |
Bruton’s tyrosine kinase (BTK) and indoleamine 2,3-dioxygenase (IDO) block differentiation of inflammatory dendritic cells in tumors |
|
| Relations |
| BioSample |
SAMN20199579 |
| SRA |
SRX11432438 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5448608_c-kit_positive_rep1.bigwig |
289.1 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
