GSM3374948: ATAC B6 Lg Ahr KO rep1; Mus musculus; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Digestive tract
Cell type
Large intestine lamina propria
NA
NA
Attributes by original data submitter
Sample
source_name
Lg. Int. Lamina Propria ILC2
tissue
Large Intestine
cell type
ILC2
strain
C57BL/6
genotype
Ahr-/-
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
[RNA-seq] Lamina propria cells were isolated and sorted by flow cytometry. Sorted ILC2s (Lin–KLRG1+CD90+) were lysed in Trizol (Invitrogen), and RNA was subsequently extracted with RNAeasy Mini Kit (Qiagen). [ATAC-seq] Lamina propria cells were isolated and ILC2s (Lin–KLRG1+CD90+) were sorted by flow cytometry. [RNA-seq] Total RNA was treated with Ribo-zero kit and RNA-seq libraries were generated using kits from Illumina. Barcoded samples were pooled and sequenced over 2 lanes on an Illumina HiSeq 2500 instrument to produce 50 bp single-end reads. [ATAC-seq] Large intestinal CD4+TCRβ+YFP+ ILC2s were sorted and subjected to ATAC-Seq according to a published protocol (Buenrostro et al., 2013) with a modification in the library purification step. Briefly, 5x10^4 sorted ILC2s were washed once with 50 ul PBS, and then lysed in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) on ice. Pelleted nuclei were resuspended in transposition reaction mix with Tn5 transposase (Illumina) and incubated at 37℃ for 30 min with gentle shaking. The DNA was purified with MinElute PCR Purification Kit (Qiagen) and was used as a template of PCR with 10 cycles of amplification. The library was cleaned up with 1.2x SPRIselect beads (Beckman Coulter), to exclude the small fragments, before sequencing with Illumia HiSeq 2500.