GSM3318544: sh-ALKBH1-6-2-ATAC; Homo sapiens; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Neural
Cell type
Glioblastoma stem cells
NA
NA
Attributes by original data submitter
Sample
source_name
Patient-Derived Glioblastoma Stem Cell
cell type
glioblastoma stem cells
shRNA
shRNA targeting ALKBH1 (shALKBH1.1551)
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
ATAC-seq was performed on 50,000 nuclei. The samples were permeabilized in cold permeabilization buffer (0.2% IGEPAL-CA630 (I8896, Sigma), 1 mM DTT (D9779, Sigma), Protease inhibitor (05056489001, Roche), 5% BSA (A7906, Sigma) in PBS (10010-23, Thermo Fisher Scientific)) for 10 minutes on the rotator in the cold room and centrifuged for 5 min at 500 xg at 4°C. The pellet was resuspended in cold tagmentation buffer (33 mM Tris-acetate (pH = 7.8) (BP-152, Thermo Fisher Scientific), 66 mM K-acetate (P5708, Sigma), 11 mM Mg- acetate (M2545, Sigma), 16% DMF (DX1730, EMD Millipore) in Molecular biology water (46000-CM, Corning)) and incubated with Tagmentation enzyme (FC-121-1030; Illumina) at 37 °C for 30 min with shaking 500 rpm. The tagementated DNA was purified using MinElute PCR purification kit (28004, Qiagen). The libraries were amplified using NEBNext High-Fidelity 2X PCR Master Mix (M0541, NEB) with primer extension at 72°C for 5 minutes, denaturation at 98°C for 30s, followed by 8 cycles of denaturation at 98°C for 10 s, annealing at 63°C for 30 seconds and extension at 72°C for 60 seconds. After the purification of amplified libraries using MinElute PCR purification kit (28004, Qiagen), the double size selection was performed using SPRIselect bead (B23317, Beckman Coulter) with 0.55X beads and 1.5X to sample volume.