title: GSM4504453: Cut_and_Run_seq_Scid.ahd.2C2_anti-ARID1a_rep2; Mus musculus; OTHER
library_construction_protocol: For RNA-seq: Total RNA was isolated by use of RNAeasy Micro Kit (Qiagen, Hilden, Germany) according to  manufacturer's recommendations. RNA-seq: Libraries were constructed using NuGEN's Ovation Ultralow Library systems (NuGEN Technologies, San Calros, CA) and were subsequently subjected to 76 cycles of NextSeq500 sequencing (Illumina, San Diego,CA). ATAC-seq: ATAC-seq library preparation was done as described in (Buenrostro et al. 2013) using Transposomes from Nextera DNA library preparation kit (Illumina, San Diego, CA) and custom primers Libraries were run single read on the Illumina NexSeq500. The following antibodies are used for Cut&Run experiment: : rabbit monoclonal aTCF1 (Cell Signaling, C63D9(2203S), Lot 8), rabbit monoclonal aARID1a (Cell Signaling, D2A8V (12354S), Lot 3) and polyclonal Normal Rabbit IgG (Millipore 12-370, Lot 3109265). Libraries for sequencing was essentially prepared as previously descried for ChIP-sequencing (Okuyama et al. PLoS Genet. 2019, PMID:31381561) with two modifications: 1) Prior to adapter ligation all purification steps were carried out using Zymo Research ChIP DNA Clean and Concentrator to not lose fragments smaller than 100 nt and 2) size-selection with Ampure XP beads was performed after adapter ligation with a targeted mean fragment size of 150-300 bp. Libraries were paired-end sequenced on an Illumina Nextseq 500 (read-length: 2 × 38 bp).
attributes.tag: GEO Accession
attributes.value: GSM4504453