alias: GSM4872459
title: GSM4872459: GFP-positive tanycytes P8 Ctrl (scATAC-seq); Mus musculus; ATAC-seq
library_construction_protocol: 2 mm thick coronal slices including the hypothalamic protruding median eminence (ME) were collected using adult mouse brain matrix (Kent Scientific).  The mediobasal hypothalamic region was microdissected using a surgical scalpel, dampened in Hibernate-A media supplemented with 0.5 mM GlutaMax and 2% B-27 (HABG) and chopped with a razor blade. Single cell ATAC-Seq was performed using the 10x Genomic single cell ATAC reagent V1 kit following the manufacturer's instructions.  Briefly, FACS-sorted cells (~30k cells) were centrifuged at 300xg for 5 min at 4oC. The cell pellet was resuspended in 100 μl of Lysis buffer, mixed 10x by pipetting and incubated on ice for 3 min.  Wash buffer (1 ml) was added to the lysed cells, and cell nuclei were centrifuged at 500xg for 5 min at 4oC. The nuclei pellet was resuspended in 250 ul of 1x Nuclei buffer.  Cell nuclei were then counted using Trypan blue staining.  Re-suspended cell nuclei (10-15k) were used for transposition and loaded into the 10x Genomics Chromium Single Cell system. Libraries were amplified with 10 PCR cycles and were sequenced on an Illumina NextSeq with ~200 million reads per library.  Sequencing data were processed through the Cell Ranger ATAC 1.1.0 pipeline (10x Genomics) with default parameters. single cell ATACseq
identifiers.namespace: GEO
identifiers.id: GSM4872459
attributes.tag: GEO Accession
attributes.value: GSM4872459