title: GSM9055795: P7_WT; Mus musculus; RNA-Seq
library_construction_protocol: For RNA-seq, cells were harvested and  using Trizol to extract total RNA. For ATAC-seq and CUT&Tag, 50,000 cells were harvested, chromosome DNA were tagmented by Tn5 transposome and then tagmented DNA was collected using Tagment DNA extract beads (Novoprotein, N248 and N249). For scRNA-seq, the dentate gyrus micro-dissected from mice was dissociated into single-cell by accutase at 37 °C for 30 min. ATAC-seq libraries were constructed by High-Sensitivity Open Chromatin Profile Kit 2.0 (for Illumina) (Novoprotein, N248) following the manufacturer's instructions.  Briefly, neurospheres were dissociated by accutase, resuspended in ATAC lysis buffer supplemented with 0.1% NP40, 0.1% Tween 20 and 0.01% digitonin, incubated for 5 min on ice, and then centrifuged for 5 min at 500 g at 4°C.  Nuclei were incubated in tagmentation buffer for 30 min at 37 °C.  Tagmented DNA was collected using Tagment DNA extract beads and amplified by PCR.   CUT&Tag-seq libraries were constructed by CUT&Tag 4.0 High-Sensitivity Kit (for Illumina) (Novoprotein, N259).  Briefly, neurospheres were dissociated by accutase.  Cells were enriched by ConA beads, and incubated with primary antibody buffer supplemented with anti-Pol II antibody (Abcam, ab817), anti-Pol II-Ser2 antibody (Abcam, ab5095), and anti-Pol II-Ser5 antibody (Abcam, ab5131), respectively.  ConA beads were then incubated with the secondary antibody buffer containing anti-mouse IgG antibody (Novoprotein, N270) for anti-Pol II-Ser5 antibody, or anti-rabbit IgG antibody (Novoprotein, N269) for anti-Pol II antibody and anti-Pol II-Ser2 antibody, respectively.  After wash, ConA beads were incubated with protein A/G-Tn5 transposome.  The DNA fragments were purified and amplified by PCR. scRNA-seq libraries were constructed following the manufacturer's instructions (single cell 3' V2 protocol, 10X Genomics).  Briefly, single-cell suspension were loaded into Chromium microfluidic chips with 3′ reagent kit (v3.1 chemistry), and barcoded with a 10X Chromium Controller (10X Genomics).