Status
Public on Oct 10, 2024
Title
RNAseq_ZT4_H3.3_Cohort1_Rep2
Sample type
SRA
Source name
Brain-TMN
Characteristics
tissue: Brain-TMN
timepoint: ZT4
virus: H3.3
genotype: C57BL/6
cohort: 1
replicate: 2
Treatment protocol
Mice brains were collected every 4 hours across the zeitgeber time following IACUC protocols. They were flash-frozen using methylbutane and stored at -80 degrees celsius. Brains were sliced and TMN punched (1 mm punches) according to previously published coordinates. TMN were frozen at -80 degrees celsius until CUT&RUN was performed.
Extracted molecule
polyA RNA
Extraction protocol
Tissue was resuspended in 800 uL of Trizol and homogenized using a small dounce homogenizer (30 strokes loose, 30 strokes tight) at room temperature. Chloroform was added and aqueos phase isolated. 70 % ethanol was added 1:1, and then passed over an RNAeasy mini-elute column. The Qiagen RNAeasy MicroKit protocol was followed, including all optional steps/DNAse treatment. RNA was eluted in 15 uL and quantitated using a nanodrop spectrophotometer. RNA quality was assessed using a tapestation RNA screentape. 100 ug of total RNA was used as input for library prep.
Illunia Stranded mRNA Prep, Ligation
Library strategy
RNA-Seq
Library source
transcriptomic
Library selection
cDNA
Instrument model
Illumina NovaSeq X Plus
Description
RNAseq_ZT4_H3.3_Cohort1_Rep2
Data processing
Samples were demultiplexed using bcl2fastq2 (Illumina, v2.20).
Samples were aligned to the GRCm38 mouse genome using STAR (2.7.11b) alignReads in mode BAM SortedByCoordinate.
Gene counts were generated using htseq-count (HTSeq 2.0.5) with the following parameters: --format=bam --minaqual=10 --type=exon --idattr=gene_name --stranded=yes --mode=union
Gene counts were normalized using DEseq2 (1.44.0) prior to analysis using JTKcycle (3.1)
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: Htseq-counts
Submission date
Jun 21, 2024
Last update date
Oct 10, 2024
Contact name
Benjamin H Weekley
Organization name
Icahn School of Medicine at Mount Sinai
Department
Neuroscience
Lab
Maze Lab, Hess 9-201
Street address
1470 Madison Ave
City
New York
State/province
NY
ZIP/Postal code
10029
Country
USA
Series (2)
GSE270429
Bidirectional histone monoaminylation dynamics regulate neural rhythmicity
GSE270434
Bidirectional histone monoaminylation dynamics regulate neural rhythmicity
Relations
Supplementary file
Size
Download
File type/resource
GSM8342727_H3-3_4_1.2_Counts.txt.gz
169.9 Kb
(ftp) (http)
TXT
Raw data are available in SRA