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| Status |
Public on May 05, 2023 |
| Title |
Brain coronal slice (1.5 mm posterior to the bregma) transcriptome [ZT14_M_Saline] |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
strain: C57BL/6J
Sex: Male
genotype: WT
treatment: control (NaCl)
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| Treatment protocol |
Rhynchophylline (RHY, 100 mg/kg; administered with a volume of 10 mL/kg) or Saline (NaCl 0.9 %) intraperitoneal injections at ZT0 or ZT11
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| Growth protocol |
Habituation to individual cage for 10 days; housing with a 12h light:12h dark cycle with food and water ad libitum.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue preparation: 10X Genomics protocol CG000240-Rev C
Slice staining: 10X Genomics protocol CG000160-Rev A (Hematoxylin-Eosin staining)
10X Genomics protocol CG000239-Rev D
Paired-end dual indexed RNA sequencing with Illumina NovaSeq 6000 (Genome Quebec Innovation Centre, Montreal, Canada), at a sequencing depth of approximately 150M read pairs per sample. RNAseq was performed according to instructions of 10x Genomics for the Visium Spatial Gene Expression kit: read 1, 28 cycles; i7 index read, 10 cycles; i5 index read, 10 cycles; read 2, 90 cycles.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
The matrix.h5 (processed data file 1) contains the columns barcodes (barcode sequences and their corresponding library identifiers, which is always -1 for spaceranger count runs), data (nonzero UMI counts in column-major order), features (gene information), indices (zero-based row index of corresponding element in data), indptr (zero-based index into data / indices of the start of each column, that is the data corresponding to each barcode sequence), shape (tuple of [# rows, # columns] indicating the matrix dimensions)
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| Data processing |
library strategy: spatial transcriptomics
Read alignment software: SpaceRanger1.2.2 (10x Genomics)
Assembly: mm10
Supplementary files format and content: Feature barcode matrices in HDF5 format that contain only tissue-associated barcodes and are used to run the Aggr pipeline and extract differentially expressed genes (DEGs)
Supplementary files format and content: Compressed file containing the spatial information: QC images to check image processing pipeline, downsampled input images, and files that describe spot barcode locations in the images. This spatial information is also used (together with the HDF5 file) to run the Aggr pipeline and extract differentially expressed genes (DEGs)
Supplementary files format and content: The matrix.h5 contains the columns barcodes (barcode sequences and their corresponding library identifiers, which is always -1 for spaceranger count runs), data (nonzero UMI counts in column-major order), features (gene information), indices (zero-based row index of corresponding element in data), indptr (zero-based index into data / indices of the start of each column, that is the data corresponding to each barcode sequence), shape (tuple of [# rows, # columns] indicating the matrix dimensions)
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| Submission date |
Nov 01, 2022 |
| Last update date |
May 06, 2023 |
| Contact name |
Valerie Mongrain |
| E-mail(s) |
valerie.mongrain@umontreal.ca
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| Phone |
514 338-2222 3323
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| Organization name |
CRCHUM
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| Department |
Research center
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| Lab |
Tour Viger, local R09-720
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| Street address |
333 rue Saint-Antoine Est
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| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H2X1R9 |
| Country |
Canada |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE217058 |
Probing pathways by which rhynchophylline modifies sleep using spatial transcriptomics |
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| Relations |
| BioSample |
SAMN31561953 |
| SRA |
SRX18114641 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6704286_ZT14_M_Saline_filtered_feature_bc_matrix.h5 |
11.5 Mb |
(ftp)(http) |
H5 |
| GSM6704286_ZT14_M_Saline_spatial.tar.gz |
6.7 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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