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| Status |
Public on Aug 21, 2024 |
| Title |
pSabatiniLabsMMrCTXM2i13d221004C |
| Sample type |
SRA |
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| Source name |
frontal cortex, brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: frontal cortex, brain
genotype: N/A
treatment: T3
mouse: sns_13
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Please see: https://www.protocols.io/view/frozen-tissue-nuclei-extraction-for-10xv3-snseq-bi62khge
10X Chromium Single Cell 3' (V3), manufacturer's protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics v.3
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| Data processing |
Sequencing was performed on Illumina NovaSeq 6000
Sequencing reads were demultiplexed and aligned to the custom-annotated GRCm38 genome using CellRanger v5
CellRanger v5 filtering was performed including 10x barcode correction, UMI correction, and cell barcode calling to produce the filtered_feature_bc_matrix
Assembly: GRCm38 (custom annotated for readout of transgenes)
Supplementary files format and content: barcodes.tsv.gz contains filtered cell barcode information corresponding to column indices of matrix.mtx.gz
Supplementary files format and content: features.tsv.gz contains filtered feature information corresponding to row indices of matrix.mtx.gz
Supplementary files format and content: matrix.mtx.gz contains filtered gene expression counts matrix
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| Submission date |
Jul 03, 2024 |
| Last update date |
Aug 21, 2024 |
| Contact name |
Evan Macosko |
| E-mail(s) |
[email protected]
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| Organization name |
Broad Institute
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| Street address |
75 Ames St
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE271421 |
Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration |
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| Relations |
| BioSample |
SAMN42159559 |
| SRA |
SRX25166431 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8376621_pSabatiniLabsMMrCTXM2i13d221004C_barcodes.tsv.gz |
26.5 Kb |
(ftp)(http) |
TSV |
| GSM8376621_pSabatiniLabsMMrCTXM2i13d221004C_features.tsv.gz |
185.6 Kb |
(ftp)(http) |
TSV |
| GSM8376621_pSabatiniLabsMMrCTXM2i13d221004C_matrix.mtx.gz |
29.4 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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