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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 05, 2024 |
| Title |
12-5-3_E12.5 BRN1/2 cKO |
| Sample type |
SRA |
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| Source name |
Cortex
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| Organism |
Mus musculus |
| Characteristics |
tissue: Cortex
genotype: BRN1/2 cKO
Sex: male
developmental stage: E12.5
collection date: 2021-03-23
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cortex of E12.5 and E14.5 embryos was dissected and dissociated into single cells using the Papain Dissociation System (#LK0031500, Worthington Biochemical). Individual collected cells were processed for scRNAseq using.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, The NextGEM protocol was run on the 10X Chromium Controller to create GEMs, composed of a single cell, gel bead with unique barcode and UMI primer, and RT reagents. 100 µl of emulsion is retrieved from the chip and incubated (45 min at 53°C, 5 min at 85°C, cool to 4°C), generating barcoded cDNA from each cell. The GEMs were broken using Recovery Agent and cDNA cleaned, following manufacturer’s instructions using MyOne SILANE beads. cDNA was amplified for 11 cycles (3 min at 98°C, 11 cycle: 15 sec at 98°C, 20 sec at 63°C, 1 min at 72°C; 1 min at 72°C, cool to 4°C). Samples were cleaned using 0.6X SPRIselect beads. Quality control (QC) was completed using Qubit and Bioanalyzer to determine size and concentrations. 10 µl of amplified cDNA was carried into library prep. Fragmentation, end repair and A-tailing were completed (5 min at 32°C, 30 min at 65°C, cool to 4°C), and samples were cleaned up using double sided size selection (0.6X, 0.8X) with SPRIselect beads. Adaptor ligation (15 min at 20°C, cool to 4°C), 0.8X cleanup and amplification were performed by PCR using unique i7 index sequences. Libraries underwent a final cleanup using double sided size selection (0.6X, 0.8X) with SPRIselect beads. Library QC was performed using Qubit, Bioanalyzer and KAPA library quantification qPCR kit.
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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
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| Data processing |
Demultiplexing and FASTQ generation was completed using Illumina’s BaseSpace software. Data were aligned to the mouse reference genome (refdata-gex-mm10-2020-A) publicly available at the 10X genomics’ website using the Cell Ranger pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Apr 06, 2023 |
| Last update date |
Jul 05, 2024 |
| Contact name |
Soraia Barao |
| Organization name |
JHU
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| Department |
Neuroscience
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| Lab |
Mueller
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| Street address |
725 N Wolfe St PCTB 1015
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| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE229129 |
Conserved transcriptional regulation by BRN1 and BRN2 in neocortical progenitors drives mammalian neural specification and neocortical expansion |
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| Relations |
| SRA |
SRX19899206 |
| BioSample |
SAMN34103830 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7153008_12-5-3_barcodes.tsv.gz |
49.9 Kb |
(ftp)(http) |
TSV |
| GSM7153008_12-5-3_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM7153008_12-5-3_matrix.mtx.gz |
129.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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