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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 12, 2018 |
| Title |
W8-8_WT_batch_2 |
| Sample type |
SRA |
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| Source name |
single cell from heart
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| Organism |
Mus musculus |
| Characteristics |
tissue: heart
genotype: wild type
strain: C57BL/6
age: Embryonic day 9.5
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| Extracted molecule |
total RNA |
| Extraction protocol |
For single cell sample preparation, Ventricular part of E9.5 heart tubes were dissected and digested into single cells by 0.04% Trypsin combined with 0.05% Collagenase IV, and then transferred into DMEM containing 10% fetal bovine serum for termination. After washed in PBS without Ca2+, the single cells were manually transferred into cell lysis buffer with a mouth pipette.
Total RNA was reverse transcribed and amplified using Smart-seq2 protocol (Picelli et al., 2014), followed by Tn5 tagmentation and PCR enrichment to generate libraries using TruePrep DNA Library Prep Kit V2 for illumina (Vazyme, TD501-503) according to the manufacturer’s suggested protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
single cell from heart
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| Data processing |
Clean reads were mapped to mouse genome (mm10) using Salmon.
TPM (Transcripts Per Kilobase Million) for genes were calculated.
1. We excluded 18 samples with the mapping rates lower than 70%, and we obtained 76 WT single cells and 76 cKO single cells
2. We included GFP and tdTomato sequences in the reference genome for mapping and expression level quantification. Among 76 cKO single cells, 7 low GFP and high tdTomato cells were considered to be WT cells that had not expressed Mesp1-Cre. In 76 WT single cells, 2 low GFP and high tdTomato cells were considered not to be WT cells. These 9 cells with abnormal reporter gene expression were excluded. Finally we obtained 143 samples for the following data analysis, so we only uploaded gene expression of 143 samples in the processed file E9.5_Mouse_embryonic_heart_single_cells_143_samples_tpm.txt. File showing sample filtering: Exclusion_of_27_samples_from_170_total_samples.xlsx
Genome_build: mm10
Supplementary_files_format_and_content: Txt files of gene names and tpm values for each sample.
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| Submission date |
Feb 07, 2018 |
| Last update date |
Sep 12, 2018 |
| Contact name |
Jie Na |
| E-mail(s) |
[email protected]
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| Phone |
+86-18618192150
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| Organization name |
Tsinghua University
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| Department |
Basic Medical Sciences, School of Medicine
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| Lab |
D115 School of Medicine
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| Street address |
Tsinghua University
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE96648 |
Transcriptome analysis of mouse primitive heart with Dgcr8 deletion |
| GSE110265 |
Single cell RNA Sequencing Analysis of Gene Expression Profile in Dgcr8 Conditional KO Embryonic Hearts |
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| Relations |
| BioSample |
SAMN08474746 |
| SRA |
SRX3656373 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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