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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 02, 2019 |
| Title |
cell types 1, 2, and 3 in plate 105102 |
| Sample type |
SRA |
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| Source name |
embryonic stem cell , blastocyst derived
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| Organism |
Mus musculus |
| Characteristics |
genotype: Mll1fl/fl; Cre-ER TM; C57BL/6J
sample group: cell type 1 - Mll1fl/fl control, cell type 2 - Mll1-/-, cell type 3 - Mll1 inhibition
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| Extracted molecule |
total RNA |
| Extraction protocol |
Selected cells were removed from low temperature and reversed to get cDNA by a reaction including 5M Betaine Solution (Sigma B0300-1VL) 56 uL, 25 mM dNTP mix (Clontech 639132) 24 uL, 1M MgCl2 (Thermo Fisher Scientific AM9530G) 3.2 uL, 100 mM DTT (Sigma 43816-10ML) 8.8 uL, SMARTScribeTM 5X First-Strand Buffer (Clontech 639537) 61.9 uL, SeqAmpTM 2X PCR Buffer (Clontech 638504) 33.3 uL, 100 uM RT E5 Oligo (WaferGen 430-000240-0001) 4.0 uL, Amp Primer (WaferGen 430-000241-0001) and 100% Triton X-100 (Sigma T8787) 1.6 uL. ,
The library were prepared by using Nextera XT Library Prep Kit (illumina, 15032350) with some modification.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1.4)
Clean reads were mapped to UCSC mm10 genome via STAR v2.5.2b
Reads were assigned to Ensembl genes by featureCounts (subread-1.4.6-p1 command line)
Genome_build: mm10
Supplementary_files_format_and_content: csv,gene expression matrix for single cell RNASeq
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| Submission date |
Mar 06, 2019 |
| Last update date |
Dec 02, 2019 |
| Contact name |
Xu hanshi |
| E-mail(s) |
[email protected]
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| Organization name |
State Key Laboratory of Cardiovascular Disease
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| Street address |
167 Beilishi Road
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| City |
beijing |
| ZIP/Postal code |
100037 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE127943 |
Single cell transcriptome of ESCs upon MLL1 inhibition/deletion |
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| Relations |
| BioSample |
SAMN11078073 |
| SRA |
SRX5486065 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3656939_105102_m_sc_merged.genematrix.csv.gz |
10.6 Mb |
(ftp)(http) |
CSV |
| GSM3656939_105102_m_sc_merged.report.csv.gz |
85.9 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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