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| Status |
Public on Feb 04, 2021 |
| Title |
P20181114 ESCA |
| Sample type |
SRA |
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| Source name |
ESCA
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Non-cancer, Tumor
patient id: P20181114
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors and adjacent normal tissues were cut into approximately 1-2 mm3 pieces in the RPMI-1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco), and enzymatically digested with gentleMACS (Miltenyi) for 60 min on a rotor at 37°C, according to manufacturer’s instruction. The dissociated cells were subsequently passed through a 100 µm SmartStrainer and centrifuged at 400 g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1× PBS (Gibco), the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
Single cell suspensions were stained with antibodies against CD45 and 7AAD for FACS sorting, performed on a BD Aria SORP instrument. Based on FACS analysis, single cells were sorted into 1.5 ml tubes (Eppendorf) and counted manually under the microscope. The concentration of single cell suspensions was adjusted to 500-1200 cells/ul. Cells were loaded between 7,000 and 15,000 cells/chip position using the 10x Chromium Single cell 5’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics, V3 barcoding chemistry) according to the manufacturer’s instructions. All the subsequent steps were performed following the standard manufacturer’s protocols. Purified libraries were analyzed by an Illumina Hiseq X Ten sequencer with 150-bp paired-end reads.
10x Chromium Single cell 5’ Library
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
ESCA_normalized_expression.csv.gz
ESCA_metadata.csv.gz
cDC2_normalized_expression.csv.gz
cDC2_metadata.csv.gz
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| Data processing |
Cell Ranger 3.0.0 was used to quantify gene expression level.
Scanpy 1.4.3 was used to conduct the scRNA-seq analysis.
Genome_build: GRCh38
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| Submission date |
Jul 20, 2020 |
| Last update date |
Feb 04, 2021 |
| Contact name |
Sijin Cheng |
| E-mail(s) |
chengsj@mail.cbi.pku.edu.cn
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| Organization name |
Peking University
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| Department |
School of Life Science
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| Lab |
Zhang Lab
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| Street address |
Haidian District, Beijing Summer Palace Road No. 5
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| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL28896 |
| Series (1) |
| GSE154763 |
A pan-cancer single-cell landscape of tumor-infiltrating myeloid cells |
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| Relations |
| BioSample |
SAMN15585186 |
| Supplementary data files not provided |
| Processed data are available on Series record |
| Raw data not provided for this record |
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