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| Status |
Public on Jan 01, 2022 |
| Title |
FAPkdCAF1 |
| Sample type |
SRA |
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| Source name |
CAFs
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| Organism |
Homo sapiens |
| Characteristics |
treatment: FAP siRNA transfected
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| Treatment protocol |
For human CD33+MDSCs isolation, single-cell suspensions of ICC tumor and blood of ICC patients were separated by gradient centrifugation using a 70%/35% Percoll gradient (GE Healthcare) and further purified by magnetic-activated cell sorting (MACS) using CD33 microbeads (#130-045-501, Miltenyi Biotech). For isolation of ICC CAFs and tumor cells, single-cell suspensions of ICC tumor were incubated with anti-human Fibroblast Microbeads (#130050601, Miltenyi Biotec) or anti-human EpCAM Microbeads (#130061101, Miltenyi Biotec), respectively, followed by magnetic beads separation. All CAFs used for in vitro experiments were cultured in advanced DMEM/F12 (#12634028, Gibco) with 1% FBS within two passages.FAP siRNA was transfected into CAFs using lipofectamine iMAX.
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| Growth protocol |
To collect CM for stimulation, 5X105 CAFs or FAPkdCAFs within two passages or blood 2X105 CD33+MDSCs were cultured in serum-free DMEM-F12 and RPMI-1640 with 1%FBS, respectively, for 24 hrs. All CM were filtered and used for further study.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells by TRIzol
RNA libraries were prepared for sequencing using standard BGI protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Raw reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke, then mapped to reference whole genome using bowtie v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
Mapped reads were count using RSEM v1.2.12, and Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
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| Submission date |
Sep 29, 2020 |
| Last update date |
Jan 01, 2022 |
| Contact name |
Qian Cai |
| E-mail(s) |
[email protected]
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| Organization name |
Fudan University
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| Department |
Immunology
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| Street address |
No.130 Dongan road
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| City |
Shanghai |
| ZIP/Postal code |
210012 |
| Country |
China |
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| Platform ID |
GPL23227 |
| Series (1) |
| GSE158755 |
RNA sequencing data of differentially treated cancer associated fibroblast, myeloid-derived supression cells, and ICC tumor cells in ICC patient |
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| Relations |
| BioSample |
SAMN16292971 |
| SRA |
SRX9215423 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4809849_FAPkd_CAF1.gene.fpkm.txt.gz |
3.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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