NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3502053 Query DataSets for GSM3502053
Status Public on Mar 16, 2020
Title C1_CAF_023219_E7
Sample type SRA
 
Source name whole cell
Organism Homo sapiens
Characteristics cell type: CAF cells
column in countmatrix: E7
Growth protocol prostate CAF cells were selected, for Fluidigm data cells were processed in two batches. Fastq files or samples with "-1" after the name are in batch 2.
Extracted molecule total RNA
Extraction protocol followed the C1 Fluidigm and 10x Chromium preparation protocols
Capture sites containing 0 or >1 cell were excluded, and cells with positive ethidium homodimer-1 staining were also excluded. Cell lysis, reverse transcription, and cDNA amplification of single cells were conducted following the protocol for mRNA sequencing (Fluidigm) or 10x Chromium.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description CAF, C1 Fluidigm platform
GeneCounts_caf_c1.csv
Data processing FastQC v.0.11.3 was used to observe read quality
FastX v. 0.0.14 was used to trim data
Fluidigm data: Tophat2 v 2.1.0 was used to align reads to the genome with max-intron-length set to 560, min-intron-length set to 60, and strandedness set to "fr-firststrand".
Fluidigm data:HTSeq Count v. 0.6.1 was used to count reads aligning to genes, feature was set to "exon" and attribute was set to "gene id", stranded was set to "reverse" and intersection-nonempty was used
Chromium data: Cellranger was used to do initial quality control, alignment, and counting
Fluidigm and chromium proceesed data: Seurat was used to normalize and perform DE analysis. The number of reads for the control and experimental groups were then compared to identify differentially expressed genes
Genome_build: Ensembl Genome Reference Consortium Human Build 38 (GRCh38.p3)
Supplementary_files_format_and_content: FASTQ files
 
Submission date Dec 04, 2018
Last update date Mar 16, 2020
Contact name Nadia Marie Atallah
Organization name Purdue University
Department Center for Cancer Research
Street address 201 S. University St
City West Lafayette
State/province IN
ZIP/Postal code 47907
Country USA
 
Platform ID GPL16791
Series (1)
GSE123359 10x and C1 CAF sequencing
Relations
BioSample SAMN10522202
SRA SRX5096390

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap