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| Status |
Public on Mar 16, 2020 |
| Title |
C1_CAF_023225_F8 |
| Sample type |
SRA |
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| Source name |
whole cell
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| Organism |
Homo sapiens |
| Characteristics |
cell type: CAF cells
column in countmatrix: F8
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
CAF, C1 Fluidigm platform
GeneCounts_caf_c1.csv
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| 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
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| Submission date |
Dec 04, 2018 |
| Last update date |
Mar 16, 2020 |
| Contact name |
Nadia Marie Atallah |
| Organization name |
Purdue University
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| Department |
Center for Cancer Research
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| Street address |
201 S. University St
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| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
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| Relations |
| BioSample |
SAMN10522196 |
| SRA |
SRX5096396 |
| 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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