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| Status |
Public on Jun 24, 2020 |
| Title |
DistA_neg_31043 |
| Sample type |
SRA |
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| Source name |
Fallopian tube fragment
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| Organism |
Homo sapiens |
| Characteristics |
fallopian tube region: distal
aldh activity: negative
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| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol-LS
Lexogen Quant-Seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
use fastp (https://github.com/OpenGene/fastp) to trim adapter sequences and move UMI sequences
align with STAR (version 2.7) 2-pass method
remove duplicate reads based on UMI
Apply GATK3 to correct sequencing bias
use featureCounts function provided by the Rsubread R package to create a count matrix
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrix of normalized counts. Each row is a gene identified by ENTREZID, each column is a sample.
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| Submission date |
May 11, 2020 |
| Last update date |
Jun 24, 2020 |
| Contact name |
Ian Michael Rose |
| E-mail(s) |
imr923@gmail.com
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| Organization name |
Cornell University
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| Street address |
Ithaca, NY 14850
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| City |
Ithaca |
| ZIP/Postal code |
14850 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE150283 |
WNT and inflammatory signaling distinguish human Fallopian tube epithelial cell populations |
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| Relations |
| BioSample |
SAMN14888022 |
| SRA |
SRX8321699 |
| 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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