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| Status |
Public on Jun 29, 2020 |
| Title |
1772159322_C05_A8 |
| Sample type |
SRA |
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| Source name |
endometrium biopsy
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| Organism |
Homo sapiens |
| Characteristics |
time in menstrual cycle: day25
tissue: endometrium biopsy
donor condition: fertile healthy
gender: female
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single cells were lysed using the reagents (Takara/Clontech) and default protocol for Fluidigm C1 mRNA Seq
RNA libraries were prepared for sequencing using Illumina Nextera-XT protocols for single cells
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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 |
bcl2fastq v2.17.1.14 was used for demultiplexing and generating *.fastq.
Raw reads in the *.fastq files were trimmed to 75bp using fastqx,
duplicate-removed using picard MarkDuplicates, and
aligned to reference using STAR with default parameters.
Aligned reads were converted to counts using HTSeq.
Genome_build: Ensembl human reference genome GRCh38.87 (dna.primary_assembly)
Supplementary_files_format_and_content: comma separated file including HTSeq count for each cell
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| Submission date |
Mar 17, 2018 |
| Last update date |
Jun 29, 2020 |
| Contact name |
Wanxin Wang |
| E-mail(s) |
wanxinw@stanford.edu
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| Phone |
4134373134
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| Organization name |
Stanford Univeristy
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| Lab |
Wanxin Wang
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| Street address |
James H Clark Center, 318 Campus Drive, room E300
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE111976 |
Single cell RNA-seq analysis on human endometrium across the natural menstrual cycle |
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| Relations |
| BioSample |
SAMN08726311 |
| SRA |
SRX3805603 |
| 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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