|
| Status |
Public on May 21, 2021 |
| Title |
72_K28_V3 |
| Sample type |
SRA |
| |
|
| Source name |
Ectocervical tissue biopsies
|
| Organism |
Homo sapiens |
| Characteristics |
subjectid: K28
locationcode: K
visit: V3
bv: F
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified using the Qiagen RNeasy Micro Kit
cDNA was generated using the Clontech SMARTseq v4 Ultra Low Input kit and libraries were prepared for sequencing using the Illumina NexteraXT DNA kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina bcl2fastq v2.17.1.14 was used for demultiplexing.
Reads were mapped to the human (GRCh38 Ensemble release 86) genomic reference with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Genome_build: GRCh38 Ensemble release 86: Homo_sapiens.GRCh38.dna.primary_assembly.fa, Homo_sapiens.GRCh38.86.gtf
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
May 20, 2021 |
| Last update date |
May 21, 2021 |
| Contact name |
Gregory K Tharp |
| E-mail(s) |
gktharp@emory.edu
|
| Phone |
404-727-7797
|
| Organization name |
Yerkes National Primate Research Center
|
| Department |
Developmental and Cognitive Neuroscience
|
| Lab |
Genomics Core
|
| Street address |
954 Gatewood Dr
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329-4208 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE174799 |
Differences in vaginal microbiota, host transcriptome and proteins in women with bacterial vaginosis are associated with metronidazole treatment response |
|
| Relations |
| BioSample |
SAMN19288992 |
| SRA |
SRX10951806 |
