|
| Status |
Public on Jun 23, 2021 |
| Title |
NBK24_repA |
| Sample type |
SRA |
| |
|
| Source name |
BAN
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: hTERT-immortalised non-balding dermal papilla cell line (BAN)
time point: 24 h
agent: 10 nM dihydrotestosterone
|
| Treatment protocol |
Fabricated MIPC scaffolds were maintained in MIPC media (3 parts DMEM media (DMEM with High Glucose, 4.0 mM L-Glutamine (Hyclone, South Logan, Utah) supplemented with 10% (v/v) fetal bovine serum (Life Technologies, Grand Island, NY), 100 U/ml penicillin G, and 100 mg/ml streptomycin (Sigma-Alrich, St Louis, MO)) and 1 part keratinocyte growth medium(Promocell GmbH, Germany)) for 9 days in an atmosphere of 10% CO2 and 90% air, conditioned in phenol red-free MIPC media (3 part phenol red-free DMEM media and 1 part keratinocyte basal medium) for 24 hr, and treated with 10 nM DHT for 6 hr and 24 hr
|
| Growth protocol |
3D fibrous hydrogel scaffolds containing DPC (BAB/BAN) and NHEK were formed by MIPC of two oppositely charged polyelectrolyte solutions. DPC (BAB/BAN) and NHEK were resuspended separately in polycationic water-soluble chitin solution and dispensed between polyanionic sodium alginate solution. The oppositely charged solutions were brought together to form an insoluble polyelectrolyte complex at an interface. Cell-containing fibres formed were drawn upwards and spooled. Each scaffold fabricated consists of DPC (BAB/BAN, 6E5 cells) and NHEK (2E5 cells) in 3:1 ratio.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from isolated BAB and BAN aggregates with Qiagen RNeasy kit according to manufacturer’s recommendation
RNA samples of high integrity (RIN value ≥ 8) were then used for RNA-seq library construction. cDNA was generated from 30 ng of extracted RNA with SMARTer Ultra Low Input RNA for Illumina Sequencing (Clontech), followed by RNA-seq library construction with NEBNext DNA Library Prep Master Mix Set for Illumina (NEB). Constructed libraries were multiplex in batches of twelve and 76 bp paired-end sequenced with Illumina HiSeq High Output v3
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Normal human epidermal keratinocyte (NHEK) co-cultured immortalised non-balding dermal papilla cell aggregates, 24 h 10 nM DHT treatment
BK24vsNBK24_gene_exp.diff.txt
BK24vsNBK24_isoform_exp.diff.txt
|
| Data processing |
Sequenced reads were aligned to the Hg19 human genome with TopHat2 (--min-anchor 8 --splice-mismatches 2 --min-intron-length 50 --max-intron-length 500000 --min-isoform-fraction 0.15 --max-multihits 20 --segment-length 25 --segment-mismatches 2 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 --mate-inner-dist 50 --mate-std-dev 20 --no-coverage-search --library-type fr-unstranded)
Transcripts were assembled with Cufflinks 2.2.1 (--frag-bias-correct hg19.fa --multi-read-correct --max-bundle-frags 100000000 --library-type fr-unstranded)
Cuffdiff2 was used to quartile normalize and identify differentially-expressed transcripts between BAB aggregates and BAN aggregates (--library-norm-method quartile)
Genome_build: Hg19
Supplementary_files_format_and_content: Cuffdiff2 output file with default settings with quartile normalised FPKM expression value of each sample type and expression level significance (q-value)
|
| |
|
| Submission date |
Jan 18, 2017 |
| Last update date |
Jun 23, 2021 |
| Contact name |
Axel HILLMER |
| E-mail(s) |
ahillmer@uni-koeln.de
|
| Organization name |
University of Cologne
|
| Department |
Institute of Pathology
|
| Street address |
Kerpener Str. 62
|
| City |
Cologne |
| ZIP/Postal code |
50937 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE93766 |
Transcriptome comparison of balding and non-balding dermal papilla aggregates from NHEK co-culturing |
|
| Relations |
| BioSample |
SAMN06238007 |
| SRA |
SRX2500383 |
