|
| Status |
Public on Jun 30, 2021 |
| Title |
H9_D5_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
hESC (H9 stem cell)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H9
genotype/variation: NA
cell type: Neuronal differenation from hESCs (Day 5)
passage: P33-P35
chip antibody: none
|
| Treatment protocol |
Total RNA was extracted with mirVana™ miRNA Isolation Kit (Thermo Fisher, Catlog: AM1560) for nanoCAGE sequencing library preparation and RNA-seq library preparation; Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody for ChIPSeq.
|
| Growth protocol |
H9 cells grows in mTeSR medium, for time-course differentiation media followed the protocol in published paper (PMID: 22976355)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
nanoCAGE library was prepared based on modified protocol from previously published paper (PMID: 21205859). ChIPSeq library was prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB); RNA-seq library was prepared using KAPA RNA HyperPrep Kit with RiboErase (HMR) Illumina® Platforms (KAPA Biosystems).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
H9D5_chr.tss.anno.txt,H9_total_peak.exp.anno.txt.filter.txt
library strategy: nanoCAGE
|
| Data processing |
NextSeq RTA version 2.4.11 software used for basecalling
For nanoCAGE data, bwa (version 0.7.13, mem default option) was used for genome mapping, duplicates were removed by samtools (version 0.1.16). TSS peaks were called and annotated based on gencode.v19.annotation.gtf with HOMER software according to the manual. Only peaks with moren than 30 reads were considered for the analyses. Gene expression was quantified using HTseq (version 0.10.0).
For ChIP-seq data, bwa (version 0.7.13, mem default option) was used for genome mapping, duplicates were removed by samtools (version 0.1.16). MACS2 (macs2 callpeak -t ZB12_flag_map_rmdup.bam -c Input_map_rmdup.bam -f BAM -g hs -n ZB12-flag -B -q 0.01) was used for peaks calling and HOMER software was used for peaks annotation based on gencode.v19.annotation.gtf.
For RNA-seq data, tophat (version 2.1.0 default parameter) was used for genome mapping, Bedtools was used for repeat coverage counting based on repeat annotation downloaded from UCSC database (hg19). Gene expression was quantified with Cufflinks (v2.2.1).
Genome_build: hg19
Supplementary_files_format_and_content: For nanoCAGE data: tab-delimited text files showing all TSS peaks (unfiltered) position with abundance measurements identified by HOMER software for each sample.
|
| |
|
| Submission date |
Aug 22, 2018 |
| Last update date |
Jun 30, 2021 |
| Contact name |
Guojing Liu |
| E-mail(s) |
guojing_liu@ucsb.edu
|
| Phone |
1-805-893-4586
|
| Organization name |
University of California, santa barbara
|
| Street address |
552 University Rd
|
| City |
santa barbara |
| State/province |
CA |
| ZIP/Postal code |
93106 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE118946 |
ZBTB12-HERVH-LncRNA axis is a molecular barrier for dedifferentiation of human stem cells |
|
| Relations |
| BioSample |
SAMN09882734 |
| SRA |
SRX4597612 |
