|
| Status |
Public on Aug 15, 2022 |
| Title |
RNAseq-CkoCT442-TAF5Lsg2-7-IAA-R2-T1 |
| Sample type |
SRA |
| |
|
| Source name |
HAP1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: auxin
genotype: endogenous CTCF KO, CTCF-AID, TIR1, TAF5L KO
|
| Treatment protocol |
For auxin treatment: 500uM auxin. For siRNA treatment: 40nM for 72H.
|
| Growth protocol |
HAP1 cells (and the derived cells lines) were cultured at 37C with 5% CO2 in IMDM GlutaMAX™ Supplement (Gibo, 31980097) with 10% FBS (Gibco, 16000069), 1% Penicillin-Streptomycin (Gibco, 15140122).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini Kit (Qiagen, 74104) with QIAshredder (Qiagen, 79654).
Total RNA was sent to the BGI Hong Kong facility (DNBseq Eukaryotic Transcriptome resequencing) for library preparation
Libraries were sequenced at the BGI Hong Kong facility on DNBseq platform (pair-ends 100bp).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
KO of endogenous CTCF. Add AID tag in N term and C term of CTCF cDNA. 4 different sgRNAs were used.
merged_clones_TPM_genes.tsv
genes_expression_expected_count_clones.tsv
|
| Data processing |
RNA-seq data was mapped using a standardized pipeline in the DolphinNext environment (Yukselen O., Turkyilmaz O., Ozturk A.R., Garber M., Kucukural A. DolphinNext: a distributed data processing platform for high throughput genomics. BMC Genomics 21, 310 (2020). https://doi.org/10.1186/s12864-020-6714-x).
Reads were mapped to hg19 using STAR (Dobin et al., 2013) with default parameters to generate BAM files. RSEM was used for transcript quantification (Li and Dewey, 2011).
Differentially Expressed genes were obtained using DESeq2 on the DEBrowser interface (Kucukural et al., 2019)
Genome_build: hg19 human genome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample
Supplementary_files_format_and_content: Bigwig
|
| |
|
| Submission date |
Jul 23, 2021 |
| Last update date |
Aug 15, 2022 |
| Contact name |
Anne-Laure Valton |
| E-mail(s) |
anne-laure.valton@umassmed.edu
|
| Organization name |
University of Massachusetts Medical School
|
| Street address |
368 Plantation St
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL28038 |
| Series (2) |
| GSE180691 |
A cohesin traffic pattern genetically linked to gene regulation |
| GSE180713 |
A cohesin traffic pattern genetically linked to gene regulation [RNA-Seq] |
|
| Relations |
| BioSample |
SAMN20360506 |
| SRA |
SRX11531671 |
