|
| Status |
Public on Jul 09, 2019 |
| Title |
1_MED1_INPUT |
| Sample type |
SRA |
| |
|
| Source name |
Cells grown in SPP liquid media
|
| Organism |
Tetrahymena thermophila |
| Characteristics |
genotype/variation: Med31-FZZ tagged cells
developmental stage: Vegetative Growth
process: Whole cell extraction
chip antibody: none
|
| Growth protocol |
30C; 100rpm; SPP liquid media
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and incubated with ANTI-FLAG® M2 Affinity Gel (Sigma) A2220
Illumina's TruSeq ChIP Sample Preparation Kit (cat# IP-202-1012)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
MED1_ORF_RACS
MED1_IRG_RACS
|
| Data processing |
ChIP-seq reads were assessed for quality using fastqc
ChIP-Seq reads were aligned using BWA and SAMtools
RACS: Reads calling from the genetic and intergenic regions were respectively counted and extracted
Genome_build: T_thermophila_June2014_assembly.fasta
Supplementary_files_format_and_content: csv files containing reads were generated using RACS
Supplementary_files_format_and_content: MED1_ORF_RACS: contains the number of reads found in all annotated genic regions of the Tetrahymena genome for the corresponding samples
Supplementary_files_format_and_content: MED2_ORF_RACS: contains the number of reads found in all annotated genic regions of the Tetrahymena genome for the corresponding samples
Supplementary_files_format_and_content: MED1_IRG_RACS: contains the number of reads found in all (RACS-pipeline generated) intergenic regions of the Tetrahymena genome for the corresponding samples
Supplementary_files_format_and_content: MED2_IRG_RACS: contains the number of reads found in all (RACS-pipeline generated) intergenic regions of the Tetrahymena genome for the corresponding samples
|
| |
|
| Submission date |
Feb 10, 2019 |
| Last update date |
Jul 09, 2019 |
| Contact name |
Alejandro Saettone |
| E-mail(s) |
alejandro.saettonechipana@sickkids.ca
|
| Organization name |
The Hospital for Sick Children
|
| Department |
Genetics & Genome Biology
|
| Lab |
Campos Lab
|
| Street address |
686 Bay Street
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G0A4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL23968 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN10908012 |
| SRA |
SRX5357051 |
