|
| Status |
Public on Jun 03, 2014 |
| Title |
Input 2 |
| Sample type |
SRA |
| |
|
| Source name |
Whoel animal extract
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: HML214
tag: GFP
antibody: n/a
|
| Growth protocol |
Worms were grown and staged on NGM plates with bacterial OP50 food at 20ยบ
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Staged worms were washed twice with M9 buffer and freezed in liquid nitrogen. Frozan worms were crushed using a pestle and a mortar and resuspended in Chip buffer. Extracts were sonicated and precleared before ChIP experiments.
Libraires were made followinf the recommended Illumina protocol for TruSeq Chip sample preparation guide (part #15023092 Rev A, August 2012).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Raw reads from the ChIP-seq and input control sequences were aligned to the ce10 version of the C elegans genome using the bowtie2 algorithm and parameters that were optimized to detect reads with approximately 3 mismatches per read and no more than 10 alignments genome-wide (-k10 -N 1)
Uniquely aligned reads were selected for input to the MACS peak calling algorithm, version 1.4, which automatically removes any duplicate sequences before calling ChIP peaks
Custom scripts were used to annotate the high confidence peaks against the Refseq list of gene models for ce10, downloaded from the UCSC genome database in April of 2013, which was supplemented with the positions of all worm microRNA genes obtained from the Wormbase genome database in April of 2013.
Genome_build: ce10
Supplementary_files_format_and_content: peaks
|
| |
|
| Submission date |
Jun 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Roberto Perales |
| E-mail(s) |
rperales@cshl.edu
|
| Organization name |
Cold Spring Harbor Laboratory
|
| Lab |
Christopher Hammell's Lab
|
| Street address |
1 Bungtown Road
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL15716 |
| Series (1) |
| GSE58171 |
LIN-42, the Caenorhabditis elegans PERIOD homolog, negatively regulates microRNA transcription |
|
| Relations |
| BioSample |
SAMN02821280 |
| SRA |
SRX560680 |
