|
| Status |
Public on Feb 27, 2024 |
| Title |
TF ChIP-seq from whole organism (ENCLB666JPW) |
| Sample type |
SRA |
| |
|
| Source name |
Caenorhabditis elegans strain OP323 hermaphrodite late embryo 5 hours post synchronization using egg bleaching insertion targeting C. elegans ceh-2
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
antibody: ceh-2
cell_type: whole organism
biomaterial_type: whole organisms
biosample encode accession: ENCBS739JKF (SAMN40085523)
collection date: not applicable
geographic location: not applicable
encode accession: ENCBS739JKF
note: Transgenic C. elegans line, stably expressing a C-terminal GFP-FLAG tag fused to CEH-2
Sex: hermaphrodite
dev stage: late embryonic
age: unknown
donor_id: ENCDO574IXR
lab: Valerie Reinke, Yale
source: Valerie Reinke
worm synchronization stage: egg bleaching
post synchronization time: 5
post synchronization time units: hour
link: ENCBS739JKF at ENCODE; https://www.encodeproject.org/ENCBS739JKF/
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
general protocol: https://www.encodeproject.org/documents/d89f19f3-31f8-4079-9635-5d3dd799471e/@@download/attachment/Reinke_Lab_ModENCODE_ChIP_protocol_%28revised%205-24-13%29_4_mg.pdf
other: https://www.encodeproject.org/documents/aa63b0ae-b1a0-41fa-9107-f6f0e439ecfa/@@download/attachment/2014-2079.pdf
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
https://www.encodeproject.org/experiments/ENCSR534TFA/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-seq of transgenic worms expressing CEH-2-eGFP fusion proteins. The IP was performed using an anti-GFP antibody.
experiment encode accession: ENCSR534TFA
assay title: TF ChIP-seq
assembly: ce11, ce10
possible controls: ENCSR767ZKR
encode release date: 2016-05-24
lab: Valerie Reinke, Yale
library encode accession: ENCLB666JPW
fragmentation methods: sonication (generic microtip)
|
| Data processing |
See GSM*_README.txt supplementary file linked below
|
| |
|
| Submission date |
Feb 26, 2024 |
| Last update date |
Feb 27, 2024 |
| Contact name |
ENCODE DCC |
| E-mail(s) |
encode-help@lists.stanford.edu
|
| Organization name |
ENCODE DCC
|
| Street address |
300 Pasteur Dr
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5120 |
| Country |
USA |
| |
|
| Platform ID |
GPL18245 |
| Series (1) |
| GSE259208 |
TF ChIP-seq from whole organism (ENCSR534TFA) |
|
| Relations |
| BioSample |
SAMN40085523 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8111296_ENCFF113RXI_signal_of_unique_reads_ce10.bigWig |
9.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM8111296_ENCFF140IGC_peaks_and_background_as_input_for_IDR_ce11.bigBed |
705.3 Kb |
(ftp)(http) |
BIGBED |
| GSM8111296_ENCFF307ZOL_peaks_and_background_as_input_for_IDR_ce11.bed.gz |
390.3 Kb |
(ftp)(http) |
BED |
| GSM8111296_ENCFF474JOI_control_normalized_signal_ce10.bigWig |
9.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM8111296_ENCFF664FXX_peaks_and_background_as_input_for_IDR_ce10.bigBed |
705.5 Kb |
(ftp)(http) |
BIGBED |
| GSM8111296_ENCFF792DUO_peaks_and_background_as_input_for_IDR_ce10.bed.gz |
390.5 Kb |
(ftp)(http) |
BED |
| GSM8111296_ENCFF878FLB_read-depth_normalized_signal_ce10.bigWig |
9.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM8111296_ENCFF880ZIM_control_normalized_signal_ce11.bigWig |
9.8 Mb |
(ftp)(http) |
BIGWIG |
| GSM8111296_ENCFF967BGN_signal_of_unique_reads_ce11.bigWig |
9.5 Mb |
(ftp)(http) |
BIGWIG |
| GSM8111296_ENCFF978KHV_read-depth_normalized_signal_ce11.bigWig |
9.6 Mb |
(ftp)(http) |
BIGWIG |
| GSM8111296_ENCLB666JPW_README.txt.gz |
1.8 Kb |
(ftp)(http) |
TXT |
| Raw data are available in SRA |
